Compiling Deep-md with GROMACS

User discussions
1

GROMACS version: 2020.2
GROMACS modification: Yes/No
I was trying to install Deep-md with GROMACS following the link
1.6. Install GROMACS with DeepMD — DeePMD-kit documentation. To do this, I have followed the link to install Deep-MD: 1.2. Install from source code — DeePMD-kit documentation
Here I have successfully completed the 1.2.1 ( install-the-python-interface) and 1.2.2. (Install the C++ interface) sections.
Then when I am running to build Gromacs with Deep-MD using the command:
#!/bin/bash
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export CMAKE_PREFIX_PATH=“/home/qzyme/Downloads/fftw-3.3.9” # fftw libraries
mkdir build
cd build

cmake … -DCMAKE_CXX_STANDARD=14 \ # not required, but c++14 seems to be more compatible with higher version of tensorflow
-DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/usr/bin/gromacs-2020.2-deepmd
make -j
make install
I am getting the error at make step which is given below:
make[2]: *** [src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make:188: src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:4813: src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

2

I think this might not be directly relevant to GROMACS installation. Given the complexity of compiling software with specific configurations, a detailed review of the error logs and cross-referencing them with the build process and requirements of Gromacs with Deep-MD would likely help in identifying and resolving the issue. It is better to consult the DeepMD team. However, here are some useful tips:

  1. Check Dependencies: Ensure that all necessary dependencies and libraries are properly installed and their paths are correctly set.
  2. Compiler Compatibility: Verify if the compilers and their versions are compatible with Gromacs and Deep-MD requirements. Sometimes, specific versions or configurations are needed for successful compilation.
  3. CMake Configuration: Double-check the CMake configuration for any missing or incorrectly set options. Ensure that paths to libraries and necessary components are accurately specified.
  4. Source Code Errors: Review the modularsimulator.cpp file for any syntax errors or issues that might be causing the compilation to fail.
  5. Build Logs: Look into the detailed build logs to pinpoint the specific error or warning messages preceding the “Error 1” to understand the cause of the build failure more precisely.