Drop support for CentOS 7, Ubuntu 16 and 18

[Tom Goddard]

Can we drop ChimeraX 1.4 distributions on older Linux distributions?

Qt 6 does not support old Linux distributions such as CentOS 7, Ubuntu 16 and 18.

​https://doc.qt.io/qt-6/supported-platforms.html

As that page says, this does not mean that Qt 6 will not run on those operating systems. But probably Qt will not provide prebuilt binaries.

[Tom Goddard]

Ticket #6593 also discusses CentOS 7 support.

[Zach Pearson]

Sounds fine to me. 18.04 is getting maintenance updates until early 2023, but I would go out on a limb and assume anyone using Ubuntu probably will have an easier time upgrading their machine to 20.04 or 22.04. I don't know of any servers running Ubuntu.

[Tom Goddard]

I asked last week RCSB, PDBe, EMDB, PDBj and SBGrid if they need ChimeraX on CentOS 7. RCSB and EMDB all responded that they do not need it on CentOS 7, PDBe and PDBj has not responded. SBGrid says half of their ChimeraX use is on CentOS 7 with 440 total ChimeraX users running it 7800 times in the last 6 months. So SBGrid is a problem. I include the email responses below.

SBGrid:

Begin forwarded message:

From: "Peter Meyer" <bugs@sbgrid.org>
Subject: [SBGrid #92958] ChimeraX dropping support for older Linux distributions
Date: April 25, 2022 at 8:45:45 AM PDT
To: goddard@sonic.net
Cc: key+rt@hkl.hms.harvard.edu
Reply-To: bugs@sbgrid.org

Hi Tom,

To answer the  easy question first; within the last six months there are ~440 unique SBGrid ChimeraX users (this is going by an encrypted/hashed user attribute) and ~7800 ChimeraX executions.

I think the relatively large number of CentOS 7 users has a few possible explanations.  We've been recommending CentOS as a linux distribution for quite a while, and standardized on it for the HMS labs where we do system support (both standard desktop/workstation systems with monitors, and compute nodes in a rack somewhere).  I don't have numbers for how many consortium CentOS systems have monitors hooked up - but I suspect a decent portion of SBGrid linux desktop use is CentOS because that's what we've been recommending (and testing on).  The change to the CentOS 8 EOL date (and general future of CentOS) caught a bunch of people by surprise; and there were likely CentOS 8 migrations that were either canceled or rolled back while searching for an alternative).  Most people I've talked to seem to be converging on Alma or Rocky as a CentOS8 alternative.

Remote graphics from ChimeraX is something we get a reasonable number of questions about; there are some solutions that seem to usually work tolerably well (realvnc, fastx, virtualgl), so I wouldn't want to rule out some of those being ChimeraX being used remotely.

Qt6 needing system calls not available in CentOS7 limits the alternatives, and it sounds like you've already looked at most of the ones I can think of (I'm a little surprised to hear that singularity didn't work, but that would've also added user setup complexity).  We've had reasonable good luck using spack internally; but that seems highly unlikely to help with syscall problems (and if it did work for Qt6/CentOS7, there'd still be the issue of the toolkit being unsupported/higher likelihood of things going wrong).  

I'll check with the rest of the group to see if there might be other ideas - I don't have a solution for Cent7/Qt6 either.

Best,
Pete

EMDB:

Begin forwarded message:

From: Gerard Kleywegt
Subject: Re: [PDBe #580574] ChimeraX dropping support for old Linux distributions
Date: April 22, 2022 at 8:24:49 AM PDT
To: goddard@sonic.net

Hi Tom,

I hope you are well.

I caught your mail to the PDBe helpdesk (thanks for asking!) and asked the EMDB folks. It seems there won't be any issues w.r.t. EMDB, but they did say that RCSB and PDBj are still using Centos 7 so they might have issues with OneDep (our OneDep version runs under Centos 8; PDBj and RCSB's not yet).

I assume someone from PDBe will send you a separate reply, but as far as EMDB goes - no problem!

Best wishes,

--Gerard

RCSB:

Begin forwarded message:

From: Rachel Kramer Green <rachel.green@rcsb.org>
Subject: Re: Use of ChimeraX on Linux by curators and RCSB web site (HELP-18610)
Date: April 26, 2022 at 11:04:46 AM PDT
To: Tom Goddard <goddard@sonic.net>
Cc: Info <info@rcsb.org>
Reply-To: Info <info@rcsb.org>

Dear Tom,

Thanks for letting us know.  This will not be an issue for us.

Best regards,

Rachel

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RACHEL KRAMER GREEN, PH.D.
Scientific Support & Customer Service Lead
RCSB Protein Data Bank
Rutgers, The State University of New Jersey
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rachel.green@rcsb.org
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On 4/21/2022 2:38 PM, Tom Goddard wrote:
We are considering dropping support for older Linux distributions in our next ChimeraX release (version 1.4, May 2022) but want to first check if the RCSB curators or RCSB web site is using ChimeraX on any of these old Linux systems: CentOS 7, Ubuntu 16, Ubuntu 18.  The reason we wish to drop these is because the Qt 6 window toolkit which ChimeraX heavily uses no longer supports those old Linux distributions.

Thanks!

	Tom Goddard
	ChimeraX developer
	UC San Francisco

[Tom Goddard]

Because this seems like a pretty sizable for SBGrid ChimeraX use with 220 users who will no longer be able to use the new version I think we could try a few more tests to support Qt 6 on CentOS 7.

1) Try installing the standard Qt 6 binary distribution from Qt on CentOS 7. They say they "don't officially support it", but lets verify that their binary installer really does not work.

2) Try building Qt 6 on CentOS 7. They have a unified source tar ball for linux (644 MBytes) here ​https://www.qt.io/offline-installers

Maybe Greg could try the Qt 6 binary install on CentOS to see what happens, and Zach or Greg could try the Qt 6 compile (Zach says he has done it before on a different Linux).

[Greg Couch]

(1) is confirmed. The binaries need newer versions of the C runtime.

(2) Should be compiled on CentOS 7 with devtoolset-9 to get a newer compiler -- our singularity container in /usr/local/projects/chimerax/nobackup/centos-7.img would work. This means that we will need to compile each new version of Qt, and that we will need to go back to bundling Qt with the commercial wheel. For the latter to work, the compilation will need to "install" Qt in the exact same layout that the Qt binaries are distributed.

[goddard@…]

Of course we don't want to compile Qt, but maybe SBGrid is worth the trouble to do it once for a ChimeraX 1.4 release.  I am not proposing doing for further daily builds.  And I am mostly wondering if the massive 644 Mbytes Qt source tar ball has everything to easily build on CentOS 7.

I don't see any other options other than dropping SBGrid from new releases.  They are pretty important.

[Greg Couch]

So is this a one time fix, or will we keep doing it until CentOS 7 reaches its end of life on June 30, 2024?

[goddard@…]

I am suggesting just trying it as a one time fix.  Although I would not rule out making a two time fix, doing it again for ChimeraX 1.5.  But mostly it is to just explore whether it is even feasible.  Otherwise we just dump SBGrid which has been an avid promoter of Chimera and ChimeraX and is rather influential in structural biology.

[Greg Couch]

According to ​https://wiki.qt.io/Building_Qt_6_from_Git, cmake 3.19 is needed to build WebEngine. CentOS 7 only has 3.17. So the first step is to get a newer version of cmake.

[Greg Couch]

Limited release candidate builds to Qt supported versions.