Molcas Forum

Kalpa

Member

Registered: 2022-04-09

Posts: 12

pymolcas verify error

Dear Openmolcas developers,

I am experiencing an issue while trying to run the "./pymolcas verify" command while working from a remote machine. I have already compiled Openmolcas and set the path in my .bash_profile. However, when I run the command, it takes a long time to complete and I have to keep my laptop connected to the server. Although most of the calculations run successfully, I am unable to fully complete the verification process as I cannot keep my laptop connected all the time.

To resolve this issue, I have created a script to run the command as follows:
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#!/bin/bash
#SBATCH -N 1
#SBATCH --ntasks-per-node=40
#SBATCH --error=job.%J.err
#SBATCH --time=40:00:00

[b]$molcas/pymolcas -np 40 verify[/b] 

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and all the test fails for this script as mentioned below.

.
.
.
2:additional:837 Failed! (gateway)
2:additional:848 Failed! (seward)
2:additional:852 Failed! (gateway)
2:additional:855 Failed! (seward)
2:additional:860 Failed! (gateway)
2:additional:863 Failed! (gateway)
2:additional:865 Failed! (gateway)
2:additional:875 Failed! (gateway)
2:additional:888 Failed! (gateway)
2:additional:893 Failed! (gateway)
2:additional:894 Failed! (gateway)
2:additional:895 Failed! (gateway)
2:additional:896 Failed! (seward)
2:additional:897 Failed! (seward)
2:additional:899 Failed! (gateway)
2:additional:918 Failed! (gateway)
2:additional:919 Failed! (gateway)
2:additional:922 Failed! (gateway)
2:additional:923 Failed! (seward)
----------
group grayzone from: /home/kalyansingh.bhu/SOFTWARES/openmolcas/OpenMolcas/test/grayzone
3:grayzone:832 Failed! (gateway)
3:grayzone:834 Skipped!
3:grayzone:898 Failed! (gateway)
3:grayzone:920 Failed! (gateway)

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However, when I simply run "./pymolcas verify" in the terminal within the build folder, the tests are successful. But, I can't complete the process in this manner. I am seeking a solution to run this command using a .bash script so that I can monitor its process ID at any time. Can anyone provide a solution for this issue?

Thank you
Kalpa

Last edited by Kalpa (2023-02-06 15:24:17)

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: pymolcas verify error

-np 40 is completely crazy. Even if you wanted to use 40 nodes, it makes no sense for the verification, which is mostly very small calculations. But then you're running apparently in a single node. 40 processes mean 40 guys competing for the disk I/O and each using the MOLCAS_MEM amount of memory (2GB by default).

I don't know if that's your problem (check the *.err files), but definitely try with a single process.