Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Trouble compiling Plumed Patched Gromacs 2023 #1079

Open
Arikite-netizen opened this issue May 19, 2024 · 0 comments
Open

Trouble compiling Plumed Patched Gromacs 2023 #1079

Arikite-netizen opened this issue May 19, 2024 · 0 comments

Comments

@Arikite-netizen
Copy link

I was trying to install gromacs patched with plumed for Metadynamics analysis as per given in the documentation however I am having problems troubleshooting the compilation error please help me figure out the issue
please follow through the commands that I had run...

cd gromacs-2023
plumed patch -p -e gromacs-2023
mkdir build && cd build
cmake .. -DGMX_BUILD_OWN_FFTW=on -DGMX_MPI=on -DCMAKE_C_COMPILER=gcc-12 -DCMAKE_CXX_COMPILER=g++-12 -DGMX_GPU=CUDA -DNVML_INCLUDE_DIR=/usr/local/cuda-12.1/targets/x86_64-linux/include/ -DNVML_LIBRARY=/usr/lib/i386-linux-gnu/libnvidia-ml.so -DCMAKE_INSTALL_PREFIX=/opt/gromacs_metad -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_metad -DGMX_LIBS_SUFFIX=_metad -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON
make -j 16

The make process remained smooth and had no errors until the plumed patching and linking , here's the few lines at the end of compilation

[ 96%] Built target libgromacs
[ 96%] Building CXX object src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o
[ 96%] Linking CXX executable ../../bin/gmx_metad
[ 96%] Building CXX object src/testutils/CMakeFiles/testutils.dir/interactivetest.cpp.o
[ 96%] Building CXX object src/testutils/CMakeFiles/testutils.dir/filematchers.cpp.o
[ 96%] Building CXX object src/testutils/CMakeFiles/testutils.dir/loggertest.cpp.o
[ 96%] Building CXX object src/testutils/CMakeFiles/testutils.dir/conftest.cpp.o
[ 96%] Building CXX object src/testutils/CMakeFiles/testutils.dir/mpi_printer.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/mpitest.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/testfilemanager.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/refdata_xml.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/simulationdatabase.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/testasserts.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/refdata.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/stdiohelper.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/stringtest.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/testfileredirector.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/test_device.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/test_hardware_environment.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/testinit.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/testmatchers.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/testoptions.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/textblockmatchers.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/topologyhelpers.cpp.o
[ 98%] Building CXX object src/testutils/CMakeFiles/testutils.dir/tprfilegenerator.cpp.o
[100%] Building CXX object src/testutils/CMakeFiles/testutils.dir/trajectoryreader.cpp.o
[100%] Building CXX object src/testutils/CMakeFiles/testutils.dir/xvgtest.cpp.o
[100%] Building CXX object src/testutils/CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o
_/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libopenblas.a(sormtr.o): undefined reference to symbol 'gfortran_concat_string@@GFORTRAN_8'
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libgfortran.so.5: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[2]: *** [src/programs/CMakeFiles/gmx.dir/build.make:104: bin/gmx_metad] Error 1
make[1]: *** [CMakeFiles/Makefile2:5853: src/programs/CMakeFiles/gmx.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[100%] Linking CXX static library ../../lib/libtestutils.a
[100%] Built target testutils
make: *** [Makefile:166: all] Error 2

I tried to add flag -LGFORTRAN in testutils section ,but it didn't make any difference please suggest a way to correct this. Would really appreciate it

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant