GROMACS version: 2021.4
GROMACS modification: Yes/No
Can anyone guide me a systematic installation of GROMACS 2021.4 in Central Supercomputing Facility ?
I want to install GROMACS into the centralised supercomputer, where I wouldn’t have any “administrative” rights. I tried to install GROMACS 2021.4 version into my user of CDAC Param - Siddhi Supercomputing facility as per installation guide. When I tried to build it with make file using following command for MPI=on.
cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
cmake … -DGMX_MPI=on
Error: – Could NOT find Python3 (missing: Python3_EXECUTABLE Interpreter) (Required is at least version “3.6”)
– Found OpenMP_C: -fopenmp
– Found OpenMP_CXX: -fopenmp
– Found OpenMP: TRUE
– MPI is not compatible with thread-MPI. Disabling thread-MPI.
– Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
– Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
– Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
CMake Error at cmake/gmxManageMPI.cmake:172 (message):
MPI support requested, but no MPI compiler found. Either set the
C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or
set the variables reported missing for MPI_C above.
Call Stack (most recent call first):
CMakeLists.txt:418 (include)
Can anyone suggest me an elaborative installation steps? What should I change in make file during make, make check and make install steps ?
Thank you in Advance.
These are the steps I have used to install gromacs in the Center supercomputing facility, Paramsanganak.
##initial step for downloading and extracting gromacs
tar xfz gromacs-2021.tar.gz
cd gromacs-2021
mkdir build
cd build
modules required for gromacs installation
module load cmake/3.14.3
module load compiler/gcc/7.3.0
module load compiler/intel/2018.2.199
module load compiler/cuda/10.1
module load python/conda-python/3.9
cmake … -DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc -DGMX_MPI=on -DGMX_OPENMP=ON -DGMX_GPU=CUDA -DGMX_USE_NVML=on -DGMX_DOUBLE=off -DBUILD_SHARED_LIBS=off -DGMX_FFT_LIBRARY=mkl -DGMX_SIMD=AVX_512 -DCMAKE_INSTALL_PREFIX=/directory/to/install/gromacs
I hope this will help.
@I_aditi ma’am , Thank you for your guidance. I tried to load needed modules listed above by using “source” command instead of module load, as Ubuntu OS is installed on ParamSiddhi. First i sourced intel compilers (source /opt/intel/env.sh), then python. But i couldn’t find .sh file to source cmake and gcc to load modules. Can you comment on this? Actually i am new to gromacs. I am only familiar with local (serial) installation of gromacs. It would be a great help, thank you in advance.
According to my understanding of CDAC supercomputing facilities, there is a section where all modules are there, which we can load according to our requirement; at least, this is the case with paramsanganak.
Try to look in the documentation provided by the CDAC or param-siddhi to locate the modules and then load them.
If things are still not working, you can always write to admin (CDAC or param-siddhi) and ask how to install Gromacs.
Thank you so much for your guidance. I’ll try to solve it with given considerations.
Respected Ma’am,
Good morning, i am please to inform you that i was able to install GROMACS into ParamSIDDHI AI successfully. But i am not aware of making script file compatible with ParamSIDDHI AI. I want to ask you that if you could guide me to prepare a sample script file (slurmm script) to run molecular dynamics simulation in parallel mode for GROMACS 2021.
Thank you so much for the help.
Regards,
Sarthak