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

[Abdourahmane D. <abd...@gm...>]

Hi Steve and Stan,

The issue is resolved by migrating all relevant data to GPFS.

I appreciate the support.

Cheers,
Abdou

On Mon, Mar 4, 2024 at 5:13 PM Moore, Stan <st...@sa...> wrote:

> >>To do this for the log file, you will need to use the "-log filename"
> command line option with a GPFS path.
>
> Or alternatively just copy all the files over to GPFS and run from there,
> i.e. make that your working directory instead of /home.
> ------------------------------
> *From:* Steve Plimpton <sj...@gm...>
> *Sent:* Monday, March 4, 2024 2:33 PM
> *To:* Moore, Stan <st...@sa...>
> *Cc:* Abdourahmane Diaw <abd...@gm...>;
> spa...@li... <spa...@li...>
> *Subject:* Re: [EXTERNAL] Re: [sparta-users] Error Opening log.sparta
> during MPI execution
>
> To do this for the log file, you will need to use the "-log filename"
> command line option with a GPFS path.
> Also, I don't recognize the --stdio_prepend option you are using (maybe
> Stan does),
> but it is possibly related to this issue for the logfile.
>
> Steve
>
> On Mon, Mar 4, 2024 at 1:10 PM Moore, Stan <st...@sa...> wrote:
>
> 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
>
> Some people who received this message don't often get email from
> abd...@gm.... Learn why this is important
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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...> 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...> 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: image.png]
>
> I have a similar problem with LAMMPS
> [image: image.png]
>
> I would appreciate any guidance or suggestions you may have to resolve
> this issue.
>
> Cheers,
> Abdou
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