[mpich-discuss] Unable to run program parallely on cluster...Its running properly on single machine...
Albert Spade
albert.spade at gmail.com
Sat May 26 15:53:41 CDT 2012
Hi Jeff,
Thanks for you reply.
N sorry I didnt changed the subject before.
I want to say, as you said I am already using gatherv then why i am getting
this error???
MPI::COMM_WORLD.Gatherv(MPI_IN_PLACE, Count[rank],
MPI::CHAR, (void*)(Data), Count, Displ, MPI::CHAR, 0);
//MPI::COMM_WORLD.Gatherv((const
void*)(Data+StartFrom[nStages-1][rank]), Count[rank], MPI::CHAR,
(void*)(Data), Count, Displ, MPI::CHAR, 0);
>
>
> Message: 2
> Date: Fri, 25 May 2012 09:46:11 -0500
> From: Jeff Hammond <jhammond at alcf.anl.gov>
> To: mpich-discuss at mcs.anl.gov
> Subject: Re: [mpich-discuss] mpich-discuss Digest, Vol 44, Issue 36
> Message-ID:
> <CAGKz=uKG+upZGHp-cZ5_2hv9von+KFjKO3QRdp3qcorJQh81_g at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> The error is pretty obvious in the output:
>
> PMPI_Gatherv(335): sendbuf cannot be MPI_IN_PLACE
>
> You cannot use MPI_IN_PLACE with MPI_Gather
> (https://svn.mpi-forum.org/trac/mpi-forum-web/ticket/163) but it is
> allowed in MPI_Gatherv as of MPI 2.2, so I don't know why the
> implementation does not allow this.
>
> Jeff
>
> On Fri, May 25, 2012 at 8:21 AM, Albert Spade <albert.spade at gmail.com>
> wrote:
> > Thanks Rajeev and Darius,
> >
> > I tried to use MPI_IN_PLACE but not getting the desired results. Can you
> > please tell me how to make it working.
> >
> > This is the previous code :
> >
> > ?? ? ? ? //MPI::COMM_WORLD.Gatherv((const
> > void*)(Data+StartFrom[nStages-1][rank]), Count[rank], MPI::CHAR,
> > (void*)(Data), Count, Displ, MPI::CHAR, 0);
> >
> > And this is how I changed it.
> >
> > ?MPI::COMM_WORLD.Gatherv(MPI_IN_PLACE, Count[rank], MPI::CHAR,
> > (void*)(Data), Count, Displ, MPI::CHAR, 0);
> >
> > Am I doing it wrong?
> >
> > Thanks.
> >
> > My output after making above changes.
> > ==============================
> > [root at beowulf programs]# mpiexec -n 1 ./output
> > Time taken for 16 elements using 1 processors = 2.81334e-05 seconds
> > [root at beowulf programs]# mpiexec -n 2 ./output
> > Fatal error in PMPI_Gatherv: Invalid buffer pointer, error stack:
> > PMPI_Gatherv(398): MPI_Gatherv failed(sbuf=MPI_IN_PLACE, scount=64,
> > MPI_CHAR, rbuf=0x879d500, rcnts=0x879d6b8, displs=0x879d6c8, MPI_CHAR,
> > root=0, MPI_COMM_WORLD) failed
> > PMPI_Gatherv(335): sendbuf cannot be MPI_IN_PLACE
> >
> >
> =====================================================================================
> > = ? BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> > = ? EXIT CODE: 256
> > = ? CLEANING UP REMAINING PROCESSES
> > = ? YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> >
> =====================================================================================
> > *** glibc detected *** mpiexec: double free or corruption (fasttop):
> > 0x094fb038 ***
> > ======= Backtrace: =========
> > /lib/libc.so.6[0x7d4a31]
> > mpiexec[0x8077b11]
> > mpiexec[0x8053c7f]
> > mpiexec[0x8053e73]
> > mpiexec[0x805592a]
> > mpiexec[0x8077186]
> > mpiexec[0x807639e]
> > mpiexec[0x80518f8]
> > mpiexec[0x804ad65]
> > /lib/libc.so.6(__libc_start_main+0xe6)[0x77cce6]
> > mpiexec[0x804a061]
> > ======= Memory map: ========
> > 00547000-00548000 r-xp 00000000 00:00 0 ? ? ? ? ?[vdso]
> > 0054b000-0068f000 r-xp 00000000 fd:00 939775 ? ?
