bwHPC Wiki - User contributions [en]

https://wiki.bwhpc.de/wiki/api.php?action=feedcontributions&feedformat=atom&user=S+Richling bwHPC Wiki - User contributions [en] 2026-06-04T14:32:31Z User contributions MediaWiki 1.39.17 https://wiki.bwhpc.de/wiki/index.php?title=Helix/Software/Matlab&diff=16089 Helix/Software/Matlab 2026-05-21T13:54:52Z

<p>S Richling: </p> <hr /> <div>{| style="border: 2px solid #d33; background-color: #fee7e6; padding: 10px; margin-bottom: 1em; width: 100%;"<br /> |-<br /> | '''⚠ MATLAB modules have been removed on March 31, 2026.'''<br /> <br /> The MathWorks state license (Landeslizenz) has expired on March 31, 2026 and will not be renewed. The MATLAB modules <code>math/matlab</code> are no longer be available on Helix.<br /> <br /> '''Alternatives:'''<br /> * '''GNU Octave''' (<code>module load math/octave</code>): MATLAB scripts that do not use special features of toolboxes may run with Octave without or with minor changes.<br /> * '''Matlab Compiler / Matlab Runtime''': Use the [https://de.mathworks.com/products/compiler.html MATLAB Compiler] to build stand-alone binaries on your local computer (with your own license) and run them with the MATLAB Runtime on the cluster — no license required at runtime (see section "Compile MATLAB binaries with mcc" below).<br /> * '''Institute license''': If your institute has its own MathWorks network license, it may be possible to use it from the cluster. This must be checked on a case-by-case basis — please [https://www.bwhpc.de/supportportal.php submit a ticket].<br /> * Other alternatives: <code>math/julia</code>, <code>math/R</code>, <code>devel/python</code><br /> |}<br /> <br /> {{Softwarepage|math/matlab}}<br /> <br /> {| width=600px class="wikitable"<br /> |-<br /> ! Description !! Content<br /> |-<br /> | module load<br /> | math/matlab<br /> |-<br /> | License<br /> | [https://de.mathworks.com/pricing-licensing/index.html?intendeduse=edu&prodcode=ML Academic License/Commercial]<br /> |-<br /> | Citing<br /> | n/a<br /> |-<br /> | Links<br /> | [https://de.mathworks.com/products/matlab/ MATLAB Homepage] &#124; [https://de.mathworks.com/index.html?s_tid=gn_logo MathWorks Homepage] &#124; [https://de.mathworks.com/support/?s_tid=gn_supp Support and more]<br /> |-<br /> | Graphical Interface<br /> | No<br /> |}<br /> <br /> <br /> <br /> = Description =<br /> <br /> '''MATLAB''' (MATrix LABoratory) is a high-level programming language and interactive computing environment for numerical calculation and data visualization.<br /> <br /> = Loading MATLAB =<br /> <br /> The preferable way is to run the MATLAB command line interface without GUI:<br /> <pre>$ matlab -nodisplay</pre><br /> <br /> An interactive MATLAB session with graphical user interface (GUI) can be started with the command (requires X11 forwarding enabled for your ssh login):<br /> <pre>$ matlab</pre><br /> <br /> Note: Do not start a long-duration interactive MATLAB session on a login node of the cluster. Submit an [[Helix/Slurm#Interactive_Jobs | interactive job]] and start MATLAB from within the dedicated compute node assigned to you by the queueing system.<br /> <br /> The following generic command will execute a MATLAB script or function named "example":<br /> <pre>$ matlab -nodisplay -batch example > result.out 2>&1</pre><br /> <br /> The output of this session will be redirected to the file result.out. The option <syntaxhighlight style="border:0px" inline=1>-batch</syntaxhighlight> executes the MATLAB statement non-interactively.<br /> <br /> = Parallel Computing Using MATLAB =<br /> <br /> Parallelization of MATLAB jobs is realized via the built-in multi-threading provided by MATLAB's BLAS and FFT implementation and the parallel computing functionality of MATLAB's Parallel Computing Toolbox (PCT).<br /> <br /> == Implicit Threading ==<br /> <br /> A large number of built-in MATLAB functions may utilize multiple cores automatically without any code modifications required. This is referred to as implicit multi-threading and must be strictly distinguished from explicit parallelism provided by the Parallel Computing Toolbox (PCT) which requires specific commands in your code in order to create threads.<br /> <br /> Implicit threading particularly takes place for linear algebra operations (such as the solution to a linear system A\b or matrix products A*B) and FFT operations. Many other high-level MATLAB functions do also benefit from multi-threading capabilities of their underlying routines. If multi-threading is not desired, single-threading can be enforced by adding the command line option <syntaxhighlight style="border:0px" inline=1>-singleCompThread</syntaxhighlight>.<br /> <br /> Whenever implicit threading takes place, MATLAB will detect the total number of cores that exist on a machine and by default makes use of all of them. This has very important implications for MATLAB jobs in HPC environments with shared-node job scheduling policy (i.e. with multiple users sharing one compute node). Due to this behaviour, a MATLAB job may take over more compute resources than assigned by the queueing system of the cluster (and thereby taking away these resources from all other users with running jobs on the same node - including your own jobs).<br /> <br /> Therefore, when running in multi-threaded mode, MATLAB always requires the user's intervention to not allocate all cores of the machine (unless requested so from the queueing system). The number of threads must be controlled from within the code by means of the <syntaxhighlight style="border:0px" inline=1>maxNumCompThreads(N)</syntaxhighlight> function or, alternatively, with the <syntaxhighlight style="border:0px" inline=1>feature('numThreads', N)</syntaxhighlight> function (which is undocumented).<br /> <br /> == Using the Parallel Computing Toolbox (PCT) ==<br /> <br /> By using the PCT one can make explicit use of several cores on multicore processors to parallelize MATLAB applications without MPI programming. Under MATLAB version 8.4 and earlier, this toolbox provides 12 workers (MATLAB computational engines) to execute applications locally on a single multicore node. Under MATLAB version 8.5 and later, the number of workers available is equal to the number of cores on a single node (up to a maximum of 512).<br /> <br /> If multiple PCT jobs are running at the same time, they all write temporary MATLAB job information to the same location. This race condition can cause one or more of the parallel MATLAB jobs fail to use the parallel functionality of the toolbox.<br /> <br /> To solve this issue, each MATLAB job should explicitly set a unique location where these files are created. This can be accomplished by the following snippet of code added to your MATLAB script.<br /> <br /> <pre><br /> % create a local cluster object<br /> pc = parcluster('local')<br /> <br /> % get the number of dedicated cores from environment<br /> nprocs = str2num(getenv('SLURM_NPROCS'))<br /> <br /> % you may explicitly set the JobStorageLocation to the tmp directory that is unique to each cluster job (and is on local, fast scratch)<br /> parpool_tmpdir = [getenv('TMP'),'/.matlab/local_cluster_jobs/slurm_jobID_',getenv('SLURM_JOB_ID')]<br /> mkdir(parpool_tmpdir)<br /> pc.JobStorageLocation = parpool_tmpdir<br /> <br /> % start the parallel pool<br /> parpool(pc, nprocs)<br /> </pre><br /> <br /> <br /> If a large number of MATLAB-jobs are run in parallel, they can also conflict when writing generic information to <syntaxhighlight style="border:0px" inline=1>~/.matlab</syntaxhighlight>. This can be circumvented by setting <syntaxhighlight style="border:0px" inline=1>$MATLAB_PREFDIR</syntaxhighlight> to different directories in your Batch-script, e.g. <br /> <br /> <pre>export MATLAB_PREFDIR=$TMP</pre><br /> <br /> == Using a different implementation of BLAS/LAPACK ==<br /> <br /> By default, Matlab uses a version of Intel MKL as its BLAS/LAPACK library. It is possible to manually change this to different libraries by setting the <syntaxhighlight style="border:0px" inline=1>BLAS_VERSION</syntaxhighlight> and <syntaxhighlight style="border:0px" inline=1>LAPACK_VERSION</syntaxhighlight> environment variables. The following lines can be added to the batch-script to change it, in this example to BLIS and Flame, which are optimized for AMD processors: <br /> <br /> <pre><br /> module load numlib/aocl/3.2.0<br /> <br /> export BLAS_VERSION=$AOCL_LIB_DIR/libblis-mt.so<br /> export LAPACK_VERSION=$AOCL_LIB_DIR/libflame.so<br /> <br /> export BLIS_NUM_THREADS=$SLURM_NTASKS<br /> </pre><br /> <br /> This can increase performance depending on the task, for example large matrix multiplications, but caution is advised.<br /> <br /> = General Performance Tips for MATLAB =<br /> <br /> MATLAB data structures (arrays or matrices) are dynamic in size, i.e. MATLAB will automatically resize the structure on demand. Although this seems to be convenient, MATLAB continually needs to allocate a new chunk of memory and copy over the data to the new block of memory as the array or matrix grows in a loop. This may take a significant amount of extra time during execution of the program.<br /> <br /> Code performance can often be drastically improved by pre-allocating memory for the final expected size of the array or matrix before actually starting the processing loop. In order to pre-allocate an array of strings, you can use MATLAB's build-in cell function. In order to pre-allocate an array or matrix of numbers, you can use MATLAB's build-in zeros function.<br /> <br /> The performance benefit of pre-allocation is illustrated with the following example code.<br /> <br /> <pre><br /> % prealloc.m<br /> <br /> clear all;<br /> <br /> num=10000000;<br /> <br /> disp('Without pre-allocation:')<br /> tic<br /> for i=1:num<br /> a(i)=i;<br /> end<br /> toc<br /> <br /> disp('With pre-allocation:')<br /> tic<br /> b=zeros(1,num);<br /> for i=1:num<br /> b(i)=i;<br /> end<br /> toc<br /> </pre><br /> <br /> On a compute node, the result may look like this:<br /> <br /> <pre><br /> Without pre-allocation:<br /> Elapsed time is 2.879446 seconds.<br /> With pre-allocation:<br /> Elapsed time is 0.097557 seconds.<br /> </pre><br /> <br /> Please recognize that the code runs almost 30 times faster with pre-allocation.<br /> <br /> == Compile MATLAB binaries with mcc ==<br /> <br /> MATLAB on Helix comes with a compiler, <code>mcc</code>, that can be used to create binaries from MATLAB-code.<br /> Stand-alone MATLAB programs compiled with <code>mcc</code> do not require any license tokens at runtime and you can start jobs in parallel without any risk of running out of licences.<br /> <br /> === Running compiled binaries with the MATLAB Runtime ===<br /> <br /> If you do not have access to a full MATLAB installation on Helix, you can still run compiled MATLAB applications using the MATLAB Runtime module:<br /> <br /> module load math/matlab-runtime<br /> ./my_compiled_app<br /> <br /> The MATLAB Runtime requires no license. To use it:<br /> <br /> # Compile your MATLAB code on a machine where you have a MATLAB license (e.g., your local workstation via an institute license):<br /> #: <code>mcc -m my_script.m</code><br /> # Transfer the compiled binary to Helix.<br /> # Load the matching Runtime module and run:<br /> #: <code>module load math/matlab-runtime/R2025b</code><br /> #: <code>./my_script</code><br /> <br /> '''Important:''' The Runtime version must '''exactly''' match the MATLAB version used for compilation. For example, code compiled with R2023a requires <code>math/matlab-runtime/R2023a</code>. Available versions:<br /> <br /> module avail math/matlab-runtime<br /> <br /> Currently installed: R2022a, R2023a, R2023b, R2024a, R2024b, R2025a, R2025b.<br /> <br /> The MATLAB Runtime is [https://de.mathworks.com/products/compiler/matlab-runtime.html freely available from MathWorks] and can also be installed locally if needed.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Main_Page&diff=15881 Main Page 2026-03-24T09:47:27Z

