[gmx-users] Problem configuring openMPI
Manik Mayur
manik.mayur at gmail.com
Tue Mar 3 20:13:03 CET 2009
On Wed, Mar 4, 2009 at 12:28 AM, Nicolas <nsapay at ucalgary.ca> wrote:
> Manik Mayur a écrit :
>
>>
>>
>> On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <nsapay at ucalgary.ca <mailto:
>> nsapay at ucalgary.ca>> 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\
thanks, I think that is what I needed. Let me try and then I will let you
know.
> CC=/path/to/gcc
> CPPFLAGS=-I/path/to/fftw/include/\
> LDFLAGS=-L/path/to/fftw/lib/
>
Why is FFTW necessary? In all my gromacs installations till now, I have
avoided this package (out of ignorance).
> 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 <nsapay at ucalgary.ca
>> <mailto:nsapay at ucalgary.ca> <mailto:nsapay at ucalgary.ca
>>
>> <mailto:nsapay at 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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>>
>> --
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
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>
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--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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