Dear Demetres, On Tue, Nov 29, 2022 at 10:25:17AM +0200, Demetres D. Leonidas wrote: > Dear Kay, > > you are right and I do apologize for the misunderstanding. Point 1 > and 2 are sufficient.
You can probably avoid doing any of this by using the LIB= feature of XDS on gzipped CBF files with the excellent xds-zcbf plugin [1]. If you have autoPROC available this will be used automatically [2]. Regards, ClAuS & Clemens [1] https://git.embl.de/nikolova/xds-zcbf [2] https://www.globalphasing.com/autoproc > > 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 > ><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 > >>----------------------------------------------- > >> > >> > >>-- > >>???????? ???? email ???????? ???????????????? ?????? ???????? ?????? ???? > >>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/ > > -- > ----------------------------------------------- > 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 > ----------------------------------------------- > > ######################################################################## > > 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/ -- *-------------------------------------------------------------- * ClAuS Flensburg, Ph.D. claus AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.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/
