Molcas Forum

angeloraymondrossi

Member

Registered: 2024-04-04

Posts: 17

OpenMolcas and Slurm Arrays - Can't get it to work

Hello everyone.

I am fairly well-versed using SLURM, and with other applications, they work with SLURM arrays.

Here is the problem.  I have an array of subdrectories dir0 ... dir9,  and each subdirectory has an OpenMolcas file, e.g. dir0.input .... dir9.input.

#!/bin/bash
...

All the SLURM stuff and definitions for MOLCAS which works for a single OpenMolcas calculation.

...

#SBATCH --array=0-9

cd dir$SLURM_ARRAY_TASK_ID
pymolcas dir$SLURM_ARRAY_TASK_ID.input -f &

The above DOES NOT WORK and pymolcas throws an error

OR

pymolcas dir$SLURM_ARRAY_TASK_ID/dir$SLURM_ARRAY_TASK_ID.input -f &

This DOES NOT WORK and pymolcas again throws an error.

BUT

cd dir$SLURM_ARRAY_TASK_ID
ls -l *

This DOES WORK and lists the dir0.input ... dir9.input files for each subdirectory.

So I know the idea is correct, but pymolcas throws an error.  I tried this with another QM calculation, and it works.

Finally, on the login node (with the same module load commands for ancillary applications loaded),  if I cd to any subdirectory and execute pymolcas, it works!

on login node:

cd dir0;
pymolcas dir0.input

Can someone please help me with this? 

Thanks so much.

Kind regards,

Angelo

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,080

Re: OpenMolcas and Slurm Arrays - Can't get it to work

What kind of error do you get? Does it work if you a common filename for your inputs (in different directories)? Does "cat dir$SLURM_ARRAY_TASK_ID.input" work?

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,080

Re: OpenMolcas and Slurm Arrays - Can't get it to work

I just tested it, and this worked for me:

cd dir$SLURM_ARRAY_TASK_ID
pymolcas test$SLURM_ARRAY_TASK_ID.input -f

angeloraymondrossi

Member

Registered: 2024-04-04

Posts: 17

Re: OpenMolcas and Slurm Arrays - Can't get it to work

Thanks so much for doing this. 

I worked on it during the morning (EST) and can't get it to work.  So I didn't want to respond.

On our cluster, I have a home directory on a separate filesystem.  My input/output files are on a another separate filesystem.  And finally there is a scratch filesystem where all the projectdir files reside. 

I will get back to you on this.

And again thanks so much for the fast turnaround.

Angelo

angeloraymondrossi

Member

Registered: 2024-04-04

Posts: 17

Re: OpenMolcas and Slurm Arrays - Can't get it to work

Hello,

I found the problem ... I think .  Even if  I run any simple OpenMolcas problem now ... no array job, this the error I am getting:

Traceback (most recent call last):
  File "/home/anr11010/OpenMolcas/build/pymolcas", line 598, in <module>
    sys.exit(main(os.path.realpath(f)))
  File "<string>", line 217, in main
  File "<string>", line 517, in read_input
  File "<string>", line 310, in setup
  File "<string>", line 908, in parallel_task
  File "<string>", line 800, in is_serial
ValueError: invalid literal for int() with base 10: ''

It seems pymolcas is not getting the data it needs to execute.

Do you think you can help with this.

OpenMolcas used to work file,  I don't know what happened.  There was maintenance on the cluster awhile ago.

Regards,

Angelo

angeloraymondrossi

Member

Registered: 2024-04-04

Posts: 17

Re: OpenMolcas and Slurm Arrays - Can't get it to work

Running the same job with pymolcas with the same input and same loaded modules works.   With SLURM I get the previous error.

angeloraymondrossi

Member

Registered: 2024-04-04

Posts: 17

Re: OpenMolcas and Slurm Arrays - Can't get it to work

First and above all,  thanks so much for helping me with this.

I finally had to recompile OpenMolcas.  There was something wrong with the module. It works now!!!!

Again, thanks so much.

Warm regards,

Angelo