Scientific Computing and Data

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Schrodinger Suite

Note that this software is open only to users who are in the groups contributing to the license cost. Please contact Professor Roberto Sanchez at roberto.sanchez@mssm.edu for more information.

Access to the Schrödinger Suite on Minerva is by way of the module system:

module load schrodinger

The current default version is 2021-3.  To see all available versions on Minerva:

module avail schrodinger

In order to use the graphics interface add an -X flag to your normal ssh connection to establish X-forwarding:

ssh -X <userid>@minerva.hpc.mssm.edu

To submit a job to a queue on Minerva, you must have a host file ‘schrodinger.hosts‘ in “~/.schrodinger” directory or the job’s working directory. This host file has to be configured properly with specific requirements about your job including the allocation account, walltime, and others. It’s supposed to be user-specific.

You may use the following example host file with required modification for your jobs. See the Installation Guide for details.

 

Name:        localhost
#
# Set "tmpdir" to a temporary directory in your work/scratch folder.
#     e.g. /sc/arion/work/your_user_ID/.tmp_schrodinger
#
tmpdir:      /sc/arion/work/choh07/.tmp_schrodinger 

Name: serial_premium_30min
Host: li03c03
Processors: 2500
Queue: LSF
Qargs: -q premium -P acc_XXX -n 1 -W 30

Name: parallel_express_1hr
Host: li03c03
Processors: 1500
Queue: LSF
Qargs: -q express -P acc_XXX -n %NPROC% -R\"span[ptile=12]\" -W 1:00

Name: gpu_1hr
Host: li03c03
processors: 2500
Queue: LSF
Qargs: -q gpu -P acc_XXX -R v100 -n %NPROC% -R\"span[ptile=24]\" -W 1:00
gpgpu: 0, Tesla v100
gpgpu: 1, Tesla v100

Name: parallel_express_1hr
Host: li03c03
Processors: 7680
Queue: LSF
Qargs: -q express -P acc_XXX -n %NPROC% -R\"span[ptile=32]\" -W 1:00

Name: bode_parallel_express_2hr
Host: li03c03
Processors: 2484
Queue: LSF
Qargs: -q express -P acc_XXX -m bode -n %NPROC% -R\"span[ptile=12]\" -W 2:00

 

If you want to run jobs on your local machine, you may install the Schrodinger Suite locally.  Download the suite compatible with your machine from the Schrodinger web site. You may need to create an account to download the suite.

Please note that job submission to the queueing system of Minerva remotely from the locally installed Schrodinger Suite on your machine is not feasible due to requirement of two-factor authentication.

To set up access to the license server from your local workstation the environment variable “SCHROD_LICENSE_FILE” has to be set to “license.hpc.mssm.edu”:

Linux

(bash) export SCHROD_LICENSE_FILE=43723@license.hpc.mssm.edu

(csh) setenv SCHROD_LICENSE_FILE 43723@license.hpc.mssm.edu

Mac/Windows
Create or update the file:

“/Library/Application Support/Schrodinger/license.txt” (Mac)
“C:\Program Files\Schrodinger2021-3\license.txt” (Windows)

to include the following two lines:

SERVER license.hpc.mssm.edu ANY 43723
USE_SERVER