bug?
>>> >>
>>> >> Is there any multicast or N to N broadcast where sender processes can
>>> >> avoid participating when they don’t need to?
>>> >>
>>> >> Thanks in advance
>>> >> Randolph
>>> >>
>>> >>
>>> >>
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>>> >
>>>
>>> --
>>> Sent from my mobile device
>>>
>>> David Zhang
>>> University of California, San Diego
>>>
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(I'll say that OMPI's ALLGATHER algorithm is probably not well optimized for
massive data transfers like you describe)
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On Aug 11, 2010, at 9:54 AM, Jeff Squyres wrote:
> (I'll say that OMPI's ALLGATHER algorithm is probably not well optimized for
> massive data transfers like you describe)
Wrong wrong wrong -- I should have checked the code before sending. I made the
incorrect assumption that OMPI stil
gorithms allow themselves to be used (e.g., O(N) may not matter if
there's a small number of peers with small messages).
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P963 -- 2455 South Road -- Poughkeepsie, NY 12601
> > Tele (845) 433-7846 Fax (845) 433-8363
> >
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loading shared libraries: libmpi.so.0: cannot open
> shared object file: No such file or directory
>
>
>
> Thanks for any help.
> Best regards,
> Sunita
>
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t have their
coredumpsize automatically reset to 0, etc.
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il thread, it's not entirely clear: are you calling abort()
or MPI_Abort()? MPI_Abort() won't drop a core file. abort() should.
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>>>>>>>> parallel computation involving the openib btl and
> > > > >>>>>>>> OpenMPI-1.4.2 (the same issue can be observed with
> > > > >>>>>>>> OpenMPI-1.3.3).
> > > > >>>>>>>>
> > > > >>>>>>>>mpirun (Open MPI) 1.4.2
> > > > >>>>>>>>Report bugs to http://www.open-mpi.org/community/help/
> > > > >>>>>>>>[pbn08:02624] *** Process received signal ***
> > > > >>>>>>>>[pbn08:02624] Signal: Segmentation fault (11)
> > > > >>>>>>>>[pbn08:02624] Signal code: Address not mapped (1)
> > > > >>>>>>>>[pbn08:02624] Failing at address: (nil)
> > > > >>>>>>>>[pbn08:02624] [ 0] /lib64/libpthread.so.0 [0x349540e4c0]
> > > > >>>>>>>>[pbn08:02624] *** End of error message ***
> > > > >>>>>>>>sh: line 1: 2624 Segmentation fault
> > > > >>>>>>>>
> > > > >>>>>>>> \/share\/hpc3\/actran_suite\/Actran_11\.0\.rc2\.41872\/RedHatE
> > > > >>>>>>>> L\ -5 \/ x 86 _6 4\ /bin\/actranpy_mp
> > > > >>>>>>>> '--apl=/share/hpc3/actran_suite/Actran_11.0.rc2.41872/RedHatEL
> > > > >>>>>>>> -5 /x 86 _ 64 /A c tran_11.0.rc2.41872'
> > > > >>>>>>>> '--inputfile=/work/st25652/LSF_130073_0_47696_0/Case1_3Dreal_m
> > > > >>>>>>>> 4_ n2 .d a t'
> > > > >>>>>>>> '--scratch=/scratch/st25652/LSF_130073_0_47696_0/scratch'
> > > > >>>>>>>> '--mem=3200' '--threads=1' '--errorlevel=FATAL' '--t_max=0.1'
> > > > >>>>>>>> '--parallel=domain'
> > > > >>>>>>>>
> > > > >>>>>>>> If I choose not to use the openib btl (by using --mca btl
> > > > >>>>>>>> self,sm,tcp on the command line, for instance), I don't
> > > > >>>>>>>> encounter any problem and the parallel computation runs
> > > > >>>>>>>> flawlessly.
> > > > >>>>>>>>
> > > > >>>>>>>> I would like to get some help to be able:
> > > > >>>>>>>> - to diagnose the issue I'm facing with the openib btl
> > > > >>>>>>>> - understand why this issue is observed only when using the
> > > > >>>>>>>> openib btl and not when using self,sm,tcp
> > > > >>>>>>>>
> > > > >>>>>>>> Any help would be very much appreciated.
