2.3.56 seg fault

[acameron]

Hi Fred,

I am trying to get version 2.3.56 but am running into an issue. Trying to execute the latest version results in a segfault, we rebuilt the software with all new versions of the dependencies and I still get the segfault.

I tried building version 2.3.54 using the same newly-built dependencies and it runs without problems.

Any insight into this issue would be greatly appreciated. I have included system information below.

Cheers,

-Alex

LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: Rocky
Description: Rocky Linux release 8.9 (Green Obsidian)
Release: 8.9
Codename: GreenObsidian

[Frederic Guillaume]

Hi Alex,

It is more likely that the seg fault is caused by a bug somewhere in the code. I would be able to help if you sent me the parameter files that you are using so I can reproduce and find the bug. Maybe some parameters are not properly set in the parameter file, which would be the easiest to fix.

Thanks, and best,

Fred

[acameron]

Hi Fred,

I have attached a parameter file that runs for 2.3.54 and fails for 2.3.56. I have also pasted my command for running below as well.

Thanks for your help.

-Alex

module load nemo/2.3.56
srun -c1 nemo2.3.56_mpi ./cwm3.ini

[Fred Guillaume]

Hi Alex,

I couldn't reproduce the seg fault in a non-mpi environment. Your simulation runs fine on a laptop with Ubuntu 22.04 and nemo2.3.56.

From your command below, it seems that you are running the MPI version of nemo with just one CPU (one process). You need at least two to properly run the mpi version of Nemo (i.e. srun -c2 nemo2.3.56_mpi ./cwm3.ini). One CPU is needed for the master, and at least one for the worker, ie., the CPU which actually runs the simulation. The master is only distributing the replicates to the workers and collects the stat data from the workers.

If you do not intend to run parallel jobs with nemo_mpi, then use the non-mpi version of nemo (i.e. srun -c1 nemo2.3.56 ./cwm3.ini).

Either of these solutions should solve the problem, hopefully. Let me know if not.

One note though. nemo2.3.56_mpi uses MPI v2 which is a pretty old version of MPI and is not guaranteed to work if your cluster has a more recent version of openmpi. Next version of Nemo (2.4.0) has an updated MPI interface. Reach out if you want to try the pre-release (alpha) version.

Best,
Fred

On 05/05/2024 20:06, acameron wrote:

Hi Fred,

I have attached a parameter file that runs for 2.3.54 and fails for 2.3.56. I have also pasted my command for running below as well.

Thanks for your help.

-Alex

module load nemo/2.3.56
srun -c1 nemo2.3.56_mpi ./cwm3.ini

On Friday, May 3, 2024 at 1:32:33 AM UTC-6 Frederic Guillaume wrote:

Hi Alex,

It is more likely that the seg fault is caused by a bug somewhere in the code. I would be able to help if you sent me the parameter files that you are using so I can reproduce and find the bug. Maybe some parameters are not properly set in the parameter file, which would be the easiest to fix.

Thanks, and best,

Fred

On Thursday 2 May 2024 at 22:07:39 UTC+3 acameron wrote:

Hi Fred,

I am trying to get version 2.3.56 but am running into an issue. Trying to execute the latest version results in a segfault, we rebuilt the software with all new versions of the dependencies and I still get the segfault.

I tried building version 2.3.54 using the same newly-built dependencies and it runs without problems.

Any insight into this issue would be greatly appreciated. I have included system information below.

Cheers,

-Alex

LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: Rocky
Description: Rocky Linux release 8.9 (Green Obsidian)
Release: 8.9
Codename: GreenObsidian

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