Re: [ccp4bb] replacement for Scientific Linux

[Guillaume Gaullier]

Hello,

I don’t know if crystallographic software is commonly GPU-accelerated. Most 
software we use to process cryoEM data is and requires CUDA, which only works 
on Nvidia hardware with their driver. Also seems to be the case for a lot of 
deep learning software. Like it or not, it’s simply a fact. So if you use such 
software, then one important criterion to help narrow down the list from 
distrowatch is to pick a distribution that Nvidia officially supports with 
their driver.

See here for supported distributions: 
https://developer.nvidia.com/cuda-downloads?target_os=Linux_arch=x86_64
This leaves the usual suspects as compatible options, with the notable 
exception of Alma Linux. So, if you hesitate between Alma and Rocky, having an 
Nvidia GPU and software using CUDA is a situation in favor of Rocky.
A recent nice development is that Nvidia now offers an open-source version of 
their driver. I have been using it on Rocky 9 and it works smoothly (and I was 
surprised it took so little time between the announcement and the actually 
usable release).

As Tim suggested, Debian would also be a fine option, with a supported Nvidia 
driver. It would be a bit less familiar than Rocky for someone coming from 
Scientific Linux. The smooth upgrade between major versions is a good reason to 
choose Debian (among other good reasons). As far as I know, Rocky doesn’t let 
you upgrade to the next major version, but with an adequate partition scheme 
you can do a "clean" installation without touching the home directories for the 
same result (it is just a bit more work than one command, and more critical to 
back up the home directories beforehand).
Regarding the heartbleed vulnerability, some versions of Debian were affected, 
but a fix was released promptly: 
https://lists.debian.org/debian-security-announce/2014/msg00071.html
CentOS as well: 
https://lists.centos.org/pipermail/centos-announce/2014-April/020248.html
Rocky and Alma didn’t exist back then.

I hope this helps,

Guillaume


On 26 Apr 2024, at 19:18, Jonathan Clinger 
mailto:clinge...@gmail.com>> wrote:

If you want to keep as close to scientific linux as possible, I would suggest 
Alma or Rocky Linux. Those were the two options my group considered when the 
writing was on the wall for scientific linux and we were ramping up our 
workstations. We ended up going with Alma, but I'm not sure it is any better 
than Rocky. We'll have to wait and see how much they diverge over time.

If you are ok with moving to something more different, Ubuntu or one of its 
derivations would probably do just fine.

Cheers! -Jonathan Clinger

On Fri, Apr 26, 2024 at 9:58 AM Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hello Harry

Any of the top 50 on distrowatch.com will basically be 
fine and the next 20 or so on the list will probably be fine. Then you start 
getting into the twilight zone. I am sure that will help greatly to narrow down 
your choice ;-0

Best wishes, Jon Cooper. 
jon.b.coo...@protonmail.com

Sent from Proton Mail mobile



 Original Message 
On 26 Apr 2024, 16:46, Harry Powell < 
193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hi folks For many years I’ve been using Scientific Linux as my OS of choice 
(when not using my Mac) - but it’s been discontinued. SL was based on RHEL, and 
had useful things like a less-buggy Fortran/C/C++ compiler than that released 
by RH. What do people here recommend as a replacement? Harry 
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Re: [ccp4bb] replacement for Scientific Linux

[Kay Diederichs]

Hi Harry,

same here. Actually we skipped RHEL8 and its alternatives, so moved directly 
from CentOS7 to Rocky9. We are happy with that decision.

Best wishes,
Kay

On Fri, 26 Apr 2024 15:57:46 +, Andy Purkiss  
wrote:

>Hi Harry,
>
>We've been migrating to Rocky Linux as it is built on RHEL in a similar way to 
>Scientific Linux. Most things compiled on Centos 7 (our default for a while) 
>work in Rocky Linux version 9. For compilers etc., I use the Software 
>Collections / devtoolsets to run later versions than the default OS.
>
>Hope this helps,
>
>Andy
>
>
>From: CCP4 bulletin board  on behalf of Harry Powell 
><193323b1e616-dmarc-requ...@jiscmail.ac.uk>
>Sent: 26 April 2024 16:46
>To: CCP4BB@JISCMAIL.AC.UK 
>Subject: [ccp4bb] replacement for Scientific Linux
>
>
>External Sender: Use caution.
>
>
>Hi folks
>
>For many years I�ve been using Scientific Linux as my OS of choice (when not 
>using my Mac) - but it�s been discontinued. SL was based on RHEL, and had 
>useful things like a less-buggy Fortran/C/C++ compiler than that released by 
>RH.
>
>What do people here recommend as a replacement?
>
>Harry
>
>
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Re: [ccp4bb] replacement for Scientific Linux

[Tim Gruene]

Hi Harry,

I started using Debian about 10-15 years ago, and never changed my
opinion since. I had tested various others before, like redhat, suse,
ubuntu etc. The stable version of Debian is indeed very stable, as
there are no version changes, only bug fixes etc. The new release
is about every three years, and upgrading does not break the system
(with rpm based systems I remember quite frequent re-installs,
because the system got messed up). The long-term support is indeed very
long.

