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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

Quantum Espresso

Quantum Espresso can be used to run various Schrödinger suites.

QE is the leading high-performance, open-source quantum mechanical software package for nanoscale modeling of material

It is recommended to load a global openmpi version available through the SPACK package manager to allow for MPI communications before loading and running Quantum Espresso.

A section on how to load openmpi through SPACK is available at the bottom of the following openmpi knowledge base article:

https://kb.uconn.edu/space/SH/26033783855/OpenMPI+Guide

To load Quantum Espresso on HPC for the use of the Schrödinger suite after openmpi has been loaded, the following module load line can called.

module load quantumespresso/7.1

The quantumespresso/7.1 module will automatically load the needed schrodinger/2022-4 module.

Quantum Espresso provides an executable that can take various command line options to run needed calculations.

Here are the command line options that are available for the Quantum Espresso run_qe executable:

run_qe
Provide EXE_NAME
Usage: run_qe EXE_NAME TPP OPENMP INPUT_FILE

The available options are:

EXE_NAME=Name Of Schrödinger EXE (maestro, desmond, etc)

TPP=# value (1, 2, 3, etc)

OPENMP=MPI command (mpirun, mpiexec, etc)

INPUT_FILE=Input File looking to be run

Example to run a maestro job with mpi:

module load openmpi/4.1.4 quantumespresso/7.1
run_qe maestro 2 mpirun code.in
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