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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: Jim Kress ORG (jimkress_58_at_[hidden])
Date: 2009-06-24 20:18:47


> 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.

I was told that 1.3.2 was used. However, I have not asked about which
OFED libraries were used nor have I asked about the use of
--enable-static for their 1.3.2 configurations.

I will have to follow-up on that.

Jim

On Wed, 2009-06-24 at 19:30 -0400, Gus Correa wrote:
> 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
> >>>> _______________________________________________
> >>>> users mailing list
> >>>> users_at_[hidden]
> >>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >>> _______________________________________________
> >>> users mailing list
> >>> users_at_[hidden]
> >>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >> _______________________________________________
> >> users mailing list
> >> users_at_[hidden]
> >> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >
> > _______________________________________________
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>
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