Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 6 Next »

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    diagnost  gfxinfo   jsc       material  phase_fq  qikprop   ska
biolumin  elements  glide     jws       mxmd      phase_hy  qiksim    ssp
blast     epik      HPC1.0Or  knime     oned_scr  phase_qs  qpld      sta
bmin      epikx     hppmap    licadmin  Original  phase_sc  qsite     structur
confgen   fep_abso  ifd       ligand_s  para_tes  pipeline  run       testapp
confgenx  fep_plus  ifd-md    ligprep   pfam      prime     schrodin  version.
consensu  fep_solu  impact    machid    phase_bu  prime_mm  shape_sc  vsw
constant  ffb_fep_  installa  macromod  phase_da  primex    shape_sc  watermap
covalent  ffbuilde  jaguar    maestro   phase_fi  qikfit    sitemap   wscore
desmond   generate  jobcontr

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

Example Application Usage

qsite

qsite -SAVE -PARALLEL 24 -HOST slurm-parallel-24 3IIS_Per1.in 
Launching JAGUAR under jobcontrol.
Exec: /apps2/schrodinger/2016-2/jaguar-v9.2/bin/Linux-x86_64
JobId: cn01-0-57b33646

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   parallel   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

schrodinger 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 Schrodinger 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 Schrodinger 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 options are:

EXE_NAME=Name Of Schrodinger 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:

run_qe maestro 2 mpirun code.in
  • No labels