Re: [ccp4bb] Acorn question
Sounds like a bug. Curing the symptoms won't help You should send full details to [EMAIL PROTECTED] Since CCP4 6.0.x there has been a substantially new version of Acorn. Source code at http://www.ccp4.ac.uk/download/prerelease_page.php#acorn or try our test 6.1 release ... Martyn On Wed, 2008-07-23 at 13:15 -0400, [EMAIL PROTECTED] wrote: > All, > > In the past couple of days I have been trying to use Acorn (in the > CCP4 suite of programs). Consistently it starts up fine and after some > small amount of time (5-10 minutes) it has taken up all the physical > memory and then it starts to slowly gobble up all the swap space until > the only option is to switch the computer off, since all processes > (including X and such) are being pushed out of memory and they somehow > are not swapped back in. > > Is there a way to restrict the amount of memory that Acorn is allowed > to use? Any other suggestions? Parameters to restrict memory I do not > see and the Acorn web page does also not mention that they exist, > neither does it have any suggestions what to do. > > We are using CentOS operating system on 64-bit hardware (I think > CentOS is vanilla Linux but 64-bit may not be vanilla). We are using > CCP4 version 6.0. > > Any suggestions are appreciated. > > Thanks, > > Mark > > Mark van der Woerd, PhD > > Research Scientist II > > Dept. of Biochemistry and Molecular Biology > > Colorado State University > > Fort Collins, CO 80523 > > Phone (970) 491-0469 > > > __ > The Famous, the Infamous, the Lame - in your browser. Get the TMZ > Toolbar Now! -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] Acorn question
shelxe can do a pretty good imitation of Acorn (amongst other things) and is kinder to your computer. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 23 Jul 2008, [EMAIL PROTECTED] wrote: > All, > > In the past couple of days I have been trying to use Acorn (in the CCP4 suite > of programs). Consistently it starts up fine and after some small amount of > time (5-10 minutes) it has taken up all the physical memory and then it > starts to slowly gobble up all the swap space until the only option is to > switch the computer off, since all processes (including X and such) are being > pushed out of memory and they somehow are not swapped back in. > > Is there a way to restrict the amount of memory that Acorn is allowed to use? > Any other suggestions? Parameters to restrict memory I do not see and the > Acorn web page does also not mention that they exist, neither does it have > any suggestions what to do. > > We are using CentOS operating system on 64-bit hardware (I think CentOS is > vanilla Linux but 64-bit may not be vanilla). We are using CCP4 version 6.0. > > Any suggestions are appreciated. > > Thanks, > > Mark > > > Mark van der Woerd, PhD > Research Scientist II > Dept. of Biochemistry and Molecular Biology > Colorado State University > Fort Collins, CO 80523 > Phone (970) 491-0469 > > > >
Re: [ccp4bb] Acorn question
On Wed, 23 Jul 2008, [EMAIL PROTECTED] wrote: All, In the past couple of days I have been trying to use Acorn (in the CCP4 suite of programs). Consistently it starts up fine and after some small amount of time (5-10 minutes) it has taken up all the physical memory and then it starts to slowly gobble up all the swap space until the only option is to switch the computer off, since all processes (including X and such) are being pushed out of memory and they somehow are not swapped back in. Is there a way to restrict the amount of memory that Acorn is allowed to use? Any other suggestions? Parameters to restrict memory I do not see and the Acorn web page does also not mention that they exist, neither does it have any suggestions what to do. If you want a fallback to stop Acorn crashing your system, you can use kernel-managed resource limits. These are controlled by shell built-in commands. If you are using csh/tcsh, the command is 'limit'; if you are using sh/ksh/bash, the command is 'ulimit'. See the 'man' page for the particular shell for details. Use 'limit' on its own (csh family), or 'ulimit -a' (sh family) to see the current limits. If memory-related ones are high or unlimited, you can try restricting them. Be aware though, that if Acorn exceeds these limits it will simply crash. If the resource limit 'coredumpsize' is unlimited, the resulting core file will be big. This is something of a last resort to protect your system of course, and not a substitute for getting Acorn to run properly. Good luck, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
