Sridhar Acharya wrote:
Hi All,
I am facing a problem for parallel mdrun.
I tried to run in 2 nodes with the following command. The program reports that
lamd is not running as follows.
####################################################################################################
mpirun -np 2 /users/soft/GromacsSingle/bin/mdrun_mpi -s b4em_1CYP_WT.tpr -o
em_1CYP_WT.trr -np 2
-----------------------------------------------------------------------------
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 MPI programs to run (the MPI
program tired to invoke the "MPI_Init" function).
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.
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n0).
mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------
##################################################################################################
But lamd is very well running, because I could get the status of lam nodes with the
"lamnodes" command.
########################################################################################
[EMAIL PROTECTED] WT_SINGLE_PARALLEL]$ lamnodes
n0 cdfd-grid-node2:1:
n1 cdfd-grid-node4:1:
n2 cdfd-grid-node12:1:
n3 cdfd-grid-node13:1:
n4 cdfd-grid-node14:1:
n5 cdfd-grid-node16:1:
n6 cdfd-grid-node17:1:origin,this_node
###########################################################################################
Do I have to define any paths so that it could recognise this?
Waiting for your suggessions.
sridhar
Hi Sridhar,
some things that I would try are:
1. stop LAM by typing lamhalt, check that there is no other lamd of you running
on that nodes,
then boot LAM again and try again
2. Paths in the startup file (assuming bash-style):
export PATH=/path-to-your-lam-installation/bin:$PATH
export LAMHOME=/path-to-your-lam-installation/
3. Can you run something like 'mpirun -np 2 ls'?
Carsten
--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/research/dep/grubmueller/
http://www.gwdg.de/~ckutzne
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