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Dear Christian,
<div class=""><br class="">
</div>
<div class="">Princeton University and the Institute for Advanced Study maintains a Linux distribution called Springdale. It’s based on Red Hat Enterprise Linux. We use it on all of our high-performance computing clusters, and also on some workstations, and
some virtual servers serving web apps and other things. It’s available to the public, here: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__springdale.math.ias.edu_&d=DwMGaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=KJGXzJpgEwv3KpnwM49PeoeDRRFhIFj_Vm4B5DjwYFm6uDE0n02VqJv93PDRLzKM&s=eVnyMT2VKkiL6eFglp2Enj6LYLg-XtKA5yj07kuWFys&e=" class="">https://springdale.math.ias.edu/</a>.</div>
<div class=""><br class="">
</div>
<div class="">I’m running CryoSPARC, RELION, and AlphaFold in this environment. The only problem I’ve had is that the Nvidia driver installation on a workstation was pretty involved, though I imagine it’s similar on other Linux distrubtions.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Matthew Cahn</div>
<div class="">Linux Administrator/Programmer/Lecturer</div>
<div class="">Princeton University</div>
<div class="">Department of Molecular Biology</div>
<div class=""><br class="">
<div class="">
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<div>|| Matthew Cahn | Linux Administrator | Dept. of Molecular Biology / Research Computing | Princeton University | (609) 258-5404 | <a href="mailto:mcahn@princeton.edu" class="">mcahn@princeton.edu</a> ||</div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On May 10, 2022, at 6:48 AM, <a href="mailto:3dem-request@ncmir.ucsd.edu" class="">
3dem-request@ncmir.ucsd.edu</a> wrote:</div>
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Today's Topics:<br class="">
<br class="">
1. Operating system for local server environment (Christian T?ting)<br class="">
2. Re: Operating system for local server environment (Grigory Sharov)<br class="">
3. Re: Operating system for local server environment<br class="">
(Guillaume Gaullier)<br class="">
4. Re: Operating system for local server environment<br class="">
(Kilian Schnelle)<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Tue, 10 May 2022 10:28:43 +0200<br class="">
From: Christian T?ting <christian.tueting@biochemtech.uni-halle.de><br class="">
To: <3dem@ncmir.ucsd.edu><br class="">
Subject: [3dem] Operating system for local server environment<br class="">
Message-ID: <627A223B020000B000063B45@gwia0.itz.uni-halle.de><br class="">
Content-Type: text/plain; charset=UTF-8<br class="">
<br class="">
Dear 3dem mailing list recipients,<br class="">
<br class="">
I would like to get your opinion on which operating system is the most<br class="">
suitable for our local server environment.<br class="">
<br class="">
To frame the question:<br class="">
We have multiple local workstations and storage servers with a very<br class="">
heterogeneous architecture:<br class="">
Different GPUs (2080Ti, 3090), different CPUs (Intel i9, Intel Xeon, AMD<br class="">
EPYC), sometimes with a cache SSD, sometimes not. Different memory<br class="">
sizes/types, different hard drive organization, etc.<br class="">
<br class="">
Currently, Centos 7 is installed on all the machines, but as you might<br class="">
know, this OS is pretty old and the EOL is just in 2 years. As some of<br class="">
the workstations needs some maintenance, I would like to not install<br class="">
Centos 7 again, just to redo this in a couple of months.<br class="">
<br class="">
Our need for the machines is the following:<br class="">
cryoSPARC, Scipion3, Relion<br class="">
AlphaFold, NAMD/Gromacs<br class="">
<br class="">
For the storage/main node servers, there is no special need. We don't<br class="">
have any workload balancer like SLURM, and also the storage servers<br class="">
"just" stores the data, without any special need. Interconnectivity is<br class="">