<p>S Richling: </p> <hr /> <div><span style="font-size:140%;>'''Welcome to the bwHPC Wiki.'''</span><br /> <br /> bwHPC represents services and resources in the State of '''B'''aden-'''W'''ürttemberg, Germany, for High Performance Computing ('''HPC'''), Data Intensive Computing ('''DIC''') and Large Scale Scientific Data Management ('''LS2DM''').<br /> <br /> The main bwHPC web page is at '''[https://www.bwhpc.de/ https://www.bwhpc.de/]'''.<br /> <br /> Many topics depend on the cluster system you use. <br /> First choose the cluster you use, then select the correct topic.<br /> <br /> <br /> <br /> {| style=" background:#B8FFB8; width:100%;" <br /> | style="padding:8px; background:#8AFF8A; font-size:120%; text-align:left" | [[Status|'''Status:''' Maintenances [0] & Outages [0]]]<br /> |}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> {| style=" background:#eeeefe; width:100%;"<br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Courses / eLearning<br /> |-<br /> | <br /> * [https://training.bwhpc.de/ eLearning and Online Courses]<br /> * [https://hpc-wiki.info/hpc/Introduction_to_Linux_in_HPC Introduction to Linux in HPC (external resource)]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | Need Access to a Cluster?<br /> |-<br /> |<br /> * [[When to use a HPC Cluster]]<br /> * [[Running Calculations]]<br /> * [[Registration]]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | HPC System Specific Documentation<br /> |-<br /> |<br /> bwHPC encompasses several HPC compute clusters at different universities in Baden-Württemberg. Each cluster is dedicated to [https://www.bwhpc.de/bwhpc-domains.php specific research domains]. <br /> <br /> Documentation differs between compute clusters, please see cluster specific overview pages:<br /> {|<br /> |-<br /> | style="padding:5px; width:30%" | [[BwUniCluster3.0|bwUniCluster 3.0]] <br /> | style="padding-left:20px;" | General Purpose, Teaching<br /> |-<br /> | style="padding:5px; width:30%" | [[BinAC2|bwForCluster BinAC 2]] <br /> | style="padding-left:20px;" | Bioinformatics, Astrophysics, Geosciences, Pharmacy, and Medical Informatics<br /> |-<br /> | style="padding:5px; width:30%" | [[Helix|bwForCluster Helix]]<br /> | style="padding-left:20px;" | Structural and Systems Biology, Medical Science, Soft Matter, Computational Humanities, and Mathematics and Computer Science<br /> |-<br /> | style="padding:5px; width:30%" | [[:JUSTUS2| bwForCluster JUSTUS 2]] <br /> | style="padding-left:20px;" | Theoretical Chemistry, Condensed Matter Physics, and Quantum Sciences<br /> |-<br /> | style="padding:5px; width:30%" | [[NEMO2|bwForCluster NEMO 2]] <br /> | style="padding-left:20px;" | Neurosciences, Particle Physics, Materials Science, and Microsystems Engineering<br /> |}<br /> |-<br /> |bwHPC Clusters: [https://www.bwhpc.de/cluster.php operational status] <br /> Further Compute Clusters in Baden-Württemberg (separate access policies):<br /> * Datenanalyse Cluster der Hochschulen (DACHS): [[DACHS | Datenanalyse Cluster der Hochschulen (DACHS)]]<br /> * bwHPC tier 1: [https://kb.hlrs.de/platforms/index.php/Hunter_(HPE) Hunter] ([https://www.hlrs.de/apply-for-computing-time getting access])<br /> * bwHPC tier 2: [https://www.nhr.kit.edu/userdocs/horeka HoreKa] ([https://www.nhr.kit.edu/userdocs/horeka/projects/ getting access])<br /> |}<br /> <br /> {| style="background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | Documentation valid for all Clusters<br /> |-<br /> |<br /> * [[Environment Modules| Software Modules]] and software documentation explained<br /> * [https://www.bwhpc.de/software.html List of Software] on all clusters<br /> * [[Development| Software Development and Parallel Programming]]<br /> * [[Energy Efficient Cluster Usage]]<br /> * [[HPC Glossary]]<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Scientific Data Storage<br /> |-<br /> |<br /> For user guides of the scientific data storage services:<br /> * [[SDS@hd]]: Everyone can join existing storage projects, entitlement needed for creating your own, [https://sds-hd.urz.uni-heidelberg.de/management/shib/sds_costs.php cost sheet]<br /> * [https://uni-tuebingen.de/einrichtungen/zentrum-fuer-datenverarbeitung/projekte/laufende-projekte/bwsfs bwSFS]<br /> Associated, but local scientific storage services are:<br /> * [https://wiki.scc.kit.edu/lsdf/index.php/Category:LSDF_Online_Storage LSDF Online Storage] (only for KIT and KIT partners)<br /> |}<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Scientific Data Archiving<br /> |-<br /> |<br /> For user guides of the scientific data archiving services:<br /> * [https://www.rda.kit.edu/english bwDataArchive]: Open to all scientists at KIT and institutions in Baden-Württemberg that have signed a service agreement with KIT<br /> Associated, but local archiving services for scientific data are:<br /> * [https://www.urz.uni-heidelberg.de/de/service-katalog/speicher/heiarchive heiARCHIVE] (only for members of Heidelberg University)<br /> For instructions on how to move the data, depending on the offered connections, can be found under [[Data Transfer | Data Transfer]].<br /> |}<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Data Management<br /> |-<br /> |<br /> * [[Data Transfer|Data Transfer]]<br /> * [https://www.forschungsdaten.org/index.php/FDM-Kontakte#Deutschland Research Data Management (RDM)] contact persons<br /> * [https://www.forschungsdaten.info Portal for Research Data Management] (Forschungsdaten.info)<br /> |}<br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Support<br /> |-<br /> | <br /> * [[BwSupportPortal|Submit a Ticket in our Support Portal]]<br /> Support is provided by the [https://www.bwhpc.de/teams.php bwHPC Competence Centers]:<br /> |}<br /> {| style=" background:#e6e9eb; width:100%;" <br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Acknowledgement<br /> |-<br /> | <br /> * Please [[Acknowledgement|acknowledge]] our resources in your publications.<br /> |}</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Main_Page&diff=15878 Main Page 2026-03-24T09:46:37Z

<p>S Richling: </p> <hr /> <div><span style="font-size:140%;>'''Welcome to the bwHPC Wiki.'''</span><br /> <br /> bwHPC represents services and resources in the State of '''B'''aden-'''W'''ürttemberg, Germany, for High Performance Computing ('''HPC'''), Data Intensive Computing ('''DIC''') and Large Scale Scientific Data Management ('''LS2DM''').<br /> <br /> The main bwHPC web page is at '''[https://www.bwhpc.de/ https://www.bwhpc.de/]'''.<br /> <br /> Many topics depend on the cluster system you use. <br /> First choose the cluster you use, then select the correct topic.<br /> <br /> <br /> <br /> {| style=" background:#B8FFB8; width:100%;" <br /> | style="padding:8px; background:#8AFF8A; font-size:120%; text-align:left" | [[Status|'''Status:''' Maintenances [0] & Outages [0]]]<br /> |}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> {| style=" background:#eeeefe; width:100%;"<br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Courses / eLearning<br /> |-<br /> | <br /> * [https://training.bwhpc.de/ eLearning and Online Courses]<br /> * [https://hpc-wiki.info/hpc/Introduction_to_Linux_in_HPC Introduction to Linux in HPC (external resource)]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | Need Access to a Cluster?<br /> |-<br /> |<br /> * [[When to use a HPC Cluster]]<br /> * [[Running Calculations]]<br /> * [[Registration]]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | HPC System Specific Documentation<br /> |-<br /> |<br /> bwHPC encompasses several HPC compute clusters at different universities in Baden-Württemberg. Each cluster is dedicated to [https://www.bwhpc.de/bwhpc-domains.php specific research domains]. <br /> <br /> Documentation differs between compute clusters, please see cluster specific overview pages:<br /> {|<br /> |-<br /> | style="padding:5px; width:30%" | [[BwUniCluster3.0|bwUniCluster 3.0]] <br /> | style="padding-left:20px;" | General Purpose, Teaching<br /> |-<br /> | style="padding:5px; width:30%" | [[BinAC2|bwForCluster BinAC 2]] <br /> | style="padding-left:20px;" | Bioinformatics, Astrophysics, Geosciences, Pharmacy, and Medical Informatics<br /> |-<br /> | style="padding:5px; width:30%" | [[Helix|bwForCluster Helix]]<br /> | style="padding-left:20px;" | Structural and Systems Biology, Medical Science, Soft Matter, Computational Humanities, and Mathematics and Computer Science<br /> |-<br /> | style="padding:5px; width:30%" | [[:JUSTUS2| bwForCluster JUSTUS 2]] <br /> | style="padding-left:20px;" | Theoretical Chemistry, Condensed Matter Physics, and Quantum Sciences<br /> |-<br /> | style="padding:5px; width:30%" | [[NEMO2|bwForCluster NEMO 2]] <br /> | style="padding-left:20px;" | Neurosciences, Particle Physics, Materials Science, and Microsystems Engineering<br /> |}<br /> |-<br /> |bwHPC Clusters: [https://www.bwhpc.de/cluster.php operational status] <br /> Further Compute Clusters in Baden-Württemberg (separate access policies):<br /> * Datenanalyse Cluster der Hochschulen (DACHS): [[DACHS | Datenanalyse Cluster der Hochschulen (DACHS)]]<br /> * bwHPC tier 1: [https://kb.hlrs.de/platforms/index.php/Hunter_(HPE) Hunter] ([https://www.hlrs.de/apply-for-computing-time getting access])<br /> * bwHPC tier 2: [https://www.nhr.kit.edu/userdocs/horeka HoreKa] ([https://www.nhr.kit.edu/userdocs/horeka/projects/ getting access])<br /> |}<br /> <br /> {| style="background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | Documentation valid for all Clusters<br /> |-<br /> |<br /> * [[Environment Modules| Software Modules]] and software documentation explained<br /> * [https://www.bwhpc.de/software.html List of Software] on all clusters<br /> * [[Development| Software Development and Parallel Programming]]<br /> * [[Energy Efficient Cluster Usage]]<br /> * [[HPC Glossary]]<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Scientific Data Storage<br /> |-<br /> |<br /> For user guides of the scientific data storage services:<br /> * [[SDS@hd]]: Everyone can join existing storage projects, entitlement needed for creating your own, [https://sds-hd.urz.uni-heidelberg.de/management/shib/sds_costs.php cost sheet]<br /> * [https://uni-tuebingen.de/einrichtungen/zentrum-fuer-datenverarbeitung/projekte/laufende-projekte/bwsfs bwSFS]<br /> Associated, but local scientific storage services are:<br /> * [https://wiki.scc.kit.edu/lsdf/index.php/Category:LSDF_Online_Storage LSDF Online Storage] (only for KIT and KIT partners)<br /> |}<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Scientific Data Archiving<br /> |-<br /> |<br /> For user guides of the scientific data archiving services:<br /> * [https://www.rda.kit.edu/english bwDataArchive]: Open to all scientists at KIT and institutions in Baden-Württemberg that have signed a service agreement with KIT<br /> Associated, but local scientific archiving services are:<br /> * [https://www.urz.uni-heidelberg.de/de/service-katalog/speicher/heiarchive heiARCHIVE] (only for members of Heidelberg University)<br /> For instructions on how to move the data, depending on the offered connections, can be found under [[Data Transfer | Data Transfer]].<br /> |}<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Data Management<br /> |-<br /> |<br /> * [[Data Transfer|Data Transfer]]<br /> * [https://www.forschungsdaten.org/index.php/FDM-Kontakte#Deutschland Research Data Management (RDM)] contact persons<br /> * [https://www.forschungsdaten.info Portal for Research Data Management] (Forschungsdaten.info)<br /> |}<br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Support<br /> |-<br /> | <br /> * [[BwSupportPortal|Submit a Ticket in our Support Portal]]<br /> Support is provided by the [https://www.bwhpc.de/teams.php bwHPC Competence Centers]:<br /> |}<br /> {| style=" background:#e6e9eb; width:100%;" <br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Acknowledgement<br /> |-<br /> | <br /> * Please [[Acknowledgement|acknowledge]] our resources in your publications.<br /> |}</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Main_Page&diff=15876 Main Page 2026-03-24T09:42:27Z

