[gmx-users] gmx 4.6 mpi installation through openmpi?
hrach at sci.am
Mon Apr 8 10:06:53 CEST 2013
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:
> 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:
> $ tar -xzvf gromacs-4.6.1.tar.gz
> $ mkdir build
> $ cd build
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
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
> 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!
> 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),
>> 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
>> 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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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
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