established over NFS or sshfs, but these should be possible in any unix<br class="">
OS.<br class="">
<br class="">
I personally have experience with [X/K/U]buntu, Centos, and some Arch<br class="">
Linux, so I am aware of the basic differences (e.g. apt vs yum).<br class="">
<br class="">
Proposed by cryoSPARC is Ubuntu, at some other point (might be in the<br class="">
Scipion mailing list), Rocky Linux was proposed. Also, afaik, Scientific<br class="">
Linux is often used.<br class="">
<br class="">
As I am used to Centos 7, handling outdated repos (e.g. GCC4 being the<br class="">
default compiler) is a daily business, I would like to avoid in the<br class="">
future. I think, this strongly points to Ubuntu, where a big and active<br class="">
community is present.<br class="">
<br class="">
Thank you for your feedback :)<br class="">
<br class="">
<br class="">
Best regards<br class="">
Christian<br class="">
Dr. rer. nat. Christian T?ting<br class="">
<br class="">
Kastritis Laboratory for Biomolecular Research<br class="">
Cryo-Electron Microscopy & Computational Structural Biology <br class="">
________________________________________________<br class="">
Martin-Luther-Universit?t Halle-Wittenberg<br class="">
Biozentrum, Room A.2.19<br class="">
IWE ZIK HALOmem NWG III<br class="">
"Kryo-Elektronenmikroskopie an Membranproteinkomplexen"<br class="">
Weinbergweg 22, 06120 Halle<br class="">
tel: +49 345 5524985<br class="">
web (Lab): <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__nam12.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fblogs.urz.uni-2D2Dhalle.de-5Fkastritislab-5F-2526d-253DDwIDaQ-2526c-253D-2D35OiAkTchMrZOngvJPOeA-2526r-253DL7-2DzyQ-2D04fFCMRqzLIOnx7H0exGZHwIQe-5FwMPuY600I-2526m-253DM5tV4i7vwtyCEWiBFwqltoUDbWfJrQ6Rq4OeG3w6Pf3szICL5sanWtIgUYWC3B5-5F-2526s-253DUJR09zZF0h0c-2DvOZd4S3RmffzgEiJ7y-5FXgkY01dJpm8-2526e-253D-26amp-3Bdata-3D05-257C01-257Cmcahn-2540princeton.edu-257C2f550a2886914885887a08da3272ba4e-257C2ff601167431425db5af077d7791bda4-257C0-257C0-257C637877765618827138-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C3000-257C-257C-257C-26amp-3Bsdata-3DNAH88OCfLYM1XJZX2-252FaOunPdawC8VEafwvAH8ivgpSY-253D-26amp-3Breserved-3D0&d=DwQGaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=KJGXzJpgEwv3KpnwM49PeoeDRRFhIFj_Vm4B5DjwYFm6uDE0n02VqJv93PDRLzKM&s=Qd6OOQyYGYWesnCtNu51irzRUCnvdsBN3SKqMHSeav8&e=">https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__blogs.urz.uni-2Dhalle.de_kastritislab_%26d%3DDwIDaQ%26c%3D-35OiAkTchMrZOngvJPOeA%26r%3DL7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I%26m%3DM5tV4i7vwtyCEWiBFwqltoUDbWfJrQ6Rq4OeG3w6Pf3szICL5sanWtIgUYWC3B5_%26s%3DUJR09zZF0h0c-vOZd4S3RmffzgEiJ7y_XgkY01dJpm8%26e%3D&data=05%7C01%7Cmcahn%40princeton.edu%7C2f550a2886914885887a08da3272ba4e%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C637877765618827138%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NAH88OCfLYM1XJZX2%2FaOunPdawC8VEafwvAH8ivgpSY%3D&reserved=0</a>
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web (HALOmem): <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__nam12.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fwww.halomem.de-5Fen-5F-2526d-253DDwIDaQ-2526c-253D-2D35OiAkTchMrZOngvJPOeA-2526r-253DL7-2DzyQ-2D04fFCMRqzLIOnx7H0exGZHwIQe-5FwMPuY600I-2526m-253DM5tV4i7vwtyCEWiBFwqltoUDbWfJrQ6Rq4OeG3w6Pf3szICL5sanWtIgUYWC3B5-5F-2526s-253DYPBQ4XfDHsZK6U3AgwzMuzhoNUcTjc4S2ntJIQ9jrJo-2526e-253D-26amp-3Bdata-3D05-257C01-257Cmcahn-2540princeton.edu-257C2f550a2886914885887a08da3272ba4e-257C2ff601167431425db5af077d7791bda4-257C0-257C0-257C637877765618827138-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C3000-257C-257C-257C-26amp-3Bsdata-3D5-252BfInG2DDmsZyUz1Q-252FTzzows5ggBcAk-252BFHUVD3VAjpA-253D-26amp-3Breserved-3D0&d=DwQGaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=KJGXzJpgEwv3KpnwM49PeoeDRRFhIFj_Vm4B5DjwYFm6uDE0n02VqJv93PDRLzKM&s=i57lYdpC7Nnonq_Js-b4