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Subject: Re: [OMPI users] 50% performance reduction due to OpenMPI v 1.3.2forcing all MPI traffic over Ethernet instead of using Infiniband
From: Gus Correa (gus_at_[hidden])
Date: 2009-06-24 19:30:57


Hi Jim

Jim Kress ORG wrote:
> Hey Gus. I was correct.
>
> If I did:
>
> ./configure --prefix=/my/dir --with-openib=/usr --enable-static
> make all install
>
...
> Wrapper extra LIBS: -lrdmacm -libverbs -ldl
> -Wl,--export-dynamic -lnsl
> -lutil -lm -ldl
...
>
> Magically, -lrdmacm -libverbs appear.
>
>

Thank you for telling us!
I was too busylazy to try it once again myself.
I built OpenMPI a lot of times, different compilers,
versions, clusters ...

In any case, the ORCA mystery remains, which is rather unsettling.
Have you investigated Jeff's question on whether the code was
compiled/linked with the same OpenMPI version (1.3.2)?
I wonder if the underlying OFED libraries must be the same as well.

Gus
---------------------------------------------------------------------
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA
---------------------------------------------------------------------

Jim Kress ORG wrote:
> Hey Gus. I was correct.
>
> If I did:
>
> ./configure --prefix=/my/dir --with-openib=/usr --enable-static
> make all install
>
> then reboot and use mpi-selector to choose openmpi-1.3.2, and then:
>
> [root_at_master ~]# ompi_info --config
> Configured by: root
> Configured on: Wed Jun 24 18:02:03 EDT 2009
> Configure host: master.org
> Built by: root
> Built on: Wed Jun 24 18:17:29 EDT 2009
> Built host: master.org
> C bindings: yes
> C++ bindings: yes
> Fortran77 bindings: yes (all)
> Fortran90 bindings: yes
> Fortran90 bindings size: small
> C compiler: gcc
> C compiler absolute: /usr/bin/gcc
> C char size: 1
> C bool size: 1
> C short size: 2
> C int size: 4
> C long size: 8
> C float size: 4
> C double size: 8
> C pointer size: 8
> C char align: 1
> C bool align: 1
> C int align: 4
> C float align: 4
> C double align: 8
> C++ compiler: g++
> C++ compiler absolute: /usr/bin/g++
> Fortran77 compiler: gfortran
> Fortran77 compiler abs: /usr/bin/gfortran
> Fortran90 compiler: gfortran
> Fortran90 compiler abs: /usr/bin/gfortran
> Fort integer size: 4
> Fort logical size: 4
> Fort logical value true: 1
> Fort have integer1: yes
> Fort have integer2: yes
> Fort have integer4: yes
> Fort have integer8: yes
> Fort have integer16: no
> Fort have real4: yes
> Fort have real8: yes
> Fort have real16: no
> Fort have complex8: yes
> Fort have complex16: yes
> Fort have complex32: no
> Fort integer1 size: 1
> Fort integer2 size: 2
> Fort integer4 size: 4
> Fort integer8 size: 8
> Fort integer16 size: -1
> Fort real size: 4
> Fort real4 size: 4
> Fort real8 size: 8
> Fort real16 size: -1
> Fort dbl prec size: 4
> Fort cplx size: 4
> Fort dbl cplx size: 4
> Fort cplx8 size: 8
> Fort cplx16 size: 16
> Fort cplx32 size: -1
> Fort integer align: 4
> Fort integer1 align: 1
> Fort integer2 align: 2
> Fort integer4 align: 4
> Fort integer8 align: 8
> Fort integer16 align: -1
> Fort real align: 4
> Fort real4 align: 4
> Fort real8 align: 8
> Fort real16 align: -1
> Fort dbl prec align: 4
> Fort cplx align: 4
> Fort dbl cplx align: 4
> Fort cplx8 align: 4
> Fort cplx16 align: 8
> Fort cplx32 align: -1
> C profiling: yes
> C++ profiling: yes
> Fortran77 profiling: yes
> Fortran90 profiling: yes
> C++ exceptions: no
> Thread support: posix (mpi: no, progress: no)
> Sparse Groups: no
> Build CFLAGS: -O3 -DNDEBUG -finline-functions
> -fno-strict-aliasing
> -pthread -fvisibility=hidden
> Build CXXFLAGS: -O3 -DNDEBUG -finline-functions -pthread
> Build FFLAGS:
> Build FCFLAGS:
> Build LDFLAGS: -export-dynamic
> Build LIBS: -lnsl -lutil -lm
> Wrapper extra CFLAGS: -pthread
> Wrapper extra CXXFLAGS: -pthread
> Wrapper extra FFLAGS: -pthread
> Wrapper extra FCFLAGS: -pthread
> Wrapper extra LDFLAGS:
> Wrapper extra LIBS: -lrdmacm -libverbs -ldl
> -Wl,--export-dynamic -lnsl
> -lutil -lm -ldl
> Internal debug support: no
> MPI parameter check: runtime
> Memory profiling support: no
> Memory debugging support: no
> libltdl support: yes
> Heterogeneous support: no
> mpirun default --prefix: no
> MPI I/O support: yes
> MPI_WTIME support: gettimeofday
> Symbol visibility support: yes
> FT Checkpoint support: no (checkpoint thread: no)
> [root_at_master ~]#
>
>
> Magically, -lrdmacm -libverbs appear.
>
> Well, that's one mystery solved.
>
> Thanks for your help.
>
> Jim
>
>
>
>
>
> On Wed, 2009-06-24 at 17:22 -0400, Gus Correa wrote:
>> Hi Jim
>>
>>
>> Jim Kress wrote:
>> > Noam, Gus and List,
>> >
>> > Did you statically link your openmpi when you built it? If you did (the
