gromacs compilation gives undefined reference error
i would like to use gromacs on my open suse 12.3 platform but am having
trouble with it. when trying to compile an analyzing tool using
gmx_template i first got this error:
g++ -L/usr/local/gromacs/lib -o msd msd.o -lmd -lgmx -lfftw3f -lxml2 -lnsl
-lm
/usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld:
/usr/local /gromacs/lib/libgmx.a(pthreads.c.o): undefined reference to
symbol 'pthread_getaffinity_np@@GLIBC_2.3.4'
/usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld:
note: 'pthread_getaffinity_np@@GLIBC_2.3.4' is defined in DSO
/lib64/libpthread.so.0 so try adding it to the linker command line
/lib64/libpthread.so.0: could not read symbols: Invalid operation
collect2: error: ld returned 1 exit status
make: * [msd] Fehler 1
then i added /lib64/libpthread.so.0 to the -L options in the makefile
but now i get a lot of errors like this:
/usr/local/gromacs/lib/libgmx.a(pbc.c.o): In function
`put_atoms_in_box_omp._omp_fn.0':
pbc.c:(.text+0x862f): undefined reference to `omp_get_num_threads'
i think they are all related to openmp. i do not understand enough of the
building process to enable openmp support (probably -fopenmp) and am at
the same time surprised in case i would have to change the cmake files in
order to make gromacs work. i used the quick and dirty install following
the gromacs installation instructions on their website.
any suggestions what i can do / did wrong so far ? i am using gcc 4.7
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