[mpich-devel] ROMIO collective i/o memory use
Kevin Harms
harms at alcf.anl.gov
Mon May 6 14:32:46 CDT 2013
sorry, haven't updated the PMR but it failed. Memory failure in PAMI. I will update the PMR today with the new results.
kevin
On May 6, 2013, at 1:41 PM, Bob Cernohous <bobc at us.ibm.com> wrote:
> I agree and suggested:
> ---------------------
> It appears they don't have enough memory for an alltoallv exchange. Try '1'...
>
> * - BGMPIO_COMM - Define how data is exchanged on collective
> * reads and writes. Possible values:
> * - 0 - Use MPI_Alltoallv.
> * - 1 - Use MPI_Isend/MPI_Irecv.
> * - Default is 0.
> ---------------------
>
> but they didn't want a work around they wanted a 'fix for o(p) allocations'. There are o(p) allocations all over collective i/o from a quick glance. Just wanted some input from the experts about scaling romio. I haven't heard if the suggestion worked.
>
> Bob Cernohous: (T/L 553) 507-253-6093
>
> BobC at us.ibm.com
> IBM Rochester, Building 030-2(C335), Department 61L
> 3605 Hwy 52 North, Rochester, MN 55901-7829
>
> > Chaos reigns within.
> > Reflect, repent, and reboot.
> > Order shall return.
>
>
> devel-bounces at mpich.org wrote on 05/04/2013 09:43:10 PM:
>
> > From: "Rob Latham" <robl at mcs.anl.gov>
> > To: devel at mpich.org,
> > Cc: mpich2-dev at mcs.anl.gov
> > Date: 05/04/2013 09:48 PM
> > Subject: Re: [mpich-devel] ROMIO collective i/o memory use
> > Sent by: devel-bounces at mpich.org
> >
> > On Mon, Apr 29, 2013 at 10:28:01AM -0500, Bob Cernohous wrote:
> > > A customer (Argonne ;) is complaining about O(p) allocations in collective
> > > i/o. A collective read is failing at larger scale.
> > >
> > > Any thoughts or comments or advice? There appears to be lots of O(p) in
> > > ROMIO collective I/O. Plus a lot of (possibly large) aggregated data
> > > buffers. A quick search shows
> >
> > The O(p) allocations are a concern, sure. For two-phase, though, the
> > real problem lies in ADIOI_R_Exchange_data_alltoallv and
> > ADIOI_W_Exchange_data_alltoallv . The O(p) allocations are the least
> > of our worries!
> >
> > around line 1063 of ad_bg_rdcoll.c
> >
> > all_recv_buf = (char *) ADIOI_Malloc( rtail );
> >
> > all_send_buf = (char *) ADIOI_Malloc( stail );
> >
> > (rtail and stail are the sum of the receive and send arrays)
> >
> > ==rob
> >
> > > The common ROMIO read collective code:
> > >
> > > Find all "ADIOI_Malloc", Match case, Regular expression (UNIX)
> > >
> > > File Z:\bgq\comm\lib\dev\mpich2\src\mpi\romio\adio\common\ad_read_coll.c
> > >
> > > 124 38: st_offsets = (ADIO_Offset *)
> > > ADIOI_Malloc(nprocs*sizeof(ADIO_Offset));
> > >
> > > 125 39: end_offsets = (ADIO_Offset *)
> > > ADIOI_Malloc(nprocs*sizeof(ADIO_Offset));
> > >
> > > 317 44: *offset_list_ptr = (ADIO_Offset *)
> > > ADIOI_Malloc(2*sizeof(ADIO_Offset));
> > >
> > > 318 41: *len_list_ptr = (ADIO_Offset *)
> > > ADIOI_Malloc(2*sizeof(ADIO_Offset));
> > >
> > > 334 44: *offset_list_ptr = (ADIO_Offset *)
> > > ADIOI_Malloc(2*sizeof(ADIO_Offset));
> > >
> > > 335 41: *len_list_ptr = (ADIO_Offset *)
> > > ADIOI_Malloc(2*sizeof(ADIO_Offset));
> > >
> > > 436 18: ADIOI_Malloc((contig_access_count+1)*sizeof(ADIO_Offset));
> > >
> > > 437 41: *len_list_ptr = (ADIO_Offset *)
> > > ADIOI_Malloc((contig_access_count+1)*sizeof(ADIO_Offset));
> > >
> > > 573 37: if (ntimes) read_buf = (char *) ADIOI_Malloc(coll_bufsize);
> > >
> > > 578 21: count = (int *) ADIOI_Malloc(nprocs * sizeof(int));
> > >
> > > 587 25: send_size = (int *) ADIOI_Malloc(nprocs * sizeof(int));
