[3dem] Operating system for local server environment

Tue May 10 02:36:59 PDT 2022

Hello Christian,

I only manage two workstations, but with very different hardware (all the types of differences you describe). They initially ran CentOS 8, but since its end of support was shifted earlier than originally scheduled, I did a fresh installation of Rocky Linux (8.4 at the time, now they are both on 8.5 through regular updates). I have had a very good experience with Rocky as the base system to run cryoSPARC and RELION (I now even have them set up to automatically queue jobs to SLURM, it works fine), and a bunch of other cryoEM programs (Topaz, cryoDRGN, etc.). It is pretty much "set up once and forget", with minimal maintenance efforts.

If you are already familiar with CentOS, Rocky will be a smooth transition. Alma Linux is probably also a sensible option (also a RHEL rebuild).

CentOS Stream is not a good option, because it updates the kernel more often than new versions of the Nvidia driver get released (because Nvidia follows RHEL updates, and CentOS Stream’s purpose is to be just ahead of RHEL; it doesn’t seem like Nvidia has any plan of supporting CentOS Stream).

Arch is updated even more often than CentOS Stream, so it will probably be the same kind of struggle to maintain than CentOS 7, but the opposite way: most things in the base OS will be too new and changing too often for the research software you want to run. Also note that Nvidia does not support Arch, so you would have to rely on the community repository. Since the Nvidia driver is so critical to a base system for GPU workstations, I would recommend limiting your choice of OS to the ones Nvidia supports, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__developer.nvidia.com_cuda-2Ddownloads-3Ftarget-5Fos-3DLinux-26target-5Farch-3Dx86-5F64&d=DwIGaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=CkvlK51L4BVJq-WOK3yXrz_7t-L3SNOr3WKUExu2ZcNWBojC7nAL5PdrAi5yHcbu&s=_cizLH5i2tmuI0nb8-uL8hV0aW0pDqboVN9toCsQZOc&e=  (knowing that you can use Rocky or Alma instead of RHEL). Moreover, I would strongly recommend installing the Nvidia driver with their RPM or DEB package, not with the "runfile", as this will ensure you never end up with incompatible driver and kernel versions (which the runfile installation does not guard against; been there, done that).

I don’t have recent experience with the Debian family to say much about them, but it would probably be fine if you limit your choice to the versions supported by Nvidia (so Debian 11 or Ubuntu 20.04 LTS).

I hope this helps,

Guillaume

On 10 May 2022, at 10:28, Christian Tüting <christian.tueting at biochemtech.uni-halle.de<mailto:christian.tueting at biochemtech.uni-halle.de>> wrote:

Dear 3dem mailing list recipients,

I would like to get your opinion on which operating system is the most
suitable for our local server environment.

To frame the question:
We have multiple local workstations and storage servers with a very
heterogeneous architecture:
Different GPUs (2080Ti, 3090), different CPUs (Intel i9, Intel Xeon, AMD
EPYC), sometimes with a cache SSD, sometimes not. Different memory
sizes/types, different hard drive organization, etc.

Currently, Centos 7 is installed on all the machines, but as you might
know, this OS is pretty old and the EOL is just in 2 years. As some of
the workstations needs some maintenance, I would like to not install
Centos 7 again, just to redo this in a couple of months.

Our need for the machines is the following:
cryoSPARC, Scipion3, Relion
AlphaFold, NAMD/Gromacs

For the storage/main node servers, there is no special need. We don't
have any workload balancer like SLURM, and also the storage servers
"just" stores the data, without any special need. Interconnectivity is
established over NFS or sshfs, but these should be possible in any unix
OS.

I personally have experience with [X/K/U]buntu, Centos, and some Arch
Linux, so I am aware of the basic differences (e.g. apt vs yum).

Proposed by cryoSPARC is Ubuntu, at some other point (might be in the
Scipion mailing list), Rocky Linux was proposed. Also, afaik, Scientific
Linux is often used.

As I am used to Centos 7, handling outdated repos (e.g. GCC4 being the
default compiler) is a daily business, I would like to avoid in the
future. I think, this strongly points to Ubuntu, where a big and active
community is present.

Thank you for your feedback :)

Best regards
Christian
Dr. rer. nat. Christian Tüting

Kastritis Laboratory for Biomolecular Research
Cryo-Electron Microscopy & Computational Structural Biology
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