Manik Mayur a écrit :
Hi,
If I have 2 mpi environments, namely LAM and openMPI, and I want
gromacs to use openMPI of the two, what extra option should I pass
during the ./configure step? In my case openMPI is installed
locally(in my /home folder).
Sorry, I've misunderstood your message. Anyway, I would first check
twice the paths to the binaries in my script. Then, I would check my
environment variables, especially PATH, LD_LIBRARY_PATH and LD_RUN_PATH.
You might need to modify them to make sure any Lam-related stuff is
loaded by default in your environment.
I've tried to use a local installation of openMPI myself, but finally
asked my sysadmin to install it for all users. I had many problems with
libraries that couldn't be loaded properly.
Cheers,
Nicolas
Thanks,
Manik
On Tue, Mar 3, 2009 at 10:58 PM, Nicolas <nsa...@ucalgary.ca
<mailto:nsa...@ucalgary.ca>> wrote:
Hi,
As mentioned by the error message:
Please run the "lamboot" command the start the LAM/MPI runtime
Before using Lam, you have to boot it. In my scripts, I've got
something like:
lamboot -v $PBS_NODEFILE
lamrun -v -np $NPROC mdrun mdargs
lamhalt
I don't use Lam often, though, you might need to use different Lam
options.
Nicolas
Manik Mayur a écrit :
Hi,
I have till now successfully used openMPI and gromacs
together. Recently I got a cluster where I tried to install
openMPI and gromacs locally as I donot have root priviledges
on it. But it turns out that it already has MPI environment on
it (LAM) which I donot want to use (as the version is quite
old.. the cluster still has gcc-3.2.3!).
So after installing openMPI 1.3 and gromacs 4.0.4 on it (in my
/home folder), I tried to execute:
$/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s eql_mpi.tpr -o
eql_mpi.trr
It gives the following error:
-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
My question is - Why it still tries to look for LAM
environment or lamd? I will be extremely thankful if somebody
gives a hint.
-Manik
--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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begin:vcard
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