[gmx-users] g_tune_pme error in blue gene

[Mark Abraham]

On 1/04/2012 4:50 AM, Albert wrote:
> Hello:
>
>   I am trying to run g_tune_pme in blue gene with following script:
>
> # @ job_name = bm
> # @ class = kdm-large
> # @ account_no = G07-13
> # @ error = gromacs.info
> # @ output = gromacs.out
> # @ environment = COPY_ALL
> # @ wall_clock_limit = 160:00:00
> # @ notification = error
> # @ job_type = bluegene
> # @ bg_size = 64
> # @ queue
> mpirun -exe /opt/gromacs/4.5.5/bin/g_tune_pme -args "-v -s md.tpr -o 
> bm.trr -cpo bm.cpt -g bm.log -launch" -mode VN -np 256
>
> but I've got the following messages as soon as I submit jobs and it 
> terminate soon:
>
> ---gromacs.info--------------
> <Mar 31 20:45:57.677742> BE_MPI (ERROR): Job execution failed
> <Mar 31 20:45:57.677803> BE_MPI (ERROR): Job 10969 is in state ERROR ('E')
> <Mar 31 20:44:58.476985> FE_MPI (ERROR): Job execution failed (error 
> code - 50)
> <Mar 31 20:44:58.477065> FE_MPI (ERROR):  - Job execution failed - job 
> switched to an error state
> <Mar 31 20:45:57.714358> BE_MPI (ERROR): The error message in the job 
> record is as follows:
> <Mar 31 20:45:57.714376> BE_MPI (ERROR):   "Load failed on 
> 192.168.101.49: Executable file is not a 32-bit ELF file"

This means the executable is unsuitable for the hardware to run. Front 
and back ends of BlueGene are different hardware, of course.

> <Mar 31 20:44:58.691897> FE_MPI (ERROR): Failure list:
> <Mar 31 20:44:58.691923> FE_MPI (ERROR):   - 1. Job execution failed - 
> job switched to an error state (failure #50)

g_tune_pme relies on being able to spawn mpirun processes and measure 
their performance. Back-end BlueGene/L jobs cannot spawn new processes, 
and I'm skeptical that BlueGene/P would be able to do this either (but P 
is less restrictive). So you will need to run g_tune_pme compiled for 
the front end in your job script, and consult g_tune_pme -h for clues on 
how to set up your job script so that g_tune_pme can correctly call 
mpirun to invoke mdrun_mpi on the back end.

Mark
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