Matter Modeling Asked on December 11, 2021
In some science fields there are efforts to provide customized distributions, so you can get a productive environment with minimum set-up overhead. For example, in high energy particle physics, we have Scientific Linux, in mathematics we have MathLibre, and in cybersecurity research we have Kali Linux.
Is there any effort like these for materials modeling? If not, which Linux distributions come the closest?
Please list only one Linux distribution per answer!
It is oriented both to desktop and to servers. It has a large collection of software repositories for scientific computing in general (you can have all of GCC 7, 9, 10, 11 at the same time, module system for different versions of MPI libraries, CAD, CFD,...) and even for matter modelling in particular (GROMACS, LAMMPS, Quantum ESPRESSO, etc.).
It supports both KDE and Gnome equally (and some more). It can be updated without re-install or one can even use the continuously-updated Tumbleweed version.
Answered by Vladimir F on December 11, 2021
I think that if you need performance Clear Linux is the best choice. It's a distribution created by Intel but give also the best performance also with PC with AMD CPU respect to other distributions. Look at phoronix.com for benchmark.
Answered by NickZ on December 11, 2021
Disclaimer: Not exactly a Linux Distibution but a Virtual Machine (VM)
Quantum Mobile is a virtual machine for computational materials science.The VM is based on Ubuntu 18.04.4 LTS with VirtualBox 6.1.4.
It comes with simulation codes - BigDFT, cp2k, fleur, Quantum ESPRESSO, Siesta, Wannier90, yambo, together with AiiDA and the AiiDA lab jupyter environment.
Tools included -
Atomistic - xcrysden, jmol, cif2cell, ase, pymatgen, seekpath, spglib, pycifrw
Visualization - grace, gnuplot, matplotlib, bokeh, jupyter
Simulation environment - slurm, OpenMPI, FFT/BLAS/LAPACK, gcc, gfortran, singularity
Answered by Thomas on December 11, 2021
As a historic note, I found an example of a effort in this direction, in the past. A modified KNOPPIX targeted at molecular modeling with Gamess-US. It was called the VigyaanCD. Unfortunately it appears to be a defunct project by now. It was released in 2005 and I could not find any updates since then. The Gamess site has the following description:
GAMESS, Vigyaan CD (obsolete):
This is a bootable CD, containing a 2005-vintage version of GAMESS. This CD, from the Vigyaan project, is a live Linux CD containing all the required software to boot the computer, and run a standard, but now quite old, version of GAMESS, Avogadro-GMS, GTK-GAMESS and other useful software. Tutorials are also available on this CD. Note, this CD does not require compilation of GAMESS. More information about the CD can be found on the Vigyaan web site. If you encounter any problems with this CD, please do not send email to Mike or our Webmaster, instead send it to Pratul Agarwal.
Perhaps someone will bring it back from the dead, someday.
Answered by ksousa on December 11, 2021
For your workstation or laptop the best linux distribution is Ubuntu. Many of the recommendations here, like CentOS, are great for servers, but you might also have a laptop or desktop computer that you use for developing your code and running simulations. Ubuntu has gone much further than other linux distributions in developing a consumer-grade user interface. It's the only linux distribution that comes close to being a user-friendly desktop operating system in the same way as Mac OS or Windows. It's broad user base also means that little things are more likely to work, like your wifi, or your laptop going to sleep when you close the lid.
Answered by taciteloquence on December 11, 2021
Susi Lehtola's answer makes some good points, and I will elaborate on two of them:
To focus this answer on just one Linux distribution, out of the Fedora/RedHat/CentOS family, I picked Fedora because:
Drawbacks:
Answered by Nike Dattani on December 11, 2021
Scientific Linux is a rebuild of Red Hat Enterprise Linux. It started out before the CentOS project really took off. Nowadays CentOS is officially supported by Red Hat, but Scientific Linux still exists on its own.
Since both CentOS and Scientific Linux are just rebuilds of RHEL, all three should be binary compatible, and you should be able to use the same software repositories for all three.
The Fedora project is where development of RHEL happens, and the Fedora project also ships software for RHEL releases that haven't been included in the official Red Hat package selection. There is a fair number of matter modeling packages in the Fedora Extra Packages for Enterprise Linux (EPEL) repositories.
However, the problem with RHEL is that since the distribution is "stable", with the current pace of development the system packages quickly become outdated. The widest and most up to date selection is within Fedora, which aims at a new stable release every 6 months.
IMNSHO there are only two distributions that can be considered at earnest for general usage: Debian/Ubuntu, and Fedora/Red Hat (and its clones like Scientific Linux and CentOS), since they are the most widely used and offer by far the widest software selections. (Knoppix is a live CD version of Debian.)
In my personal experience the Debian world tends to lag a bit behind, but it should be noted I am not impartial: I've been packaging for Fedora/Red Hat for over a decade, by addressing any deficiencies wherever I've noticed them; this is why my needs are best served by Fedora and Red Hat.
In any case, the situation dependends highly on the package and its maintainer. If the distribution has a contributor who needs package X for their interests, it's highly likely that the distribution's package X is up to date and includes all features. If not, then it might be that X is not included in the distro, or that the version of X is super old...
Answered by Susi Lehtola on December 11, 2021
There isn't a silver bullet for this, so in my humble opinion there isn't a "best" Linux distribution for this. Just as Kali is not "the best" for security and Scientific Linux is also not advertised as the "best" for HEP. They are just good enough alternatives that tackle some issues that may seem helpful for many users, such as including many things and not having to install them by hand.
Personally, I tend to use popular big distributions, that I know are well documented and won't cease to exist anytime soon. Any Linux distribution could be used for Matter Modelling. The features of the software and tools for Modelling are independent of the choice of distribution (in general). Also take into account that a lot of Matter Modelling involves generic tools that are not specific for the area (shell, modern python versions, up-to-date BLAS libraries, etc.).
Answered by IvanP on December 11, 2021
(to simulate continuous material)
CAELinux's official page states:
Based on the open-source CAD/CAM software such as Freecad, LibreCAD, PyCAM and Slic3r and CAE softwares like Salomé, Code_Aster, Code_Saturne, Calculix, OpenFOAM and Elmer , you can design your CAD geometry, perform multiphysics simulations to optimize your design, generate G-code for prototyping with 3D printing & milling, and even develop your own PCBs & microcontroller based electronic circuits for automation.
Answered by Camps on December 11, 2021
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