JUSTUS2/Software/Schrodinger: Difference between revisions
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{{Softwarepage|chem/schrodinger}} |
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| Availability |
| Availability |
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| [[BwForCluster_Chemistry]] |
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| Links |
| Links |
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| [https://www.schrodinger.com Homepage] | [ |
| [https://www.schrodinger.com Homepage] | [https://www.schrodinger.com/supportdocs/18/ Documentation] |
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| Graphical Interface |
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'''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. |
'''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. |
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= Versions and Availability = |
= Versions and Availability = |
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A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the |
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the |
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<br> |
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<big> |
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[https://cis-hpc.uni-konstanz.de Cluster Information System CIS] |
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<big>[https://cis-hpc.uni-konstanz.de Cluster Information System CIS]</big> |
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</big> |
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{{#widget:Iframe |
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|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/schrodinger |
|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/schrodinger |
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On the command line interface of any bwHPC cluster you'll get a list of available versions by using |
On the command line interface of any bwHPC cluster you'll get a list of available versions by using |
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the command |
the command |
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module avail chem/schrodinger |
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The module is called ''''schrodinger'''' and '''not''' 'schoedinger' or 'schrödinger'! |
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<br> |
<br> |
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''''module avail chem/schrodinger''''. |
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= Availability = |
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Schrödinger is available on the HPC cluster Justus2 to users of the system for no charge. |
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= Remote Visualization = |
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You can connect to the visualization hosts |
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<pre> |
<pre> |
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justus2-vis01.rz.uni-ulm.de |
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: UniCluster |
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justus2-vis02.rz.uni-ulm.de |
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$ module avail chem/schrodinger |
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------------------------ /opt/bwhpc/common/modulefiles ------------------------- |
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chem/schrodinger/2014u1 chem/schrodinger/2015u3 |
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chem/schrodinger/2014u2 chem/schrodinger/2015u4 |
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: Justus |
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$ module avail chem/schrodinger |
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------------------------ /opt/bwhpc/common/modulefiles ------------------------- |
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chem/schrodinger/2015u4 |
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</pre> |
</pre> |
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of the system to access the graphical interface "maestro" using a vnc viewer. |
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<br> |
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Please follow the documentation on our page on [[VNC]] |
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= License and Registering = |
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Schrödinger, especially Maestro, is available after registering for academical use for no charge. Downloadable here: [https://www.schroedinger.com/downloadcenter/ Download Center]<br> |
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Your request will be verified and after that you can download Maestro for academical use. That will take about 48 hours. |
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== |
== Running == |
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If you are on one of the vis servers inside VNC: |
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=== Requesting the License Key === |
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After installing Maestro you need a license key which you can request from the „Competence Center for Bioinformatics“. Please contact |
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==== Set environment variable for the license server ==== |
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When you got the licence server information, set it as an environment variable, editing $LICENSE_SERVER$ in the following command. |
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<pre>export LM_LICENSE_FILE=$LICENSE_SERVER$</pre> |
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On a Mac system you should additionally execute following tasks |
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<pre>sudo vi /etc/launchd.conf</pre> |
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Insert: <pre>setenv LM_LICENSE_FILE $LICENSE_SERVER$</pre> and save the file. |
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Execute following command and start Maestro from Sportlight: |
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<pre>launchctl setenv LM_LICENSE_FILE $LICENSE_FILE$</pre> |
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=== bwGRiD/bwUni/JUSTUS specific installation === |
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Follow the instruction for your operating system. |
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==== Linux/Mac ==== |
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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 |
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<pre>chmod u+x post-install.sh</pre> |
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and execute it. |
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<pre>./post-install.sh</pre> |
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You will be asked for the License Server, your usernames on the cluster and the schrodinger path/version. |
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==== Windows ==== |
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$SCHRODINGER ist the path to your schrodinger installation. |
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Download [https://codeload.github.com/marekdynowski/MOAB-Schroedinger-Submitter/zip/master this zipfile], extract it and copy the MOAB folder to $SCHRODINGER/queues/. |
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Download the [https://raw.githubusercontent.com/marekdynowski/bwSchrodingerHosts/master/schrodinger.hosts sample schrodinger.hosts] |
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and change the entries |
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* %LICENSE_SERVER% the address of the license server |
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* %USER_BWGRID% your username on the bwhpc cluster |
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* %USER_BWUNI% your username on the bwUni cluster |
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* %USER_BWJUSTUS% your username on the Justus cluster |
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* %SCHROD_VERSION% the schrodinger version (e.g. 2015u4) |
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You can delete sections of the schrodinger.hosts if you don't have an account on these clusters. |
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Please execute these commands in your windows shell. (Close Schrodinger before executing these commands!) |
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<pre> |
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cd $SCHRODINGER/utilities |
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feature_flags.exe -d JOBCON_JSERVER_GO |
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jserver.exe -cleanall |
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jserver.exe -shutdown |
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</pre> |
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<code>vglrun maestro -NOSGL</code> |
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== Usage == |
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on normal login hosts inside VNC without hardware accelerations |
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=== Copy your public key === |
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Maestro needs a passwordless login for submitting jobs on the cluster. |
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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. |
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<code>maestro -SGL</code> |
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=== Using Maestro with the offered example === |
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First start Maestro and choose the following menu items:<br> |
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[[File:Schrodinger-Usage01.jpg]] |
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To start maestro in the mode for the other suites: |
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* <code>vglrun maestro -profile BioLuminate &</code> |
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Then load the molecularDynamicsExample.cms from your filesystem:<br> |
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[[File:Schrodinger-Usage02.jpg]] |
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* <code>vglrun maestro -profile Elements & </code> |
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* <code>vglrun maestro -profile MaterialsScience &</code> |
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Choose your desired host and click "Run".<br> |
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[[File:Schrodinger-Usage03.jpg]] |
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=== Monitoring your Job === |
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Maestro offers an job monitoring interface, which you can start in the left corner of the molecule window. |
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[[File:Schrodinger-Monitor01.jpg]] |
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Furthermore you are able to manipulate you job on the cluster. |
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== Submitting Jobs == |
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[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]] |
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You can submit jobs from within the Schrödinger GUI Maestro. |
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Make sure to only run calculations on localhost directly for short minimalizations and submit to the compute nodes for any longer runs. |
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Latest revision as of 11:44, 6 December 2022
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The main documentation is available via |
| Schrödinger | |
|---|---|
| module load | chem/schrodinger |
| Availability | BwForCluster_Chemistry |
| License | commercial |
| Citing | 5. See Schrodinger manual |
| Links | Homepage | 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.
Availability
Schrödinger is available on the HPC cluster Justus2 to users of the system for no charge.
Remote Visualization
You can connect to the visualization hosts
justus2-vis01.rz.uni-ulm.de justus2-vis02.rz.uni-ulm.de
of the system to access the graphical interface "maestro" using a vnc viewer.
Please follow the documentation on our page on VNC
Running
If you are on one of the vis servers inside VNC:
vglrun maestro -NOSGL
on normal login hosts inside VNC without hardware accelerations
maestro -SGL
To start maestro in the mode for the other suites:
vglrun maestro -profile BioLuminate &
vglrun maestro -profile Elements &
vglrun maestro -profile MaterialsScience &
Submitting Jobs
You can submit jobs from within the Schrödinger GUI Maestro. Make sure to only run calculations on localhost directly for short minimalizations and submit to the compute nodes for any longer runs.