On Aug 6, 2007, at 7:00 PM, Glenn Carver wrote:
Just to clarify, the MPI applications exit cleanly. We have our own f90 code (in various configurations) and I'm also testing using Intel's IMB. If I watch the applications whilst they run, there is a drop in free memory as our code begins, the free memory then steadily drops as the code runs. When it exits normally, free memory increases but falls short of where it was before the code started. The longer we run the code for the bigger the final drop in memory. Taking the machine down to single user mode doesn't help so it's not an issue of processes still running. Neither can I find any files still open with lsof. We installed Sun's clustertools 6 (not based on openmpi) and we don't see the same problem. I'm currently testing whether setting btl_udapl_flags=1 makes a difference. I'm guessing that registered memory is leaking? We're also trying some mca parameters to turn off features we don't need to see if that makes a difference. I'll report back on point 2. below and further tests later. If there's specific mca parameters you'd like to see specified let me know? Thanks, GlennGuess I don't see how stale shared memory files would cause swapping to occur. Besides, the user provided no indication that the applications were abnormally terminating, which makes it likely we cleaned up the sessiondirectories as we should.However, we definitely leak memory (i.e., we don't free all memory we malloc while supporting execution of an application), so if the OS isn't cleaningup after us, it is quite possible we could be causing the problem asdescribed. It would appear exactly as described - a slow leak that gradually builds up until the "dead" area was so big that it forces applications toswap to find enough room to work. So I guess we should ask for clarification:1. are the Open MPI applications exiting cleanly? Do you see any stale"orted" executables still in the process table?2. can you check the temp directory where we would be operating? This is usually your /tmp directory, unless you specified some other location. Look for our session directories - they have a name that includes "openmpi" in them. Are they being cleaned up (i.e., removed) when the applications exit?Thanks Ralph On 8/6/07 5:53 PM, "Jeff Squyres" <jsquy...@cisco.com> wrote:Unless there's something weird going on in the Solaris kernel, theonly memory that we should be leaking after MPI processes exit would be shared memory files that are [somehow] not getting removed properly.Right? On Aug 6, 2007, at 8:15 AM, Ralph H Castain wrote:Hmmm...just to clarify as I think there may be some confusion here.Orte-clean will kill any outstanding Open MPI daemons (which shouldkill their local apps) and will cleanup their associated temporary file systems.If you are having problems with zombied processes or stale daemons,then this will hopefully help (it isn't perfect, but it helps). However, orte-clean will not do anything about releasing memory that hasbeen "leaked" by Open MPI. We don't have any tools for doing that, I'mafraid. On 8/6/07 8:08 AM, "Don Kerr" <don.k...@sun.com> wrote:Glenn,With CT7 there is a utility which can be used to clean up left overcruft from stale MPI processes. % man -M /opt/SUNWhpc/man -s 1 orte-clean Achtung: This will remove current running jobs as well. Use of "- v" for verbose recommended. I would be curious if this helps. -DONp.s. orte-clean does not exist in the ompi v1.2 branch, it is in thetrunk but I think there is an issue with it currently Ralph H Castain wrote:On 8/5/07 6:35 PM, "Glenn Carver" <glenn.car...@atm.ch.cam.ac.uk>wrote:I'd appreciate some advice and help on this one. We're having serious problems running parallel applications on our cluster. After each batch job finishes, we lose a certain amount of available memory. Additional jobs cause free memory to gradually go down until the machine starts swapping and becomes unusable or hangs. Taking the machine to single user mode doesn't restore the memory, only a reboot returns all available memory. This happens on all our nodes. We've been doing some testing to try to pin the problems down, although we still don't fully know where the problem is coming from.We have ruled out our applications (fortran codes); we see the same behaviour with Intel's IMB. We know it's not a network issue as a parallel job running solely on the 4 cores on each node producesthesame effect. All nodes have been brought up to the very latest OSpatches and we still see the same problem.Details: we're running Solaris 10/06, Sun Studio 12, Clustertools 7(open-mpi 1.2.1) and Sun Gridengine 6.1. Hardware is Sun X4100/ X4200. Kernel version: SunOS 5.10 Generic_125101-10 on all nodes. I read in the release notes that a number of memory leaks were fixedfor the 1.2.1 release but none have been noticed since so I'm notsure where the problem might be.I'm not sure where that claim came from, but it is certainly not true thatwe haven't noticed any leaks since 1.2.1. We know we have quite afew memoryleaks in the code base, many of which are small in themselves butcan add up depending upon exactly what the application does (i.e., which code paths ittravels). Running a simple hello_world app