| I am having problems with a docking computational program running for large ligands either parallel or serial on amd64. The error message is "out of memory" and the authors of the program agree that the OS is not furnishing all the RAM available. With smaller ligands (i.e., with less memory needed to rotate the molecule) the program completes the task. The system consists of a couple of dual opteron cpu and 16 GB ecc memory (shared memory). That was set with shmmax kernel.shmmax = 16000000000 kernel.shmall = 16000000000 sysctl -p and when using ab initio computational programs, "top -i" shows that all 15 GB let for use are effectively used (1 GB for the OS). The failing computational program also indicated to set memory with the limit ulimit or unlimit commands and to pay attention to "datasize" and "stacksize". Command "ulimit" returns "Unlimited". I did nothing for datasize and stacksize. Well, I would be much obliged for suggesting where to learn how to set memory on debian linux amd64. Currently I am at updated "etch". Thanks francesco pietra |