Page Comparison

...

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

Multisim example:

$SCHRODINGER/utilities/multisim < rest Of command options here >

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

...

"${SCHRODINGER}/utilities/multisim" -JOBNAME desmond_md_job_TREK1model_1ms < restOfCommandOptions >

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:

fisbatch -N 1 -n 126 -p general --constraint='epyc128'

FISBATCH -- waiting for JOBID jobidhere to start on cluster=slurm and partition=general
.........................!
Warning: Permanently added 'cXX,137.99.x.x' (ECDSA) to the list of known hosts.
FISBATCH -- Connecting to head node (cnXX)

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

module load schrodinger/2023-3

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:

 fisattach jobidhere

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