[GE users] estrange messages from mpich2 (tight integrated)

Baudilio Tejerina tejerina at chem.northwestern.edu
Thu Sep 6 01:01:42 BST 2007


Fixed, Reuti:

Even though the image 'main.x' was in the path and accessible and  
executable from all the nodes I interactively logged in, it didn't  
suffice. However, from your suggestions, I explicitly stated the path  
along the executable and it turned out to fixed the problem:

mpiexec -rsh -nopm -np $NSLOTS -machinefile $TMPDIR/machines /home/ 
bta/MPICH2/F90/main.x         (Works)

  instead of

mpiexec -rsh -nopm -np $NSLOTS -machinefile $TMPDIR/machines   
main.x                                                   (Does not)


Thank you, Reuti

Baudilio



On Sep 5, 2007, at 5:25 PM, Reuti wrote:

> Am 05.09.2007 um 22:53 schrieb Baudilio Tejerina:
>
>> Hi ALL:
>>
>> I have just installed MPICH2 (1.0.5) in a cluster (ROCKS) and I'd  
>> like to have all the parallel jobs under GE control. For that,  
>> I've followed Reuti's "demonless" procedure described in
>> http://gridengine.sunsource.net/howto/mpich2-integration/mpich2- 
>> integration.html
>>
>> The script bellow is the one I used for testing the installation  
>> and next is the contents of the error file.
>>
>> The weird messages that i don't know how to interpret nor where  
>> they may come from are those with permission denied.
>>
>> Does anyone have any explanation for this?
>
> Assuming the path to main.x is in your default $PATH, can you read  
> this file if you login to a node? Is the mountpoint not mounted  
> with "noexec" on the node?
>
> -- Reuti
>
>>
>> Thank you
>> Baudilio
>>
>>
>>
>>
>> #!/bin/sh
>> #$ -S /bin/sh
>> #$ -cwd
>> #$ -j y
>> #$ -pe mpich2 4
>> #$ -o TEST_MPICH2.err
>>
>> #export MPIEXEC_RSH=rsh
>> #export PATH=/home/reuti/local/mpich2_smpd/bin:$PATH
>>
>> export MPIEXEC_RSH=rsh
>> #Make sure we use the rsh wrapper provided by the PE. A copy of it  
>> will be placed on $TMPDIR:
>> export PATH=$TMPDIR:$PATH
>> echo BTA: my RSH is: `which rsh`
>>
>>
>> export PATH=/opt/local/mpich2-1.0.5/bin:$PATH
>> echo BTA: my MPIEXEC is: `which mpiexec`
>> mpiexec -rsh -nopm -np $NSLOTS -machinefile $TMPDIR/machines main.x
>>
>> exit 0
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> THIS IS THE CONTENTS of the error FILE:
>>
>>
>>
>>
>>
>>
>>
>> -catch_rsh /opt/gridengine/default/spool/compute-0-1/active_jobs/ 
>> 565.1/pe_hostfile
>> compute-0-1
>> compute-0-1
>> compute-0-0
>> compute-0-0
>> BTA: my RSH is: /state/partition1/565.1.all.q/rsh
>> BTA: my MPIEXEC is: /opt/local/mpich2-1.0.5/bin/mpiexec
>> env: main.x: Permission deniedenv: main.x: Permission denied
>> env: main.x: Permission denied
>> env: main.x: Permission denied/opt/gridengine/bin/lx26-x86/qrsh - 
>> inherit compute-0-1 env PMI_RANK=0 PMI_SIZE=4 PM\
>> I_KVS=19B130D14D0B84936F8CE02422E66098  
>> PMI_ROOT_HOST=compute-0-1.local PMI_ROOT_PORT=33703  
>> PMI_ROOT_LOCAL=0 PMI_A\
>> PPNUM=0 main.x
>> /opt/gridengine/bin/lx26-x86/qrsh -inherit compute-0-1 env  
>> PMI_RANK=1 PMI_SIZE=4 PMI_KVS=19B130D14D0B84936F8CE024\
>> 22E66098 PMI_ROOT_HOST=compute-0-1.local PMI_ROOT_PORT=33703  
>> PMI_ROOT_LOCAL=0 PMI_APPNUM=0 main.x
>> /opt/gridengine/bin/lx26-x86/qrsh -inherit compute-0-0 env  
>> PMI_RANK=2 PMI_SIZE=4 PMI_KVS=19B130D14D0B84936F8CE024\
>> 22E66098 PMI_ROOT_HOST=compute-0-1.local PMI_ROOT_PORT=33703  
>> PMI_ROOT_LOCAL=0 PMI_APPNUM=0 main.x
>> /opt/gridengine/bin/lx26-x86/qrsh -inherit compute-0-0 env  
>> PMI_RANK=3 PMI_SIZE=4 PMI_KVS=19B130D14D0B84936F8CE024\
>> 22E66098 PMI_ROOT_HOST=compute-0-1.local PMI_ROOT_PORT=33703  
>> PMI_ROOT_LOCAL=0 PMI_APPNUM=0 main.x
>>
>>
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