<p>S Richling: </p> <hr /> <div><span style="font-size:140%;>'''Welcome to the bwHPC Wiki.'''</span><br /> <br /> bwHPC represents services and resources in the State of '''B'''aden-'''W'''ürttemberg, Germany, for High Performance Computing ('''HPC'''), Data Intensive Computing ('''DIC''') and Large Scale Scientific Data Management ('''LS2DM''').<br /> <br /> The main bwHPC web page is at '''[https://www.bwhpc.de/ https://www.bwhpc.de/]'''.<br /> <br /> Many topics depend on the cluster system you use. <br /> First choose the cluster you use, then select the correct topic.<br /> <br /> <br /> <br /> {| style=" background:#B8FFB8; width:100%;" <br /> | style="padding:8px; background:#8AFF8A; font-size:120%; text-align:left" | [[Status|'''Status:''' Maintenances [0] & Outages [0]]]<br /> |}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> {| style=" background:#eeeefe; width:100%;"<br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Courses / eLearning<br /> |-<br /> | <br /> * [https://training.bwhpc.de/ eLearning and Online Courses]<br /> * [https://hpc-wiki.info/hpc/Introduction_to_Linux_in_HPC Introduction to Linux in HPC (external resource)]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | Need Access to a Cluster?<br /> |-<br /> |<br /> * [[When to use a HPC Cluster]]<br /> * [[Running Calculations]]<br /> * [[Registration]]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | HPC System Specific Documentation<br /> |-<br /> |<br /> bwHPC encompasses several HPC compute clusters at different universities in Baden-Württemberg. Each cluster is dedicated to [https://www.bwhpc.de/bwhpc-domains.php specific research domains]. <br /> <br /> Documentation differs between compute clusters, please see cluster specific overview pages:<br /> {|<br /> |-<br /> | style="padding:5px; width:30%" | [[BwUniCluster3.0|bwUniCluster 3.0]] <br /> | style="padding-left:20px;" | General Purpose, Teaching<br /> |-<br /> | style="padding:5px; width:30%" | [[BinAC2|bwForCluster BinAC 2]] <br /> | style="padding-left:20px;" | Bioinformatics, Astrophysics, Geosciences, Pharmacy, and Medical Informatics<br /> |-<br /> | style="padding:5px; width:30%" | [[Helix|bwForCluster Helix]]<br /> | style="padding-left:20px;" | Structural and Systems Biology, Medical Science, Soft Matter, Computational Humanities, and Mathematics and Computer Science<br /> |-<br /> | style="padding:5px; width:30%" | [[:JUSTUS2| bwForCluster JUSTUS 2]] <br /> | style="padding-left:20px;" | Theoretical Chemistry, Condensed Matter Physics, and Quantum Sciences<br /> |-<br /> | style="padding:5px; width:30%" | [[NEMO2|bwForCluster NEMO 2]] <br /> | style="padding-left:20px;" | Neurosciences, Particle Physics, Materials Science, and Microsystems Engineering<br /> |}<br /> |-<br /> |bwHPC Clusters: [https://www.bwhpc.de/cluster.php operational status] <br /> Further Compute Clusters in Baden-Württemberg (separate access policies):<br /> * Datenanalyse Cluster der Hochschulen (DACHS): [[DACHS | Datenanalyse Cluster der Hochschulen (DACHS)]]<br /> * bwHPC tier 1: [https://kb.hlrs.de/platforms/index.php/Hunter_(HPE) Hunter] ([https://www.hlrs.de/apply-for-computing-time getting access])<br /> * bwHPC tier 2: [https://www.nhr.kit.edu/userdocs/horeka HoreKa] ([https://www.nhr.kit.edu/userdocs/horeka/projects/ getting access])<br /> |}<br /> <br /> {| style="background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | Documentation valid for all Clusters<br /> |-<br /> |<br /> * [[Environment Modules| Software Modules]] and software documentation explained<br /> * [https://www.bwhpc.de/software.html List of Software] on all clusters<br /> * [[Development| Software Development and Parallel Programming]]<br /> * [[Energy Efficient Cluster Usage]]<br /> * [[HPC Glossary]]<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Scientific Data Storage<br /> |-<br /> |<br /> For user guides of the scientific data storage services:<br /> * [[SDS@hd]]: Everyone can join existing storage projects, entitlement needed for creating your own, [https://sds-hd.urz.uni-heidelberg.de/management/shib/sds_costs.php cost sheet]<br /> * [https://uni-tuebingen.de/einrichtungen/zentrum-fuer-datenverarbeitung/projekte/laufende-projekte/bwsfs bwSFS]<br /> Associated, but local scientific storage services are:<br /> * [https://wiki.scc.kit.edu/lsdf/index.php/Category:LSDF_Online_Storage LSDF Online Storage] (only for KIT and KIT partners)<br /> |}<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Scientific Data Archiving<br /> |-<br /> |<br /> For user guides of the scientific data archiving services:<br /> * [https://www.rda.kit.edu/english bwDataArchive]: Open to all scientists at KIT and institutions in Baden-Württemberg that have signed a service agreement with KIT<br /> Associated, but local scientific storage services are:<br /> * [https://www.urz.uni-heidelberg.de/de/service-katalog/speicher/heiarchive heiARCHIVE] (only for members of Heidelberg University)<br /> For instructions on how to move the data, depending on the offered connections, can be found under [[Data Transfer | Data Transfer]].<br /> |}<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Data Management<br /> |-<br /> |<br /> * [[Data Transfer|Data Transfer]]<br /> * [https://www.forschungsdaten.org/index.php/FDM-Kontakte#Deutschland Research Data Management (RDM)] contact persons<br /> * [https://www.forschungsdaten.info Portal for Research Data Management] (Forschungsdaten.info)<br /> |}<br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Support<br /> |-<br /> | <br /> * [[BwSupportPortal|Submit a Ticket in our Support Portal]]<br /> Support is provided by the [https://www.bwhpc.de/teams.php bwHPC Competence Centers]:<br /> |}<br /> {| style=" background:#e6e9eb; width:100%;" <br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Acknowledgement<br /> |-<br /> | <br /> * Please [[Acknowledgement|acknowledge]] our resources in your publications.<br /> |}</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Main_Page&diff=15875 Main Page 2026-03-24T09:41:44Z