> > > > >>>>>>>>
> > > > >>>>>>>> The outputs of ompi_info and the configure scripts of OpenMPI
> > > > >>>>>>>> are enclosed to this email, and some information on the
> > > > >>>>>>>> infiniband drivers as well.
> > > > >>>>>>>>
> > > > >>>>>>>> Here is the command line used when launching a parallel
> > > > >>>>>>>> computation
> > > > >>>>>>>>
> > > > >>>>>>>> using infiniband:
> > > > >>>>>>>>path_to_openmpi/bin/mpirun -np $NPROCESS --hostfile
> > > > >>>>>>>>host.list --mca
> > > > >>>>>>>>
> > > > >>>>>>>> btl openib,sm,self,tcp --display-map --verbose --version
> > > > >>>>>>>> --mca mpi_warn_on_fork 0 --mca btl_openib_want_fork_support 0
> > > > >>>>>>>> [...]
> > > > >>>>>>>>
> > > > >>>>>>>> and the command line used if not using infiniband:
> > > > >>>>>>>>path_to_openmpi/bin/mpirun -np $NPROCESS --hostfile
> > > > >>>>>>>>host.list --mca
> > > > >>>>>>>>
> > > > >>>>>>>> btl self,sm,tcp --display-map --verbose --version --mca
> > > > >>>>>>>> mpi_warn_on_fork 0 --mca btl_openib_want_fork_support 0 [...]
> > > > >>>>>>>>
> > > > >>>>>>>> Thanks,
> > > > >>>>>>>> Eloi
> > > > >>>>>>
> > > > >>>>>> ___
> > > > >>>>>> users mailing list
> > > > >>>>>> us...@open-mpi.org
> > > > >>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
> --
>
>
> Eloi Gaudry
>
> Free Field Technologies
> Company Website: http://www.fft.be
> Company Phone: +32 10 487 959
>
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he entire MPI job. abort() drops core when I'm running
> on 1 processor, but not in a multiprocessor run. In addition, a node
> calling abort() doesn't lead to the entire run being killed off.
>
> David
> O
> n Mon, 2010-08-16 at 08:51 -0700, Jeff Squyres wrote:
>> On Aug 13,
ies.c:179:
> restoreTL: Assertion `n >= 0 && n < rl->max' failed. "
>
> Any help is appreciated,
>
> Thanks,
>
> --
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>
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suggestions, it would be appreciated.
>> Many thanks.
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not believe that the IB/iWARP vendors have cleaned up the openib BTL much
in this regard recently. But then again, we branched for v1.3 a long time ago,
so I don't remember offhand if any valgrind cleanups occurred since then...
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ashes.
>
> Is this a known issue? I found related problem (of around May, 2010) when
> people were using the same option but in a SLURM environment.
>
> regards
>
> Michael
>
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> Tel: +49 241/80-24915
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> us...
gt; |>
>> |> but it failed. I am attaching the configure and make logs.
>> |>
>> |> regards
>> |>
>> |> Michael
>> |>
>> |>
>> |> On 08/23/10 20:53, Ralph Castain wrote:
>> |>>
>> |>&g
ariable. i.e. 10GigE might be eth0 on one and
> eth2 on the next. In case this matters. I was told this shouldn't be
> an issue.
Are all the eth0's on one subnet and all the eth2's on a different subnet?
Or are all eth0's and eth2's all on the same subnet?
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all 1GigE's are on 10.0.x.x
It would simplify testing if you could get all the eth0's to be of one type and
on the same subnet, and the same for eth1.
Once you do that, try using just one of the networks by telling OMPI to use
only one of the devices, something like this:
mpirun --mca btl_tcp_if
se then your is safe for both C and
C++, and you keep contained inside it (assumedly preserving some
abstraction barriers in your code by keeping the MPI prototypes bundled with
).
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a long time but never implemented.
Are your jobs hanging because of deadlock (i.e., application error), or
infrastructure error? If they're hanging because of deadlock, there are some
PMPI-based tools that might be able to help.
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easiest / least total time spent to just build another copy of OMPI against
10.8. :-\
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>> > > > > > > ___
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>>>
>> -- next part --
>> HTML attachment scrubbed and removed
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>
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, argv=0x7fffe008)
> at test.c:4
>
> I can't figure out what's going on here! It says MPI_Init is segfaulting, but
> I think it is probably some kind of misconfiguration.
