Iu W BRET CHURCH Sydney Pharmacy School A15 THE UNIVERSITY OF SYDNEY
E [email protected] | W http://sydney.edu.au Get Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Demetres D. Leonidas <[email protected]> Sent: Tuesday, November 29, 2022 6:34:49 PM To: [email protected] <[email protected]> Subject: Re: [ccp4bb] xds crashes 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 >>> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://protect-au.mimecast.com/s/Uo06CZY1NqiMg1KlZTzx1F8?domain=jiscmail.ac.uk >> >> This message was issued to members of >> www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list >> hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions >> are available at >> https://protect-au.mimecast.com/s/F-D-C1WLPxcpGrJ3yTG9B2_?domain=jiscmail.ac.uk > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://protect-au.mimecast.com/s/Uo06CZY1NqiMg1KlZTzx1F8?domain=jiscmail.ac.uk > > This message was issued to members of > www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list > hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions > are available at > https://protect-au.mimecast.com/s/F-D-C1WLPxcpGrJ3yTG9B2_?domain=jiscmail.ac.uk/ -- ----------------------------------------------- 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 ----------------------------------------------- -- Αυτό το email έχει ελεγχθεί για ιούς από το Avast antivirus. www.avast.com<http://www.avast.com> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://protect-au.mimecast.com/s/Uo06CZY1NqiMg1KlZTzx1F8?domain=jiscmail.ac.uk This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://protect-au.mimecast.com/s/F-D-C1WLPxcpGrJ3yTG9B2_?domain=jiscmail.ac.uk/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 https://www.jiscmail.ac.uk/policyandsecurity/