z48DcFsJrEeZrC22tI6bWDw&e=">https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.halomem.de_en_%26d%3DDwIDaQ%26c%3D-35OiAkTchMrZOngvJPOeA%26r%3DL7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I%26m%3DM5tV4i7vwtyCEWiBFwqltoUDbWfJrQ6Rq4OeG3w6Pf3szICL5sanWtIgUYWC3B5_%26s%3DYPBQ4XfDHsZK6U3AgwzMuzhoNUcTjc4S2ntJIQ9jrJo%26e%3D&data=05%7C01%7Cmcahn%40princeton.edu%7C2f550a2886914885887a08da3272ba4e%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C637877765618827138%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5%2BfInG2DDmsZyUz1Q%2FTzzows5ggBcAk%2BFHUVD3VAjpA%3D&reserved=0</a>
<br class="">
<br class="">
<br class="">
<br class="">
------------------------------<br class="">
<br class="">
Message: 2<br class="">
Date: Tue, 10 May 2022 09:47:35 +0100<br class="">
From: Grigory Sharov <sharov.grigory@gmail.com><br class="">
To: Christian T?ting <christian.tueting@biochemtech.uni-halle.de><br class="">
Cc: 3dem@ncmir.ucsd.edu<br class="">
Subject: Re: [3dem] Operating system for local server environment<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><CAJZ7w0dQQaRBgXh9Jtokap47fqFWVYV8xyv+MWy2z0fyC-TvJg@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Christian,<br class="">
<br class="">
I personally have experience with [X/K/U]buntu, Centos, and some Arch<br class="">
<blockquote type="cite" class="">Linux, so I am aware of the basic differences (e.g. apt vs yum).<br class="">
</blockquote>
<br class="">
<br class="">
If you are going to manage this server then this is your answer. Use the OS<br class="">
that you have most experience with.<br class="">
<br class="">
I wouldn't use Arch Linux for a server (it is mostly for "bleeding edge"<br class="">
desktop enthusiasts) and if you go for Ubuntu, in my opinion a server does<br class="">
not have GUI, so no X/Kubuntu. Personally, I'm not an Ubuntu fan and use<br class="">
Debian.<br class="">
<br class="">
Proposed by cryoSPARC is Ubuntu, at some other point (might be in the<br class="">
<blockquote type="cite" class="">Scipion mailing list), Rocky Linux was proposed. Also, afaik, Scientific<br class="">
Linux is often used.<br class="">
</blockquote>
<br class="">
<br class="">
CentOS has been buried by Red Hat/IBM, so Rocky linux, Alma linux or<br class="">
VZlinux are the alternatives currently being developed by the community.<br class="">
<br class="">
Hope this helps,<br class="">
Grigory<br class="">
<br class="">
--------------------------------------------------------------------------------<br class="">
Grigory Sharov, Ph.D.<br class="">
<br class="">
MRC Laboratory of Molecular Biology,<br class="">
Francis Crick Avenue,<br class="">
Cambridge Biomedical Campus,<br class="">
Cambridge CB2 0QH, UK.<br class="">
tel. +44 (0) 1223 267228 <+44%201223%20267228><br class="">
e-mail: gsharov@mrc-lmb.cam.ac.uk<br class="">
<br class="">
<br class="">
On Tue, May 10, 2022 at 9:29 AM Christian T?ting <<br class="">
christian.tueting@biochemtech.uni-halle.de> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Dear 3dem mailing list recipients,<br class="">
<br class="">
I would like to get your opinion on which operating system is the most<br class="">
suitable for our local server environment.<br class="">
<br class="">
To frame the question:<br class="">
We have multiple local workstations and storage servers with a very<br class="">
heterogeneous architecture:<br class="">
Different GPUs (2080Ti, 3090), different CPUs (Intel i9, Intel Xeon, AMD<br class="">
EPYC), sometimes with a cache SSD, sometimes not. Different memory<br class="">
sizes/types, different hard drive organization, etc.<br class="">
<br class="">
Currently, Centos 7 is installed on all the machines, but as you might<br class="">
know, this OS is pretty old and the EOL is just in 2 years. As some of<br class="">
the workstations needs some maintenance, I would like to not install<br class="">
Centos 7 again, just to redo this in a couple of months.<br class="">