<p>S Richling: </p> <hr /> <div><span style="font-size:140%;>'''Welcome to the bwHPC Wiki.'''</span><br /> <br /> bwHPC represents services and resources in the State of '''B'''aden-'''W'''ürttemberg, Germany, for High Performance Computing ('''HPC'''), Data Intensive Computing ('''DIC''') and Large Scale Scientific Data Management ('''LS2DM''').<br /> <br /> The main bwHPC web page is at '''[https://www.bwhpc.de/ https://www.bwhpc.de/]'''.<br /> <br /> Many topics depend on the cluster system you use. <br /> First choose the cluster you use, then select the correct topic.<br /> <br /> <br /> <br /> {| style=" background:#B8FFB8; width:100%;" <br /> | style="padding:8px; background:#8AFF8A; font-size:120%; text-align:left" | [[Status|'''Status:''' Maintenances [0] & Outages [0]]]<br /> |}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> {| style=" background:#eeeefe; width:100%;"<br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Courses / eLearning<br /> |-<br /> | <br /> * [https://training.bwhpc.de/ eLearning and Online Courses]<br /> * [https://hpc-wiki.info/hpc/Introduction_to_Linux_in_HPC Introduction to Linux in HPC (external resource)]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | Need Access to a Cluster?<br /> |-<br /> |<br /> * [[When to use a HPC Cluster]]<br /> * [[Running Calculations]]<br /> * [[Registration]]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | HPC System Specific Documentation<br /> |-<br /> |<br /> bwHPC encompasses several HPC compute clusters at different universities in Baden-Württemberg. Each cluster is dedicated to [https://www.bwhpc.de/bwhpc-domains.php specific research domains]. <br /> <br /> Documentation differs between compute clusters, please see cluster specific overview pages:<br /> {|<br /> |-<br /> | style="padding:5px; width:30%" | [[BwUniCluster3.0|bwUniCluster 3.0]] <br /> | style="padding-left:20px;" | General Purpose, Teaching<br /> |-<br /> | style="padding:5px; width:30%" | [[BinAC2|bwForCluster BinAC 2]] <br /> | style="padding-left:20px;" | Bioinformatics, Astrophysics, Geosciences, Pharmacy, and Medical Informatics<br /> |-<br /> | style="padding:5px; width:30%" | [[Helix|bwForCluster Helix]]<br /> | style="padding-left:20px;" | Structural and Systems Biology, Medical Science, Soft Matter, Computational Humanities, and Mathematics and Computer Science<br /> |-<br /> | style="padding:5px; width:30%" | [[:JUSTUS2| bwForCluster JUSTUS 2]] <br /> | style="padding-left:20px;" | Theoretical Chemistry, Condensed Matter Physics, and Quantum Sciences<br /> |-<br /> | style="padding:5px; width:30%" | [[NEMO2|bwForCluster NEMO 2]] <br /> | style="padding-left:20px;" | Neurosciences, Particle Physics, Materials Science, and Microsystems Engineering<br /> |}<br /> |-<br /> |bwHPC Clusters: [https://www.bwhpc.de/cluster.php operational status] <br /> Further Compute Clusters in Baden-Württemberg (separate access policies):<br /> * Datenanalyse Cluster der Hochschulen (DACHS): [[DACHS | Datenanalyse Cluster der Hochschulen (DACHS)]]<br /> * bwHPC tier 1: [https://kb.hlrs.de/platforms/index.php/Hunter_(HPE) Hunter] ([https://www.hlrs.de/apply-for-computing-time getting access])<br /> * bwHPC tier 2: [https://www.nhr.kit.edu/userdocs/horeka HoreKa] ([https://www.nhr.kit.edu/userdocs/horeka/projects/ getting access])<br /> |}<br /> <br /> {| style="background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | Documentation valid for all Clusters<br /> |-<br /> |<br /> * [[Environment Modules| Software Modules]] and software documentation explained<br /> * [https://www.bwhpc.de/software.html List of Software] on all clusters<br /> * [[Development| Software Development and Parallel Programming]]<br /> * [[Energy Efficient Cluster Usage]]<br /> * [[HPC Glossary]]<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Scientific Data Storage<br /> |-<br /> |<br /> For user guides of the scientific data storage services:<br /> * [[SDS@hd]]: Everyone can join existing storage projects, entitlement needed for creating your own, [https://sds-hd.urz.uni-heidelberg.de/management/shib/sds_costs.php cost sheet]<br /> * [https://uni-tuebingen.de/einrichtungen/zentrum-fuer-datenverarbeitung/projekte/laufende-projekte/bwsfs bwSFS]<br /> Associated, but local scientific storage services are:<br /> * [https://wiki.scc.kit.edu/lsdf/index.php/Category:LSDF_Online_Storage LSDF Online Storage] (only for KIT and KIT partners)<br /> |}<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Scientific Data Archiving<br /> |-<br /> |<br /> For user guides of the scientific data archiving services:<br /> * [https://www.rda.kit.edu/english bwDataArchive]: Open to all scientists at KIT and institutions in Baden-Württemberg that have signed a service agreement with KIT<br /> Associated, but local scientific storage services are:<br /> * [https://www.urz.uni-heidelberg.de/de/service-katalog/speicher/heiarchive heiARCHIVE] (only for members of the University of Heidelberg)<br /> For instructions on how to move the data, depending on the offered connections, can be found under [[Data Transfer | Data Transfer]].<br /> |}<br /> <br /> {| style="height:100%; background:#ffeaef; width:100%"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | Data Management<br /> |-<br /> |<br /> * [[Data Transfer|Data Transfer]]<br /> * [https://www.forschungsdaten.org/index.php/FDM-Kontakte#Deutschland Research Data Management (RDM)] contact persons<br /> * [https://www.forschungsdaten.info Portal for Research Data Management] (Forschungsdaten.info)<br /> |}<br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Support<br /> |-<br /> | <br /> * [[BwSupportPortal|Submit a Ticket in our Support Portal]]<br /> Support is provided by the [https://www.bwhpc.de/teams.php bwHPC Competence Centers]:<br /> |}<br /> {| style=" background:#e6e9eb; width:100%;" <br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Acknowledgement<br /> |-<br /> | <br /> * Please [[Acknowledgement|acknowledge]] our resources in your publications.<br /> |}</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/Software/Matlab&diff=15855 Helix/Software/Matlab 2026-03-20T08:46:02Z

<p>S Richling: </p> <hr /> <div>{| style="border: 2px solid #d33; background-color: #fee7e6; padding: 10px; margin-bottom: 1em; width: 100%;"<br /> |-<br /> | '''⚠ MATLAB modules will be removed on March 31, 2026.'''<br /> <br /> The MathWorks state license (Landeslizenz) expires on March 31, 2026 and will not be renewed. After this date, the MATLAB modules under <code>math/matlab</code> will no longer be available on Helix.<br /> <br /> '''Alternatives:'''<br /> * '''GNU Octave''' (<code>module load math/octave</code>): MATLAB scripts that do not use special features of toolboxes may run with Octave without or with minor changes.<br /> * '''Matlab Compiler / Matlab Runtime''': Use the [https://de.mathworks.com/products/compiler.html MATLAB Compiler] to build stand-alone binaries on your local computer (with your own license) and run them with the MATLAB Runtime on the cluster — no license required at runtime (see section "Compile MATLAB binaries with mcc" below).<br /> * '''Institute license''': If your institute has its own MathWorks network license, it may be possible to use it from the cluster. This must be checked on a case-by-case basis — please [https://www.bwhpc.de/supportportal.php submit a ticket].<br /> * Other alternatives: <code>math/julia</code>, <code>math/R</code>, <code>devel/python</code><br /> |}<br /> <br /> {{Softwarepage|math/matlab}}<br /> <br /> {| width=600px class="wikitable"<br /> |-<br /> ! Description !! Content<br /> |-<br /> | module load<br /> | math/matlab<br /> |-<br /> | License<br /> | [https://de.mathworks.com/pricing-licensing/index.html?intendeduse=edu&prodcode=ML Academic License/Commercial]<br /> |-<br /> | Citing<br /> | n/a<br /> |-<br /> | Links<br /> | [https://de.mathworks.com/products/matlab/ MATLAB Homepage] &#124; [https://de.mathworks.com/index.html?s_tid=gn_logo MathWorks Homepage] &#124; [https://de.mathworks.com/support/?s_tid=gn_supp Support and more]<br /> |-<br /> | Graphical Interface<br /> | No<br /> |}<br /> <br /> <br /> <br /> = Description =<br /> <br /> '''MATLAB''' (MATrix LABoratory) is a high-level programming language and interactive computing environment for numerical calculation and data visualization.<br /> <br /> = Loading MATLAB =<br /> <br /> The preferable way is to run the MATLAB command line interface without GUI:<br /> <pre>$ matlab -nodisplay</pre><br /> <br /> An interactive MATLAB session with graphical user interface (GUI) can be started with the command (requires X11 forwarding enabled for your ssh login):<br /> <pre>$ matlab</pre><br /> <br /> Note: Do not start a long-duration interactive MATLAB session on a login node of the cluster. Submit an [[Helix/Slurm#Interactive_Jobs | interactive job]] and start MATLAB from within the dedicated compute node assigned to you by the queueing system.<br /> <br /> The following generic command will execute a MATLAB script or function named "example":<br /> <pre>$ matlab -nodisplay -batch example > result.out 2>&1</pre><br /> <br /> The output of this session will be redirected to the file result.out. The option <syntaxhighlight style="border:0px" inline=1>-batch</syntaxhighlight> executes the MATLAB statement non-interactively.<br /> <br /> = Parallel Computing Using MATLAB =<br /> <br /> Parallelization of MATLAB jobs is realized via the built-in multi-threading provided by MATLAB's BLAS and FFT implementation and the parallel computing functionality of MATLAB's Parallel Computing Toolbox (PCT).<br /> <br /> == Implicit Threading ==<br /> <br /> A large number of built-in MATLAB functions may utilize multiple cores automatically without any code modifications required. This is referred to as implicit multi-threading and must be strictly distinguished from explicit parallelism provided by the Parallel Computing Toolbox (PCT) which requires specific commands in your code in order to create threads.<br /> <br /> Implicit threading particularly takes place for linear algebra operations (such as the solution to a linear system A\b or matrix products A*B) and FFT operations. Many other high-level MATLAB functions do also benefit from multi-threading capabilities of their underlying routines. If multi-threading is not desired, single-threading can be enforced by adding the command line option <syntaxhighlight style="border:0px" inline=1>-singleCompThread</syntaxhighlight>.<br /> <br /> Whenever implicit threading takes place, MATLAB will detect the total number of cores that exist on a machine and by default makes use of all of them. This has very important implications for MATLAB jobs in HPC environments with shared-node job scheduling policy (i.e. with multiple users sharing one compute node). Due to this behaviour, a MATLAB job may take over more compute resources than assigned by the queueing system of the cluster (and thereby taking away these resources from all other users with running jobs on the same node - including your own jobs).<br /> <br /> Therefore, when running in multi-threaded mode, MATLAB always requires the user's intervention to not allocate all cores of the machine (unless requested so from the queueing system). The number of threads must be controlled from within the code by means of the <syntaxhighlight style="border:0px" inline=1>maxNumCompThreads(N)</syntaxhighlight> function or, alternatively, with the <syntaxhighlight style="border:0px" inline=1>feature('numThreads', N)</syntaxhighlight> function (which is undocumented).<br /> <br /> == Using the Parallel Computing Toolbox (PCT) ==<br /> <br /> By using the PCT one can make explicit use of several cores on multicore processors to parallelize MATLAB applications without MPI programming. Under MATLAB version 8.4 and earlier, this toolbox provides 12 workers (MATLAB computational engines) to execute applications locally on a single multicore node. Under MATLAB version 8.5 and later, the number of workers available is equal to the number of cores on a single node (up to a maximum of 512).<br /> <br /> If multiple PCT jobs are running at the same time, they all write temporary MATLAB job information to the same location. This race condition can cause one or more of the parallel MATLAB jobs fail to use the parallel functionality of the toolbox.<br /> <br /> To solve this issue, each MATLAB job should explicitly set a unique location where these files are created. This can be accomplished by the following snippet of code added to your MATLAB script.<br /> <br /> <pre><br /> % create a local cluster object<br /> pc = parcluster('local')<br /> <br /> % get the number of dedicated cores from environment<br /> nprocs = str2num(getenv('SLURM_NPROCS'))<br /> <br /> % you may explicitly set the JobStorageLocation to the tmp directory that is unique to each cluster job (and is on local, fast scratch)<br /> parpool_tmpdir = [getenv('TMP'),'/.matlab/local_cluster_jobs/slurm_jobID_',getenv('SLURM_JOB_ID')]<br /> mkdir(parpool_tmpdir)<br /> pc.JobStorageLocation = parpool_tmpdir<br /> <br /> % start the parallel pool<br /> parpool(pc, nprocs)<br /> </pre><br /> <br /> <br /> If a large number of MATLAB-jobs are run in parallel, they can also conflict when writing generic information to <syntaxhighlight style="border:0px" inline=1>~/.matlab</syntaxhighlight>. This can be circumvented by setting <syntaxhighlight style="border:0px" inline=1>$MATLAB_PREFDIR</syntaxhighlight> to different directories in your Batch-script, e.g. <br /> <br /> <pre>export MATLAB_PREFDIR=$TMP</pre><br /> <br /> == Using a different implementation of BLAS/LAPACK ==<br /> <br /> By default, Matlab uses a version of Intel MKL as its BLAS/LAPACK library. It is possible to manually change this to different libraries by setting the <syntaxhighlight style="border:0px" inline=1>BLAS_VERSION</syntaxhighlight> and <syntaxhighlight style="border:0px" inline=1>LAPACK_VERSION</syntaxhighlight> environment variables. The following lines can be added to the batch-script to change it, in this example to BLIS and Flame, which are optimized for AMD processors: <br /> <br /> <pre><br /> module load numlib/aocl/3.2.0<br /> <br /> export BLAS_VERSION=$AOCL_LIB_DIR/libblis-mt.so<br /> export LAPACK_VERSION=$AOCL_LIB_DIR/libflame.so<br /> <br /> export BLIS_NUM_THREADS=$SLURM_NTASKS<br /> </pre><br /> <br /> This can increase performance depending on the task, for example large matrix multiplications, but caution is advised.<br /> <br /> = General Performance Tips for MATLAB =<br /> <br /> MATLAB data structures (arrays or matrices) are dynamic in size, i.e. MATLAB will automatically resize the structure on demand. Although this seems to be convenient, MATLAB continually needs to allocate a new chunk of memory and copy over the data to the new block of memory as the array or matrix grows in a loop. This may take a significant amount of extra time during execution of the program.<br /> <br /> Code performance can often be drastically improved by pre-allocating memory for the final expected size of the array or matrix before actually starting the processing loop. In order to pre-allocate an array of strings, you can use MATLAB's build-in cell function. In order to pre-allocate an array or matrix of numbers, you can use MATLAB's build-in zeros function.<br /> <br /> The performance benefit of pre-allocation is illustrated with the following example code.<br /> <br /> <pre><br /> % prealloc.m<br /> <br /> clear all;<br /> <br /> num=10000000;<br /> <br /> disp('Without pre-allocation:')<br /> tic<br /> for i=1:num<br /> a(i)=i;<br /> end<br /> toc<br /> <br /> disp('With pre-allocation:')<br /> tic<br /> b=zeros(1,num);<br /> for i=1:num<br /> b(i)=i;<br /> end<br /> toc<br /> </pre><br /> <br /> On a compute node, the result may look like this:<br /> <br /> <pre><br /> Without pre-allocation:<br /> Elapsed time is 2.879446 seconds.<br /> With pre-allocation:<br /> Elapsed time is 0.097557 seconds.<br /> </pre><br /> <br /> Please recognize that the code runs almost 30 times faster with pre-allocation.<br /> <br /> == Compile MATLAB binaries with mcc ==<br /> <br /> MATLAB on Helix comes with a compiler, <code>mcc</code>, that can be used to create binaries from MATLAB-code.<br /> Stand-alone MATLAB programs compiled with <code>mcc</code> do not require any license tokens at runtime and you can start jobs in parallel without any risk of running out of licences.<br /> <br /> === Running compiled binaries with the MATLAB Runtime ===<br /> <br /> If you do not have access to a full MATLAB installation on Helix, you can still run compiled MATLAB applications using the MATLAB Runtime module:<br /> <br /> module load math/matlab-runtime<br /> ./my_compiled_app<br /> <br /> The MATLAB Runtime requires no license. To use it:<br /> <br /> # Compile your MATLAB code on a machine where you have a MATLAB license (e.g., your local workstation via an institute license):<br /> #: <code>mcc -m my_script.m</code><br /> # Transfer the compiled binary to Helix.<br /> # Load the matching Runtime module and run:<br /> #: <code>module load math/matlab-runtime/R2025a</code><br /> #: <code>./my_script</code><br /> <br /> '''Important:''' The Runtime version must '''exactly''' match the MATLAB version used for compilation. For example, code compiled with R2023a requires <code>math/matlab-runtime/R2023a</code>. Available versions:<br /> <br /> module avail math/matlab-runtime<br /> <br /> Currently installed: R2022a, R2023a, R2024a, R2025a.<br /> <br /> The MATLAB Runtime is [https://de.mathworks.com/products/compiler/matlab-runtime.html freely available from MathWorks] and can also be installed locally if needed.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/Software/Matlab&diff=15794 Helix/Software/Matlab 2026-03-05T20:41:41Z

