Slurm script fails when I request mpirun/ntasks

[slabhan1]

I am trying to run a LIS (module openmpi_5.0.0) with the following slurm script on Milan:

#!/bin/bash

#SBATCH -J cold_30node
#SBATCH --constraint=mil 
#SBATCH --ntasks=1

#SBATCH --time=00:00:40
#SBATCH --output=./LDAS_irri/lisjob.out
#SBATCH -D ./wd/
#SBATCH --no-requeue
#SBATCH --mail-type=ALL
#SBATCH --error=./LDAS_irri/error.log
module purge
source $HOME/.profile


module use --append $HOME/privatemodules

module load lisf_7.5_intel_2023.2.1_openmpi_5.0.0

time mpirun -np 1 ./LIS -f ./LDAS_irri/lis_config_2001

exit 0

Which throws the error:

I have tried to run this without "mpirun -np 1" and "ntasks = 1" and it works just fine, so I imagine it's not an issue with the executable/config. I can't figure out why I can't run this with mpirun, please help!
mpirun --version
mpirun (Open MPI) 5.0.0

sinfo --version
slurm 22.05.11

[dmocko]

Hi @slabhan1

Sorry for the delay in responding. If you are only running with 1 task, you can just run with this command:

./LIS -f ./LDAS_irri/lis_config_2001

It sounds like this is already working for you. I think "mpirun" can cause errors when running with just 1 task.

If that's not the issue, are you sure that you have both compiled and submitted the job from a Milan node?

I see you are on Discover. You can point me to your LISF/lis/make/configure.lis (ensure permissions are open) and I'll take a look.

I just posted a separate discussion. Please see if Issue 5 in it might apply to you. #1642

My apologies, I see that we never responded to your question from March: #1503

Would you still like us to respond to that other question?

[slabhan1]

Hi David, Thank you, those were helpful leads, and solved the issue. I don't think I need help to use ERA5 anymore, I have been using MERRA2. Both these discussions can be closed! Thank you!

…

________________________________ From: David Mocko ***@***.***> Sent: Thursday, November 21, 2024 2:33 PM To: NASA-LIS/LISF ***@***.***> Cc: Sakshi Labhane ***@***.***>; Mention ***@***.***> Subject: Re: [NASA-LIS/LISF] Slurm script fails when I request mpirun/ntasks (Discussion #1641) External Email - Use Caution Hi @slabhan1<https://github.com/slabhan1> Sorry for the delay in responding. If you are only running with 1 task, you can just run with this command: ./LIS -f ./LDAS_irri/lis_config_2001 It sounds like this is already working for you. I think "mpirun" can cause errors when running with just 1 task. If that's not the issue, are you sure that you have both compiled and submitted the job from a Milan node? I see you are on Discover. You can point me to your LISF/lis/make/configure.lis (ensure permissions are open) and I'll take a look. I just posted a separate discussion. Please see if Issue 5 in it might apply to you. #1642<#1642> My apologies, I see that we never responded to your question from March: #1503<#1503> Would you still like us to respond to that other question? — Reply to this email directly, view it on GitHub<#1641 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXQLRRE7ZI3MR67CN4NWZ6L2BYYQ3AVCNFSM6AAAAABSA2KI6KVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTCMZUGA2TINA>. You are receiving this because you were mentioned.Message ID: ***@***.***>