[gmx-users] gmx 4.6 mpi installation through openmpi?

[Zhikun]

Sorry, Hrachya Astsatryan, I have no idea in such case.
Why not just try to install openmpi and fftw ahead by yourself before
installing groamcs?



On Mon, Apr 8, 2013 at 4:06 PM, Hrachya Astsatryan <hrach at sci.am> wrote:

> Dear Zhikun Cai,
>
> Thank you for your quick response.
>
>
> On 4/8/13 11:15 AM, Zhikun Cai wrote:
> > Hi, see installation instruction with CMAKE here:
> >
> > http://www.gromacs.org/Documentation/Installation_Instructions
> >
> > I guess that maybe you need to specify your Openmpi and FFTW installation
> > directories using options CMAKE_PREFIX_PATH.
> > For example, my Openmpi and FFTW were firstly installed in
> >  "/home/ucaizk/ComTools/openmpi" and "/home/ucaizk/ComTools/fftw
> > Then, I installed gromacs with command lines below:
> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.1.tar.gz
> >      $ tar -xzvf gromacs-4.6.1.tar.gz
> >      $ mkdir build
> >      $ cd build
> Done
> >      $
> >
> CMAKE_PREFIX_PATH=/home/ucaizk/ComTools/openmpi:/home/ucaizk/ComTools/fftw
> export CMAKE_PREFIX_PATH=/opt/mpi (I use an option below to download and
> install the fftw by gromacs)
> >  cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX
> > =/home/ucaizk/ComTools/gromacs  ../gromacs-4.6.1
> cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/backup/sicnas/gromacs
> -DGMX_BUILD_OWN_FFTW=ON (I want to install on /backup/sicnas/gromacs,
> which is shared by nodes)
> >      $ make
> >      $ make install
> done!
>
> And finally get the following error:
> /backup/sicnas/gromacs/bin/mdrun_mpi: error while loading shared
> libraries: libblas.so.3: cannot open shared object file: No such file or
> directory
>
> > When above was done, cd to your home directory and add one line to
> > ".bashrc" file
> >      export PATH=$PATH:/home/ucaizk/ComTools/gromacs/bin
> >
> > restart bash shell, then all are done!
> >
> > Hope it helps!
> >
> > Zhikun
> >
> >
> > On Fri, Apr 5, 2013 at 11:12 PM, 라지브간디 <rajiv at kaist.ac.kr> wrote:
> >
> >> Dear gmx users,
> >>
> >>
> >> I could able to install gmx4.6.1 without MPI option in my cluster,
> whereas
> >> the MPI fails to install and gives the following error ( used command
> line
> >> cmake .. -DGMX_MPI=ON  -DGMX_BUILD_OWN_FFTW=ON )
> >>
> >>
> >> CMake Error at cmake/gmxManageMPI.cmake:161 (message):
> >>   MPI support requested, but no MPI compiler found.  Either set the
> >>   C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called
> mpicc),
> >> or
> >>   set the variables reported missing for MPI_C above.
> >> Call Stack (most recent call first):
> >>   CMakeLists.txt:494 (include)
> >>
> >>
> >>
> >>
> >> I have also installed openmpi 1.5 version. which mpirun shows
> >> /usr/bin/mpirun.
> >> It seems openmpi installed in /usr/bin/openmpi/
> >>
> >>
> >> I dont know how to do link this cmake.
> >>
> >>
> >> Please need some suggestion. Thanks.
> >>
> >> --
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>
>
> --
> Hrachya Astsatryan
> Head of HPC Laboratory,
> Institute for Informatics and Automation Problems,
> National Academy of Sciences of the Republic of Armenia
> 1, P. Sevak str., Yerevan 0014, Armenia
> t: 374 10 284780
> f: 374 10 285812
> e: hrach at sci.am
> skype: tighra
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