<br class="">
Our need for the machines is the following:<br class="">
cryoSPARC, Scipion3, Relion<br class="">
AlphaFold, NAMD/Gromacs<br class="">
<br class="">
For the storage/main node servers, there is no special need. We don't<br class="">
have any workload balancer like SLURM, and also the storage servers<br class="">
"just" stores the data, without any special need. Interconnectivity is<br class="">
established over NFS or sshfs, but these should be possible in any unix<br class="">
OS.<br class="">
<br class="">
I personally have experience with [X/K/U]buntu, Centos, and some Arch<br class="">
Linux, so I am aware of the basic differences (e.g. apt vs yum).<br class="">
<br class="">
Proposed by cryoSPARC is Ubuntu, at some other point (might be in the<br class="">
Scipion mailing list), Rocky Linux was proposed. Also, afaik, Scientific<br class="">
Linux is often used.<br class="">
<br class="">
As I am used to Centos 7, handling outdated repos (e.g. GCC4 being the<br class="">
default compiler) is a daily business, I would like to avoid in the<br class="">
future. I think, this strongly points to Ubuntu, where a big and active<br class="">
community is present.<br class="">
<br class="">
Thank you for your feedback :)<br class="">
<br class="">
<br class="">
Best regards<br class="">
Christian<br class="">
Dr. rer. nat. Christian T?ting<br class="">
<br class="">
Kastritis Laboratory for Biomolecular Research<br class="">
Cryo-Electron Microscopy & Computational Structural Biology<br class="">
________________________________________________<br class="">
Martin-Luther-Universit?t Halle-Wittenberg<br class="">
Biozentrum, Room A.2.19<br class="">
IWE ZIK HALOmem NWG III<br class="">
"Kryo-Elektronenmikroskopie an Membranproteinkomplexen"<br class="">
Weinbergweg 22, 06120 Halle<br class="">
tel: +49 345 5524985<br class="">
web (Lab):<br class="">
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------------------------------<br class="">
<br class="">
Message: 3<br class="">
Date: Tue, 10 May 2022 09:36:59 +0000<br class="">
From: Guillaume Gaullier <guillaume.gaullier@icm.uu.se><br class="">
To: Christian T?ting <christian.tueting@biochemtech.uni-halle.de><br class="">
Cc: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br class="">
Subject: Re: [3dem] Operating system for local server environment<br class="">
Message-ID: <0857AEA3-1EC9-4F95-A48E-100BBF895E7E@icm.uu.se><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Hello Christian,<br class="">
<br class="">
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.<br class="">
<br class="">
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).<br class="">
<br class="">
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).<br class="">
<br class="">
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:
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__nam12.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fdeveloper.nvidia.com-5Fcuda-2D2Ddownloads-2D3Ftarget-2D5Fos-2D3DLinux-2D26target-2D5Farch-2D3Dx86-2D5F64-2526d-253DDwIGaQ-2526c-253D-2D35OiAkTchMrZOngvJPOeA-2526r-253DL7-2DzyQ-2D04fFCMRqzLIOnx7H0exGZHwIQe-5FwMPuY600I-2526m-253DCkvlK51L4BVJq-2DWOK3yXrz-5F7t-2DL3SNOr3WKUExu2ZcNWBojC7nAL5PdrAi5yHcbu-2526s-253D-5FcizLH5i2tmuI0nb8-2DuL8hV0aW0pDqboVN9toCsQZOc-2526e-253D-26amp-3Bdata-3D05-257C01-257Cmcahn-2540princeton.edu-257C2f550a2886914885887a08da3272ba4e-257C2ff601167431425db5af077d7791bda4-257C0-257C0-257C637877765618827138-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C3000-257C-257C-257C-26amp-3Bsdata-3D-252BvUfjaPbYi8FAJ2Ecz-252BsgQpMaFKuRvR8kfgb6bblPSI-253D-26amp-3Breserved-3D0&d=DwQGaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=KJGXzJpgEwv3KpnwM49PeoeDRRFhIFj_Vm4B5DjwYFm6uDE0n02VqJv93PDRLzKM&s=KChAWsYUjG6CIx3PJR0Fhc8FhnV_Hyo0V_scQmoI4ME&e=">https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__developer.nvidia.com_cuda-2Ddownloads-3Ftarget-5Fos-3DLinux-26target-5Farch-3Dx86-5F64%26d%3DDwIGaQ%26c%3D-35OiAkTchMrZOngvJPOeA%26r%3DL7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I%26m%3DCkvlK51L4BVJq-WOK3yXrz_7t-L3SNOr3WKUExu2ZcNWBojC7nAL5PdrAi5yHcbu%26s%3D_cizLH5i2tmuI0nb8-uL8hV0aW0pDqboVN9toCsQZOc%26e%3D&data=05%7C01%7Cmcahn%40princeton.edu%7C2f550a2886914885887a08da3272ba4e%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C637877765618827138%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2BvUfjaPbYi8FAJ2Ecz%2BsgQpMaFKuRvR8kfgb6bblPSI%3D&reserved=0</a>