> I have tried reinstalling the openmpi package. I have an AMD Turion X2
> M500(64 bit) process
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t-to-point
functions (MPI_SEND and the like). They may *also* act as the lowest layers
for all of the collective functions. Some collective algorithms call MPI_SEND
to do their individual sends, for example. Others may invoke BTL send/receive
functions directly. Others don't use the BTLs at all.
-
as to enable automatic path migration over
> lmc, but this is only for failover, if I remember rightly.
>
> Regards,
> Jens
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PI 1.4.2 is built with GCC (GCC 4.1.2).
> No problems are found with Open MPI 1.2.6 and PathScale either.
>
> Best regards,
>
> Rafa
>
> --
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>
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uld be welcome! :-)
I believe that the first step would be to get some assembly for the ARM
platform for some of OMPI's key routines (locks, atomics, etc.). Beyond that,
it *might* "just work"...?
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matter), you may not see much difference.
That being said, if you were watching OMPI's behavior with regard to LIDs and
only saw the base LIDs go by, then perhaps something is wrong. Shrug.
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ne
> to know the specifics.
FWIW: here's a brief writeup of MPI_Ibarrier -
http://blogs.cisco.com/ciscotalk/performance/comments/ibarrier/
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does, relax, have a beer^H^H^H^Hnon-cafinated tea
- if it does not work, you may have to go the recompile-everything route
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erious ways (e.g., if a
struct changed size somewhere that OMPI uses to interact with the system, then
it may work in some cases and may fail in other seemingly unrelated cases.
Such things are a total bugger to track down).
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puts (mystring);
> }
> pclose (pFile);
>}
> }
>
> MPI_Finalize();
>return 0;
> }
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Yes, the built-in GCC atomics might work. I don't know if anyone has tried
them; they would be most useful because they would allow us to use multiple
different platforms.
Patches would definitely be appreciated here.
On Sep 22, 2010, at 12:25 PM, Dave Love wrote:
> Jeff Squyres <
that will do all the same things
that MPI_SEND does: eager sends for short messages, striping across multiple
devices, using RDMA when appropriate, etc.
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>
> On Wed, 2010-09-22 at 14:54 +0200, Ake Sandgren wrote:
>> On Wed, 2010-09-22 at 14:16 +0200, Ake Sandgren wrote:
>>> On Wed, 2010-09-22 at 07:42 -0400, Jeff Squyres wrote:
>>>> This is a problem with the Pathscale compiler and old versions of
>> GCC. See:
>&
on-blocking collectives on a
single communicator -- it doesn't matter if they are the same or different
collective operations. They will each be unique instances and will be satisfied
in order.
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1:
MPI_IBcast(MPI_COMM_WORLD, request_2) // first Bcast
MPI_IBcast(MPI_COMM_WORLD, request_1) // second Bcast
MPI_Wait(_1, ...);
MPI_Wait(_2, ...);
That may/will deadlock.
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t;
> ( I don't think these information are relevant here, but just in case: I am
> using openMPI 1.4.2, on a Mandriva 2008 system )
>
> Thanks in advance for any help/info/advice.
>
> Olivier
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uses hwloc internally, but you could also link your application
against hwloc and call its C functions to get information about your process'
locality, etc.
On Sep 24, 2010, at 8:14 AM, Jeff Squyres wrote:
> On the OMPI SVN trunk, we have an "Open MPI extension" call named
> O
On Sep 23, 2010, at 1:24 PM, Ken Mighell wrote:
> Would a hack written in C suffice?
Assembly is always better, but C should be fine. If you really want to, could
you write it in C and have the compiler generate optimized assembly for you.
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0D
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trip these from the command.
This might well be directly related to the version of Libtool that HDF
bootstraps their build process with -- you really should talk to them.
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nd.
Strange.
Be sure to see: http://www.open-mpi.org/faq/?category=mpi-apps#cant-use-wrappers
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's not too much that
OMPI can do there.
The heterogeneous flag is more traditionally used for endian flipping kinds of
things.
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e I think we have done basic testing to ensure
this stuff works, but it is used so infrequently (in reality, most people don't
mix and match too often) that we don't stress test it, nor do we test it in
exotic environments.
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On Oct 8, 2010, at 2:21 PM, Jeff Squyres wrote:
> No. Open MPI does not have MPD -- I think you're thinking of a different MPI
> implementation. :-)
Someone pointed out to me off-list that I wasn't quite clear here...
