CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> wrote on 04/30/2008 03:33:32 PM:
> Hi > Since I am not on the cnsbb yet I am posting this here. > I downloaded the cns 1.2.2 intel build and was trying to run a > simulated annealing refinement on my macbook pro ( Intel) running 10.5.2 . > (snip) > > The detailed error is posted below > (snip) > cns_solve(93676) malloc: *** mmap(size=3000000512) failed (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > ALLHP: request for -1294967296 bytes You're asking for 3 billion bytes of memory here according to the first line. (The negative number in the last line also equals 3 billion bytes, but the 32-bit signed long(?) rolls over at 2 GB.) It's possible you simply don't have enough physical memory + free swap space to satisfy this demand. I don't have an OS X Mac in front of me to verify what I'm telling you, but: you can use 'hinv' to check how much physical + virtual memory you have available. Also, you should monitor (using top) the memory usage of your cns job as it's running. It's possible this map request comes on top of some already substantial memory allocation. You should first verify that you need this much memory for the annealing job. Are your unit cell dimensions, FFT grid spacing, space group, etc. correct? If you do in fact need such a big map, you should probably find a computer with more memory to run this job. It is possible to allocate more swap space (virtual memory) on your hard disk, but a compute job that's running mostly in virtual memory will be so slow that you'll collect Social Security before it's done... Let me know if you need more detailed help. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
