I have no real experience with oom-killer. However, it is not set intrinsically by siesta. I believe it must be from openmpi or the compiler in itself. I have just checked my values of oom_adj, and they are all 0 (also debian 6). So maybe you have set a system setting.
Please check if it is siesta which is set to -17 or not, just to be sure of its origin. Nevertheless, to circumvent you can when you start siesta catch the pid and set the oom_adj value manually. Do: cat "0" > /proc/<pid>/oom_adj Then you should be just fine. Kind regards Nick 2012/5/10 Iván Pulido Sanchez <[email protected]> > Hello, > > I've been having problem with Siesta in Linux (Debian) when it needs a lot > of RAM, specially in the case when it take all the available memory of > the system (ram + swap). The problem is that when it does that the linux > oom-killer gets invoked and then it start killing processes. The following > are the relevant lines in the kernel log (kern.log) explaining this: > > May 8 21:00:16 nodo4 kernel: [8217579.288562] siesta invoked oom-killer: > gfp_mask=0x200da, order=0, oom_adj=-17 > ... > May 8 21:00:16 nodo4 kernel: [8217579.306967] Out of memory: kill process > 1975 (dbus-daemon) score 646 or a child > ... > May 8 21:00:16 nodo4 kernel: [8217579.856575] rsyslogd invoked > oom-killer: gfp_mask=0x200da, order=0, oom_adj=0 > ... > May 8 21:00:16 nodo4 kernel: [8217579.875127] Out of memory: kill process > 1599 (rpc.statd) score 399 or a child > May 8 21:00:16 nodo4 kernel: [8217579.875934] Killed process 1599 > (rpc.statd) > May 9 11:48:08 nodo4 kernel: imklog 4.6.2, log source = /proc/kmsg > started. > > And thats how it ends (as you can see in the jump in the date). > > There is something that worries me and that's in the first line of the > previous ones. It basically says that siesta is using a oom_adj value > of -17 meaning that it can't be killed by the oom-killer, I don't know > why is Siesta running with this value for oom_adj. > > Processes like ssh or rpc.statd (NFS) shouldn't get killed before > Siesta, this is why the node "dies" when this happens. > > Here is my siesta version and/or configuration: > > Siesta Version: siesta-3.1 > Architecture : x86_64-debian6 > Compiler flags: mpif90 -g -O2 > PARALLEL version > > > Any idea, help or suggestions are very much appreciated. > > Thanks > > -- > Iván José Pulido Sánchez > Estudiante de Física > Universidad Nacional de Colombia > >
