Manik Mayur a écrit :
On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <[email protected]
<mailto:[email protected]>> wrote:
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.
ok, is there any specific option or environment variable through which
I can make gromacs aware of openMPI and not LAM while installation? If
I carry on the default --enable-mpi thing, upon executing the following:
Just a silly question: Did you recompile Gromacs with openMPI? If not,
you should with the correct CPPFLAGS, LDFLAGS and MPICC. Typically, you
should have something like:
./configure\
--prefix /home/local/gromacs\
--enable-mpi\
--program-suffix="_mpi"\
--without-x\
--disable-nice\
MPICC=/path/to/mpicc\
CC=/path/to/gcc
CPPFLAGS=-I/path/to/fftw/include/\
LDFLAGS=-L/path/to/fftw/lib/
mpicc is located in the bin/ directory of openMPI. gcc is the regular
gcc installation (gcc 3). As I said, your issue is probably due to a
path uncorrectly pointing to Lam. So check/modify your environment
variables, especially the paths to loaded libraries.
$/home/openmpi/bin/mpirun -np 4 mdrun_mpi -s eql_mpi.tpr -o
eql_mpi.trr
I get 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.
-----------------------------------------------------------------------------
so it is like mdrun_mpi was configured with LAM and hence it is
looking for it.
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 <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>> 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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--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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