BwUniCluster2.0/Software/Mathematica

2016-11-03T16:34:10Z

R Rutka: /* Parallel Computation */

{| width=600px class="wikitable"
|-
! Description !! Content
|-
| module load
| math/mathematica
|-
| Availability
| [[bwUniCluster]] | [[bwForCluster_MLS&WISO_Production]]
|-
| License
| Commercial. See [http://www.wolfram.com/mathematica/pricing/ Mathematica Pricing].
|-
| Citing
| n/a
|-
| Links
| [http://www.wolfram.com/mathematica/ Homepage] | [http://www.wolfram.com/support/?source=nav Documentation]
|-
| Graphical Interface
| Yes (See [[VNC]])
|-
| Comments
| Mathematica might not be available on all locations and clusters.
|}

== Description ==
'''Mathematica''' is a software from Wolfram for symbolic and numerical computation with many features such as powerful visualization and application specific functions.
 
 
== Versions and Availability ==
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
 
<big>
[https://cis-hpc.uni-konstanz.de/prod.cis/ Cluster Information System CIS]
</big>
{{#widget:Iframe
|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/math/mathematica
|width=90%
|height=330
|border=0
}}

= Loading =
To check if Mathematica is available execute
$ module avail math/mathematica

If Mathematica is available you can load a specific version or you can load the default version with
$ module load math/mathematica

= General Usage =
Mathematica can be used interactively on the command line or with a graphical front-end.
Alternatively Mathematica can run a script in batch mode which is useful when submitting batch jobs to the cluster.
After loading Mathematica the different modes can be used as follows.

*Interactive with GUI (needs [[X11 forwarding]] or [[VNC]]): <pre>$ mathematica</pre>

*Interactive with command line: <pre>$ math</pre>

*Non-Interactive. Looks like interactive with command line but input is taken from script.m: <pre>$ math < script.m</pre>

*Non-Interactive. You have to explicitly specify what you want to print <pre>$ math -script script.m</pre>However, the output is done in InputForm which is suitable for input in other Mathematica calculations but if you want pretty output you have to change the output format to OutputForm like this <pre>SetOptions[$Output, FormatType -> OutputForm]</pre>

For an introduction to Mathematica we refer to the online documentation ([http://reference.wolfram.com/mathematica/guide/Mathematica.html Mathematica Documentation Center]). Specific information on the use in a compute cluster is in the next section.

= Parallel Computation =
Obviously parallel computation can be useful to speed up time-consuming computations, but it should also be used for multiple computations with different input data files (e.g. for parametric studies). The reason for this
is the license model from Wolfram. There are two types of licenses.
* Each time an instance of Mathematica starts, a so called MathKernel license is used up.
* Each time Mathematica spawns a subprocess, a license called SubMathKernel is used up.
Because usually there are much more SubMathKernel licenses than MathKernel licenses it is recommended to start multiple subprocesses instead of submitting multiple jobs.

Remember to request the correct amount of processors in your [[Batch Jobs]] script but note that Mathematica will not automatically use these processors.
In general you have to adjust your code to benefit from more cores.
To do this you first have to start a number of kernels which are then used by ParallelTable to run the computations in parallel.
This basic example computes the first eight square numbers in parallel.
<pre>
LaunchKernels[8]
f[i_] := i^2
DistributeDefinitions[f]
ParallelTable[f[i], {i,0,7}]
CloseKernels[]
</pre>
Note that the use of DistributeDefinitions is necessary for f is a user defined function and the definition of this function must be available to all kernels.

The next example is the computation of a numerical solution for the following initial value problem
x'(t) = x(t)^2 - x(t)^3
x(0) = d
It is difficult to solve this equation with high accuracy at the point 1/d.
We decrease the step size of the algorithm to see how the execution time and the relative error at the point 1/d change.

<pre>
d = 0.00001

y[t_] := 1/(ProductLog[(1/d-1)*Exp[1/d-1-t]]+1) (* analytical solution *)
relerr[t_, s_] := Abs[(y[t] - x[t]/.s)/y[t]] (* relative error of solution s at time t *)
g[v_] := {v[[1]], v[[2]][[1]], relerr[1/d, v[[2]][[2]][[1]]]} (* helper function *)

(* compute numerical solutions for 6 different step sizes *)
LaunchKernels[6]
tbl = ParallelTable[{step, Timing[NDSolve[{x'[t] == x[t]^2 - x[t]^3, x[0] == d}, x, {t, 0, 2/d}, MaxStepSize->step, MaxSteps->10000000]]}, {step,5,3,-0.4}]
CloseKernels[]