*If* all of your architectures are the same endian and oth
s doing this
>> from the glut display call back causing the problem? Any suggestions would
>> be greatly appreciated.
>> Thanks,
>> Ed
>>
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>
>
roblem was but it wasn't the called to MPI_Send
> blocking.
> Ed
>
>
> From: users-boun...@open-mpi.org on behalf of Jeff Squyres
> Sent: Tue 10/12/2010 6:52 AM
> To: Open MPI Users
> Subject: Re: [OMPI users] nonblocking send/receive question
>
> On Oct 11, 2010, at 1
er, PACKBUFFER_SIZE, , MPI_COMM_WORLD);
> MPI_PACK(data->subData3->data1, sizeof(data->subDat2->data1), MPI_FLOAT,
> packBuffer, PACKBUFFER_SIZE, , MPI_COMM_WORLD);
> MPI_Send(packBuffer, packSize, MPI_PACKED, 1, 100, , MPI_COMM_WORLD);
>
> Ed
>
>
>
> root process and a "root" parameter name (which doesn't exist for
> MPI_Allreduce). Should I add this to Trac?
>
> -- Jeremiah Willcock
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tion* that the
process will never move and might be able to use the native x86 timer (there's
some complications here, but we might be able to figure it out). Bad Things
could happen if the process ever moved, though (e.g., if the application ever
manually changed the binding).
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j
have
> found had to do with different version of OpenMPI installed, but I only have
> one version, and I believe it is the one being used.
>
> Thank you,
> Kalin
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going through the pain right now of upgrading to Autoconf 2.68 /
Libtool 2.4; hopefully we'll have fixes on the trunk RSN for the
newest-of-the-new autotools.
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explicitly listed in the link line, which should contain MPI_Abort. Can you nm
on that file and ensure that it is actually listed there?
VT guys -- any ideas here?
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On Oct 14, 2010, at 5:38 PM, Jed Brown wrote:
> $ nm -D
> /home/jed/src/openmpi-1.5/bclang/ompi/contrib/vt/vt/../../../.libs/libmpi.so
> |grep MPI_Abort
> 00074380 T PMPI_Abort
>
> In contrast, with gcc:
>
> $ nm -D
>
d-to-self case, but it should perform well.
You might want to benchmark memcpy vs. MPI_Sendrecv() to self (for example) and
see if there's a noticeable difference.
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iting MPI programs
> in Fortran90.
>From my understanding of Fortran, that would violate the MPI spec.
You could, I think, use an array subsection when you call MPI_STARALL that
would give you a 1D array of integers, right?
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mo' betta than the
existing MPI F90 bindings. We plan to prototype the F08 module in OMPI when we
finish specifying it in the Forum, and revamp the F90 support in OMPI at
more-or-less the same time.
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the rendered text.
>
> -- Jeremiah Willcock
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rogram-suffix or --program-transform-name. Users
> are recommended to instead use --prefix with a unique directory and make
> symbolic links as desired for renaming." >&2;}
>
> If I remove the new control on --program-prefix in openmpi-1.5 configure
> script, the 1.5 build
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pty machines?
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.
>
> --td
>
>
> On 10/21/2010 06:47 AM, Terry Dontje wrote:
>> On 10/21/2010 06:43 AM, Jeff Squyres (jsquyres) wrote:
>>> Also, i'm not entirely sure what all the commands are that you are showing.
>>> Some of those warnings (eg in config.log) are normal.
>
code A seems to run faster. I do have a
> lot of communications in code B too. It involves 500 procs. I had thought
> code B should have no effect on the time spent on code A if I use MPI_Barrier.
>
> Linbao
> On Thu, Oct 21, 2010 at 5:17 AM, Jeff Squyres <jsquy...@cisco.com>
erence to 'MPI::Datatype::Free()'
>
> So could I get some help? Thanks!
>
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For co
s the possible reason ?
>
>
> Any help is appreciated.
>
> thanks
>
> jack
>
> Oct. 22 1010
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a little suspect of what you sent already (e.g., you didn't
include the waitall, which is kinda important :-) ).
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t the ZOMBIE_PID ?
>
> "ps" from the command line, or getpid() from C code.
>
> Jed
>
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> __
> > > better in a non-interactive environment.
