Sorry for the delay in replying back. I start the job using the
following script file:
#$ -S /bin/bash
#$ -l h_rt=47:59:00
#$ -j y
#$ -pe mpich2 8
#$ -cwd
cd /home/jwillia4/GRO/gromacs-4.0.7/JJW_003/PH_TORUN
/home/jwillia4/GRO/bin/mpirun -np 8 /home/jwillia4/GRO/bin/mdrun_mpi
-v -s md.tpr
The strange thing is that sometimes it works and the job runs to
completion and sometimes it crashes immediately with the orte error so
I know that it is not the input files causing the problems. It seems
entirely random.
Has it to do with the -pe mpich2 8 line? I was previously using Open
MPI installed on the cluster for common use but now have downloaded
everything into my home directory. The script has been adapted from
the time when I didn't have my own OpenMPI in my home directory.
Perhaps it needs further alteration but I don't know what.
How would I do about checking whether MPI is running?
If you spot anything suspicious in the above commands please let me know.
Thanks
Jenny
Quoting Chandan Choudhury <iitd...@gmail.com>:
As Justin said give the command line options for mdrun and also check that
your mpi environment is running. Better to run a parallel job and check its
output.
Chadnan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 8, 2010 at 8:02 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
Jennifer Williams wrote:
Dear All,
I am having problems compiling gromacs 4.0.7 in parallel. I am following
the
Quick and Dirty Installation instructions on the gromacs webpage.
I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 following
these instructions.
Everything seems to compile OK and I get all the serial executables
including mdrun written to my bin directory and they seem to run fine.
However when I try to run mdrun_mpi on 6 nodes I get the following:
[vlxbig16:08666] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
[vlxbig16:08667] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
[vlxbig16:08700] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
[vlxbig16:08670] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
[vlxbig16:08681] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
[vlxbig16:08659] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_rml_base_select failed
--> Returned value -13 instead of ORTE_SUCCESS
Does anyone have any idea what is causing this? Computer support at my
University is not sure.
How are you launching mdrun_mpi (command line)?
-Justin
Thanks
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Dr. Jennifer Williams
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