# GROMACS Installation in Centralised Supercomputing Facility **URL:** \ **Category:** User discussions\ **Tags:** installation-guide, installation\ **Created:** [August 16, 2023, 2:12pm UTC](https://gromacs.bioexcel.eu/t/gromacs-installation-in-centralised-supercomputing-facility/7029 "2023-08-16T14:12:20Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![SarthakTrivedi](https://avatars.discourse-cdn.com/v4/letter/s/58956e/32.png) [@SarthakTrivedi](https://gromacs.bioexcel.eu/u/SarthakTrivedi)\ **Post date:** [August 16, 2023, 2:12pm UTC](https://gromacs.bioexcel.eu/t/gromacs-installation-in-centralised-supercomputing-facility/7029/1 "2023-08-16T14:12:20Z")
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. ---
**Author:** ![l\_aditi](https://avatars.discourse-cdn.com/v4/letter/l/b38774/32.png) [@l\_aditi](https://gromacs.bioexcel.eu/u/l_aditi)\ **Post date:** [August 17, 2023, 10:35am UTC](https://gromacs.bioexcel.eu/t/gromacs-installation-in-centralised-supercomputing-facility/7029/2 "2023-08-17T10:35:55Z")
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. ---
**Author:** ![SarthakTrivedi](https://avatars.discourse-cdn.com/v4/letter/s/58956e/32.png) [@SarthakTrivedi](https://gromacs.bioexcel.eu/u/SarthakTrivedi)\ **Post date:** [August 17, 2023, 2:15pm UTC](https://gromacs.bioexcel.eu/t/gromacs-installation-in-centralised-supercomputing-facility/7029/3 "2023-08-17T14:15:19Z")
@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. ---
**Author:** ![l\_aditi](https://avatars.discourse-cdn.com/v4/letter/l/b38774/32.png) [@l\_aditi](https://gromacs.bioexcel.eu/u/l_aditi)\ **Post date:** [August 18, 2023, 6:17am UTC](https://gromacs.bioexcel.eu/t/gromacs-installation-in-centralised-supercomputing-facility/7029/4 "2023-08-18T06:17:56Z")
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. ---
**Author:** ![SarthakTrivedi](https://avatars.discourse-cdn.com/v4/letter/s/58956e/32.png) [@SarthakTrivedi](https://gromacs.bioexcel.eu/u/SarthakTrivedi)\ **Post date:** [August 23, 2023, 7:09am UTC](https://gromacs.bioexcel.eu/t/gromacs-installation-in-centralised-supercomputing-facility/7029/5 "2023-08-23T07:09:05Z")
Thank you so much for your guidance. I’ll try to solve it with given considerations. ---
**Author:** ![SarthakTrivedi](https://avatars.discourse-cdn.com/v4/letter/s/58956e/32.png) [@SarthakTrivedi](https://gromacs.bioexcel.eu/u/SarthakTrivedi)\ **Post date:** [August 26, 2023, 5:42am UTC](https://gromacs.bioexcel.eu/t/gromacs-installation-in-centralised-supercomputing-facility/7029/6 "2023-08-26T05:42:09Z")
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