How did you verify this?
cexec "ps -aux | grep mpiblast"
and i see that ALL processes are on the same node
So it should work, but did now work. why ?You should not need to do any patching.
I simply installed Oscar 4, and i'm using default LAM/MPI that comes with Oscar 4What version of OSCAR are you running, and what version of LAM/MPI?
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
