GROMACS version:2018.8
GROMACS modification: No
Here post your question :
When I try to compile gromacs, I always get an error in the last step of make install. How can I solve this problem?
The following output is the result of the command “make install”
[ 98%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/thread_mpi/src/numa_malloc.c.o
[ 98%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/thread_mpi/src/once.c.o
[ 98%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/__/external/lmfit/lmmin.cpp.o
[ 98%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
[ 98%] Linking CXX shared library ../../lib/libgromacs.so
[ 98%] Built target libgromacs
Scanning dependencies of target template
[ 98%] Building CXX object share/template/CMakeFiles/template.dir/template.cpp.o
[ 98%] Linking CXX executable ../../bin/template
../../lib/libgromacs.so.3.5.0: undefined reference to `srot_'
../../lib/libgromacs.so.3.5.0: undefined reference to `strsm_'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2
The following output is the result of the command “make install -j”
[100%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
[100%] Linking CXX shared library ../../lib/libgromacs.so
[100%] Built target libgromacs
Scanning dependencies of target gmx
Scanning dependencies of target template
[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o
[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o
[100%] Building CXX object share/template/CMakeFiles/template.dir/template.cpp.o
[100%] Linking CXX executable ../../bin/gmx
../../lib/libgromacs.so.3.5.0: undefined reference to `srot_'
../../lib/libgromacs.so.3.5.0: undefined reference to `strsm_'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/gmx] Error 1
make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[100%] Linking CXX executable ../../bin/template
../../lib/libgromacs.so.3.5.0: undefined reference to `srot_'
../../lib/libgromacs.so.3.5.0: undefined reference to `strsm_'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2
The key commands executed throughout the process are:
cd fftw-3.3.8/
./configure --prefix=/data/home/software/fftw-3.3.8 --enable-sse2 --enable-avx --enable-float --enable-shared --enable-avx2
tar -zxvf gromacs-2018.8.tar.gz
cd gromacs-2018.8/
mkdir build
cd build/
export CMAKE_PREFIX_PATH=/data/home/software/fftw-3.3.8
cmake3 .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/share/cuda/9.2 -DCMAKE_INSTALL_PREFIX=/data/home/software/gromacs-2018.8/gmx2018.8-gpu -DGMX_SIMD=AVX2_256
which cmake3
alias cmake3='/share/apps/cmake/3.7.1/bin/cmake'
/share/apps/cmake/3.7.1/bin/cmake
I can’t find any similar problem on google. How can I solve it?
Any advice would be appreciated!