On Wed, Jun 12, 2013 at 12:42 AM, sirishkaushik <kaushik.lakkar...@gmail.com > wrote:
> Note that this works fine with 4.5.5. > > when I installed using: > > ./configure CPPFLAGS="-I/home/kaushik/fftw-new/include" > LDFLAGS="-L/home/kaushik/fftw-new/lib" --enable-mpi --prefix > /home/kaushik/gromacs_executable/gromacs-old > > ldd mdrun on the 4.5.5 version correctly points to the fftw and the mpi > locations: > > > linux-vdso.so.1 => (0x00007fff6a302000) > libfftw3f.so.3 => /home/kaushik/fftw-new/lib/libfftw3f.so.3 > (0x00007f2e7a6e2000) > libmpi.so.1 => /usr/local/lib/libmpi.so.1 (0x00007f2e7a340000) > libnsl.so.1 => /lib/libnsl.so.1 (0x00007f2e7a11b000) > libm.so.6 => /lib/libm.so.6 (0x00007f2e79e99000) > libdl.so.2 => /lib/libdl.so.2 (0x00007f2e79c95000) > libnuma.so.1 => /usr/lib/libnuma.so.1 (0x00007f2e79a8c000) > librt.so.1 => /lib/librt.so.1 (0x00007f2e79884000) > libutil.so.1 => /lib/libutil.so.1 (0x00007f2e79681000) > libpthread.so.0 => /lib/libpthread.so.0 (0x00007f2e79464000) > libc.so.6 => /lib/libc.so.6 (0x00007f2e79102000) > libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f2e78e52000) > /lib64/ld-linux-x86-64.so.2 (0x00007f2e7a9f4000) > libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f2e78c05000) > libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f2e789b0000) > > > However, with 4.6.2, when I install using: > > cmake -DCMAKE_INSTALL_PREFIX=/home/kaushik/gromacs_executable/gromacs-mpi > -DGMX_THREADS=DGMX_X11=OFF -DGMX_MPI=ON > -DCMAKE_PREFIX_PATH=/home/kaushik/fftw-new -DGMX_DEFAULT_SUFFIX=OFF > -DMPI_INCLUDE_PATH=/usr/local/include -DMPI_COMPILER=/usr/local/bin/mpicxx > cmake -DCMAKE_C_COMPILER=/usr/local/bin/mpicc should Just Work. its now pointing to the wrong MPI libraries causing the crash with the > mpirun: > > ldd mdrun: > linux-vdso.so.1 => (0x00007fffba9ff000) > libfftw3f.so.3 => /home/kaushik/fftw-new/lib/libfftw3f.so.3 > (0x00007f32c6785000) > libmpi_cxx.so.0 => /usr/lib/libmpi_cxx.so.0 (0x00007f32c655e000) > libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f32c62ae000) > libdl.so.2 => /lib/libdl.so.2 (0x00007f32c60aa000) > libm.so.6 => /lib/libm.so.6 (0x00007f32c5e27000) > libnuma.so.1 => /usr/lib/libnuma.so.1 (0x00007f32c5c1f000) > librt.so.1 => /lib/librt.so.1 (0x00007f32c5a17000) > libnsl.so.1 => /lib/libnsl.so.1 (0x00007f32c57fe000) > libutil.so.1 => /lib/libutil.so.1 (0x00007f32c55fb000) > libpthread.so.0 => /lib/libpthread.so.0 (0x00007f32c53df000) > libgomp.so.1 => /usr/local/lib64/libgomp.so.1 (0x00007f32c51d0000) > libc.so.6 => /lib/libc.so.6 (0x00007f32c4e6e000) > libstdc++.so.6 => /usr/local/lib64/libstdc++.so.6 > (0x00007f32c4b67000) > libgcc_s.so.1 => /usr/local/lib64/libgcc_s.so.1 > (0x00007f32c4951000) > libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f32c4705000) > /lib64/ld-linux-x86-64.so.2 (0x00007f32c6a97000) > libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f32c44af000) > > > Is this a potential bug, as in the gromacs compilation is picking up the > /usr/lib/ and /usr/include (old MPI locations) despite manually specifying > it using -DMPI_INCLUDE, etc? > Perhaps, but it is not yet clear where the problem lies. In cmake, we try to compile an MPI test program with the compiler you've made available, and just use that compiler if it works. This combines nicely with modern MPI wrapper compilers, hence the above suggestion. Otherwise, in cmake we try to do some detection, and that presumably leads to your symptoms. It might be possible to work around that by setting CMAKE_PREFIX_PATH=/usr/local, so that the detection finds the version you want. Mark -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