> /usr/lib/libxml2.so.2.7.6
> > 0068f000-00694000 rw-p 00143000 fd:00 939775 ? ?
> /usr/lib/libxml2.so.2.7.6
> > 00694000-00695000 rw-p 00000000 00:00 0
> > 00740000-0075e000 r-xp 00000000 fd:00 2105890 ? ?/lib/ld-2.12.so
> > 0075e000-0075f000 r--p 0001d000 fd:00 2105890 ? ?/lib/ld-2.12.so
> > 0075f000-00760000 rw-p 0001e000 fd:00 2105890 ? ?/lib/ld-2.12.so
> > 00766000-008ef000 r-xp 00000000 fd:00 2105891 ? ?/lib/libc-2.12.so
> > 008ef000-008f0000 ---p 00189000 fd:00 2105891 ? ?/lib/libc-2.12.so
> > 008f0000-008f2000 r--p 00189000 fd:00 2105891 ? ?/lib/libc-2.12.so
> > 008f2000-008f3000 rw-p 0018b000 fd:00 2105891 ? ?/lib/libc-2.12.so
> > 008f3000-008f6000 rw-p 00000000 00:00 0
> > 008f8000-008fb000 r-xp 00000000 fd:00 2105893 ? ?/lib/libdl-2.12.so
> > 008fb000-008fc000 r--p 00002000 fd:00 2105893 ? ?/lib/libdl-2.12.so
> > 008fc000-008fd000 rw-p 00003000 fd:00 2105893 ? ?/lib/libdl-2.12.so
> > 008ff000-00916000 r-xp 00000000 fd:00 2105900 ? ?/lib/libpthread-2.12.so
> > 00916000-00917000 r--p 00016000 fd:00 2105900 ? ?/lib/libpthread-2.12.so
> > 00917000-00918000 rw-p 00017000 fd:00 2105900 ? ?/lib/libpthread-2.12.so
> > 00918000-0091a000 rw-p 00000000 00:00 0
> > 0091c000-0092e000 r-xp 00000000 fd:00 2105904 ? ?/lib/libz.so.1.2.3
> > 0092e000-0092f000 r--p 00011000 fd:00 2105904 ? ?/lib/libz.so.1.2.3
> > 0092f000-00930000 rw-p 00012000 fd:00 2105904 ? ?/lib/libz.so.1.2.3
> > 00932000-0095a000 r-xp 00000000 fd:00 2098429 ? ?/lib/libm-2.12.so
> > 0095a000-0095b000 r--p 00027000 fd:00 2098429 ? ?/lib/libm-2.12.so
> > 0095b000-0095c000 rw-p 00028000 fd:00 2098429 ? ?/lib/libm-2.12.so
> > 00bb0000-00bcd000 r-xp 00000000 fd:00 2105914
> > ?/lib/libgcc_s-4.4.6-20110824.so.1
> > 00bcd000-00bce000 rw-p 0001d000 fd:00 2105914
> > ?/lib/libgcc_s-4.4.6-20110824.so.1
> > 00c18000-00c24000 r-xp 00000000 fd:00 2098123 ? ?/lib/
> libnss_files-2.12.so
> > 00c24000-00c25000 r--p 0000b000 fd:00 2098123 ? ?/lib/
> libnss_files-2.12.so
> > 00c25000-00c26000 rw-p 0000c000 fd:00 2098123 ? ?/lib/
> libnss_files-2.12.so
> > 00ce9000-00d00000 r-xp 00000000 fd:00 2105929 ? ?/lib/libnsl-2.12.so
> > 00d00000-00d01000 r--p 00016000 fd:00 2105929 ? ?/lib/libnsl-2.12.so
> > 00d01000-00d02000 rw-p 00017000 fd:00 2105929 ? ?/lib/libnsl-2.12.so
> > 00d02000-00d04000 rw-p 00000000 00:00 0
> > 08048000-080a0000 r-xp 00000000 fd:00 656990
> > /opt/mpich2-1.4.1p1/bin/bin/mpiexec.hydra
> > 080a0000-080a1000 rw-p 00058000 fd:00 656990
> > /opt/mpich2-1.4.1p1/bin/bin/mpiexec.hydra
> > 080a1000-080a3000 rw-p 00000000 00:00 0
> > 094ee000-0950f000 rw-p 00000000 00:00 0 ? ? ? ? ?[heap]
> > b7893000-b7896000 rw-p 00000000 00:00 0
> > b78a4000-b78a7000 rw-p 00000000 00:00 0
> > bff80000-bff95000 rw-p 00000000 00:00 0 ? ? ? ? ?[stack]
> > Aborted (core dumped)
> > [root at beowulf programs]#
> >
> >
> > On Tue, May 22, 2012 at 10:30 PM, <mpich-discuss-request at mcs.anl.gov>
> wrote:
> >>
> >> Send mpich-discuss mailing list submissions to
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> >>
> >> Today's Topics:
> >>
> >> ? 1. ?Unable to run program parallely on cluster... Its running
> >> ? ? ?properly on single machine... (Albert Spade)
