Dear Justin:
Thank you very much for your reply, but I have another problem.
After I install the fftw package, and remove the argument of the --enable-mpi
when installing the gromacs package by using the follow commands:
export CPPFLAGS=-I/my_path/
export LDFFLAGS=-L/my_path/
./configure --prefix=my_path --enable-shared --disable-float --enable-mpi
make mdrun
then I encountered the following errors:
libtool: link: cannot find the library `../mdlib/libmd_mpi_d.la' or unhandled
argument `../mdlib/libmd_mpi_d.la'
make[1]: *** [libgmxpreprocess_mpi_d.la] Error 1
make[1]: directory `/home/dw11-sg007/dying/gromacs-4.5.4/src/kernel'
what does this mean? Does it mean there is some problem with the mpi I used?
Thanks in advance!!
R-X Gu
Message: 2
Date: Wed, 04 Jan 2012 09:44:53 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] a installation problem of gromacs4.5.4 using
mpi
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4f0465e5.6090...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
mirc...@sjtu.edu.cn wrote:
> Dear All:
>
> I encountered a problem when installing gromacs4.5.4 by using mpi. When
>
> I finished the installation successfully, I submit a job by assigning 8
> processes. However, the job was not run by 8 processes, by generate 8 same
> jobs each use only 1 process (I have encountered the same problem before, but
> it is solved by using the same mpirun path during the installation and the
> simulation. However, this time i am sure the path of mpirun assigned during
> the installation is the same of that assigned in the simulation command and
> this problem occures again.). The followings are the commonds used in my
> installation:
>
> ########################install fftw#######
> ./configure --prefix=my_path --enable-thread --disable-float --enable-shared
> make
> make install
>
> #######################install gromacs#####
>
> export CPPFLAGS=-I/my_path/
> export LDFFLAGS=-L/my_path/
>
> ./configure --prefix=my_path --enable-shared --disable-float
> --enable-mpi=the_path_of_mpirun
The --enable-mpi flag does not take any argument. It is also advisable to
append
a suffix (e.g. _mpi) to the mdrun executable so you can unambiguously use the
commands.
> make
> make install
There is no need to try to compile the entire Gromacs package with MPI support;
only mdrun is MPI-aware. Instead, use:
make mdrun
make install-mdrun
-Justin
> ###########################################
>
> then I used the following command to do the simulations
>
> /the_path_of_mpirun/mpirun -np 8 mdrun -s myfile.tpr
>
> I am sure the path of mpirun assigned during the installation is the same of
> that assigned in the simulation command.
>
> Could anyone tell me how to solve this problem?
>
> Thanks in advance!!
>
> R-X Gu
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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