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Hi everyone, I've run into a memory allocation problem with fffear I'm hoping that I can get some pointers on fixing. Specifically, fffear will run on a linux machine (~600MB physical memory; ~1GB swap) although it hits the swap space pretty hard (job size is ~1.5GB). When I try to run the same script on an alpha with ~1GB physical memory and ~3GB swap, fffear exits with a CCPALC message saying that it can't allocate memory. Both systems are running ccp4-6.0.0 (installed from the same source tarball), although the alpha exits with the same error message with versions 5.0.2 and 4.2.1. I checked the limit/ulimit outputs (below), and as near as I can tell these don't seem to be the problem (but I could be wrong about this). On the tru64 system, the process size seems to max out at ~500MB. My two working hypothesis were that either it was the user memory limits, or a bug in CCPALC dynamic memory allocation on tru64. But, I seem to have eliminated both of them (ulimit on the alpha should allow a 1.5GB job to run by using swap space, and it's highly unlikely that there's a bug in CCPALC because 1. I see the same behaviour with multiple ccp4 versions, after reasonably big changes in the organization of the libraries, 2. the same source version produces different behaviour on different machines, 3. the ccp4 people are better programmers than me, and probably tested each of these on an alpha). So, I'm stumped at this point. (But then again, I'd though that gcc-4 wasn't object compatible with g77-3.3, so I don't know what that proves.) Anyhow, I'd greatly appreciate any ideas for how to go about troubleshooting this. Thanks, Pete linux> ulimit -a: core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited file size (blocks, -f) unlimited max locked memory (kbytes, -l) 32 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 stack size (kbytes, -s) unlimited cpu time (seconds, -t) unlimited max user processes (-u) 5050 virtual memory (kbytes, -v) unlimited alpha> ulimit -a: time(seconds) unlimited file(blocks) unlimited data(kbytes) 1048576 stack(kbytes) 1048576 memory(kbytes) 1261488 coredump(blocks) unlimited nofiles(descriptors) 4096 vmemory(kbytes) 4194304 Pete Meyer Fu Lab BMCB grad student Cornell University