(knowing that you can use Rocky or Alma instead of RHEL). Moreover, I would strongly recommend installing the Nvidia driver with their R!<br class="">
PM or DEB<br class="">
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).<br class="">
<br class="">
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).<br class="">
<br class="">
I hope this helps,<br class="">
<br class="">
Guillaume<br class="">
<br class="">
<br class="">
On 10 May 2022, at 10:28, Christian T?ting <christian.tueting@biochemtech.uni-halle.de<mailto:christian.tueting@biochemtech.uni-halle.de>> wrote:<br class="">
<br class="">
Dear 3dem mailing list recipients,<br class="">
<br class="">
I would like to get your opinion on which operating system is the most<br class="">
suitable for our local server environment.<br class="">
<br class="">
To frame the question:<br class="">
We have multiple local workstations and storage servers with a very<br class="">
heterogeneous architecture:<br class="">
Different GPUs (2080Ti, 3090), different CPUs (Intel i9, Intel Xeon, AMD<br class="">
EPYC), sometimes with a cache SSD, sometimes not. Different memory<br class="">
sizes/types, different hard drive organization, etc.<br class="">
<br class="">
Currently, Centos 7 is installed on all the machines, but as you might<br class="">
know, this OS is pretty old and the EOL is just in 2 years. As some of<br class="">
the workstations needs some maintenance, I would like to not install<br class="">
Centos 7 again, just to redo this in a couple of months.<br class="">
<br class="">
Our need for the machines is the following:<br class="">
cryoSPARC, Scipion3, Relion<br class="">
AlphaFold, NAMD/Gromacs<br class="">
<br class="">
For the storage/main node servers, there is no special need. We don't<br class="">
have any workload balancer like SLURM, and also the storage servers<br class="">
"just" stores the data, without any special need. Interconnectivity is<br class="">
established over NFS or sshfs, but these should be possible in any unix<br class="">
OS.<br class="">
<br class="">
I personally have experience with [X/K/U]buntu, Centos, and some Arch<br class="">
Linux, so I am aware of the basic differences (e.g. apt vs yum).<br class="">
<br class="">
Proposed by cryoSPARC is Ubuntu, at some other point (might be in the<br class="">
Scipion mailing list), Rocky Linux was proposed. Also, afaik, Scientific<br class="">
Linux is often used.<br class="">
<br class="">
As I am used to Centos 7, handling outdated repos (e.g. GCC4 being the<br class="">
default compiler) is a daily business, I would like to avoid in the<br class="">
future. I think, this strongly points to Ubuntu, where a big and active<br class="">
community is present.<br class="">
<br class="">
Thank you for your feedback :)<br class="">
<br class="">
<br class="">
Best regards<br class="">
Christian<br class="">
Dr. rer. nat. Christian T?ting<br class="">
<br class="">
Kastritis Laboratory for Biomolecular Research<br class="">
Cryo-Electron Microscopy & Computational Structural Biology<br class="">
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Message: 4<br class="">
Date: Tue, 10 May 2022 12:48:27 +0200<br class="">
From: Kilian Schnelle <kilian.schnelle@uni-osnabrueck.de><br class="">
To: Christian T?ting <christian.tueting@biochemtech.uni-halle.de><br class="">
Cc: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br class="">
