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I have just started studying DFT. I did some basic calculations using a Windows system. How will Ubuntu help me if I install it on my system? How much space should I allocate on drive for the Ubuntu system as to run it in parallel with Windows?

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  • $\begingroup$ I move the discussion here to our High performance computing chat room. Just didn't want to discussion under the post getting too long, but feel free to continue in the chat room. $\endgroup$
    – Tyberius
    Jul 9 at 16:58
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As previously commented, any Linux distro will be much better than Windows to run simulations.

About your first question:

Is Ubuntu a better option for DFT calculations?

No, it is not. But there is nothing special about Ubuntu, any Linux distribution would be a better choice than Windows. You can use Ubuntu or other distros like Mint or the father of them, Debian. Also, you can use Fedora, a daughter of RedHat or OpenSUSE. There are many other variants (in this link you will find 12.)

About your second question:

How will Ubuntu help me if I install it on my system?

Yes, it will. Normally, Ubuntu will recognize your Windows installation and will suggest you how to partition the hard disk space in order to install it together with Windows. Also, it will setup the boot loader with the two options so you can select at boot.

About your third question:

How much space should I allocate on drive for the Ubuntu system as to run it parallel with Windows.

You can have a Linux installation with only the main developer packages (C, C++, and fortran compilers and also Python, etc.) in 5GB-10GB (less than a 16GB memory stick). For that, avoid to use the install recommendation packages and select yourself. Then you can mount your Windows partition and use it to put your working files.

My recommendation is to look for the software requirements of your simulation package. You will be free of headache trying to compile/install if the requirements are not fulfilled. Even if you can put your code to work, it is possible that after a system update (that is very common in distros like (or based on) Ubuntu), your software stop working.

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    $\begingroup$ Thank you so much for this detailed answer. It definitely helps and I appreciate it so much. On my learning process such help is going to give me proper direction. $\endgroup$ Jul 8 at 17:45
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    $\begingroup$ I think OpenSUSE has no relation to Red Hat. Another "daughter" of Red Hat was CentOS though it may be discontinued, at least in current form. $\endgroup$
    – Gherman
    Jul 8 at 19:28
  • $\begingroup$ @Gherman thanks for your comment. I edited the post. $\endgroup$
    – Camps
    Jul 8 at 19:39
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"Is Ubuntu a better option than Windows for DFT calculations?"

The vast majority of quantum chemistry and solid-state physics software were designed/developed for Linux. Your comment says you're specifically interested in Quantum ESPRESSO, and we recently had someone else complain that Quantum ESPRESSO was not performing the way they expected when using Windows: Running Quantum ESPRESSO on a GPU in Windows. The same will be the case for most of the programs listed in the link I provided in the beginning of this paragraph.

The most highly upvoted comment on this question: What software is available to do molecular dynamics on Windows? said this very accurately:

"Although it's possible to run molecular dynamics on Windows, if you are serious about computational science it's best to get comfortable with Linux. It costs nothing monetarily. Most high-performance computing platforms (clusters and supercomputers) are Linux-based. Most molecular simulation software and ancillary codes (system building and analysis tools) are developed on Linux. Even where Windows compatibility exists, it is often incomplete (some features are missing) or poorly supported."

Another similar question to yours was asked before (and my answer was similar to my answer to you here): GUI for DFT calculations.

Finally (since Camps already answered the part in your question about how much space you'll need to allocate for Linux), I'll say that Ubuntu isn't the only option, and that there's some Linux distributions that are specifically designed for matter modeling, and other more general distributions like Fedora which already have a lot of matter modeling software packaged: Which Linux distribution is best for Matter Modeling?. Ubuntu does likely have more than 40 million users though (Does Ubuntu have 40 million users?) and by far has the largest number of users out of all Linux distributions, and there's an entire Stack Exchange site called Ask Ubuntu just for Ubuntu, so there's advantages in terms of getting help if you run into any problems. However, if you're considering to build a compute server (see "https://mattermodeling.stackexchange.com/q/5018/5" and "https://mattermodeling.stackexchange.com/q/6165/5" first), the most popular Linux distribution for that purpose would no longer be Ubuntu: Red Hat (not free), CentOS (basically a free version of Red Hat that was unfortunately discontinued a few months ago) and OpenSUSE (mainly used in Germany) are more popular for that.

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    $\begingroup$ Thank you for your detailed answer. On my personal system I have to work with free open source Quantum espresso and certainly as a starter Ubuntu community will help me if I have any questions at this stage. $\endgroup$ Jul 12 at 4:47
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Well, my advice is to always check benchmarks before doing any consideration. I suggest you to follow the phoronix website because here you can read a lot about Linux benchmark in terms of different distributions, different hardware and also some comparison with windows OS. For example here you can find performance benchmarks comparing Ubuntu and Ubuntu on Windows wsl. Here you can find for example some recent benchmark between different Linux distributions. DFT software are not usually tested, but these tests are good starting point.

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    $\begingroup$ Thank you for your answer, it was indeed useful to know more about Linux distributions. $\endgroup$ Jul 12 at 4:34
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Another advantage of using Linux is that it's more portable if you later end up switching to supercomputing facilities.

Most jobs I've been involved with have had just enough shell scripting etc. in there for things to go wrong if not tested on a sufficiently similar system. Running a long job is no fun if your script copied the wrong input file over, or (if you're queued on a busy supercomputer) if the job script fails on the 2nd line when your turn arrives. I tend to check basic operation on a desktop, with very coarse parameters, then refine the parameters and launch the job on the cluster.

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    $\begingroup$ Thank you for your answer. $\endgroup$ Jul 12 at 4:48
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If you want to use quantum chemical programs as packaged for and distributed by your Linux distribution of choice, the long term support (LTS) releases of the Ubuntu familiy are typically good to familiarize with the program in question, and to perform many types of computation. If you opt for a light-weight desktop environment (e.g., Xfce as in Xubuntu) instead of GNOME (as in default Ubuntu), a less performant computer may dedicate some resources not used for graphics for the scientific computations ahead.

Still assuming you use the program as distributed by the LTS distribution you may become interested in more recent versions of the program in question for that they adjust present / introduce new features, or correct errors. Then, the lag until a new release of the LTS distribution hopefully including version ($n + 1$) of your program of interest may be noticeable. E.g., still supported Linux Xubuntu 18.04 LTS includes NWChem in version 6.6, current Xubuntu 20.04 LTS in version 7.0.0 (tracker), while the program (by October 2020) was released as version 7.0.2. If you report a bug in the corresponding user forums, you may receive an answer in lines of «the issue reported by you (already) was resolved in the past with version X. Since version X no longer is supported, please update and use version Y instead».

This may be an incentive to either a) learn how to compile / install the program from what the developers distribute. Or b), to use a distribution with a more continious integration and upgrade of the packaged programs, e.g., Linux Debian branch testing, where you may track which (new) relases are available for you (example from the DebiChem collection). You may chose a), b), as well as a) and b).

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    $\begingroup$ Thank you for your answer, it certainly was something I needed to know about. $\endgroup$ Jul 12 at 4:49

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