A workaround for this is to use lamboot / mpirun / lamhalt (instead of mpiexec), but to use the hostfile $PBS_NODEFILE, which is created specially for each PBS job and contains a list of all the nodes just in your job. For example:
----- lamboot $PBS_NODEFILE mpirun ... lamhalt ------
On Mar 4, 2005, at 9:46 AM, Salvatore Di Nardo wrote:
How did you verify this?
cexec "ps -aux | grep mpiblast" and i see that ALL processes are on the same node
You should not need to do any patching. So it should work, but did now work. why ?
What version of OSCAR are you running, and what version of LAM/MPI?�
I simply installed Oscar 4, and i'm using default LAM/MPI that comes with Oscar 4
Can you send the output of laminfo?
=============================================== ���������� LAM/MPI: 7.0.6 ����������� Prefix: /opt/lam-7.0.6 ����� Architecture: i686-redhat-linux-gnu ���� Configured by: root ���� Configured on: Tue Nov� 2 23:56:09 EST 2004 ��� Configure host: headnode ������� C bindings: yes ����� C++ bindings: yes � Fortran bindings: yes ������ C profiling: yes ���� C++ profiling: yes Fortran profiling: yes ���� ROMIO support: yes ����� IMPI support: no ���� Debug support: no ����� Purify clean: no ��������� SSI boot: globus (Module v0.5) ��������� SSI boot: rsh (Module v1.0) ��������� SSI coll: lam_basic (Module v7.0) ��������� SSI coll: smp (Module v1.0) ���������� SSI rpi: crtcp (Module v1.0.1) ���������� SSI rpi: lamd (Module v7.0) ���������� SSI rpi: sysv (Module v7.0) ���������� SSI rpi: tcp (Module v7.0) ���������� SSI rpi: usysv (Module v7.0) ===============================================
Just to explain u better, mpiblast works well if i dont use torque/PBS using
>lamboot <my_hostfile> >mpirun -np mpiblast -p blastx -d nr -i frag.0 -o frag.0.out6p_pbs >lamhalt
As far i understood is that mpirun is unable to retrieve list of free nodes from PBS so all jobs are sent on first node reserved by pbs. What i need is to bea ble to retrieve a list from PBS and that PBS know that there are some jobs running in those node. If i run mpiblast outside from pbs environment, not only i need to check previusly what nodes are working or not, but the main problem is that also if i find free nodes, PBS can submit other jobs during mpiblast execution.�
Salvatore Di Nardo
-- {+} Jeff Squyres {+} [EMAIL PROTECTED] {+} http://www.lam-mpi.org/
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