Dear Kay,
many thanks for your suggestions. We will look into this.
best
Demetres
On 11/29/2022 2:35 PM, Kay Diederichs wrote:
Dear Demetres,
I googled the Ubuntu 22.04 release notes and found
https://discourse.ubuntu.com/t/jammy-jellyfish-release-notes/24668 which says "We’ve enabled
the userspace OOMD service and are shipping the systemd-oomd package by default on the “Ubuntu
Desktop” flavour, to avoid overloaded systems and the need of the kernel’s OOM killer to kick in.
The OOMD status can be checked using oomctl." Then googling "Ubuntu 22.04 oomctl"
takes me e.g. to https://askubuntu.com/questions/1405021/firefox-closes-by-itself-in-ubuntu-22-04
and https://bugs.launchpad.net/ubuntu/+source/systemd/+bug/1972159 which confirms that there may be
a problem in Ubuntu 22.04 with processes being killed without good reason, and some hints on how to
configure your system to avoid that.
Maybe the systems-oomd package can simply be removed.
Hope that helps,
Kay
On Tue, 29 Nov 2022 10:25:17 +0200, Demetres D. Leonidas
<[email protected]> wrote:
Dear Kay,
you are right and I do apologize for the misunderstanding. Point 1 and 2
are sufficient.
best
Demetres
On 11/29/2022 10:00 AM, Kay Diederichs wrote:
Dear Demetres,
sounds a bit drastic!
The second point alone would certainly suffice, because then no forking is done.
What kind of hardware is that?
I would expect that on a contemporary workstation you have 8GB of RAM or more;
that would allow for 8 or more processes.
Do you have a swapfile? If not, create one.
Please check out
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Performance
Best wishes,
Kay
On Tue, 29 Nov 2022 09:34:49 +0200, Demetres D. Leonidas
<[email protected]> wrote:
Dear Kay,
after some digging and help from Max Nanao we found that the problem
was the memory. It was fulling rapidly. The workaround was to:
1. unzip the cbf files prior to processing
2. use maximum number of jobs 1
3. use number of processors 4
4. run xds_par
Many thanks for all your help
Demetres
On 11/29/2022 9:03 AM, Kay Diederichs wrote:
Dear Demetres,
I agree with what James says: this is the operating system trying to to
prevent, in an over-zealous way, the
forking of too many or too big (in terms of memory) processes.
In other words, XDS hasn't changed, but the operating system changed - it
applies different limits to its processes.
Your friendly system administrator should try to find out exactly which
limit(s) changed, and reset the value(s).
Perhaps a hint is in the Release Notes of Ubuntu 22.04 ?
Pls report here when you've found it - currently you are the only one reporting
it.
Best wishes,
Kay
On Mon, 28 Nov 2022 12:06:43 -0800, James Holton <[email protected]> wrote:
Sounds like your kernel might think "forkxds" is creating a "fork
bomb". Too many sub-processes firing off in too short a time triggers
this. On one of my systems, I fixed it by editing
/etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more
pids than normal. This tends to prevent these mysterious "Killed" errors.
HTH?
-James Holton
MAD Scientist
On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote:
Dear all,
I do not know if this is the right list and I would like to apologize
if it is not.
We have repeatedly experienced xds crashes in machines running ubuntu
22.04.1 with the following message repeated several times at the
INTEGRATE step
/usr/local/bin/forkxds: line 60: 3427 Done echo "$itask"
3428 Killed | $amain
We are trying to process data from P13 at EMBL-Hamburg.
We are running XDS version Jan 10, 2022 BUILT=20220820
Any ideas ?
Demetres
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Dr. Demetres D. Leonidas
Professor in Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis 41500 Larissa, Greece
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Dr. Demetres D. Leonidas
Professor in Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis 41500 Larissa, Greece
---------------------------------------------
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Tel. +304210 565263 (X-ray)
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E-mail: [email protected]
ORCID ID orcid.org/0000-0002-3874-2523
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--
-----------------------------------------------
Dr. Demetres D. Leonidas
Professor in Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis 41500 Larissa, Greece
---------------------------------------------
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Tel. +304210 565263 (X-ray)
Fax. +302410 565290
E-mail: [email protected]
ORCID ID orcid.org/0000-0002-3874-2523
-----------------------------------------------
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