I haven't begun using MPI yet on my cluster but maybe you need to export
environment variables?
If that is the case then the following snippet of a PBS script my help
# export all my environment variables to the job
#PBS -V
#
#
# Using PBS - Environment Variables
# When a batch job starts execution, a number of environment variables
are
# predefined, which include:
#
# Variables defined on the execution host.
# Variables exported from the submission host with
# -v (selected variables) and -V (all variables).
# Variables defined by PBS.
#
# The following reflect the environment where the user ran qsub:
# PBS_O_HOST The host where you ran the qsub command.
# PBS_O_LOGNAME Your user ID where you ran qsub.
# PBS_O_HOME Your home directory where you ran qsub.
# PBS_O_WORKDIR The working directory where you ran qsub.
#
# These reflect the environment where the job is executing:
# PBS_ENVIRONMENT Set to PBS_BATCH to indicate the job is a batch
job, or
# to PBS_INTERACTIVE to indicate the job is a PBS
interactive job.
# PBS_O_QUEUE The original queue you submitted to.
# PBS_QUEUE The queue the job is executing from.
# PBS_JOBID The job's PBS identifier.
# PBS_JOBNAME The job's name.
###
|Message: 3
|From: [EMAIL PROTECTED]
|To: [EMAIL PROTECTED]
|Date: Thu, 03 Apr 2003 18:08:08 +0000
|Subject: [Oscar-users] mpirun wont run within pbs
|
|When I try to run mpirun within a PBS script I get the
|following message in my
|error file:
|
|It seems that there is no lamd running on this host,
|which indicates that the
|LAM/MPI runtime enviornment is not operating. The
|LAM/MPI runtime enviornment
|is necessary for MPI programs to run (the MPI program
|tried to invoke
|the "MPI_Init" function).
|
|Please run the "lamboot" command the start the LAM/MPI
|runtime environment.
|See the LAM/MPI documentation for how to invoke
|"lamboot" across multiple
|machines.
|
|When I go to the command line and execute the same
|command that is in my PBS
|script mpirun executes normally and my program
|produces the expected output.
|So I am assuming the LAM/MPI is running fine when the
|script is exectuing.
|
|Are there an commands that I am missing in the script?
|
|Thanks for the help.
|
|-Chris
|
|------------------------------SCRIPT-------------------
|----------------
|
|#PBS -o /home/cluster/output.txt
|#PBS -e /home/cluster/error.txt
|#
|#
|cd ~/cluster/biomap
|#
|mpirun -np 3 biomap
|#
|#
|
|
|
|
|--__--__--
|
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|s
|
|
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