On 6/01/2012 12:37 AM, [email protected] wrote: > 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?
Maybe. Shared libraries and MPI do not always work well together. Also, be sure to use "make distclean" between attempts. Mark > > Thanks in advance!! > > R-X Gu > Message: 2 > Date: Wed, 04 Jan 2012 09:44:53 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] a installation problem of gromacs4.5.4 using > mpi > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > [email protected] 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 >> -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