The main repositories of Debian
include a great number of scientific / crystallographic packages, e.g.
raster3d, pymol, clipper-, ccp4-, mmdb2-libraries and what not.

Due to the philosophy of sticking to a version, and only to bug fixes
and security releases, Debian is often not affected by security holes,
e.g. the SHELX server was save from heart-bleed when it came out,
because heart-bleed require more modern versions of whatever library
was affected (SSL?). Same is true for the recent foul version of XZ.

Debian is POSIX compliant, so it doesn't mess around with standards,
and for configuration you can rely on what you find on the web. There
is a saying 'even a chicken can install Debian, as you only need to hit
Enter', which is not far from true.

Cheers,
Tim


On Fri, 26 Apr 2024 16:46:17 +0100 Harry Powell
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi folks
> 
> For many years I’ve been using Scientific Linux as my OS of choice
> (when not using my Mac) - but it’s been discontinued. SL was based on
> RHEL, and had useful things like a less-buggy Fortran/C/C++ compiler
> than that released by RH.
> 
> What do people here recommend as a replacement? 
> 
> Harry
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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-- 
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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Re: [ccp4bb] replacement for Scientific Linux

[Jonathan Clinger]

If you want to keep as close to scientific linux as possible, I would
suggest Alma or Rocky Linux. Those were the two options my group considered
when the writing was on the wall for scientific linux and we were ramping
up our workstations. We ended up going with Alma, but I'm not sure it is
any better than Rocky. We'll have to wait and see how much they diverge
over time.

If you are ok with moving to something more different, Ubuntu or one of its
derivations would probably do just fine.

Cheers! -Jonathan Clinger

On Fri, Apr 26, 2024 at 9:58 AM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello Harry
>
> Any of the top 50 on distrowatch.com will basically be fine and the next
> 20 or so on the list will probably be fine. Then you start getting into the
> twilight zone. I am sure that will help greatly to narrow down your choice
> ;-0
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>
>
>  Original Message 
> On 26 Apr 2024, 16:46, Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Hi folks For many years I’ve been using Scientific Linux as my OS of
> choice (when not using my Mac) - but it’s been discontinued. SL was based
> on RHEL, and had useful things like a less-buggy Fortran/C/C++ compiler
> than that released by RH. What do people here recommend as a replacement?
> Harry
>  To
> unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This
> message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing
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> --
>
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>



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Re: [ccp4bb] replacement for Scientific Linux

[Jon Cooper]

Hello Harry

Any of the top 50 on distrowatch.com will basically be fine and the next 20 or 
so on the list will probably be fine. Then you start getting into the twilight 
zone. I am sure that will help greatly to narrow down your choice ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 26 Apr 2024, 16:46, Harry Powell wrote:

> Hi folks For many years I’ve been using Scientific Linux as my OS of choice 
> (when not using my Mac) - but it’s been discontinued. SL was based on RHEL, 
> and had useful things like a less-buggy Fortran/C/C++ compiler than that 
> released by RH. What do people here recommend as a replacement? Harry 
>  To 
> unsubscribe from the CCP4BB list, click the following link: 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message 
> was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by 
> www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] replacement for Scientific Linux

[Andy Purkiss]

Hi Harry,

We've been migrating to Rocky Linux as it is built on RHEL in a similar way to 
Scientific Linux. Most things compiled on Centos 7 (our default for a while) 
work in Rocky Linux version 9. For compilers etc., I use the Software 
Collections / devtoolsets to run later versions than the default OS.

Hope this helps,

Andy


From: CCP4 bulletin board  on behalf of Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: 26 April 2024 16:46
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] replacement for Scientific Linux


External Sender: Use caution.


Hi folks

For many years I’ve been using Scientific Linux as my OS of choice (when not 
using my Mac) - but it’s been discontinued. SL was based on RHEL, and had 
useful things like a less-buggy Fortran/C/C++ compiler than that released by RH.

What do people here recommend as a replacement?

Harry


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[ccp4bb] replacement for Scientific Linux

[Harry Powell]

Hi folks

For many years I’ve been using Scientific Linux as my OS of choice (when not 
using my Mac) - but it’s been discontinued. SL was based on RHEL, and had 
useful things like a less-buggy Fortran/C/C++ compiler than that released by RH.

What do people here recommend as a replacement? 

Harry


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