Schrödinger¶

Schrödinger aims to provide integrated software solutions and services that truly meet its customers needs. We want to empower researchers around the world to achieve their goals of improving human health and quality of life through advanced computational techniques that transform the way chemists design compounds and materials.

Policy¶

Schrodinger is available to users at HPC2N who have their own license.

SCHROD_LICENSE_FILE=port@your.license.server

Overview¶

The Schrodinger suite is collection of programs for computational chemistry and molecular modelling.

The suite contains programs such as Maestro, Desmond and Jaguar.

• Maestro is a molecular modelling environment.
• Desmond is a molecular dynamics simulation tool.
• Jaguar is a ab initio electronic structure package.

Usage at HPC2N¶

On HPC2N we have Schrodinger available as a module.

Loading¶

To use the Schrodinger module, add it to your environment. You can find versions with

module spider Schrodinger

and you can then find how to load a specific version (including prerequisites), with

module spider Schrodinger/<VERSION> 

Using the maestro GUI¶

To be able to submit batch jobs directly from inside the maestro GUI there are two extra environment variables that must be set before starting maestro.

export SBATCH_ACCOUNT=your-account
export SBATCH_TIMELIMIT=required-timelimit-for-all-batchjobs

Example for Jaguar¶

Most of the tools creates a submit file and submits it when given the correct parameters.

Here is a typical invocation of jaguar using 28 cores (suitable for a regular Intel Skylake node on Kebnekaise - change for the other node types), note the -QARGS parameter which is passed to the sbatch command.

$SCHRODINGER/jaguar run -HOST batch -PARALLEL 28 -QARGS "-t <hh:mm:ss> -A <YOUR-ACCOUNT-ID>" somefile.in

Submit example for Prime¶

When using Prime one should take advantage of the OpenMP capability it has.

The following submit file is an example of how to run Prime.

#!/bin/bash
#SBATCH -A <your-hpc2n-account>
#SBATCH -J <your-job-name>
#SBATCH -t hh:mm:ss
# Can only run on a single node at the moment so make sure to specify -N 1
#SBATCH -N 1
#SBATCH -n <your-selected-number-of-simultaneous-subjobs-to-use>
#SBATCH -c <your-selected-number-of-OpenMP-threads-to-use>

export LM_LICENSE_FILE="port@your.license.server"

# This example loads Schrodinger 2019-1
module add Schrodinger/2019-1_Advanced_Linux-x86_64  

export SCHRODINGER_NODEFILE=`mktemp`
echo localhost:$SLURM_NTASKS > $SCHRODINGER_NODEFILE

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

$SCHRODINGER/prime_mmgbsa -WAIT -LOCAL -NJOBS <number-of-subjobs-to-split-the-workload-into> <your-parameters>

You can set the number-of-subjobs-to-split-workload-into as high as you like, but there is no reason to choose it larger then the total number of subjobs in the workload. The more sub jobs you split the workload into, the less work is needed during a restart.

To restart a failed or otherwise stopped prime_mmgbsa job, just add -RESTART to the arguments of prime_mmgbsa in the above submit file. Any complaints about any -out.maegz file being incorrect format should be resolved by simply deleting the offending file and the job restarted again.

Submit example for Glide¶

When using Glide we have to create a more complicated submit file. It can only run on a single node at the moment.

#!/bin/bash
#SBATCH -A <your-hpc2n-account>
#SBATCH -J <your-job-name>
#SBATCH -t hh:mm:ss
#SBATCH -N 1
#SBATCH -n <number-of-processors>

export LM_LICENSE_FILE="port@your.license.server"

# This example loads Schrodinger 2019-1 
module add Schrodinger/2019-1_Advanced_Linux-x86_64 

export SCHRODINGER_NODEFILE=`mktemp`
echo localhost:$SLURM_NTASKS > $SCHRODINGER_NODEFILE

# Run with 16 subjobs
$SCHRODINGER/glide -NJOBS 16 -NOJOBID <your-input-file-and-parameters>

Submit example for Multisim¶

#!/bin/bash
#SBATCH -A <your-project-id>
#SBATCH -J <your-job-name>
#SBATCH -t hh:mm:ss
#SBATCH --gpus-per-node=v100:1
#SBATCH -n 1

export LM_LICENSE_FILE="port@your.license.server"

module purge > /dev/null 2>&1  # Clean the environment from any loaded modules
module load Schrodinger/2019-1_Advanced_Linux-x86_64 

$SCHRODINGER/utilities/multisim -WAIT -HOST localhost -maxjob 1 -cpu 1 -m MD-GBP3C5-AL560.msj -c MD-GBP3C5-AL560.cfg MD-GBP3C5-AL560.cms -mode umbrella -set stage[1].set_family.md.jlaunch_opt=["-gpu"] -o MD-GBP3C5-AL560-out.cms -lic DESMOND_GPGPU:1

The important options here are -WAIT -HOST localhost -mode umbrella -set stage... -lic DESMOND_GPGPU:1

Additional info¶

More information can be found

• The official website for Schrödinger
• Schrödinger documentation - requires sign in