AMBER Archive (2005)

Subject: AMBER: problem with running AMBER with lam-mpi though PBS script

From: Ru-Zhen Li (r.li_at_qmul.ac.uk)
Date: Wed Mar 09 2005 - 08:01:24 CST

Dear all,

I am having strange errors when i tried to use mpirun (mpiexec) with PBS script,

there are 13 nodes on the linux cluster, lam-7.0.3 v8
1)i used lamboot -v lamhosts, with the master and all the slave nodes listed in lamhosts, and lam is runing successfuly
2)i used mpirun -np 8 sander..... and it works ok
3)i used the same command, but put it in a PBS script, and then it complained that
it seems that there is no lamd running on the host node13
..........

i tried many work arounds including
mpirun n1-8 -np 8 sander
mpiexec -machinefile hostfile sander (with master and node1-8 listed in hostfile)

i also tried to use lower version of lam which is v7

but no matter what i tried, the same error always came out, what i am really confused about are:
I am not using node13 at all, why it complained about node13,
the lam seems to work on node13 since when i do lamboot, it shows node13 is successufully done
why i can use mpirun through interactive mode, but can't do it through PBS?

anybody have any idea of why?

Thanks a lot

Ruzhen

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