> >> ? 2. ?Not able to run program parallely on cluster... (Albert Spade)
> >> ? 3. Re: ?Unable to run program parallely on cluster... ? ? ? ?Its
> >> ? ? ?running properly on single machine... (Darius Buntinas)
> >> ? 4. Re: ?Not able to run program parallely on cluster...
> >> ? ? ?(Rajeev Thakur)
> >> ? 5. ?replication of mpi applications (Thomas Ropars)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Tue, 22 May 2012 00:12:24 +0530
> >> From: Albert Spade <albert.spade at gmail.com>
> >> To: mpich-discuss at mcs.anl.gov
> >> Subject: [mpich-discuss] Unable to run program parallely on cluster...
> >> ? ? ? ?Its running properly on single machine...
> >> Message-ID:
> >>
> >> ?<CAP2uaQopgOwaFNfCF49gcnW9REw8CQtWGMgf0U8RyNYStTFw1A at mail.gmail.com>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >> Hi everybody,
> >>
> >> I am using mpich2-1.4.1p1 and mpiexec from hydra-1.5b1
> >> I have a cluster of 5 machines.
> >> When I am trying to run the program for parallel fast fourier transform
> on
> >> single machine it runs correctly but on a cluster it gives error.
> >> Can you please tell me why its happening.
> >>
> >> Thanks.
> >>
> >> Here is my sample output:
> >>
> >>
> ---------------------------------------------------------------------------------------
> >>
> >> [root at beowulf programs]# mpiexec -n 1 ./Radix2
> >> Time taken for 16 elements using 1 processors = 2.7895e-05 seconds
> >> [root at beowulf programs]#
> >> [root at beowulf programs]# mpiexec -n 4 ./Radix2
> >> [mpiexec at beowulf.master] control_cb (./pm/pmiserv/pmiserv_cb.c:197):
> >> assert
> >> (!closed) failed
> >> [mpiexec at beowulf.master] HYDT_dmxu_poll_wait_for_event
> >> (./tools/demux/demux_poll.c:77): callback returned error status
> >> [mpiexec at beowulf.master] HYD_pmci_wait_for_completion
> >> (./pm/pmiserv/pmiserv_pmci.c:205): error waiting for event
> >> [mpiexec at beowulf.master] main (./ui/mpich/mpiexec.c:437): process
> manager
> >> error waiting for completion
> >> [root at beowulf programs]# mpiexec -n 2 ./Radix2
> >> [mpiexec at beowulf.master] control_cb (./pm/pmiserv/pmiserv_cb.c:197):
> >> assert
> >> (!closed) failed
> >> [mpiexec at beowulf.master] HYDT_dmxu_poll_wait_for_event
> >> (./tools/demux/demux_poll.c:77): callback returned error status
> >> [mpiexec at beowulf.master] HYD_pmci_wait_for_completion
> >> (./pm/pmiserv/pmiserv_pmci.c:205): error waiting for event
> >> [mpiexec at beowulf.master] main (./ui/mpich/mpiexec.c:437): process
> manager
> >> error waiting for completion
> >> [root at beowulf programs]# mpiexec -n 4 ./Radix2
> >> [mpiexec at beowulf.master] control_cb (./pm/pmiserv/pmiserv_cb.c:197):
> >> assert
> >> (!closed) failed
> >> [mpiexec at beowulf.master] HYDT_dmxu_poll_wait_for_event
> >> (./tools/demux/demux_poll.c:77): callback returned error status
> >> [mpiexec at beowulf.master] HYD_pmci_wait_for_completion
> >> (./pm/pmiserv/pmiserv_pmci.c:205): error waiting for event
> >> [mpiexec at beowulf.master] main (./ui/mpich/mpiexec.c:437): process
> manager
> >> error waiting for completion
> >> [root at beowulf programs]#
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL:
> >> <
