Re: [sparta-users] [EXTERNAL] Re: Error Opening log.sparta during MPI execution

[Moore, S. <st...@sa...>]

In other words, try writing the log file and any other files to scratch GPFS instead of NFS /home, pretty sure that will fix the issue on Summit.
________________________________
From: Moore, Stan <st...@sa...>
Sent: Monday, March 4, 2024 1:08 PM
To: Abdourahmane Diaw <abd...@gm...>; Steve Plimpton <sj...@gm...>
Cc: spa...@li... <spa...@li...>
Subject: Re: [EXTERNAL] Re: [sparta-users] Error Opening log.sparta during MPI execution

Are you running out of your home directory or on the NFS file system? If I recall correctly, on Summit you cannot write to the NFS file system during a compute job (e.g. your home directory), you have to use the GPFS scratch filesystem instead. Maybe that is enforced by jsrun but not mpiexec?
________________________________
From: Abdourahmane Diaw <abd...@gm...>
Sent: Monday, March 4, 2024 1:00 PM
To: Steve Plimpton <sj...@gm...>
Cc: spa...@li... <spa...@li...>
Subject: [EXTERNAL] Re: [sparta-users] Error Opening log.sparta during MPI execution

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Hi Steve,

Thank you for taking the time to respond to my question. I have looked at the permissions, which was not the issue. I also added a line in my script to cd into my folder. But the problem remains. Interestingly, the problem disappears when using mpirun rather than jsrun. However, folks at olcf recommend using jsrun on the Summit.

Yes, I can % touch log.sparta.

I run via a batch script with "cd" to my folder.

#BSUB -W 00:10
#---------------------------------------
cd /ccs/home/abdou/test_spa
jsrun --stdio_mode=prepend -D CUDA_VISIBLE_DEVICES   -E OMP_NUM_THREADS=4   --nrs 2   --tasks_per_rs 21   --cpu_per_rs 21   --gpu_per_rs 0   --bind=proportional-packed:1   -d plane:21    /ccs/home/abdou/sparta/build/src/spa_mpi -in in.free



Hopefully, the olcf folks can help fix this problem as it seems to be something other than a SPARTA/LAMMPS problem.

Abdou

On Mon, Mar 4, 2024 at 1:05 PM Steve Plimpton <sj...@gm...<mailto:sj...@gm...>> wrote:
This is typically not a SPARTA or LAMMPS problem.  The problem is that you do not
have write access to the directory you are running from.  What directory is the
code trying to create the logfile in?

Can you do the following successfully from that directory?
% touch log.sparta

If you are running via a batch script on a big system, you may need to "cd" to
one of your own directories before trying to launch SPARTA.

Steve


On Fri, Mar 1, 2024 at 5:38 PM Abdourahmane Diaw <abd...@gm...<mailto:abd...@gm...>> wrote:

Dear SPARTA USERS,

I am experiencing an issue when attempting to run SPARTA on a new machine.

Specifically, SPARTA cannot open the required log file and subsequently aborts the MPI processes, while LAMMPS outputs a warning but continues to run.

SPARTA Issue: When executing the command below for SPARTA, I encounter this error:

[image.png]

I have a similar problem with LAMMPS

[image.png]

I would appreciate any guidance or suggestions you may have to resolve this issue.

Cheers,
Abdou

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