Error: ‘useDeepmd’, 'deepmdPlugin', 'c_dp2gmx' were not declared in this scope, while Installing gromacs2023 with Deepmd-kit #4641
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wangshuai-simulation
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I think you need to confirm that if every line is patched. |
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I think you need to confirm that if every line is patched. |
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As the gromacs2020.2 is too old to be compiled using newer compiler (it causes error ‘numeric_limits’ is not a member of ‘std’), I have to install gromacs2023 with Deepmd-kit. Here is my protocol of the whole installing process bellow:
`
SOFTWARE=/data2/shuaiwang/deep-potential-md
wget https://github.com/deepmodeling/deepmd-kit/releases/latest/download/libdeepmd_c.tar.gz
tar xzvf libdeepmd_c.tar.gz
git clone https://github.com/deepmodeling/deepmd-kit.git deepmd-kit
cd $SOFTWARE/deepmd-kit/source
mkdir build
cd build
cmake -DDEEPMD_C_ROOT=$SOFTWARE/libdeepmd_c -DCMAKE_INSTALL_PREFIX=$SOFTWARE/deepmd-kit/source/install-wangshuai ..
make -j8
make install
cd $SOFTWARE
tar -zxvf gromacs-2023.2.tar.gz
export PATH=$PATH:$SOFTWARE/deepmd-kit/source/install-wangshuai/bin
dp_gmx_patch -d $SOFTWARE/gromacs-2023.2 -v 2020.2 -p
mkdir build
cd build
cmake .. -DGMX_CUDA_TARGET_COMPUTE=89 -DCMAKE_CXX_STANDARD=14 -DGMX_MPI=OFF -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-12.6/ -DCMAKE_INSTALL_PREFIX=$SOFTWARE/gromacs-2023.2/gromacs-2023.2-deepmd -DCMAKE_PREFIX_PATH=/data2/shuaiwang/deepmd/fftw-3.3.10/install-wangshuai/bin -DCMAKE_LIBRARY_PATH=/data2/shuaiwang/deepmd/fftw-3.3.10/install-wangshuai/lib/ -DCMAKE_INCLUDE_PATH=/data2/shuaiwang/deepmd/fftw-3.3.10/install-wangshuai/include/ -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Release -DGMX_DOUBLE=OFF -DREGRESSIONTEST_DOWNLOAD=ON
make -j20
when i went to the last step of make -j20, it outputted error as shown bellow:
[ 81%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o
[ 83%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o
/data2/shuaiwang/deep-potential-md/gromacs-2023.2/src/gromacs/mdlib/forcerec.cpp: In function ‘void init_forcerec(FILE*, const gmx::MDLogger&, const gmx::SimulationWorkload&, t_forcerec*, const t_inputrec&, const gmx_mtop_t&, const t_commrec*, real ()[3], const char, const char*, gmx::ArrayRef<const std::__cxx11::basic_string >, real)’:
/data2/shuaiwang/deep-potential-md/gromacs-2023.2/src/gromacs/mdlib/forcerec.cpp:1085:5: error: ‘deepmdPlugin’ was not declared in this scope
1085 | deepmdPlugin = new deepmd::DeepmdPlugin;
| ^~~~~~~~~~~~
/data2/shuaiwang/deep-potential-md/gromacs-2023.2/src/gromacs/mdlib/forcerec.cpp:1085:24: error: ‘deepmd’ does not name a type
1085 | deepmdPlugin = new deepmd::DeepmdPlugin;
| ^~~~~~
/data2/shuaiwang/deep-potential-md/gromacs-2023.2/src/gromacs/mdlib/forcerec.cpp:1089:9: error: ‘useDeepmd’ was not declared in this scope
1089 | useDeepmd = false;
| ^~~~~~~~~
/data2/shuaiwang/deep-potential-md/gromacs-2023.2/src/gromacs/mdlib/forcerec.cpp:1094:9: error: ‘useDeepmd’ was not declared in this scope
1094 | useDeepmd = true;
| ^~~~~~~~~
...
`
Appreciate if anyone can help me avoid this error !
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