under valgrind will showsignificant unreleased memory. I doubt you will see much, if any, improvement in 1.2.4. There have probably been a few patches applied, but a comprehensive effort to eradicate the problem has not been made. It is something we are trying to cleanup over time, but hasn't been a crash priority as most OS's do a fairly good job of cleaning up when the app completes.My next move is to try the very latest release (probably 1.2.4pre-release). As CT7 is built with sun studio 11 rather than 12 which we're using, I might also try downgrading. At the moment we'rerebooting our cluster nodes every day to keep things going. So anysuggestions are appreciated. Thanks, Glenn $ ompi_info Open MPI: 1.2.1r14096-ct7b030r1838 Open MPI SVN revision: 0 Open RTE: 1.2.1r14096-ct7b030r1838 Open RTE SVN revision: 0 OPAL: 1.2.1r14096-ct7b030r1838 OPAL SVN revision: 0 Prefix: /opt/SUNWhpc/HPC7.0 Configured architecture: i386-pc-solaris2.10 Configured by: root Configured on: Fri Mar 30 13:40:12 EDT 2007 Configure host: burpen-csx10-0 Built by: root Built on: Fri Mar 30 13:57:25 EDT 2007 Built host: burpen-csx10-0 C bindings: yes C++ bindings: yes Fortran77 bindings: yes (all) Fortran90 bindings: yes Fortran90 bindings size: trivial C compiler: cc C compiler absolute: /ws/ompi-tools/SUNWspro/SOS11/bin/cc C++ compiler: CC C++ compiler absolute: /ws/ompi-tools/SUNWspro/SOS11/bin/CC Fortran77 compiler: f77 Fortran77 compiler abs: /ws/ompi-tools/SUNWspro/SOS11/bin/f77 Fortran90 compiler: f95 Fortran90 compiler abs: /ws/ompi-tools/SUNWspro/SOS11/bin/f95 C profiling: yes C++ profiling: yes Fortran77 profiling: yes Fortran90 profiling: yes C++ exceptions: yes Thread support: no Internal debug support: no MPI parameter check: runtime Memory profiling support: no Memory debugging support: no libltdl support: yes Heterogeneous support: yes mpirun default --prefix: yes MCA backtrace: printstack (MCA v1.0, API v1.0, Component v1.2.1)MCA paffinity: solaris (MCA v1.0, API v1.0, Componentv1.2.1) MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2.1)MCA timer: solaris (MCA v1.0, API v1.0, Componentv1.2.1) MCA allocator: basic (MCA v1.0, API v1.0, Component v1.0) MCA allocator: bucket (MCA v1.0, API v1.0, Component v1.0) MCA coll: basic (MCA v1.0, API v1.0, Component v1.2.1) MCA coll: self (MCA v1.0, API v1.0, Component v1.2.1)MCA coll: sm (MCA v1.0, API v1.0, Component v1.2.1)MCA coll: tuned (MCA v1.0, API v1.0, Component v1.2.1) MCA io: romio (MCA v1.0, API v1.0, Component v1.2.1)MCA mpool: sm (MCA v1.0, API v1.0, Component v1.2.1)MCA mpool: udapl (MCA v1.0, API v1.0, Component v1.2.1)MCA pml: cm (MCA v1.0, API v1.0, Component v1.2.1)MCA pml: ob1 (MCA v1.0, API v1.0, Component v1.2.1)MCA bml: r2 (MCA v1.0, API v1.0, Component v1.2.1) MCA rcache: rb (MCA v1.0, API v1.0, Component v1.2.1)MCA rcache: vma (MCA v1.0, API v1.0, Component v1.2.1) MCA btl: self (MCA v1.0, API v1.0.1, Component v1.2.1) MCA btl: sm (MCA v1.0, API v1.0.1, Component v1.2.1) MCA btl: tcp (MCA v1.0, API v1.0.1, Component v1.0) MCA btl: udapl (MCA v1.0, API v1.0, Component v1.2.1) MCA topo: unity (MCA v1.0, API v1.0, Component v1.2.1) MCA osc: pt2pt (MCA v1.0, API v1.0, Component v1.2.1) MCA errmgr: hnp (MCA v1.0, API v1.3, Component v1.2.1) MCA errmgr: orted (MCA v1.0, API v1.3, Component v1.2.1) MCA errmgr: proxy (MCA v1.0, API v1.3, Component v1.2.1) MCA gpr: null (MCA v1.0, API v1.0, Component v1.2.1) MCA gpr: proxy (MCA v1.0, API v1.0, Component v1.2.1)MCA gpr: replica (MCA v1.0, API v1.0, Componentv1.2.1) MCA iof: proxy (MCA v1.0, API v1.0, Component v1.2.1) MCA iof: svc (MCA v1.0, API v1.0, Component v1.2.1) MCA ns: proxy (MCA v1.0, API v2.0, Component v1.2.1)MCA ns: replica (MCA v1.0, API v2.0, Componentv1.2.1)MCA oob: tcp (MCA v1.0, API v1.0, Component v1.0)MCA ras: dash_host (MCA v1.0, API v1.3, Component v1.2.1) MCA ras: gridengine (MCA v1.0, API v1.3, Component v1.2.1) MCA ras: localhost (MCA v1.0, API v1.3, Component v1.2.1)MCA ras: tm (MCA v1.0, API v1.3, Component v1.2.1)MCA rds: hostfile (MCA v1.0, API v1.3, Component v1.2.1) MCA rds: proxy (MCA v1.0, API v1.3, Component v1.2.1)MCA rds: resfile (MCA v1.0, API v1.3, Componentv1.2.1) MCA rmaps: round_robin (MCA v1.0, API v1.3, Component v1.2.1) MCA rmgr: proxy (MCA v1.0, API v2.0, Component v1.2.1) MCA rmgr: urm (MCA v1.0, API v2.0, Component v1.2.1) MCA rml: oob (MCA v1.0, API v1.0, Component v1.2.1) MCA pls: gridengine (MCA v1.0, API v1.3, Component v1.2.1) MCA pls: proxy (MCA v1.0, API v1.3, Component v1.2.1) MCA pls: rsh (MCA v1.0, API v1.3, Component v1.2.1)MCA pls: tm (MCA v1.0, API v1.3, Component v1.2.1)MCA sds: env (MCA v1.0, API v1.0, Component v1.2.1) MCA sds: pipe (MCA v1.0, API v1.0, Component v1.2.1) MCA sds: seed (MCA v1.0, API v1.0, Component v1.2.1) MCA sds: singleton (MCA v1.0, API v1.0, Component v1.2.1) _______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users_______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users_______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users_______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users_______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users_______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
-- Jeff Squyres Cisco Systems