> > >
> > > Where should I put the (gdb --batch -ex 'bt full' -ex 'info reg' -pid
> > > ZOMBIE_PID) in the script ?
> > >
> > > Is control returning to your script after rank 0 has exited? In
elp would be greatly
> regarded, since I'm supposed to meet a deadline, and half of my semester has
> been spent trying to get either LAM-MPI or Open MPI (which I was suggested I
> shift to) to work.
> Thank you very much.
>
> Regards,
> Saahil___
> =NwEP
> -END PGP SIGNATURE-
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and libmpi.so from
v1.4.3 on other nodes). This is absolutely not guaranteed to work -- we don't
even try to maintain this kind of compatibility.
Does that make sense?
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not CXXFLAGS to the configure script?
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On Nov 2, 2010, at 4:57 AM, jody wrote:
> So i guess the basic question is:
> is it permitted to rename openMPI installations, and if yes how is
> this porperly done (since a simple mv doesn't work)
Yes: http://www.open-mpi.org/faq/?category=building#installdirs
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**
> ** This warning was added by the IU Computer Science Dept. mail scanner. **
> *
>
>
>
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ssions about this topic, but have never really addressed it
-- the need for low latency has been greater than the need for
blocking/not-consuming-CPU progress.
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to proceed? (the specific version of openmpi in
>> this case is the one available for download on Nov 2 from the main
>> website; obtained via the src.rpm download)
>> --Jim
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hem. But seriously, I try to use printf's for
only truly trivial things; I use various kinds of debugging tools for
everything else (e.g., I'll frequently use gdb to examine corefiles and/or
attach to individual processes in parallel jobs to do heavy-lifting debugging).
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f OpenMPI, and it seems to correctly support my
> existing software.
>
> So, now for my question:
>
> Should FCFLAGS show up on these links lines and, if so, how would I get
> 64-bit objects?
>
> Thanks,
>
> Brian Price
>
>
>
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nks,
>
> Brian Price
>
>
>
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parameter is not being set in cases of oversubscription,
> with or without an explicit hostfile.
>
> Jed
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d9c60 in PMPI_Send () from /home/gmaj/openmpi/lib/libmpi.so.0
> #8 0x0804e900 in main ()
> --
>
> If anybody knows what may cause this problem or what may I do to find
> the reason, any help is appreciated.
>
> My open-mpi is version 1.4.1.
>
>
> Regards,
> Grzegorz Maj
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>
>
> --
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> University of California, San Diego
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on both hosts (i.e., eth1 on hostA is
reachable by eth1 on hostB; ditto for eth2).
See the FAQ for more details on other ways of setting MCA parameters
(environment vars, files, etc.).
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s much better debug/error
messages, but I've never had the time to finish it (indeed, I think there's a
bug in that development branch right now, otherwise I'd recommend giving it a
whirl). :-\
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s on MPI-3.
http://sc10.supercomputing.org/schedule/event_detail.php?evid=bof122
Many other Open MPI organizations who will also have a presence at SC; be sure
to stop by their booths and say hello.
See you there!
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find what the error codes mean?
>
> Thanks,
> Ondrej Marsalek
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___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
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Total time: " << total_time << " secs\n"
> << "MPI_Test calls: " << time_res.size() << '\n'
> << std::fixed << std::setprecision(10)
> << "Average: " << average << &quo
e differnece between these two versions, or
> what affects the "SYSTEM CPU" and execution speed?
There shouldn't be any noticeable difference in performance between these
versions.
Assumedly you're running your tests on otherwise-idle machines. Is the
difference repeatable
e_options
> --with-tm=/opt/torque' --define '_name openmpi-gcc' openmpi-1.4.3.spec
Weird -- you're saying that *without* --enable-contrib-no-build=vt, the 1.4.3
SRPM fails to build?
Can you send the output from the rpmbuild command so that we can see the error?
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s...@selfip.ru>
> Selfip.Ru
>
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.obj) : error LNK2001: unresolved
> external symbol _MPI_Bcast@20
>
>
> is boostpro's mpi lib against openmpi or another MPI implementation?
>
>
> regards,
>
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You
should contact your IB vendor for assistance.
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PI
should do the Right Thing under the covers in this case.
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's just a mistake, please fix it in the next version.
>
> Regards,
> Tetsuya Mishima
>
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