SetOptions[$Output, FormatType -> OutputForm] (* better output when called with -script *)
Print[ Grid[Join[{{"Stepsize", "Time", "Error at 1/d"}}, Map[g, tbl]]] ] (* print the result *)
</pre>
Mathematica features some further functions similar to ParallelTable which are documented on the [http://reference.wolfram.com/mathematica/guide/ParallelComputing.html Mathematica parallel computing webpage] from Wolfram. One such function is ParallelSubmit which can be used to start two (or more) completely unrelated functions in parallel. But bear in mind that the functions should have similar running times because the scheduler reserves the requested resources for the runtime of the whole job. The following code shows how to pack two 1-core jobs into one 2-core job.
<pre>
f[r_] := (
d = 0.000001;
{time, sol} = Timing[NDSolve[{x'[t] == r*x[t]^2 - x[t]^3, x[0] == d}, x, {t, 0, 2/d}, MaxStepSize->3, MaxSteps->10000000]];
{time, x[1/d]/.sol[[1]]}
)

g[r_] := (
{time, sol} = Timing[NDSolve[{y''[t] + (r+1)*y'[t] + r*y[t] == 0, y[0] == 1, y'[0] == 0}, y, {t, 0, 30}, MaxStepSize->0.000002, MaxSteps->10000000000]];
{time, y[30]/.sol[[1]]}
)

kernel1 := (
file = OpenWrite["out1.txt", FormatType -> OutputForm];
$Output = {file};
Print[f[1.2]];
Close[file];
)

kernel2 := (
file = OpenWrite["out2.txt", FormatType -> OutputForm];
$Output = {file};
Print[g[1000]];
Close[file];
)

LaunchKernels[2]
DistributeDefinitions[kernel1, kernel2]
e = {ParallelSubmit[kernel1], ParallelSubmit[kernel2]}
WaitAll[e]
</pre>
The helper functions kernel1 and kernel2 get started in different threads and then they execute f and g. The output of these functions is redirected to different files so the results can clearly be distinguished and examined as soon as one function is done.

[[Category:Mathematics software]] [[Category:bwUniCluster]][[Category:BwForCluster_BinAC]] [[Category:bwForCluster_MLS&WISO_Production]]

2016-06-01T14:26:33Z

R Rutka: /* Versions and Availability */

{| width=600px class="wikitable"
|-
! Description !! Content
|-
| module load
| chem/orca
|-
| Availability
| [[bwUniCluster]] | [[BwForCluster_Chemistry]]
|-
| License
| [https://orcaforum.cec.mpg.de/license.html "Research group" license]
|-
|Citing
| [https://orcaforum.cec.mpg.de/OrcaManual.pdf As described in the manual]
|-
| Links
| [https://orcaforum.cec.mpg.de/ ORCA Forum Homepage] | [https://orcaforum.cec.mpg.de/OrcaManual.pdf Documentation]
|-
| Graphical Interface
| No
|}
 
= Description =
'''ORCA''' is a modern electronic structure program package. It is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.
 
ORCA is able to carry out geometry optimizations and to predict a large number of spectroscopic parameters at different levels of theory. Besides the use of Hartee Fock theory, density functional theory (DFT) and semiempirical methods, high level ab initio quantum chemical methods, based on the configuration interaction and coupled cluster methods, are included into ORCA to an increasing degree.
 
Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.
 
Implemented Methods
* Semiempirical INDO/S, MNDO, AM1, PM3, NDDO/1
* Hartee Fock theory (RHF, UHF, ROHF and CASSCF) all in direct, semidirect, or conventional mode, different RI approximations
* DFT including a reasonably large number of exchange and correlation functionals including hybrid DFT and the most recent double hybrid functionals (see below).
* High level single reference correlation models: CCSD(T), QCISD(T), CEPA, CPF (with and without RI, Local)
* High level ab-initio individual selecting multireference methods (MRCI, MRMP2, MRMP3, MRMP4, MRACPF, MRAQCC, SORCI, DDCI) for ground- and excited-states.
* Geometry optimization in redundant internal coordinates using analytical gradient techniques for all SCF methods as well as MP2.
* Excited state calculations via TD-DFT and CI-singles (CIS). For CIS an analytic gradient is also available. The doubles correction is available for CIS(D) in an efficient implementation.
* Scalar relativistic ZORA, IORA and Douglas-Kroll-Hess (DKH) approaches, picture change effects, all-electron basis sets, effective core potentials
* The COSMO model is available throughout the package for continuum dielectric modeling of the environment.
* QM/MM interface to GROMACS
* Double hybrid functionals including a fraction of nonlocal correlation. Analytic gradients are also available (these methods were invented by the Grimme group).
* Van der Waals correct density functionals.
 
