Hello Phil and thanks for your email..I was running a VMware fusion Ubuntu session which was grabbing onto a large chunk of memory ( entirely my fault). I didnt realize that virtualized sessions can divert memory away from even the OS and make it essentially unavailable.
I am waiting for my ubuntu job to finish to retry the phaser run. Sorry I jumped the gun and emailed ccp4bb Thanks again hari On Thu, Aug 21, 2008 at 2:55 PM, Phil Jeffrey <[EMAIL PROTECTED]>wrote: > I would take a look at how much physical memory is on the machine, how much > disk space there is on the system drive (often used as virtual swap), and > what other processes are running. This would seem to be a failure to > allocate 2Gb of memory, which isn't the smallest chunk I've ever seen. > > Phil > > > hari jayaram wrote: > >> Hello, >> I am running phaser from the ccp4 6.0.99 suite on an OSX 10.5.4 Leopard , >> Mac Pro machine . >> I get the rather ominous error given below . >> We have gotten similar malloc errors with large datasets before on this >> machine. In those cases the same jobs ran fine on regular linux. >> Thought I would write in. I can send the mtz and search model over if >> needed for testing/ reproducing this error >> >> Thanks a lot for your help >> Hari Jayaram >> Postdoc , Brandeis Univerity >> >> >> -------------------- >> EXIT STATUS: SUCCESS >> -------------------- >> >> CPU Time: 0 days 0 hrs 9 mins 0.67 secs (540.67 secs) >> Finished: Thu Aug 21 13:45:26 2008 >> >> </pre> >> </html> >> >> *************************************************************************** >> * Information from CCP4Interface script >> >> *************************************************************************** >> The program run with command: /sw/share/xtal/ccp4-6.0.99e/bin/phaser >> has failed with error message >> phaser(36682) malloc: *** mmap(size=1999872000) failed (error code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> >> *************************************************************************** >> >> >> #CCP4I TERMINATION STATUS 0 "phaser(36682) malloc: *** >> mmap(size=1999872000) failed (error code=12) *** error: can't allocate >> region *** set a breakpoint in malloc_error_break to debug" >> #CCP4I TERMINATION TIME 21 Aug 2008 13:45:26 >> #CCP4I MESSAGE Task failed >> > >
