Hello Ethan Meritt, Thanks for your reply, I have only recently started using the 8 core Mac pro , and in the last three days have faced many such issues with swapsize and running out of memory (the machine has 4GB total). Just Yesterday I had a problem on a different dataset with a cns simulated annealing run which stopped because of swapsize issues. I know that phenix on this machine has a setting in the com file which uses ulimit (csh tcsh) to unlimit everything . On a related note, I think Apple also changed its csh such that unlimit requires an argument such as unlimit stacksize etc..and not just unlimit
Since I am an OSX leopard newbie, Should I ( or could I ) use ulimit or unlimit as a systemwide shell setting and should I put this into the ccp4.setup.sh and ccp4.setup or in /etc/bashrc or /etc/cshrc so that I dont run into such problems. From the seetings it seems like I have a very small swapsize of 8192 kbytes At the present moment the limit command on this machine when run in csh returns cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 266 I am wondering why I havent had to mess with similar settings on linux while this multi-core machine with a massive disk and reasonable amount of memory , seems a little touchy with its swap size and other settings. Thank you for your help, Hari On Thu, May 1, 2008 at 2:49 PM, Ethan Merritt <[EMAIL PROTECTED]> wrote: > On Thursday 01 May 2008 11:37, hari jayaram wrote: > > Hi > > I was running phaser on an 8 core Mac pro using the fink 10.5 (intel) > ccp4 > > binaries provided by W.G Scott . > > Today I saw a very strange error and phaser FAILED. > > > > #CCP4I TERMINATION STATUS 0 "phaser(88098) malloc: *** > mmap(size=1185792000) > > failed (error code=12) *** error: can't allocate region *** set a > breakpoint > > in malloc_error_break to debug" > > This is telling you that you ran out of memory. > Perhaps you had more jobs running than usual, and not enough swap space. > Perhaps something in the Phaser run caused it to calculate a map with > finer grid spacing than your other runs. Perhaps something else entirely. > I would start by checking the swap space. > > Ethan Merritt > > -- > Ethan A Merritt Courier Deliveries: 1959 NE Pacific > Dept of Biochemistry Regular Mail: Mailstop 357742 > Health Sciences Building > University of Washington - Seattle WA 98195-7742 >
