Gromacs installation error - deepmd.hpp: No such file or directory

[yazaydin]

Hello, 

I am trying to install Gromcas with DeepMD, but I get the following error
---------------------
[ 24%] Building CXX object src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o
In file included from /home/ucecoya/software/gromacs-2020.2/src/gromacs/mdlib/forcerec.h:47,
                 from /home/ucecoya/software/gromacs-2020.2/src/gromacs/modularsimulator/modularsimulator.cpp:56:
/home/ucecoya/software/deepmd/include/deepmd/gmx_plugin.h:8:10: fatal error: deepmd.hpp: No such file or directory
    8 | #include "deepmd.hpp"
      |          ^~~~~~~~~~~~
compilation terminated.
make[2]: *** [src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o] Error 1
make[1]: *** [src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/all] Error 2
make: *** [all] Error 2
-----------------------------

There is no deepmd.hpp in "$deepmd_root/include/deepmd/". The script that I ran to get to the above stage is below. Not sure where I did a mistake. Thanks.


# Clone deepmd-kit from GitHub to $HOME/software
cd $HOME/software
git clone https://github.com/deepmodeling/deepmd-kit.git deepmd-kit 
deepmd_source_dir=$HOME/software/deepmd-kit

# Download pre-compiled DeepMD C library
wget https://github.com/deepmodeling/deepmd-kit/releases/latest/download/libdeepmd_c.tar.gz -q
tar -xf libdeepmd_c.tar.gz 

# Create deepmd directory in $HOME/software
mkdir $HOME/software/deepmd
deepmd_root=$HOME/software/deepmd

# Build the GROMACS patch
cd $deepmd_source_dir/source
mkdir build
cd build
cmake -DDEEPMD_C_ROOT=$HOME/software/libdeepmd_c -DCMAKE_INSTALL_PREFIX=$deepmd_root ..
make -j8
make install

# Download GROMACS 2020.2 to $HOME
cd $HOME/software
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.2.tar.gz -q
tar -xf gromacs-2020.2.tar.gz
gromacs_root=$HOME/software/gromacs-2020.2
version=2020.2

# Patch GROMACS source code with DeepMD
export PATH=$PATH:$deepmd_root/bin
dp_gmx_patch -d $gromacs_root -v $version -p

# Compile Gromacs 
 cd $gromacs_root
mkdir build
cd build

#MPI double precision
cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON -DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_X11=ON -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs2020.2deepmdkit $CMAKE_FLAGS
make

[njzjz]

deepmd.hpp is in $HOME/software/libdeepmd_c. It seems the CMake file needs to be fixed.

[njzjz]

I see, the correct include directive is #include "deepmd/deepmd.hpp". It's not a problem when deepmd.hpp and gmx_plugin.h are in the same directory, otherwise, it will fail to find deepmd.hpp.

[yazaydin]

Thanks. I understand, but despite setting TENSORFLOW_ROOT=$HOME/software/libdeepmd_c
deepmd.hpp is under libdeepmd_c/include/deepmd/
but
gmx_plugin.h is under deepmd/include/deepmd/

what should I do to have both of them under the same directory? 

[njzjz]

Moving or copying into the same directory should be a fast workaround to make it work. I also submitted #3221 to fix it.

[yazaydin]

Thanks. I copied "deepmd.hpp" and "c_api.h" to deepmd/include/deepmd/ so that they are now with "gmx_plugin.h" in the same directory. 
cp $HOME/software/libdeepmd_c/include/deepmd/* $deepmd_root/include/deepmd/

I also had to do 
cp $HOME/software/libdeepmd_c/lib/* $deepmd_root/lib/

After the above actions, I think I successfully built Gromacs with DeepMDKit

[ucecoya@login01 bin]$ ls $HOME/software/gromacs2020.2deepmdkit/bin
demux.pl  gmx-completion.bash  gmx-completion-gmx_mpi.bash  gmx_mpi  GMXRC  GMXRC.bash  GMXRC.csh  GMXRC.zsh  xplor2gmx.pl

[yazaydin]

Infact, it seems, there was no need to set TENSORFLOW_ROOT=$HOME/software/libdeepmd_c in first place.

cp $HOME/software/libdeepmd_c/include/deepmd/* $deepmd_root/include/deepmd/
cp $HOME/software/libdeepmd_c/lib/* $deepmd_root/lib/

does the trick.