> http://lists.mcs.anl.gov/pipermail/mpich-discuss/attachments/20120522/25975b06/attachment-0001.html
> >
> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Tue, 22 May 2012 00:59:27 +0530
> >> From: Albert Spade <albert.spade at gmail.com>
> >> To: mpich-discuss at mcs.anl.gov
> >> Subject: [mpich-discuss] Not able to run program parallely on
> >> ? ? ? ?cluster...
> >> Message-ID:
> >>
> >> ?<CAP2uaQpiMV0yqHsHfsWpgAQ=_K3M_ZGxsCm-S5BPvzbxH+Z9zQ at mail.gmail.com>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >> This is my new error after making few changes...
> >> Results are quite similar... No succes with cluster...
> >>
> >> Sample run
> >> --------------------------------------------------------
> >>
> >> [root at beowulf testing]# mpiexec -n 1 ./Radix
> >> Time taken for 16 elements using 1 processors = 4.72069e-05 seconds
> >> [root at beowulf testing]# mpiexec -n 2 ./Radix
> >> Fatal error in PMPI_Gatherv: Internal MPI error!, error stack:
> >> PMPI_Gatherv(398).....: MPI_Gatherv failed(sbuf=0x97d0500, scount=64,
> >> MPI_CHAR, rbuf=0x97d0500, rcnts=0x97d06b8, displs=0x97d06c8, MPI_CHAR,
> >> root=0, MPI_COMM_WORLD) failed
> >> MPIR_Gatherv_impl(210):
> >> MPIR_Gatherv(104).....:
> >> MPIR_Localcopy(357)...: memcpy arguments alias each other, dst=0x97d0500
> >> src=0x97d0500 len=64
> >>
> >>
> >>
> =====================================================================================
> >> = ? BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> >> = ? EXIT CODE: 256
> >> = ? CLEANING UP REMAINING PROCESSES
> >> = ? YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> >>
> >>
> =====================================================================================
> >> [proxy:0:1 at beowulf.node1] HYD_pmcd_pmip_control_cmd_cb
> >> (./pm/pmiserv/pmip_cb.c:927): assert (!closed) failed
> >> [proxy:0:1 at beowulf.node1] HYDT_dmxu_poll_wait_for_event
> >> (./tools/demux/demux_poll.c:77): callback returned error status
> >> [proxy:0:1 at beowulf.node1] main (./pm/pmiserv/pmip.c:221): demux engine
> >> error waiting for event
> >> [mpiexec at beowulf.master] HYDT_bscu_wait_for_completion
> >> (./tools/bootstrap/utils/bscu_wait.c:77): one of the processes
> terminated
> >> badly; aborting
> >> [mpiexec at beowulf.master] HYDT_bsci_wait_for_completion
> >> (./tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting
> >> for
> >> completion
> >> [mpiexec at beowulf.master] HYD_pmci_wait_for_completion
> >> (./pm/pmiserv/pmiserv_pmci.c:225): launcher returned error waiting for
> >> completion
> >> [mpiexec at beowulf.master] main (./ui/mpich/mpiexec.c:437): process
> manager
> >> error waiting for completion
> >> [root at beowulf testing]#
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL:
> >> <
> http://lists.mcs.anl.gov/pipermail/mpich-discuss/attachments/20120522/7b1db8c0/attachment-0001.html
> >
> >>
> >> ------------------------------
> >>
> >> Message: 3
> >> Date: Tue, 22 May 2012 03:36:44 +0800
> >> From: Darius Buntinas <buntinas at mcs.anl.gov>
> >> To: mpich-discuss at mcs.anl.gov
> >> Subject: Re: [mpich-discuss] Unable to run program parallely on
> >> ? ? ? ?cluster... ? ? ?Its running properly on single machine...
