The Schrödinger Suite is a collection of software for chemical and biochemical use. It offers various tools that facilitate the investigation of the structures, reactivity and properties of chemical systems. There is a campus site license for this software, supported by UITS. More information is available here: http://software.uconn.edu/schrodinger/ .
Load Modules
module load schrodinger/2022-4
You can then see a list of executable programs:
find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/2022-4/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t autots desmond gfxinfo jsc material phase_hy qiksim ska biolumin elements glide jws mxmd phase_qs qpld ssp blast epik hppmap knime oned_scr phase_sc qsite sta bmin epikx ifd licadmin para_tes pipeline run structur confgen fep_abso ifd-md ligand_s pfam prime schrodin testapp confgenx fep_plus impact ligprep phase_bu prime_mm shape_sc vsw consensu fep_solu installa machid phase_da primex shape_sc watermap constant ffbuilde jaguar macromod phase_fi qikfit shape_sc wscore covalent generate jobcontr maestro phase_fq qikprop sitemap
Host Configuration
The Schrödinger Suite is configured to submit jobs directly to the SLURM job scheduler. Therefore, you do not need to wrap your commands in a submission script. You can execute Schrödinger commands directly from a login node. When you submit Schrödinger jobs, you do so to hosts. We have created the following hosts: slurm-parallel-24, slurm-parallel-48, slurm-parallel-96, slurm-parallel-192, slurm-parallel-384. Each one of these hosts will submit a job to SLURM's hi-core parallel partition for the number of cores specified by the number at the end of its name.
Below is a table listing the available Schrodinger hosts on HPC, what partition each host submits the Schrodinger job on, and how many cores are allocated for each host/job.
Host | Partition | Cores being allocated to job |
|---|---|---|
slurm-single | general | 24 |
slurm-parallel-24 | hi-core | 24 |
Example Application Usage
qsite
qsite -SAVE -PARALLEL 24 -HOST slurm-parallel-24 3IIS_Per1.in Launching JAGUAR under jobcontrol. Exec: /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/2022-4/jaguar-v11.8/bin/Linux-x86_64 JobId: job60-login5-1674022
Note that the numeric value of -PARALLEL should match the numeric value of the -HOST that you specified.
You can then view the status of your running job with sacct.
sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
39148 j3IIS_Per1 hi-core abc12345 24 RUNNING 0:0
391148.0 hostname abc12345 24 COMPLETED 0:0
Run Test Suite
testapp -HOST slurm-parallel-24 -DEBUG para_testapp -HOST slurm-parallel-48 -DEBUG
Installation Oddities
Schrödinger comes pre-packaged with an outdated version of mpi(< 1.8.1), meaning an old bug in the MPI->SLURM interface needs to be manually patched by appending the following line to schrodinger's mpi's default config file:
plm_slurm_args = --cpu_bind=boards
Example Submission Script
#!/bin/bash
#SBATCH --partition=general-gpu # Name of Partition
#SBATCH --ntasks=20 # Maximum CPU cores for job
#SBATCH --nodes=1 # Ensure all cores are from the same node
#SBATCH --mem=128G # Request 128 GB of available RAM
#SBATCH --gres=gpu:2 # Request 2 GPU cards for the job
#SBATCH --mail-type=END # Event(s) that triggers email notification (BEGIN,END,FAIL,ALL)
#SBATCH --mail-user=first.lastname@uconn.edu # Destination email address
module load schrodinger/2022-4
host=`srun hostname|head -1`
nproc=`srun hostname|wc -l`
<schrodinger program> -HOST ${host}:${nproc} <other options>