Hi everyone and thanks for your help with my cns problems. I am sure that some settings in my file were leading to an escalation in the memory requirement. Since a significant portion of my model was polyala , I had edited my anneal.inp file and increased the torsion_maxlength , torsion_maxtree and torsion_maxchain to very high values . This probably resulted in the explosive requirement for memory , which even my quad core Mac pro with 4 GB of RAM was not able to satisfy.
On this machine I am showing numbers similar to what phil saw when I ran limit. Regardless, I still have not arrived at a comfortable value for maxtree , maxchain and maxlength and have instead switched to running cartesian molecular dynamics, which is working fine. Thanks everyone for your help Hari Jayaram On Wed, Apr 30, 2008 at 5:12 PM, <[EMAIL PROTECTED]> wrote: > > 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. > >
