[gmx-users] MPI installation

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 9 05:11:17 CEST 2012

On 8/04/2012 12:41 PM, bharat gupta wrote:
> Hi,
> I am trying to enable mpi fro mdrun in an already installed gromacs-4.5.5.

Using a freshly unpacked tarball will eliminate some sources of 
problems. Shouldn't be necessary, of course, but since nobody can 
warrant something hasn't been broken accidentally...

> But while executing the command make mdrun , I am getting the 
> following errorn:-
> mv -f .deps/xlate.Tpo .deps/xlate.Plo
> /bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3 
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
> -funroll-all-loops -std=gnu99 -fexcess-precision=fast -no-undefined 
> -version-info 6:0:0   -o libgmxpreprocess_mpi.la 
> <http://libgmxpreprocess_mpi.la> -rpath /usr/local/gromacs/lib 
> add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo 
> gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo 
> hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo 
> resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo 
> topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo 
> vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la <http://libmd_mpi.la> 
> -lnsl -lm
> libtool: link: cannot find the library `../mdlib/libmd_mpi.la 
> <http://libmd_mpi.la>' or unhandled argument `../mdlib/libmd_mpi.la 
> <http://libmd_mpi.la>'
> make[1]: *** [libgmxpreprocess_mpi.la 
> <http://libgmxpreprocess_mpi.la>] Error 1
> make[1]: Leaving directory `/usr/local/gromacs-4.5.5/src/kernel'

The original error occurred earlier - this error is triggered by libmd 
not being built earlier because of some other problem.

> I used this command to configure , before issuing make mdrun :  
> ./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3. Also 
> I have mpich2 installed in my system. So, what could be reason for 
> this error ??

Unknown at this stage.

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