For more information on features please visit [https://orcaforum.cec.mpg.de/ ''The ORCA Portal of the Max-Planck Institute''] web page.
 
 

= Versions and Availability =
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
 
<big>

[https://cis-hpc.uni-konstanz.de Cluster Information System CIS]

</big>
{{#widget:Iframe
|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/orca
|width=99%
|height=230
|border=0
}}
On the command line interface of any bwHPC cluster you'll get a list of available versions by using
the command
 
''''module avail chem/orca''''.
<pre>
$ module avail chem/orca # bwUniCluster
------------------------ /opt/bwhpc/common/modulefiles -------------------------
chem/orca/3.0.1 chem/orca/3.0.3
</pre>
 

= License =
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.
 
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.
 
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]
 
 
= Usage =
== Loading the module ==
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.
<pre>
$ module load chem/orca
module avail chem/orca
------------------------ /opt/bwhpc/common/modulefiles ----------------------
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)
$ module load chem/orca
</pre>
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.
 
If you wish to load a specific (older) version, you can do so using e.g.
 
''''module load chem/orca/'''version' to load the version you desires.
<pre>
$ module load chem/orca/3.0.1 # bwUniCluster example
Please do not use this module if you do not own a valid ORCA group license.
Please cite ORCA in your publications according to ORCA documentation.
Please read 'module help chem/orca/3.0.1' before using ORCA.
</pre>
 
Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler!
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen. 
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca! 
This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!
 

== Program Binaries ==
You can find the ORCA binaries in the main folder of the ORCA system.
 
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].
<pre>
$ ls -x $ORCA_BIN_DIR
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot
otool_cosmo otool_gcp otool_smd
$
</pre>
Only the programs with the suffix '''_mpi''' are compiled including OPENMPI functionality.
 

== Disk Usage ==
Scratch files are written to the current directory by default. 
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations.
 
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.
<pre>
$ cd $(ws_find calc_repo)
['your-id'-calc_repo-0]$ pwd
/work/workspace/scratch/'your-id'-calc_repo-0
['your-id'-calc_repo-0]$
</pre>

== Examples ==
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'
<pre>
$ cd $(ws_find calc_repo)
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .
$ cp bwhpc-orca-example.moab myorcajob.moab
§ vi myorcajob.moab # do your own modifications
$ msub myorcajob.moab # start job submission
</pre>
 
= ORCA-Specific Environments =
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,
use ''''env | grep ORCA'''' 
Or try the command ''''module show 'chem/orca'''/version'.
<pre>
$ module load chem/orca/3.0.3
$ env | grep ORCA
ORCA_VERSION=3.0.3
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3
</pre>
 
= Version-Specific Information =
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.
 
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.
 
Examples
<pre>
$ module avail chem/orca
------------------------------ /opt/bwhpc/common/modulefiles ---------------------------------------
chem/orca/3.0.1 chem/orca/3.0.3

$ module whatis chem/orca/3.0.1
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')

$ module help chem/orca/3.0.1
----------- Module Specific Help for 'chem/orca/3.0.1' ------------
This module provides the quantum chemistry package ORCA version 3.0.1
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca'
[...]
Documentation:
* Max-Planck-Institut fuer Chemische Energiekonversion
https://cec.mpg.de/forum/portal.php
* New features for version 3.0.1
https://cec.mpg.de/forum/portal.php#a3
* Manuals in pdf format:
/opt/bwhpc/common/chem/orca/3.0.1/manual
* Example data and a Moab example script can be found here:
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples
[...]
</pre>
 
----
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]

2016-03-14T08:42:45Z

R Rutka:

{| width=600px class="wikitable"
|-
! colspan="2" style="text-align:center" | Schrödinger
|-
| module load
| chem/schrodinger

|-
| Availability
| [[bwUniCluster]] | [[BwForCluster_Chemistry]] | bwGRiD Tuebingen

|-
| License
| commercial
|-
|Citing
| 5. See Schrodinger manual
|-
| Links
| [https://www.schrodinger.com Homepage] | [http://www.schrodinger.com/supportdocs/18/ Documentation]
|-
| Graphical Interface
| Yes, Maestro, Desmond
|}

== Description ==
'''Schrödinger''' is a collection of software chemical or biochemical use. It offers various tools, like Maestro, that acts like an interface to all other schrödinger software and it is supposed to be used for material science, to investigate the structure, the reactivity and properties of chemical systems. Maestro is part of the Materials science suite.

