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plumed / plumed2

Development version of plumed 2
https://www.plumed.org
GNU Lesser General Public License v3.0
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Trouble compiling Plumed Patched Gromacs 2023 #1079

Open Arikite-netizen opened 4 months ago

Arikite-netizen commented 4 months ago

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