>> > default is NOT to do this) then that could explain the discrepancy.
>> >
>> > Jim
>>
>> No, I didn't link statically.
>>
>> Did you link statically?
>>
>> Actually, I tried to do it, and it didn't work.
>> I wouldn't get OpenMPI with IB if I tried to
>> link statically (i.e. by passing -static or equivalent to CFLAGS,
>> FFLAGS, etc).
>> When I removed the "-static" I got OpenMPI with IB.
>> I always dump the configure output (and the make output, etc) to
>> log files to check these things out after it is done.
>> I really suggest you do this, it pays off, saves time, costs nothing.
>> I don't remember exactly what symptoms I found on the log,
>> whether the log definitely said that there was no IB support,
>> or if it didn't have the right flags (-libverbs, etc) like yours.
>> However, when I suppressed the "-static" from the compiler flags
>> then I've got all the IB goodies! :)
>>
>> Here is how I run configure (CFLAGS etc only have optimization flags,
>> no "-static"):
>>
>> ./configure \
>> --prefix=/my/directory \
>> --with-libnuma=/usr \
>> --with-tm=/usr \
>> --with-openib=/usr \
>> --enable-static \
>> 2>&1 configure.log
>>
>> Note, "--enable-static" means OpenMPI will build static libraries
>> (besides the shared ones).
>> OpenMPI is not being linked statically to system libraries,
>> or to IB libraries, etc.
>>
>> Some switches may not be needed,
>> in particularly the explicit use of /usr directory.
>> However, at some point the OpenMPI configure
>> would not work without being
>> told this (at least for libnuma).
>>
>> BTW, I didn't claim your OpenMPI doesn't have IB support.
>> Not a categorical syllogism like
>> "you don't have the -libverbs flag, hence you don't have IB".
>> It is hard to make definitive statements like this
>> in a complex environment like this (OpenMPI build, parallel programs),
>> and with limited information via email.
>> After all, the list is peer reviewed! :)
>> Hence, I only guessed, as I usually do in these exchanges.
>> However, considering all the trouble you've been through, who knows,
>> maybe it was a guess in the right direction.
>>
>> I wonder if there may still be a glitch in the OpenMPI configure
>> script, on how it searches for and uses libraries like IB, NUMA, etc,
>> which may be causing the problem.
>> Jeff: Is this possible?
>>
>> In any case, we have different "Wrapper extra LIBS".
>> I have -lrdmacm -libverbs, you and Noam don't have them.
>> (Noam: I am not saying you don't have IB support! :))
>> My configure explicitly asks for ib support, Noam's (and maybe yours)
>> doesn't.
>> Somehow, slight differences in how one invokes
>> the configure script seems to produce different results.
>>
>> I hope this helps,
>> Gus Correa
>> ---------------------------------------------------------------------
>> Gustavo Correa
>> Lamont-Doherty Earth Observatory - Columbia University
>> Palisades, NY, 10964-8000 - USA
>> ---------------------------------------------------------------------
>>>> -----Original Message-----
>>>> From: users-bounces_at_[hidden]
>>>> [mailto:users-bounces_at_[hidden]] On Behalf Of Noam Bernstein
>>>> Sent: Wednesday, June 24, 2009 9:38 AM
>>>> To: Open MPI Users
>>>> Subject: Re: [OMPI users] 50% performance reduction due to
>>>> OpenMPI v 1.3.2forcing all MPI traffic over Ethernet instead
>>>> of using Infiniband
>>>>
>>>>
>>>> On Jun 23, 2009, at 6:19 PM, Gus Correa wrote:
>>>>
>>>>> Hi Jim, list
>>>>>
>>>>> On my OpenMPI 1.3.2 ompi_info -config gives:
>>>>>
>>>>> Wrapper extra LIBS: -lrdmacm -libverbs -ltorque -lnuma -ldl -Wl,--
>>>>> export-dynamic -lnsl -lutil -lm -ldl
>>>>>
>>>>> Yours doesn't seem to have the IB libraries: -lrdmacm -libverbs
>>>>>
>>>>> So, I would guess your OpenMPI 1.3.2 build doesn't have IB support.
>>>> The second of these statements doesn't follow from the first.
>>>>
>>>> My "ompi_info -config" returns
>>>>
>>>> ompi_info -config | grep LIBS
>>>> Build LIBS: -lnsl -lutil -lm
>>>> Wrapper extra LIBS: -ldl -Wl,--export-dynamic
>>>> -lnsl -lutil -
>>>> lm -ldl
>>>>
>>>> But it does have openib
>>>>
>>>> ompi_info | grep openib
>>>> MCA btl: openib (MCA v2.0, API v2.0,
>>>> Component v1.3.2)
>>>>
>>>> and osu_bibw returns
>>>>
>>>> # OSU MPI Bi-Directional Bandwidth Test v3.0
>>>> # Size Bi-Bandwidth (MB/s)
>>>> 4194304 1717.43
>>>>
>>>> which it's sure not getting over ethernet. I think Jeff
>>>> Squyres' test (ompi_info | grep openib) must be more definitive.
>>>>
>>>>
>>>> Noam
>>>> _______________________________________________
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>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
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