How to configure a new system with supporting libraries for compiling MHD models?

Often when migrating to new systems, it can get difficult to setup all the necessary libraries and packages in the target system for continuing working on the mddelling. In this post I will try to summarize the libraries required for setting up some of the simulations codes e.g., SWMF, MPI-AMRVAC, SFT-1D. Some of these codes require hdf5, netcdf-c/fortran, zlib, curl, OPENMPI and GCC.

GCC

It is quite simple to build up on the existing system libraries (on Linux/Mac systems). The bash script file build_gcc_13.2.0.sh is the best resource for this. Download the file and run it in a bash shell. Add fortran language to the list of languages inside the shell script. At the end of the building, it will show the instructions to append the installed libraries to the system $PATH. The script downloads and installs the libraries on the system. A note of caution, the whole process may take about ~3 hrs., so be patient.

After this, you can build the OPENMPI libraries. The installation version openmpi-4.1.5 seem to work for me with the GCC installation versions. I prefer building the libraries with a local prefix.

Inside the openmpi-4.1.5 directory run the following,

./configure --prefix=~/opt/openmpi-4.1.5
make -j 4
make install

Here are a few lines that you can add to the ~/.bashrc or ~/.zshrc file after the OPENMPI installation.

export PATH=~/openmpi-4.1.5/bin:~/opt/gcc-13.2.0/bin:$PATH
export LD_LIBRARY_PATH=~/openmpi-4.1.5/lib:~/opt/gcc-13.2.0/lib:~/opt/gcc-13.2.0/lib64:$LD_LIBRARY_PATH
export MANPATH=~/opt/gcc-13.2.0/share/man:$MANPATH
export INFOPATH=~/opt/gcc-13.2.0/share/info:$INFOPATH

After the installation you can check the version of the gcc by typing gcc -v. Similarly for fortran as well. At the end of this the system should have all the mpicc, mpif90, gcc, gfortran executables in the default $PATH variable.

netCDF

Installation of netcdf libraries is dependent on multiple other libraries e.g., curl, zlib, hdf5, netcdf-c and netcdf-fortran. Here is a shell script install_netcdf.sh for this. A few extra install flags and versions are suggested for a system-wide installation.

Suggested versions

• hdf5-1.14.6, build with --enable-fortran, --enable-cxx/--enable-parallel.
• netcdf-c-4.9.3
• netcdf-fortran-4.6.1
• zlib-1.3.1
• curl-8.14.1

Again the shell script downloads the required files and builds the libraries at a user location.

None of the scripts require admin privileges, so building these libraries should be self-sufficient.

After building these libraries, you must update the system $PATH$ variable for future use. Individual simulation codes require independent path to the libraries. I will write create other posts for installing and testing individual widely used codes.

Hope this helps!