JUSTUS2/Software/Schrodinger: Difference between revisions
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= Availability = |
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= License and Registering = |
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Schrödinger |
Schrödinger is available on the HPC cluster Justus2 to users of the system for no charge. |
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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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You can connect to the visualization hosts of the system to access the graphical interface "maestro" via [[VNC]] |
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== Prerequirements == |
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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“ or CompChem. Please contact us via https://bw-support.scc.kit.edu/ |
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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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[[Category:Chemistry software]] |
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Insert: <pre>setenv LM_LICENSE_FILE $LICENSE_SERVER$</pre> and save the file. |
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[[Category:bwForCluster_Chemistry]] |
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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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=== bwUni/JUSTUS specific installation === |
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Copy project files to the cluster after building. Request an interactive node and use [[vnc]] to continue working interactively. |
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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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== Usage == |
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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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=== 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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Then load the molecularDynamicsExample.cms from your filesystem:<br> |
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[[File:Schrodinger-Usage02.jpg]] |
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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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[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]] |
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Revision as of 13:50, 29 June 2020
| Schrödinger | |
|---|---|
| module load | chem/schrodinger |
| Availability | bwUniCluster | BwForCluster_Chemistry | bwGRiD Tuebingen |
| 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.
Versions and Availability
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
Cluster Information System CIS {{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/schrodinger |width=95% |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
The module is called 'schrodinger' and not 'schoedinger' or 'schrödinger'!
Availability
Schrödinger is available on the HPC cluster Justus2 to users of the system for no charge.
You can connect to the visualization hosts of the system to access the graphical interface "maestro" via VNC