Subject: Re: [3dem] Operating system for local server environment<br class="">
Message-ID: <BFE7853A-3C61-4841-A13F-DA9A05D3F821@uni-osnabrueck.de><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
We are running Ubuntu 20.04 LTS on our HPC without any problems so far.<br class="">
<br class="">
I self had experience with CentOS 7 before but switching to Ubuntu was not that much of a difference for most, I mean mostly you may have to google the corresponding package name since they differ in yum/apt. I choose Ubuntu over Rocky/Alma since I didn?t knew
what would ?win? and also the support times of Ubuntu LTS versions is great, same as the obvious advantage of having a huge user base.<br class="">
<br class="">
Cheers<br class="">
Kilian<br class="">
<br class="">
<br class="">
Kilian Schnelle<br class="">
Department of Structural Biology<br class="">
University of Osnabrueck<br class="">
Barbarastr. 13<br class="">
D-49076 Osnabrueck, Germany<br class="">
Phone: +49 541 969 7508<br class="">
Email: kilian.schnelle@uni-osnabrueck.de<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On 10. May 2022, at 10:28, Christian T?ting <christian.tueting@biochemtech.uni-halle.de> wrote:<br class="">
<br class="">
Dear 3dem mailing list recipients,<br class="">
<br class="">
I would like to get your opinion on which operating system is the most<br class="">
suitable for our local server environment.<br class="">
<br class="">
To frame the question:<br class="">
We have multiple local workstations and storage servers with a very<br class="">
heterogeneous architecture:<br class="">
Different GPUs (2080Ti, 3090), different CPUs (Intel i9, Intel Xeon, AMD<br class="">
EPYC), sometimes with a cache SSD, sometimes not. Different memory<br class="">
sizes/types, different hard drive organization, etc.<br class="">
<br class="">
Currently, Centos 7 is installed on all the machines, but as you might<br class="">
know, this OS is pretty old and the EOL is just in 2 years. As some of<br class="">
the workstations needs some maintenance, I would like to not install<br class="">
Centos 7 again, just to redo this in a couple of months.<br class="">
<br class="">
Our need for the machines is the following:<br class="">
cryoSPARC, Scipion3, Relion<br class="">
AlphaFold, NAMD/Gromacs<br class="">
<br class="">
For the storage/main node servers, there is no special need. We don't<br class="">
have any workload balancer like SLURM, and also the storage servers<br class="">
"just" stores the data, without any special need. Interconnectivity is<br class="">
established over NFS or sshfs, but these should be possible in any unix<br class="">
OS.<br class="">
<br class="">
I personally have experience with [X/K/U]buntu, Centos, and some Arch<br class="">
Linux, so I am aware of the basic differences (e.g. apt vs yum).<br class="">
<br class="">
Proposed by cryoSPARC is Ubuntu, at some other point (might be in the<br class="">
Scipion mailing list), Rocky Linux was proposed. Also, afaik, Scientific<br class="">
Linux is often used.<br class="">
<br class="">
As I am used to Centos 7, handling outdated repos (e.g. GCC4 being the<br class="">
default compiler) is a daily business, I would like to avoid in the<br class="">
future. I think, this strongly points to Ubuntu, where a big and active<br class="">
community is present.<br class="">
<br class="">
Thank you for your feedback :)<br class="">
<br class="">
<br class="">
Best regards<br class="">
Christian<br class="">
Dr. rer. nat. Christian T?ting<br class="">
<br class="">
Kastritis Laboratory for Biomolecular Research<br class="">
Cryo-Electron Microscopy & Computational Structural Biology <br class="">
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Subject: Digest Footer<br class="">
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End of 3dem Digest, Vol 177, Issue 11<br class="">
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