I believe the result of the tests is greatly influenced by the hardware and the cmake options and thus there is no way to know that’s wrong by just reading the error message…
However, you can very well install GROMACS even without running make check: just do sudo make install, source the binary and try it out! It may be that the failures highlited in make check are completely bening and won’t affect your runs. It happens to me every time I try to install a customized GROMACS version on a cluster or a supercomputer.
Hello sir
please do help me out with this error
Error occurred when make was runned
[ 97%] Linking CXX shared library …/…/lib/libgromacs.so
/usr/bin/ld: /usr/local/lib/libfftw3f.a(lt7-conf.o): warning: relocation against fftwf_solvtab_rdft_r2r' in read-only section .text’
/usr/bin/ld: /usr/local/lib/libfftw3f.a(assert.o): relocation R_X86_64_PC32 against symbol `stdout@@GLIBC_2.2.5’ can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/build.make:13361: lib/libgromacs.so.7.0.0] Error 1
make[1]: *** [CMakeFiles/Makefile2:4633: src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [Makefile:166: all] Error 2
Thank you in advance.
This is the error which I got when i run make check
It looks like there is something wrong with your compiler toolchain or the libraries you are linking against.
As Michele said, HPC environments can be difficult because the architecture of the login nodes and compute nodes can be different. If you are compiling for a compute node, it is best to do cmake, build, and make check all on a compute node, such as through an interactive job.
If this is not the problem, then it is hard to guess about the problem without more information about your computing environment and the CMake command line you used.
/usr/bin/ld: /usr/local/lib/libfftw3f.a(assert.o): relocation R_X86_64_PC32 against symbol stdout@@GLIBC_2.2.5’ can not be used when making a shared object; recompile with -fPIC
It looks like you are building GROMACS with shared libraries, but only a static library archive was found for libfftw3f. You can either