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Schrodinger

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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

1 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.

2 Versions and Availability

A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS

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'.

: 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

The module is called 'schrodinger' and not 'schoedinger' or 'schrödinger'!

3 License and Registering

Schrödinger, especially Maestro, is available after registering for academical use for no charge. Downloadable here: Download Center
Your request will be verified and after that you can download Maestro for academical use. That will take about 48 hours.

3.1 Prerequirements

3.1.1 Requesting the License Key

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

3.1.1.1 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.

export LM_LICENSE_FILE=$LICENSE_SERVER$

On a Mac system you should additionally execute following tasks

sudo vi /etc/launchd.conf
Insert:
setenv LM_LICENSE_FILE $LICENSE_SERVER$
and save the file.

Execute following command and start Maestro from Sportlight:

launchctl setenv LM_LICENSE_FILE $LICENSE_FILE$

3.1.2 bwGRiD/bwUni/JUSTUS specific installation

Follow the instruction for your operating system.

3.1.2.1 Linux/Mac

Download this file and open a terminal in the download folder. Make the bash-script executable

chmod u+x post-install.sh

and execute it.

./post-install.sh

You will be asked for the License Server, your usernames on the cluster and the schrodinger path/version.

3.1.2.2 Windows

$SCHRODINGER ist the path to your schrodinger installation. Download this zipfile, extract it and copy the MOAB folder to $SCHRODINGER/queues/.

Download the 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!)

cd $SCHRODINGER/utilities
feature_flags.exe -d JOBCON_JSERVER_GO
jserver.exe -cleanall
jserver.exe -shutdown

3.2 Usage

3.2.1 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 .ssh/id_rsa.pub into .ssh/authorized_keys file on the cluster.

3.2.2 Using Maestro with the offered example

First start Maestro and choose the following menu items:
Schrodinger-Usage01.jpg


Then load the molecularDynamicsExample.cms from your filesystem:
Schrodinger-Usage02.jpg


Choose your desired host and click "Run".
Schrodinger-Usage03.jpg

3.2.3 Monitoring your Job

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