[gmx-users] Re: gromacs 4.6.2 MPI distribution location problems

[sirishkaushik]

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

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?




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