AMBER Archive (2005)

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

From: Karol Miaskiewicz (miaskiew_at_ncifcrf.gov)
Date: Wed Mar 09 2005 - 07:57:46 CST

> 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?

The list of hosts to run on is set by PBS. You must use this list and
not the hostfile that you created yourself. The file with a list of
hosts for your job is pointed to by the variable PBS_NODEFILE, so your
mpirun command should look something like this:

  mpirun -machinefile $PBS_NODEFILE sander -np 8

Of course, you must also indicate to PBS that you want to use 8
processors. In the most common case of a cluster of 2-way nodes, this is
done with:

  #PBS -l nodes=4:ppn=2

    

-- 
 Karol Miaskiewicz [Contractor]                            
 Advanced Biomedical Computing Center                      
 NCI-Frederick, PO Box B, Frederick, MD 21702
 miaskiew_at_ncifcrf.gov, phone 301-8465664, fax 301-8465762 

 
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