From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Fri Mar 11 2005 - 22:21:55 CST
add the lamboot command to the script before you start the job like the
example below
#PBS -S /bin/sh
#PBS -N Namd
#PBS -V
lamboot
lamnodes
/usr/bin/mpirun n1-14 /usr/local/bin/namd_mpi hiv1.conf >hiv1.out
oOn Friday 11 March 2005 06:29 pm, you wrote:
> Hi all,
> The system Admin of the computer cluster I'm using just compiled and
> installed NAMD on a myrinet linux cluster (GM 2 libraries).
>
> I'm testing if it works, but it doesn't, I get the following error in
> the log file:
>
> Running on 4 processors:
> /NAMD-tim/Linux-i686-g++/namd2 ++nodelist nodelist myrinet_test.namd
> ---------------------------------------------------------------------------
>-- It seems that there is no lamd running on this host, which indicates that
> the LAM/MPI runtime environment is not operating. The LAM/MPI runtime
> environment is necessary for the "mpirun" command.
>
> Please run the "lamboot" command the start the LAM/MPI runtime
> environment. See the LAM/MPI documentation for how to invoke
> "lamboot" across multiple machines.
> ---------------------------------------------------------------------------
>--
>
> Here is my call in pbs script:
>
> $dir/charmrun $dir/namd2 +p4 ++nodelist $nodelist myrinet_test.namd >&
> myrinet_test.log
>
> Is my call to namd2 erroneous? or do you think the above error is caused
> by an installation error?
>
> Any comments/suggestions would be appreciated,
> Ed
-- Jerry Ebalunode Ph.D. Candidate (Advisor: Asoc. Professor James Briggs Ph.D.) RM 402F Houston Science Center Phone: 713-743-8367 Dept. of Biology and Biochemistry University of Houston 4800 Calhoun Road Houston, TX 77204
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