Run AEM3D by command line on linux-ubuntu with parallel algorithms on multiple cores.

Question

Hello

Please guide me on how to run AEM3D by command line on linux-ubuntu with parallel algorithms on multiple cores.

Thank you very much.

Jason Ha.

Answer 1

Hi Jason,

You would have two options:

1. You copy aem3d_openmp.exe into your run directory, and run it using the terminal by the command:
srun aem3d_openmp.exe

or as a more efficient choice (if you are on a cluster):
 

2. you create a bash script, in which you define your simulation parameters e.g. simulation (allocation) time, number of cores/threads, and also as you are going to run an openmp structure, you would also need to setup the "OMP_NUM_THREADS"
the last line of your script will be: srun aem3d_openmp.exe

If you are on a cluster, with the second approach you can submit your job and the bash will do the rest for you.

You can setup your number of threads within the run_aem3d.dat file, and I recommend to set it same as the threads you are setting in your bash script

Behnam

Comments

Hello, thank you for your reply.
I entered the command srun aem3d_openmp.exe but it failed.

~/#_INSTALL/AEM3D/test/RoundLake/run$ srun aem3d_openmp.exe
=============================================================
|                 STARTING AEM3D RUN                        |
=============================================================
 Aquatic Ecosystem Model 3D (AEM3D)
 Hydronumerics PTY LTD

  aem3d built:                      2024-02-09 02:28:26 UTC
  aem3d built on machine:           jenkins
  aem3d built on os:                LINUX
  aem3d built using compiler:       ifort
  aem3d built using debug level:    0
  aem3d built using compiler flags: -O3 -no-prec-div -g -traceback -qopenmp -align array64byte -static -nothread

  aem3d Build Version:              1.1.2
  aem3d Auto Build Number:           721
Simulation Started : 2024-02-16 11:26:13
 ***** FATAL ERROR **** FATAL ERROR **** FATAL ERROR *****
 * multiple values found for key nthreads in file run_aem3d.dat
 *********************************************************
1
srun: error: localhost: task 0: Exited with exit code 1

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I think you need to check out your run_aem3d.dat. Look at the comment below FATAL error. You should check if you either have multiple lines of nthreads field or multiplem values for nthread in one line.

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Hello
I checked again, this is the run_aem3d.dat file downloaded from the test website. It seems to me that it is not defective.

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two things to check:

1. you should check inside of your run_aem3d.dat not to have more than one nthreads lines nor more than one value for it. You will need to change the file based on your settings and files, anyway.

2.Are you sure you are running linux (dev) executables (and not windows nor macOS)?