<p>S Richling: </p> <hr /> <div>{| style="border: 2px solid #d33; background-color: #fee7e6; padding: 10px; margin-bottom: 1em; width: 100%;"<br /> |-<br /> | '''⚠ MATLAB modules will be removed on March 31, 2026.'''<br /> <br /> The MathWorks state license (Landeslizenz) expires on March 31, 2026 and will not be renewed. After this date, the MATLAB modules under <code>math/matlab</code> will no longer be available on Helix.<br /> <br /> '''Alternatives:'''<br /> * '''GNU Octave''' (<code>module load math/octave</code>): MATLAB scripts that do not use special features of toolboxes may run with Octave without or with minor changes.<br /> * '''Matlab Compiler / Matlab Runtime''': Use the [https://de.mathworks.com/products/compiler.html MATLAB Compiler] to build stand-alone binaries on your local computer and run them with the MATLAB Runtime on the cluster — no license required at runtime (see section "Compile MATLAB binaries with mcc" below).<br /> * '''Institute license''': If your institute has its own MathWorks network license, it may be possible to use it from the cluster. This must be checked on a case-by-case basis — please [https://www.bwhpc.de/supportportal.php submit a ticket].<br /> * Other alternatives: <code>math/julia</code>, <code>math/R</code>, <code>devel/python</code><br /> |}<br /> <br /> {{Softwarepage|math/matlab}}<br /> <br /> {| width=600px class="wikitable"<br /> |-<br /> ! Description !! Content<br /> |-<br /> | module load<br /> | math/matlab<br /> |-<br /> | License<br /> | [https://de.mathworks.com/pricing-licensing/index.html?intendeduse=edu&prodcode=ML Academic License/Commercial]<br /> |-<br /> | Citing<br /> | n/a<br /> |-<br /> | Links<br /> | [https://de.mathworks.com/products/matlab/ MATLAB Homepage] &#124; [https://de.mathworks.com/index.html?s_tid=gn_logo MathWorks Homepage] &#124; [https://de.mathworks.com/support/?s_tid=gn_supp Support and more]<br /> |-<br /> | Graphical Interface<br /> | No<br /> |}<br /> <br /> <br /> <br /> = Description =<br /> <br /> '''MATLAB''' (MATrix LABoratory) is a high-level programming language and interactive computing environment for numerical calculation and data visualization.<br /> <br /> = Loading MATLAB =<br /> <br /> The preferable way is to run the MATLAB command line interface without GUI:<br /> <pre>$ matlab -nodisplay</pre><br /> <br /> An interactive MATLAB session with graphical user interface (GUI) can be started with the command (requires X11 forwarding enabled for your ssh login):<br /> <pre>$ matlab</pre><br /> <br /> Note: Do not start a long-duration interactive MATLAB session on a login node of the cluster. Submit an [[Helix/Slurm#Interactive_Jobs | interactive job]] and start MATLAB from within the dedicated compute node assigned to you by the queueing system.<br /> <br /> The following generic command will execute a MATLAB script or function named "example":<br /> <pre>$ matlab -nodisplay -batch example > result.out 2>&1</pre><br /> <br /> The output of this session will be redirected to the file result.out. The option <syntaxhighlight style="border:0px" inline=1>-batch</syntaxhighlight> executes the MATLAB statement non-interactively.<br /> <br /> = Parallel Computing Using MATLAB =<br /> <br /> Parallelization of MATLAB jobs is realized via the built-in multi-threading provided by MATLAB's BLAS and FFT implementation and the parallel computing functionality of MATLAB's Parallel Computing Toolbox (PCT).<br /> <br /> == Implicit Threading ==<br /> <br /> A large number of built-in MATLAB functions may utilize multiple cores automatically without any code modifications required. This is referred to as implicit multi-threading and must be strictly distinguished from explicit parallelism provided by the Parallel Computing Toolbox (PCT) which requires specific commands in your code in order to create threads.<br /> <br /> Implicit threading particularly takes place for linear algebra operations (such as the solution to a linear system A\b or matrix products A*B) and FFT operations. Many other high-level MATLAB functions do also benefit from multi-threading capabilities of their underlying routines. If multi-threading is not desired, single-threading can be enforced by adding the command line option <syntaxhighlight style="border:0px" inline=1>-singleCompThread</syntaxhighlight>.<br /> <br /> Whenever implicit threading takes place, MATLAB will detect the total number of cores that exist on a machine and by default makes use of all of them. This has very important implications for MATLAB jobs in HPC environments with shared-node job scheduling policy (i.e. with multiple users sharing one compute node). Due to this behaviour, a MATLAB job may take over more compute resources than assigned by the queueing system of the cluster (and thereby taking away these resources from all other users with running jobs on the same node - including your own jobs).<br /> <br /> Therefore, when running in multi-threaded mode, MATLAB always requires the user's intervention to not allocate all cores of the machine (unless requested so from the queueing system). The number of threads must be controlled from within the code by means of the <syntaxhighlight style="border:0px" inline=1>maxNumCompThreads(N)</syntaxhighlight> function or, alternatively, with the <syntaxhighlight style="border:0px" inline=1>feature('numThreads', N)</syntaxhighlight> function (which is undocumented).<br /> <br /> == Using the Parallel Computing Toolbox (PCT) ==<br /> <br /> By using the PCT one can make explicit use of several cores on multicore processors to parallelize MATLAB applications without MPI programming. Under MATLAB version 8.4 and earlier, this toolbox provides 12 workers (MATLAB computational engines) to execute applications locally on a single multicore node. Under MATLAB version 8.5 and later, the number of workers available is equal to the number of cores on a single node (up to a maximum of 512).<br /> <br /> If multiple PCT jobs are running at the same time, they all write temporary MATLAB job information to the same location. This race condition can cause one or more of the parallel MATLAB jobs fail to use the parallel functionality of the toolbox.<br /> <br /> To solve this issue, each MATLAB job should explicitly set a unique location where these files are created. This can be accomplished by the following snippet of code added to your MATLAB script.<br /> <br /> <pre><br /> % create a local cluster object<br /> pc = parcluster('local')<br /> <br /> % get the number of dedicated cores from environment<br /> nprocs = str2num(getenv('SLURM_NPROCS'))<br /> <br /> % you may explicitly set the JobStorageLocation to the tmp directory that is unique to each cluster job (and is on local, fast scratch)<br /> parpool_tmpdir = [getenv('TMP'),'/.matlab/local_cluster_jobs/slurm_jobID_',getenv('SLURM_JOB_ID')]<br /> mkdir(parpool_tmpdir)<br /> pc.JobStorageLocation = parpool_tmpdir<br /> <br /> % start the parallel pool<br /> parpool(pc, nprocs)<br /> </pre><br /> <br /> <br /> If a large number of MATLAB-jobs are run in parallel, they can also conflict when writing generic information to <syntaxhighlight style="border:0px" inline=1>~/.matlab</syntaxhighlight>. This can be circumvented by setting <syntaxhighlight style="border:0px" inline=1>$MATLAB_PREFDIR</syntaxhighlight> to different directories in your Batch-script, e.g. <br /> <br /> <pre>export MATLAB_PREFDIR=$TMP</pre><br /> <br /> == Using a different implementation of BLAS/LAPACK ==<br /> <br /> By default, Matlab uses a version of Intel MKL as its BLAS/LAPACK library. It is possible to manually change this to different libraries by setting the <syntaxhighlight style="border:0px" inline=1>BLAS_VERSION</syntaxhighlight> and <syntaxhighlight style="border:0px" inline=1>LAPACK_VERSION</syntaxhighlight> environment variables. The following lines can be added to the batch-script to change it, in this example to BLIS and Flame, which are optimized for AMD processors: <br /> <br /> <pre><br /> module load numlib/aocl/3.2.0<br /> <br /> export BLAS_VERSION=$AOCL_LIB_DIR/libblis-mt.so<br /> export LAPACK_VERSION=$AOCL_LIB_DIR/libflame.so<br /> <br /> export BLIS_NUM_THREADS=$SLURM_NTASKS<br /> </pre><br /> <br /> This can increase performance depending on the task, for example large matrix multiplications, but caution is advised.<br /> <br /> = General Performance Tips for MATLAB =<br /> <br /> MATLAB data structures (arrays or matrices) are dynamic in size, i.e. MATLAB will automatically resize the structure on demand. Although this seems to be convenient, MATLAB continually needs to allocate a new chunk of memory and copy over the data to the new block of memory as the array or matrix grows in a loop. This may take a significant amount of extra time during execution of the program.<br /> <br /> Code performance can often be drastically improved by pre-allocating memory for the final expected size of the array or matrix before actually starting the processing loop. In order to pre-allocate an array of strings, you can use MATLAB's build-in cell function. In order to pre-allocate an array or matrix of numbers, you can use MATLAB's build-in zeros function.<br /> <br /> The performance benefit of pre-allocation is illustrated with the following example code.<br /> <br /> <pre><br /> % prealloc.m<br /> <br /> clear all;<br /> <br /> num=10000000;<br /> <br /> disp('Without pre-allocation:')<br /> tic<br /> for i=1:num<br /> a(i)=i;<br /> end<br /> toc<br /> <br /> disp('With pre-allocation:')<br /> tic<br /> b=zeros(1,num);<br /> for i=1:num<br /> b(i)=i;<br /> end<br /> toc<br /> </pre><br /> <br /> On a compute node, the result may look like this:<br /> <br /> <pre><br /> Without pre-allocation:<br /> Elapsed time is 2.879446 seconds.<br /> With pre-allocation:<br /> Elapsed time is 0.097557 seconds.<br /> </pre><br /> <br /> Please recognize that the code runs almost 30 times faster with pre-allocation.<br /> <br /> == Compile MATLAB binaries with mcc ==<br /> <br /> MATLAB on Helix comes with a compiler, <code>mcc</code>, that can be used to create binaries from MATLAB-code.<br /> Stand-alone MATLAB programs compiled with <code>mcc</code> do not require any license tokens at runtime and you can start jobs in parallel without any risk of running out of licences.<br /> <br /> === Running compiled binaries with the MATLAB Runtime ===<br /> <br /> If you do not have access to a full MATLAB installation on Helix, you can still run compiled MATLAB applications using the MATLAB Runtime module:<br /> <br /> module load math/matlab-runtime<br /> ./my_compiled_app<br /> <br /> The MATLAB Runtime requires no license. To use it:<br /> <br /> # Compile your MATLAB code on a machine where you have a MATLAB license (e.g., your local workstation via an institute license):<br /> #: <code>mcc -m my_script.m</code><br /> # Transfer the compiled binary to Helix.<br /> # Load the matching Runtime module and run:<br /> #: <code>module load math/matlab-runtime/R2025a</code><br /> #: <code>./my_script</code><br /> <br /> '''Important:''' The Runtime version must '''exactly''' match the MATLAB version used for compilation. For example, code compiled with R2023a requires <code>math/matlab-runtime/R2023a</code>. Available versions:<br /> <br /> module avail math/matlab-runtime<br /> <br /> Currently installed: R2022a, R2023a, R2024a, R2025a.<br /> <br /> The MATLAB Runtime is [https://de.mathworks.com/products/compiler/matlab-runtime.html freely available from MathWorks] and can also be installed locally if needed.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=SDS@hd&diff=15403 SDS@hd 2025-11-12T19:44:20Z

