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 <jmhol...@lbl.gov> 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
---------------------------------------------
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Tel. +304210 565263 (X-ray)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
ORCID ID orcid.org/0000-0002-3874-2523
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