= Versions and Availability =
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
 
<big>

[https://cis-hpc.uni-konstanz.de Cluster Information System CIS]

</big>
{{#widget:Iframe
|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/schrodinger
|width=99%
|height=330
|border=0
}}
On the command line interface of any bwHPC cluster you'll get a list of available versions by using
the command
 
''''module avail chem/schrodinger''''.
<pre>
: UniCluster
$ module avail chem/schrodinger
------------------------ /opt/bwhpc/common/modulefiles -------------------------
chem/schrodinger/2014u1 chem/schrodinger/2015u3
chem/schrodinger/2014u2 chem/schrodinger/2015u4
: Justus
$ module avail chem/schrodinger
------------------------ /opt/bwhpc/common/modulefiles -------------------------
chem/schrodinger/2015u4
</pre>
 

= License and Registering =
Schrödinger, especially Maestro, is available after registering for academical use for no charge. Downloadable here: [https://www.schroedinger.com/downloadcenter/ Download Center] 
Your request will be verified and after that you can download Maestro for academical use. That will take about 48 hours.

== Prerequirements ==
=== Requesting the License Key ===
After installing Maestro you need a license key which you can request from the „Competence Center for Bioinformatics“. Please contact

==== Set environment variable for the license server ====
When you got the licence server information, set it as an environment variable, editing $LICENSE_SERVER$ in the following command.
<pre>export LM_LICENSE_FILE=$LICENSE_SERVER$</pre>

On a Mac system you should additionally execute following tasks
<pre>sudo vi /etc/launchd.conf</pre>

Insert: <pre>setenv LM_LICENSE_FILE $LICENSE_SERVER$</pre> and save the file.

Execute following command and start Maestro from Sportlight:
<pre>launchctl setenv LM_LICENSE_FILE $LICENSE_FILE$</pre>

=== bwGRiD/bwUni/JUSTUS specific installation ===

Follow the instruction for your operating system.

==== Linux/Mac ====

Download [https://raw.githubusercontent.com/marekdynowski/bwSchrodingerHosts/master/post-install.sh this file] and open a terminal in the download folder. Make the bash-script executable
<pre>chmod u+x post-install.sh</pre>
and execute it.
<pre>./post-install.sh</pre>
You will be asked for the License Server, your usernames on the cluster and the schrodinger path/version.

==== Windows ====

$SCHRODINGER ist the path to your schrodinger installation.
Download [https://codeload.github.com/marekdynowski/MOAB-Schroedinger-Submitter/zip/master this zipfile], extract it and copy the MOAB folder to $SCHRODINGER/queues/.

Download the [https://raw.githubusercontent.com/marekdynowski/bwSchrodingerHosts/master/schrodinger.hosts sample schrodinger.hosts]
and change the entries
* %LICENSE_SERVER% the address of the license server
* %USER_BWGRID% your username on the bwhpc cluster
* %USER_BWUNI% your username on the bwUni cluster
* %USER_BWJUSTUS% your username on the Justus cluster
* %SCHROD_VERSION% the schrodinger version (e.g. 2015u4)
You can delete sections of the schrodinger.hosts if you don't have an account on these clusters.

Please execute these commands in your windows shell. (Close Schrodinger before executing these commands!)
<pre>
cd $SCHRODINGER/utilities
feature_flags.exe -d JOBCON_JSERVER_GO
jserver.exe -cleanall
jserver.exe -shutdown
</pre>

== Usage ==

=== Copy your public key ===
Maestro needs a passwordless login for submitting jobs on the cluster.
Login to the cluster and copy your public key of your host system from <tt>.ssh/id_rsa.pub</tt> into <tt>.ssh/authorized_keys</tt> file on the cluster.

=== Using Maestro with the offered example ===
First start Maestro and choose the following menu items: 
[[File:Schrodinger-Usage01.jpg|200px]]

Then load the molecularDynamicsExample.cms from your filesystem: 
[[File:Schrodinger-Usage02.jpg|200px]]

Choose your desired host and click "Run". 
[[File:Schrodinger-Usage03.jpg|200px]]

=== Monitoring you job ===
Maestro offers an job monitoring interface, which you can start in the left corner of the molecule window.
[[File:Schrodinger-Monitor01.jpg]]
Furthermore you are able to manipulate you job on the cluster.

[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]