I have investigated further, its definitely an MPI issue. Thanks for taking a look at this.
Nichols A. Romero, Ph.D. Argonne Leadership Computing Facility Argonne National Laboratory Building 240 Room 2-127 9700 South Cass Avenue Argonne, IL 60490 (630) 252-3441 ----- Original Message ----- From: "Quincey Koziol" <[email protected]> To: "HDF Users Discussion List" <[email protected]> Sent: Thursday, August 25, 2011 10:14:38 AM Subject: Re: [Hdf-forum] memory usage in H5Dwrite Hi Nichols, On Aug 18, 2011, at 10:43 AM, Nichols A. Romero wrote: > This is the test case that I sent to IBM for analysis. They assert that there > is no memory leaked according to mallinfo. However, mmap/munmap are not > recorded > to mallinfo (AFAIK). If I analyze the sequence of mmap/munmap and translate > the > addresses, then I see heap memory (O(100 MB)) which is not freed. Yes, it doesn't look like memory should be leaked, given your usage. Can you push the leak analysis further down inside HDF5, to see if it's in the MPI library, or actually in HDF5? Thanks, Quincey > Nichols A. Romero, Ph.D. > Argonne Leadership Computing Facility > Argonne National Laboratory > Building 240 Room 2-127 > 9700 South Cass Avenue > Argonne, IL 60490 > (630) 252-3441 > > > ----- Original Message ----- > From: "Quincey Koziol" <[email protected]> > To: "HDF Users Discussion List" <[email protected]> > Sent: Tuesday, August 16, 2011 2:49:05 PM > Subject: Re: [Hdf-forum] memory usage in H5Dwrite > > Hi Nichols, > > On Jul 28, 2011, at 5:44 PM, Nichols A. Romero wrote: > >> Hi, >> >> I am trying to figure out if there is a memory leak or a lack of >> understanding on my part >> with respect to the HDF5 internals. My simple test case writes a >> 4-dimensional uniformly >> distributed array using H5Dwrite. I measure the heap memory before and after >> the write. >> I would expect the heap memory utilization to not change substantially. >> >> I have measured the heap memory a couple of different ways, e.g. using >> mallinfo or some tool. >> Naively it looks like the MPI I/O aggregators are not releasing memory but >> some tools >> have reported no leak at all, while others have report a large one (> 200 >> MB). I finally >> resorted to using mpirun -strace to track the series of mmap/munmap in the >> H5Dwrite. >> I was surprised to see a large number of calls to mmap/munmap which >> ultimately results >> in 60 MB of heap memory not being released. >> >> First question: Is this the intended behavior? >> >> Second question: If this behavior is intentional, is there away to force >> HDF5 to release >> these internal buffers after the H5Dwrite. > > It's a bit hard to tell from your description - could you send a short > program that demonstrates the issue? > > Quincey > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org > <hdf5_4D.tar>_______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