<p>S Richling: </p> <hr /> <div>[[File:sds-hd-logo.png|350px]]<br /> <br /> SDS@hd is a central service for securely storing scientific data (Scientific Data Storage). The service is provided as a state service to researchers of higher education institutions of Baden-Württemberg. It is intended to be used for data that is frequently accessed ('hot data').<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> * November 2022: No special entitlement is needed anymore to participate in an existing storage project.<br /> * September 2023: Service has now been opened for DFN AAI & eduGAIN federation members to participate on existing storage projects.<br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [https://www.urz.uni-heidelberg.de/en/service-catalogue/storage/sdshd-scientific-data-storage Service description & FAQ]<br /> * [mailto:sds-hd-support@urz.uni-heidelberg.de Submit a Ticket]<br /> |}<br /> <br /> {| style=" background:#ffeaef; width:100%;"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | User Documentation<br /> |-<br /> |<br /> * [[SDS@hd/Registration|Registration]]<br /> * [[SDS@hd/Access|Access]]<br /> * [[SDS@hd/Security|Data Security]]<br /> * [[Helix/bwVisu|bwVisu]] for visualization and interactive data analysis<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Storage Funding<br /> |-<br /> |<br /> * Please [[SDS@hd/Acknowledgement|acknowledge]] SDS@hd in your publications.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix&diff=15402 Helix 2025-11-12T19:44:00Z

<p>S Richling: </p> <hr /> <div>[[File:Helix-logo.png|300px]]<br /> <br /> The '''bwForCluster Helix''' is dedicated to research in the bwHPC domains Structural and Systems Biology, Medical Science, Soft Matter, Computational Humanities, and Mathematics and Computer Science.<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> * June 2025: [https://www.bwhpc.de/897.php Important notice regarding the use of MathWorks products]<br /> * April 2025: Cluster extension with 3x gpu8 nodes (Nvidia H200)<br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [[Helix/Getting Started|Getting Started]]<br /> * E-Learning Course [https://training.bwhpc.de/goto.php/crs/695 Introduction to bwForCluster Helix]<br /> <br /> * [https://www.bwhpc.de/supportportal.php Submit a Ticket] to support unit 'bwHPC - Support > bwForCluster Helix'<br /> <br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | User Documentation<br /> |-<br /> |<br /> * [[Registration/bwForCluster|Registration]] ([[Registration/bwForCluster/RV/Management|RV Management]])<br /> * [[Helix/Login|Login]]<br /> * [[Helix/Hardware|Hardware and Architecture]]<br /> * [[Helix/Filesystems|File Systems and Workspaces]] <br /> * [[Helix/Software|Cluster Specific Software]]<br /> * [[Helix/Slurm|Batch System (Slurm)]] <br /> * [[Helix/bwVisu|bwVisu]] for visualization and interactive applications<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Cluster Funding<br /> |-<br /> |<br /> * Please [[Helix/Acknowledgement|acknowledge]] the cluster in your publications.<br /> |}</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu&diff=15401 Helix/bwVisu 2025-11-12T19:43:43Z

<p>S Richling: </p> <hr /> <div>[[File:BwVisu wide.svg|300px]]<br /> <br /> [https://bwvisu.bwservices.uni-heidelberg.de/ bwVisu] is a scalable service for remote visualization and interactive applications. This easy-to-use, web-based platform provides interactive access to scientific work environments utilizing massive compute and storage resources.<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> * December 2024: The [https://bwvisu.bwservices.uni-heidelberg.de/ new bwVisu version] based on Open OnDemand is now in operation. You can write feedback to [mailto:bwvisu-support@urz.uni-heidelberg.de bwvisu-support].<br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [https://www.urz.uni-heidelberg.de/en/service-catalogue/software-and-applications/bwvisu Service Description &amp; FAQ]<br /> * [mailto:bwvisu-support@urz.uni-heidelberg.de Submit a Ticket]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left;" | User Documentation<br /> |-<br /> |<br /> * [https://bwvisu.bwservices.uni-heidelberg.de/ <span style="text-decoration: underline;"> Link to Webservice</span>]<br /> * [[Helix/bwVisu/Getting_Started|Getting Started]]<br /> * [[Helix/bwVisu/Usage|Usage]]<br /> * Available applications and user guides:<br /> <br /> {| class="wikitable" style="text-align: center; margin-left: 30px;"<br /> |- style="font-weight:bold;"<br /> ! Application<br /> ! [[Helix/bwVisu/Usage#noVNC_Applications|noVNC App]]<br /> |-<br /> | [[Helix/bwVisu/CryoSPARC|CryoSPARC]]<br /> | ✓<br /> |-<br /> | [https://imagej.net/software/fiji/ Fiji]<br /> | ✓<br /> |-<br /> | [https://www.ilastik.org/ Ilastik]<br /> | ✓<br /> |-<br /> | [https://bio3d.colorado.edu/imod/ IMOD]<br /> | ✓<br /> |-<br /> | [https://docs.mitk.org/2024.12/UserManualPortal.html MITK]<br /> | ✓<br /> |-<br /> | [https://phy.readthedocs.io/en/latest/ Phy]<br /> | ✓<br /> |-<br /> | [https://qgis.org/ QGIS]<br /> | ✓<br /> |-<br /> | [https://qupath.readthedocs.io/en/stable/index.html QuPath]<br /> | ✓<br /> |-<br /> | [[Helix/bwVisu/JupyterLab|JupyterLab]]<br /> | ☓<br /> |-<br /> | [[Helix/bwVisu/RStudio|RStudio]]<br /> | ☓<br /> |-<br /> | [[Helix/bwVisu/KI-Morph|KI-Morph]]<br /> | ☓<br /> |}<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Acknowledgement<br /> |-<br /> |<br /> * Please [[Helix/bwVisu/Acknowledgement|acknowledge]] bwVisu in your publications</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu&diff=15380 Helix/bwVisu 2025-11-04T09:54:04Z