> >> Message-ID: <B411B6C1-CB5A-4A1C-AEBB-71680C9AF8C5 at mcs.anl.gov>
> >> Content-Type: text/plain; charset=us-ascii
> >>
> >> It may be that one of your processes is failing, but also check to make
> >> sure every process is calling MPI_Finalize before exiting.
> >>
> >> -d
> >>
> >> On May 22, 2012, at 2:42 AM, Albert Spade wrote:
> >>
> >> > Hi everybody,
> >> >
> >> > I am using mpich2-1.4.1p1 and mpiexec from hydra-1.5b1
> >> > I have a cluster of 5 machines.
> >> > When I am trying to run the program for parallel fast fourier
> transform
> >> > on single machine it runs correctly but on a cluster it gives error.
> >> > Can you please tell me why its happening.
> >> >
> >> > Thanks.
> >> >
> >> > Here is my sample output:
> >> >
> >> >
> ---------------------------------------------------------------------------------------
> >> >
> >> > [root at beowulf programs]# mpiexec -n 1 ./Radix2
> >> > Time taken for 16 elements using 1 processors = 2.7895e-05 seconds
> >> > [root at beowulf programs]#
> >> > [root at beowulf programs]# mpiexec -n 4 ./Radix2
> >> > [mpiexec at beowulf.master] control_cb (./pm/pmiserv/pmiserv_cb.c:197):
> >> > assert (!closed) failed
> >> > [mpiexec at beowulf.master] HYDT_dmxu_poll_wait_for_event
> >> > (./tools/demux/demux_poll.c:77): callback returned error status
> >> > [mpiexec at beowulf.master] HYD_pmci_wait_for_completion
> >> > (./pm/pmiserv/pmiserv_pmci.c:205): error waiting for event
> >> > [mpiexec at beowulf.master] main (./ui/mpich/mpiexec.c:437): process
> >> > manager error waiting for completion
> >> > [root at beowulf programs]# mpiexec -n 2 ./Radix2
> >> > [mpiexec at beowulf.master] control_cb (./pm/pmiserv/pmiserv_cb.c:197):
> >> > assert (!closed) failed
> >> > [mpiexec at beowulf.master] HYDT_dmxu_poll_wait_for_event
> >> > (./tools/demux/demux_poll.c:77): callback returned error status
> >> > [mpiexec at beowulf.master] HYD_pmci_wait_for_completion
> >> > (./pm/pmiserv/pmiserv_pmci.c:205): error waiting for event
> >> > [mpiexec at beowulf.master] main (./ui/mpich/mpiexec.c:437): process
> >> > manager error waiting for completion
> >> > [root at beowulf programs]# mpiexec -n 4 ./Radix2
> >> > [mpiexec at beowulf.master] control_cb (./pm/pmiserv/pmiserv_cb.c:197):
> >> > assert (!closed) failed
> >> > [mpiexec at beowulf.master] HYDT_dmxu_poll_wait_for_event
> >> > (./tools/demux/demux_poll.c:77): callback returned error status
> >> > [mpiexec at beowulf.master] HYD_pmci_wait_for_completion
> >> > (./pm/pmiserv/pmiserv_pmci.c:205): error waiting for event
> >> > [mpiexec at beowulf.master] main (./ui/mpich/mpiexec.c:437): process
> >> > manager error waiting for completion
> >> > [root at beowulf programs]#
> >> > _______________________________________________
> >> > mpich-discuss mailing list ? ? mpich-discuss at mcs.anl.gov
> >> > To manage subscription options or unsubscribe:
> >> > https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
> >>
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 4
> >> Date: Mon, 21 May 2012 20:14:35 -0500
> >> From: Rajeev Thakur <thakur at mcs.anl.gov>
> >> To: mpich-discuss at mcs.anl.gov
> >> Subject: Re: [mpich-discuss] Not able to run program parallely on
> >> ? ? ? ?cluster...
