[gmx-users] Trouble compiling gromacs 5.1.2 with plumed 2.2.3

Anna Vernon lappala.anna at gmail.com
Tue Oct 25 16:39:23 CEST 2016


So... I compiled and installed  gmx 5.1.2 on its own and it was fine. I
patched it up with plumed 2.2.3 and it could not compile anymore.

The error message was this:

usr/bin/ld: ../../lib/libgromacs.so.1.2.0: undefined reference to symbol
'MPI_Isend'
//usr/lib/x86_64-linux-gnu/libmpich.so.12: error adding symbols: DSO
missing from command line
collect2: error: ld returned 1 exit status
share/template/CMakeFiles/template.dir/build.make:99: recipe for target
'bin/template' failed
make[2]: *** [bin/template] Error 1
CMakeFiles/Makefile2:1745: recipe for target
'share/template/CMakeFiles/template.dir/all' failed
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

this is my gromacs cmake:

cmake .. -DGMX_MPI=on -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
-DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np -DNUMPROC=2, -DNUMPROC=3,
-DNUMPROC=4, -DNUMPROC=5, -DNUMPROC=6, -DNUMPROC=7,-DNUMPROC=8
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

after which i do make  and make, upon which the error message appears.

this is how I configure plumed:

./configure --enable-mpi CXX="$MPICXX" --prefix=/usr/local

What is going on?

Anna


More information about the gromacs.org_gmx-users mailing list