GROMACS version: 2021.4
GROMACS modification: Yes, with PLUMED 2.8.0
Hi,
I was trying to install PLUMED 2.8.0 and patch it with GROMACS 2021.4 with the following workflow:
(1) First I installed PLUMED with the following commands:
git clone --single-branch --branch v2.8 https://github.com/plumed/plumed2.git
mkdir plumed2_build
cd plumed2 && ./configure --prefix=/home/wei-tse/Documents/Software/PLUMED/plumed2_build CXX=g++ CC=gcc
make -j 16
make install
(2) Then, I installed GROMACS 2021.4 and tried to patch PLUMED with the following commands:
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2021.4.tar.gz && tar zxf gromacs-2021.4.tar.gz
cd gromacs-2021.4 && mkdir build && cd build
cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7
make -j 16
cd ../ && source /home/wei-tse/Documents/Software/PLUMED/plumed2/sourceme.sh
plumed patch -p
cd build
sudo make install
source /usr/local/gromacs/bin/GMXRC
However, when running make install for GROMACS, I had the following error when the command was 98% done:
/usr/bin/ld: warning: libplumed.so, needed by /home/wei-tse/Documents/Software/GROMACS/gromacs-2021.4/build/lib/libgromacs.so.6, not found (try using -rpath or -rpath-link)
/home/wei-tse/Documents/Software/GROMACS/gromacs-2021.4/build/lib/libgromacs.so.6: undefined reference to `plumed_installed'
/home/wei-tse/Documents/Software/GROMACS/gromacs-2021.4/build/lib/libgromacs.so.6: undefined reference to `plumed_cmd_nothrow'
/home/wei-tse/Documents/Software/GROMACS/gromacs-2021.4/build/lib/libgromacs.so.6: undefined reference to `plumed_cmd_safe_nothrow'
/home/wei-tse/Documents/Software/GROMACS/gromacs-2021.4/build/lib/libgromacs.so.6: undefined reference to `plumed_finalize'
/home/wei-tse/Documents/Software/GROMACS/gromacs-2021.4/build/lib/libgromacs.so.6: undefined reference to `plumed_create' collect2: error: ld returned 1 exit status api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make:97: recipe for target 'bin/argon-forces-integration' failed
make[2]: *** [bin/argon-forces-integration] Error 1
CMakeFiles/Makefile2:4116: recipe for target 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/all' failed
make[1]: *** [api/nblib/samples/CMakeFiles/argon-forces-integration.dir/all] Error 2
Makefile:165: recipe for target 'all' failed make: *** [all] Error 2
I didn’t have any errors when installing PLUMED or executing the patch command. I think I might have accidentally messed up something but I’m not entirely sure how this error occurred. I’m wondering if anyone could provide some guidance. Thanks a lot!