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 <ddleoni...@bio.uth.gr> 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 <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 >>>> >>> ######################################################################## >>> >>> 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/ >> ######################################################################## >> >> 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/ > >-- >----------------------------------------------- >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 >----------------------------------------------- > > >-- >Αυτό το email έχει ελεγχθεί για ιούς από το Avast antivirus. >www.avast.com > >######################################################################## > >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/ ######################################################################## 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/