<p>S Richling: </p> <hr /> <div>[[File:BwVisu wide.svg|300px]]<br /> <br /> [https://bwvisu.bwservices.uni-heidelberg.de/ bwVisu] is a scalable service for remote visualization and interactive applications. This easy-to-use, web-based platform provides interactive access to scientific work environments utilizing massive compute and storage resources.<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> * December 2024: The [https://bwvisu.bwservices.uni-heidelberg.de/ new bwVisu version] based on Open OnDemand is now in operation. You can write feedback to [mailto:bwvisu-support@urz.uni-heidelberg.de bwvisu-support].<br /> * <span style="color:red">8. November 2025: Maintenance 8 am - 8 pm</span><br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [https://www.urz.uni-heidelberg.de/en/service-catalogue/software-and-applications/bwvisu Service Description &amp; FAQ]<br /> * [mailto:bwvisu-support@urz.uni-heidelberg.de Submit a Ticket]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left;" | User Documentation<br /> |-<br /> |<br /> * [https://bwvisu.bwservices.uni-heidelberg.de/ <span style="text-decoration: underline;"> Link to Webservice</span>]<br /> * [[Helix/bwVisu/Getting_Started|Getting Started]]<br /> * [[Helix/bwVisu/Usage|Usage]]<br /> * Available applications and user guides:<br /> <br /> {| class="wikitable" style="text-align: center; margin-left: 30px;"<br /> |- style="font-weight:bold;"<br /> ! Application<br /> ! [[Helix/bwVisu/Usage#noVNC_Applications|noVNC App]]<br /> |-<br /> | [[Helix/bwVisu/CryoSPARC|CryoSPARC]]<br /> | ✓<br /> |-<br /> | [https://imagej.net/software/fiji/ Fiji]<br /> | ✓<br /> |-<br /> | [https://www.ilastik.org/ Ilastik]<br /> | ✓<br /> |-<br /> | [https://bio3d.colorado.edu/imod/ IMOD]<br /> | ✓<br /> |-<br /> | [https://docs.mitk.org/2024.12/UserManualPortal.html MITK]<br /> | ✓<br /> |-<br /> | [https://phy.readthedocs.io/en/latest/ Phy]<br /> | ✓<br /> |-<br /> | [https://qgis.org/ QGIS]<br /> | ✓<br /> |-<br /> | [https://qupath.readthedocs.io/en/stable/index.html QuPath]<br /> | ✓<br /> |-<br /> | [[Helix/bwVisu/JupyterLab|JupyterLab]]<br /> | ☓<br /> |-<br /> | [[Helix/bwVisu/RStudio|RStudio]]<br /> | ☓<br /> |-<br /> | [[Helix/bwVisu/KI-Morph|KI-Morph]]<br /> | ☓<br /> |}<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Acknowledgement<br /> |-<br /> |<br /> * Please [[Helix/bwVisu/Acknowledgement|acknowledge]] bwVisu in your publications</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu&diff=15379 Helix/bwVisu 2025-11-04T09:53:56Z

<p>S Richling: </p> <hr /> <div>[[File:BwVisu wide.svg|300px]]<br /> <br /> [https://bwvisu.bwservices.uni-heidelberg.de/ bwVisu] is a scalable service for remote visualization and interactive applications. This easy-to-use, web-based platform provides interactive access to scientific work environments utilizing massive compute and storage resources.<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> * December 2024: The [https://bwvisu.bwservices.uni-heidelberg.de/ new bwVisu version] based on Open OnDemand is now in operation. You can write feedback to [mailto:bwvisu-support@urz.uni-heidelberg.de bwvisu-support].<br /> * * <span style="color:red">8. November 2025: Maintenance 8 am - 8 pm</span><br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [https://www.urz.uni-heidelberg.de/en/service-catalogue/software-and-applications/bwvisu Service Description &amp; FAQ]<br /> * [mailto:bwvisu-support@urz.uni-heidelberg.de Submit a Ticket]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left;" | User Documentation<br /> |-<br /> |<br /> * [https://bwvisu.bwservices.uni-heidelberg.de/ <span style="text-decoration: underline;"> Link to Webservice</span>]<br /> * [[Helix/bwVisu/Getting_Started|Getting Started]]<br /> * [[Helix/bwVisu/Usage|Usage]]<br /> * Available applications and user guides:<br /> <br /> {| class="wikitable" style="text-align: center; margin-left: 30px;"<br /> |- style="font-weight:bold;"<br /> ! Application<br /> ! [[Helix/bwVisu/Usage#noVNC_Applications|noVNC App]]<br /> |-<br /> | [[Helix/bwVisu/CryoSPARC|CryoSPARC]]<br /> | ✓<br /> |-<br /> | [https://imagej.net/software/fiji/ Fiji]<br /> | ✓<br /> |-<br /> | [https://www.ilastik.org/ Ilastik]<br /> | ✓<br /> |-<br /> | [https://bio3d.colorado.edu/imod/ IMOD]<br /> | ✓<br /> |-<br /> | [https://docs.mitk.org/2024.12/UserManualPortal.html MITK]<br /> | ✓<br /> |-<br /> | [https://phy.readthedocs.io/en/latest/ Phy]<br /> | ✓<br /> |-<br /> | [https://qgis.org/ QGIS]<br /> | ✓<br /> |-<br /> | [https://qupath.readthedocs.io/en/stable/index.html QuPath]<br /> | ✓<br /> |-<br /> | [[Helix/bwVisu/JupyterLab|JupyterLab]]<br /> | ☓<br /> |-<br /> | [[Helix/bwVisu/RStudio|RStudio]]<br /> | ☓<br /> |-<br /> | [[Helix/bwVisu/KI-Morph|KI-Morph]]<br /> | ☓<br /> |}<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Acknowledgement<br /> |-<br /> |<br /> * Please [[Helix/bwVisu/Acknowledgement|acknowledge]] bwVisu in your publications</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=SDS@hd&diff=15378 SDS@hd 2025-11-04T09:53:31Z

<p>S Richling: </p> <hr /> <div>[[File:sds-hd-logo.png|350px]]<br /> <br /> SDS@hd is a central service for securely storing scientific data (Scientific Data Storage). The service is provided as a state service to researchers of higher education institutions of Baden-Württemberg. It is intended to be used for data that is frequently accessed ('hot data').<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> * November 2022: No special entitlement is needed anymore to participate in an existing storage project.<br /> * September 2023: Service has now been opened for DFN AAI & eduGAIN federation members to participate on existing storage projects.<br /> * <span style="color:red">8. November 2025: Maintenance 8 am - 8 pm</span><br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [https://www.urz.uni-heidelberg.de/en/service-catalogue/storage/sdshd-scientific-data-storage Service description & FAQ]<br /> * [mailto:sds-hd-support@urz.uni-heidelberg.de Submit a Ticket]<br /> |}<br /> <br /> {| style=" background:#ffeaef; width:100%;"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | User Documentation<br /> |-<br /> |<br /> * [[SDS@hd/Registration|Registration]]<br /> * [[SDS@hd/Access|Access]]<br /> * [[SDS@hd/Security|Data Security]]<br /> * [[Helix/bwVisu|bwVisu]] for visualization and interactive data analysis<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Storage Funding<br /> |-<br /> |<br /> * Please [[SDS@hd/Acknowledgement|acknowledge]] SDS@hd in your publications.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix&diff=15377 Helix 2025-11-04T09:53:11Z

<p>S Richling: </p> <hr /> <div>[[File:Helix-logo.png|300px]]<br /> <br /> The '''bwForCluster Helix''' is dedicated to research in the bwHPC domains Structural and Systems Biology, Medical Science, Soft Matter, Computational Humanities, and Mathematics and Computer Science.<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> * June 2025: [https://www.bwhpc.de/897.php Important notice regarding the use of MathWorks products]<br /> * April 2025: Cluster extension with 3x gpu8 nodes (Nvidia H200)<br /> * <span style="color:red">8. November 2025: Maintenance 8 am - 8 pm</span><br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [[Helix/Getting Started|Getting Started]]<br /> * E-Learning Course [https://training.bwhpc.de/goto.php/crs/695 Introduction to bwForCluster Helix]<br /> <br /> * [https://www.bwhpc.de/supportportal.php Submit a Ticket] to support unit 'bwHPC - Support > bwForCluster Helix'<br /> <br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | User Documentation<br /> |-<br /> |<br /> * [[Registration/bwForCluster|Registration]] ([[Registration/bwForCluster/RV/Management|RV Management]])<br /> * [[Helix/Login|Login]]<br /> * [[Helix/Hardware|Hardware and Architecture]]<br /> * [[Helix/Filesystems|File Systems and Workspaces]] <br /> * [[Helix/Software|Cluster Specific Software]]<br /> * [[Helix/Slurm|Batch System (Slurm)]] <br /> * [[Helix/bwVisu|bwVisu]] for visualization and interactive applications<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Cluster Funding<br /> |-<br /> |<br /> * Please [[Helix/Acknowledgement|acknowledge]] the cluster in your publications.<br /> |}</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=SDS@hd&diff=15376 SDS@hd 2025-11-04T09:40:15Z

<p>S Richling: </p> <hr /> <div>[[File:sds-hd-logo.png|350px]]<br /> <br /> SDS@hd is a central service for securely storing scientific data (Scientific Data Storage). The service is provided as a state service to researchers of higher education institutions of Baden-Württemberg. It is intended to be used for data that is frequently accessed ('hot data').<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> * November 2022: No special entitlement is needed anymore to participate in an existing storage project.<br /> * September 2023: Service has now been opened for DFN AAI & eduGAIN federation members to participate on existing storage projects.<br /> * 8. November 2025: Maintenance<br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [https://www.urz.uni-heidelberg.de/en/service-catalogue/storage/sdshd-scientific-data-storage Service description & FAQ]<br /> * [mailto:sds-hd-support@urz.uni-heidelberg.de Submit a Ticket]<br /> |}<br /> <br /> {| style=" background:#ffeaef; width:100%;"<br /> | style="padding:8px; background:#f5dfdf; font-size:120%; font-weight:bold; text-align:left" | User Documentation<br /> |-<br /> |<br /> * [[SDS@hd/Registration|Registration]]<br /> * [[SDS@hd/Access|Access]]<br /> * [[SDS@hd/Security|Data Security]]<br /> * [[Helix/bwVisu|bwVisu]] for visualization and interactive data analysis<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Storage Funding<br /> |-<br /> |<br /> * Please [[SDS@hd/Acknowledgement|acknowledge]] SDS@hd in your publications.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix&diff=15375 Helix 2025-11-04T09:38:50Z

<p>S Richling: </p> <hr /> <div>[[File:Helix-logo.png|300px]]<br /> <br /> The '''bwForCluster Helix''' is dedicated to research in the bwHPC domains Structural and Systems Biology, Medical Science, Soft Matter, Computational Humanities, and Mathematics and Computer Science.<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> * June 2025: [https://www.bwhpc.de/897.php Important notice regarding the use of MathWorks products]<br /> * April 2025: Cluster extension with 3x gpu8 nodes (Nvidia H200)<br /> * 8. November 2025: Cluster Maintenance<br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [[Helix/Getting Started|Getting Started]]<br /> * E-Learning Course [https://training.bwhpc.de/goto.php/crs/695 Introduction to bwForCluster Helix]<br /> <br /> * [https://www.bwhpc.de/supportportal.php Submit a Ticket] to support unit 'bwHPC - Support > bwForCluster Helix'<br /> <br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | User Documentation<br /> |-<br /> |<br /> * [[Registration/bwForCluster|Registration]] ([[Registration/bwForCluster/RV/Management|RV Management]])<br /> * [[Helix/Login|Login]]<br /> * [[Helix/Hardware|Hardware and Architecture]]<br /> * [[Helix/Filesystems|File Systems and Workspaces]] <br /> * [[Helix/Software|Cluster Specific Software]]<br /> * [[Helix/Slurm|Batch System (Slurm)]] <br /> * [[Helix/bwVisu|bwVisu]] for visualization and interactive applications<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Cluster Funding<br /> |-<br /> |<br /> * Please [[Helix/Acknowledgement|acknowledge]] the cluster in your publications.<br /> |}</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14979 Helix/bwVisu/CryoSPARC 2025-06-23T12:58:09Z