> >> Message-ID: <8C80534E-3611-40D7-BBAF-F66110D25EE1 at mcs.anl.gov>
> >> Content-Type: text/plain; charset=us-ascii
> >>
> >> You are passing the same buffer as the sendbuf and recvbuf to
> MPI_Gatherv,
> >> which is not allowed in MPI. Use MPI_IN_PLACE as described in the
> standard.
> >>
> >>
> >> On May 21, 2012, at 2:29 PM, Albert Spade wrote:
> >>
> >> > This is my new error after making few changes...
> >> > Results are quite similar... No succes with cluster...
> >> >
> >> > Sample run
> >> > --------------------------------------------------------
> >> >
> >> > [root at beowulf testing]# mpiexec -n 1 ./Radix
> >> > Time taken for 16 elements using 1 processors = 4.72069e-05 seconds
> >> > [root at beowulf testing]# mpiexec -n 2 ./Radix
> >> > Fatal error in PMPI_Gatherv: Internal MPI error!, error stack:
> >> > PMPI_Gatherv(398).....: MPI_Gatherv failed(sbuf=0x97d0500, scount=64,
> >> > MPI_CHAR, rbuf=0x97d0500, rcnts=0x97d06b8, displs=0x97d06c8, MPI_CHAR,
> >> > root=0, MPI_COMM_WORLD) failed
> >> > MPIR_Gatherv_impl(210):
> >> > MPIR_Gatherv(104).....:
> >> > MPIR_Localcopy(357)...: memcpy arguments alias each other,
> dst=0x97d0500
> >> > src=0x97d0500 len=64
> >> >
> >> >
> =====================================================================================
> >> > = ? BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> >> > = ? EXIT CODE: 256
> >> > = ? CLEANING UP REMAINING PROCESSES
> >> > = ? YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> >> >
> >> >
> =====================================================================================
> >> > [proxy:0:1 at beowulf.node1] HYD_pmcd_pmip_control_cmd_cb
> >> > (./pm/pmiserv/pmip_cb.c:927): assert (!closed) failed
> >> > [proxy:0:1 at beowulf.node1] HYDT_dmxu_poll_wait_for_event
> >> > (./tools/demux/demux_poll.c:77): callback returned error status
> >> > [proxy:0:1 at beowulf.node1] main (./pm/pmiserv/pmip.c:221): demux
> engine
> >> > error waiting for event
> >> > [mpiexec at beowulf.master] HYDT_bscu_wait_for_completion
> >> > (./tools/bootstrap/utils/bscu_wait.c:77): one of the processes
> terminated
> >> > badly; aborting
> >> > [mpiexec at beowulf.master] HYDT_bsci_wait_for_completion
> >> > (./tools/bootstrap/src/bsci_wait.c:23): launcher returned error
> waiting for
> >> > completion
> >> > [mpiexec at beowulf.master] HYD_pmci_wait_for_completion
> >> > (./pm/pmiserv/pmiserv_pmci.c:225): launcher returned error waiting for
> >> > completion
> >> > [mpiexec at beowulf.master] main (./ui/mpich/mpiexec.c:437): process
> >> > manager error waiting for completion
> >> > [root at beowulf testing]#
> >> >
>
>
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