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/ .

It is recommended currently to use Schrodinger through an interactive session because of some issues encountered when submitting jobs through submission scripts.

Start an interactive session:

srun --x11 -N 1 -n 126 -p general --constraint=epyc128 --pty bash

Make sure to include the “--x11” flag for the GUI

Load Modules

Once a node is assigned to the interactive srun job in the previous section, schrodinger can be loaded from one of the various modules available on HPC.

module load schrodinger/2023-3

You can then see a list of executable programs:

find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/2023-3/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t
autots    elements  hppmap    knime     mxmd      phase_qs  qpld      ska
biolumin  epik      ifd       lambda_d  oned_scr  phase_sc  qsite     ssp
blast     epikx     ifd-md    licadmin  para_tes  pipeline  quick_sh  sta
bmin      fep_abso  impact    ligand_s  pfam      prime     run       structur
confgen   fep_plus  installa  ligprep   phase_bu  prime_mm  schrodin  testapp
confgenx  fep_solu  jaguar    machid    phase_da  primex    shape_sc  vsw
consensu  ffbuilde  jobcontr  macromod  phase_fi  qikfit    shape_sc  watermap
constant  generate  jsc       maestro   phase_fq  qikprop   shape_sc  wscore
covalent  gfxinfo   jws       material  phase_hy  qiksim    sitemap   xtb
desmond   glide

You can also see a list of utilities with the same find command above:

Example Application Usage

qsite

Note that the numeric value of -PARALLEL should match the numeric value of the -n declaration that you specified in the previous srun command.

Jaguar

There is a way to target a specific Schrodinger application or utility with the following syntax:

You can then view the status of your running job with sacct.

Run Test Suite

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Schrödinger comes pre-packaged with an outdated version of mpi(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:

Command to call a Schrodinger utility

Launching and disconnecting from an interactive fisbatch Schrodinger job

Schrodinger can be run interactively through srun or fisbatch.

The srun solution above is good for a single interactive calculation that can be left up and running without any disconnections.

If there are network or power interruptions while the Interactive Schrodinger srun job is running, the srun job will end and progress will be lost.

An alternative to avoid potential network/power interruptions for an interactive SLURM srun job would be to submit an interactive fisbatch job to HPC.

Fisbatch is older and it does have some bugs.

Fisbatch allocates a compute node to the job session, which allows users to spawn a calculation interactively through a screen session that launches on the assigned compute node,.

Users can also disconnect from the fisbatch job, and reattach to the job to track the progress of various calculations.

Here is an example to allocate an AMD EPYC compute node with 126 cores through fisbatch under the general partition:

Once a compute node is assigned and the fisbatch job is running, schrodinger can be loaded normally through the module.

Once schrodinger is loaded, the Schrodinger commands will become available and the Schrodinger calculations can be called through one of the many Schrodinger suites.

To disconnect from a fisbatch job, enter the following key strokes:

“Ctrl-a then Ctrl-d”

The screen session that fisbatch spawns on the compute node should detach and the fisbatch job will continue running.

To confirm that the job is still running, the following SLURM command can be entered:

shist

To reattach to the fisbatch job, the following command can be entered:

The fisbatch screen session should reattach and the session enabled for the specific job and the Schrodinger calculation should still be running.

If a network/power interruption happens while a fisbatch job is up and running, the job could potentially end. The network/power interruptions will not affect a job that is detached and running unless the specific assigned node runs into hardware/network problems.