code_saturne User's Forum

Hi Yvan,

I'm trying to install Code_Saturne on my school's local cluster which uses the SGE batch system. I compiled Code_Saturne and have managed to run jobs with it, but it doesn't recongize mpi. I tried to edit the code_saturne.cfg file for Code_Saturne, which is attached. Changing the batch system to SGE doesn't appear to help and adding mpirun to mpiexec field causes error. If I initialize and create the RESU folder first and then submit the job from the RESU folder, instead of trying to run the job from DATA folder, I can get to run with mpi but it doesn't recognize the allocated time of the job. Do you have any suggested changes I could make to the config file or is there other changes that I need to make to the source code to make it work on a cluster with SGE?

Thank you,
Andrew

Hello Andrew,

of all the batch systems Code_Saturne tries to support, SGE is the one that has caused us most pain, or at least the one we do not know how to automate well.

Using MPI with SGE often requires declaring a specific program environment (-pe option), in addition to the queue. As the name of the environment depends on the administrator's choice, and I am not an expert on this, it is a pain to automate. Most other systems are also complex and can handle similar things, but have a clearer syntax, with the possibility of handling specific environment aspects and choosing the number of MPI ranks in a less messy fashion.

So you probably need to adapt the batch.SGE template (you can use an absolute path in the code_satutne.cfg to point to your version).

Also, which MPI library are you using ? Is it configured/does it need extra configuration to work with SGE ?

Best regards,

Yvan

Hi Yvan,

Yeah, reading through the previous posting related SGE, it appeared that it was pain for Code_Saturne.

The mpi library being used is openmpi v1.6.5. I will email my IT department about whether mpi is specially configured to work with the SGE batch system.

Regards,
Andrew