<p>S Richling: </p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> === The application ===<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> === The database ===<br /> The CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> === Downloads ===<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == CryoSPARC Documentation ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].<br /> <br /> == Known Issues ==<br /> * For the default lane 'localhost', the total installed memory of a compute node is displayed. Note that you can only use the memory that you requested for the CryoSPARC application.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu&diff=14941 Helix/bwVisu 2025-06-05T22:02:46Z

<p>S Richling: </p> <hr /> <div>[[File:BwVisu wide.svg|300px]]<br /> <br /> [https://bwvisu.bwservices.uni-heidelberg.de/ bwVisu] is a scalable service for remote visualization and interactive applications. This easy-to-use, web-based platform provides interactive access to scientific work environments utilizing massive compute and storage resources.<br /> <br /> {| style=" background:#FEF4AB; width:100%;" <br /> | style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News<br /> |-<br /> | <br /> * December 2024: The [https://bwvisu.bwservices.uni-heidelberg.de/ new bwVisu version] based on Open OnDemand is now in operation. You can write feedback to [mailto:bwvisu-support@urz.uni-heidelberg.de bwvisu-support].<br /> |}<br /> <br /> {| style=" background:#eeeefe; width:100%;" <br /> | style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support<br /> |-<br /> | <br /> * [https://www.urz.uni-heidelberg.de/en/service-catalogue/software-and-applications/bwvisu Service Description &amp; FAQ]<br /> * [mailto:bwvisu-support@urz.uni-heidelberg.de Submit a Ticket]<br /> |}<br /> <br /> {| style=" background:#deffee; width:100%;"<br /> | style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left;" | User Documentation<br /> |-<br /> |<br /> * [https://bwvisu.bwservices.uni-heidelberg.de/ <span style="text-decoration: underline;"> Link to Webservice</span>]<br /> * [[Helix/bwVisu/Getting_Started|Getting Started]]<br /> * [[Helix/bwVisu/Usage|Usage]]<br /> * Available applications and user guides:<br /> <br /> {| class="wikitable" style="text-align: center; margin-left: 30px;"<br /> |- style="font-weight:bold;"<br /> ! Application<br /> ! [[Helix/bwVisu/Usage#noVNC_Applications|noVNC App]]<br /> |-<br /> | [[Helix/bwVisu/CryoSPARC|CryoSPARC]]<br /> | ✓<br /> |-<br /> | [https://imagej.net/software/fiji/ Fiji]<br /> | ✓<br /> |-<br /> | [https://www.ilastik.org/ Ilastik]<br /> | ✓<br /> |-<br /> | [https://bio3d.colorado.edu/imod/ IMOD]<br /> | ✓<br /> |-<br /> | [https://docs.mitk.org/2024.12/UserManualPortal.html MITK]<br /> | ✓<br /> |-<br /> | [https://phy.readthedocs.io/en/latest/ Phy]<br /> | ✓<br /> |-<br /> | [https://qgis.org/ QGIS]<br /> | ✓<br /> |-<br /> | [[Helix/bwVisu/JupyterLab|JupyterLab]]<br /> | ☓<br /> |-<br /> | [[Helix/bwVisu/RStudio|RStudio]]<br /> | ☓<br /> |-<br /> | [[Helix/bwVisu/KI-Morph|KI-Morph]]<br /> | ☓<br /> |}<br /> |}<br /> <br /> {| style=" background:#e6e9eb; width:100%;"<br /> | style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Acknowledgement<br /> |-<br /> |<br /> * Please [[Helix/bwVisu/Acknowledgement|acknowledge]] bwVisu in your publications</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14940 Helix/bwVisu/CryoSPARC 2025-06-05T21:58:17Z

<p>S Richling: /* CryoSPARC Documenation */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> === The application ===<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> === The database ===<br /> The CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> === Downloads ===<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == CryoSPARC Documentation ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14939 Helix/bwVisu/CryoSPARC 2025-06-05T21:57:16Z

<p>S Richling: /* The database */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> === The application ===<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> === The database ===<br /> The CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> === Downloads ===<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == CryoSPARC Documenation ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14938 Helix/bwVisu/CryoSPARC 2025-06-05T21:56:28Z

<p>S Richling: /* Documentation for CryoSPARC */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> === The application ===<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> === The database ===<br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> === Downloads ===<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == CryoSPARC Documenation ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14937 Helix/bwVisu/CryoSPARC 2025-06-05T21:56:05Z

<p>S Richling: </p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> === The application ===<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> === The database ===<br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> === Downloads ===<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Documentation for CryoSPARC ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14936 Helix/bwVisu/CryoSPARC 2025-06-05T21:52:28Z

<p>S Richling: /* CryoSPARC in bwVisu */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Documentation for CryoSPARC ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14935 Helix/bwVisu/CryoSPARC 2025-06-05T21:51:33Z

<p>S Richling: /* CryoSPARC License */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Documentation for CryoSPARC ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14934 Helix/bwVisu/CryoSPARC 2025-06-05T21:46:38Z

<p>S Richling: /* CryoSPARC License */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Documentation for CryoSPARC ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14933 Helix/bwVisu/CryoSPARC 2025-06-05T21:40:30Z

<p>S Richling: /* CryoSPARC@bwVisu */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Documentation for CryoSPARC ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14932 Helix/bwVisu/CryoSPARC 2025-06-05T21:40:02Z

<p>S Richling: /* The CryoSPARC Application */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC@bwVisu ==<br /> The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Documentation for CryoSPARC ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14931 Helix/bwVisu/CryoSPARC 2025-06-05T21:38:53Z

<p>S Richling: /* Usage documentation and tutorials */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == The CryoSPARC Application ==<br /> The CryoSPARC application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Documentation for CryoSPARC ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14930 Helix/bwVisu/CryoSPARC 2025-06-05T21:35:01Z

<p>S Richling: /* CryoSPARC@bwVisu */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == The CryoSPARC Application ==<br /> The CryoSPARC application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage documentation and tutorials ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14929 Helix/bwVisu/CryoSPARC 2025-06-05T21:32:16Z

<p>S Richling: /* CryoSPARC in bwVisu */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC@bwVisu ==<br /> The CryoSPARC application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage documentation and tutorials ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14928 Helix/bwVisu/CryoSPARC 2025-06-05T21:30:13Z

<p>S Richling: /* Information about the application */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == CryoSPARC in bwVisu ==<br /> The CryoSPARC application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage documentation and tutorials ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14927 Helix/bwVisu/CryoSPARC 2025-06-05T21:29:49Z

<p>S Richling: /* CryoSPARC License */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start CryoSPARC in bwVisu.<br /> <br /> == Information about the application ==<br /> The CryoSPARC application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage documentation and tutorials ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14926 Helix/bwVisu/CryoSPARC 2025-06-05T21:29:36Z

<p>S Richling: /* CryoSPARC License */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC in bwVisu.<br /> <br /> == Information about the application ==<br /> The CryoSPARC application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage documentation and tutorials ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14925 Helix/bwVisu/CryoSPARC 2025-06-05T21:27:01Z

<p>S Richling: /* Usage Documentation and Tutorials */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the application ==<br /> The CryoSPARC application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage documentation and tutorials ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14924 Helix/bwVisu/CryoSPARC 2025-06-05T21:23:45Z

<p>S Richling: /* Information about the application */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the application ==<br /> The CryoSPARC application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage Documentation and Tutorials ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14923 Helix/bwVisu/CryoSPARC 2025-06-05T21:23:28Z

<p>S Richling: </p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage Documentation and Tutorials ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14922 Helix/bwVisu/CryoSPARC 2025-06-05T21:22:18Z

<p>S Richling: /* Usage Documentation and Tutorials */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage Documentation and Tutorials ==<br /> You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14921 Helix/bwVisu/CryoSPARC 2025-06-05T21:21:58Z

<p>S Richling: /* Documentation and Tutorials */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Usage Documentation and Tutorials ==<br /> You can find usage documentation and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14920 Helix/bwVisu/CryoSPARC 2025-06-05T21:19:42Z

<p>S Richling: </p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.<br /> <br /> == Documentation and Tutorials ==<br /> You can find documation and tutorials for CryoSPARC at [https://cryosparc.com/docs].</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14919 Helix/bwVisu/CryoSPARC 2025-06-05T21:17:18Z

<p>S Richling: </p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14918 Helix/bwVisu/CryoSPARC 2025-06-05T21:12:46Z

<p>S Richling: </p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == CryoSPARC and Topaz ==<br /> CryoSPARC can use an existing installation of Topaz. The path to the Topaz executable is: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code><br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14917 Helix/bwVisu/CryoSPARC 2025-06-05T21:01:29Z

<p>S Richling: </p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14916 Helix/bwVisu/CryoSPARC 2025-06-05T21:00:48Z

<p>S Richling: /* Downloads from CryoSPARC */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory. From there, you can download the results to your own system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14915 Helix/bwVisu/CryoSPARC 2025-06-05T20:59:28Z

<p>S Richling: </p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory. From there, you can download the results to your system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14914 Helix/bwVisu/CryoSPARC 2025-06-05T20:59:05Z

<p>S Richling: </p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the <code>.cryosparc<code> directory in your home directory the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory. From there, you can download the results to your system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14913 Helix/bwVisu/CryoSPARC 2025-06-05T20:57:09Z

<p>S Richling: /* Information about the CryoSPARC Application */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the .cryosparc directory in your home directory the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory. From there, you can download the results to your system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14912 Helix/bwVisu/CryoSPARC 2025-06-05T20:56:48Z

<p>S Richling: /* CryoSPARC License */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC Application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the .cryosparc directory in your home directory the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory. From there, you can download the results to your system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14911 Helix/bwVisu/CryoSPARC 2025-06-05T20:53:13Z

<p>S Richling: /* CryoSPARC Application */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting a CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == Information about the CryoSPARC Application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the .cryosparc directory in your home directory the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory. From there, you can download the results to your system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14910 Helix/bwVisu/CryoSPARC 2025-06-05T20:52:37Z

<p>S Richling: /* Downloads */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting a CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == CryoSPARC Application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the .cryosparc directory in your home directory the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == Downloads from CryoSPARC ==<br /> When you download results from the CryoSPARC application, they are initially saved in your home directory. From there, you can download the results to your system via the file browser in bwVisu.</div>

S Richling https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/CryoSPARC&diff=14909 Helix/bwVisu/CryoSPARC 2025-06-05T20:52:00Z

<p>S Richling: /* CryoSPARC Job */</p> <hr /> <div>[https://cryosparc.com/ CryoSPARC] is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.<br /> <br /> == CryoSPARC License ==<br /> For starting a CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start a CryoSPARC job in bwVisu.<br /> <br /> == CryoSPARC Application ==<br /> The CryoSPACE application starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. <br /> <br /> Note that the CryoSPARC application creates a database in the .cryosparc directory in your home directory the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.<br /> <br /> == Downloads ==<br /> When you download results, they are initially saved in your home directory. From there, you can download the results to your system via the file browser in bwVisu.</div>

S Richling