> > >
> > > 590 25: recv_size = (int *) ADIOI_Malloc(nprocs * sizeof(int));
> > >
> > > 598 25: start_pos = (int *) ADIOI_Malloc(nprocs*sizeof(int));
> > >
> > > 739 32: tmp_buf = (char *) ADIOI_Malloc(for_next_iter);
> > >
> > > 744 33: read_buf = (char *)
> > > ADIOI_Malloc(for_next_iter+coll_bufsize);
> > >
> > > 805 9: ADIOI_Malloc((nprocs_send+nprocs_recv+1)*sizeof(MPI_Request));
> > >
> > > 827 30: recv_buf = (char **) ADIOI_Malloc(nprocs * sizeof(char*));
> > >
> > > 830 44: (char *)
> > > ADIOI_Malloc(recv_size[i]);
> > >
> > > 870 31: statuses = (MPI_Status *)
> > > ADIOI_Malloc((nprocs_send+nprocs_recv+1) * \
> > >
> > > 988 35: curr_from_proc = (unsigned *) ADIOI_Malloc(nprocs *
> > > sizeof(unsigned));
> > >
> > > 989 35: done_from_proc = (unsigned *) ADIOI_Malloc(nprocs *
> > > sizeof(unsigned));
> > >
> > > 990 35: recv_buf_idx = (unsigned *) ADIOI_Malloc(nprocs *
> > > sizeof(unsigned));
> > >
> > > Total found: 22
> > >
> > >
> > > Our BG version of read collective:
> > >
> > > File Z:\bgq\comm\lib\dev\mpich2\src\mpi\romio\adio\ad_bg\ad_bg_rdcoll.c
> > >
> > > 179 40: st_offsets = (ADIO_Offset *)
> > > ADIOI_Malloc(nprocs*sizeof(ADIO_Offset));
> > >
> > > 180 40: end_offsets = (ADIO_Offset *)
> > > ADIOI_Malloc(nprocs*sizeof(ADIO_Offset));
> > >
> > > 183 43: bg_offsets0 = (ADIO_Offset *)
> > > ADIOI_Malloc(2*nprocs*sizeof(ADIO_Offset));
> > >
> > > 184 43: bg_offsets = (ADIO_Offset *)
> > > ADIOI_Malloc(2*nprocs*sizeof(ADIO_Offset));
> > >
> > > 475 37: if (ntimes) read_buf = (char *) ADIOI_Malloc(coll_bufsize);
> > >
> > > 480 21: count = (int *) ADIOI_Malloc(nprocs * sizeof(int));
> > >
> > > 489 25: send_size = (int *) ADIOI_Malloc(nprocs * sizeof(int));
> > >
> > > 492 25: recv_size = (int *) ADIOI_Malloc(nprocs * sizeof(int));
> > >
> > > 500 25: start_pos = (int *) ADIOI_Malloc(nprocs*sizeof(int));
> > >
> > > 676 32: tmp_buf = (char *) ADIOI_Malloc(for_next_iter);
> > >
> > > 681 33: read_buf = (char *)
> > > ADIOI_Malloc(for_next_iter+coll_bufsize);
> > >
> > > 761 9: ADIOI_Malloc((nprocs_send+nprocs_recv+1)*sizeof(MPI_Request));
> > >
> > > 783 30: recv_buf = (char **) ADIOI_Malloc(nprocs * sizeof(char*));
> > >
> > > 786 44: (char *)
> > > ADIOI_Malloc(recv_size[i]);
> > >
> > > 826 31: statuses = (MPI_Status *)
> > > ADIOI_Malloc((nprocs_send+nprocs_recv+1) * \
> > >
> > > 944 35: curr_from_proc = (unsigned *) ADIOI_Malloc(nprocs *
> > > sizeof(unsigned));
> > >
> > > 945 35: done_from_proc = (unsigned *) ADIOI_Malloc(nprocs *
> > > sizeof(unsigned));
> > >
> > > 946 35: recv_buf_idx = (unsigned *) ADIOI_Malloc(nprocs *
> > > sizeof(unsigned));
> > >
> > > 1058 23: rdispls = (int *) ADIOI_Malloc( nprocs * sizeof(int) );
> > >
> > > 1063 29: all_recv_buf = (char *) ADIOI_Malloc( rtail );
> > >
> > > 1064 26: recv_buf = (char **) ADIOI_Malloc(nprocs * sizeof(char *));
> > >
> > > 1068 23: sdispls = (int *) ADIOI_Malloc( nprocs * sizeof(int) );
> > >
> > > 1073 29: all_send_buf = (char *) ADIOI_Malloc( stail );
> > >
> > > Total found: 23
> > >
> > >
> > > Bob Cernohous: (T/L 553) 507-253-6093
> > >
> > > BobC at us.ibm.com
> > > IBM Rochester, Building 030-2(C335), Department 61L
> > > 3605 Hwy 52 North, Rochester, MN 55901-7829
> > >
> > > > Chaos reigns within.
> > > > Reflect, repent, and reboot.
> > > > Order shall return.
> >
> > --
> > Rob Latham
> > Mathematics and Computer Science Division
> > Argonne National Lab, IL USA
> >
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