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Subject: Re: [OMPI users] OpenMPI-ROMIO-OrangeFS
From: Edgar Gabriel (gabriel_at_[hidden])
Date: 2014-02-26 15:07:22


not sure whether its the problem or not, but usually have an additional
flag set :

 --with-io-romio-flags="--with-file-system=pvfs2+ufs+nfs
--with-pvfs2=/opt/pvfs-2.8.2"

compilation is a bit slow for me today...

Edgar

On 2/26/2014 2:05 PM, vithanousek wrote:
> Now I compiled by doing this:
> OrangeFS (original, withou editing):
>
> ./configure --prefix=/usr/local/orangefs
> --with-kernel=/usr/src/kernels/2.6.32-431.5.1.el6.x86_64
> --with-openib=/usr --without-bmi-tcp --enable-shared
> make
> make kmod
> make install
> make kmod_install
>
> Without error.
> OpenMPI (with edited switch to ifs):
>
> ./configure --prefix=/usr/local/openmpi_1.6.5_romio
> --with-io-romio-flags='--with-pvfs2=/usr/local/orangefs'
> make
> make install
>
> Without error.
> parallel FS mount work. But I still cant use MPIIO.
> I compiled simple MPIIO program and run it by this:
>
> mpicc -o mpiio mpiio.c
> mpirun -np 1 -host node18 mpiio
> [node18:02334] mca: base: component_find: unable to open
> /usr/local/openmpi_1.6.5_romio/lib/openmpi/mca_io_romio:
> /usr/local/openmpi_1.6.5_romio/lib/openmpi/mca_io_romio.so: undefined
> symbol: ADIOI_PVFS2_IReadContig (ignored)
>
> And no file is created.
> I tried compile it with:
> mpicc -o mpiio mpiio.c -lpvfs2 -L/usr/local/orangefs/lib
>
> but i got the same results, have You any idea?
>
> Thank for reply
> Hanousek Vít
>
>
>
>
>
> ---------- Původní zpráva ----------
> Od: vithanousek <vithanousek_at_[hidden]>
> Komu: Open MPI Users <users_at_[hidden]>
> Datum: 26. 2. 2014 20:30:17
> Předmět: Re: [OMPI users] OpenMPI-ROMIO-OrangeFS
>
>
> Thanks for your Time,
>
> I'm little bit confused, what is diferent between pvfs2 and
> orangefs. I was thinking, that only project changes name.
>
> I get hint from OrangeFS maillist, to compile OrangeFs with
> --enable-shared. This produce a some shared library (.so) in
> /usr/local/orangefs/lib and I can compile OpenMPI 1.6.5 now (with
> fixed "switch =>ifs" in ROMIO).
>
> I will test if it is working in next hour (some configuration steps
> is needed).
>
> Thanks.
> Hanousek Vít
>
> ---------- Původní zpráva ----------
> Od: Edgar Gabriel <gabriel_at_[hidden]>
> Komu: Open MPI Users <users_at_[hidden]>
> Datum: 26. 2. 2014 20:18:03
> Předmět: Re: [OMPI users] OpenMPI-ROMIO-OrangeFS
>
>
> so we had ROMIO working with PVFS2 (not OrangeFS, which is however
> registered as PVFS2 internally). We have one cluster which uses
> OrangeFS, on that machine however we used OMPIO, not ROMIO. I am
> currently compiling the 1.6 version of Open MPI to see whether I can
> reproduce your problem.
>
> Thanks
> Edgar
>
> On 2/26/2014 12:23 PM, vithanousek wrote:
> > Thanks for reply,
> >
> > Is it possible that the patch solvs all this problems, not
> only "switch
> > => ifs" problem?
> > I realy dont know, wher the problem is now (OpenMPI, ROMIO,
> OrangeFS).
> >
> > Thanks
> > Hanousek Vít
> >
> > ---------- Původní zpráva ----------
> > Od: Ralph Castain <rhc_at_[hidden]>
> > Komu: Open MPI Users <users_at_[hidden]>
> > Datum: 26. 2. 2014 19:16:36
> > Předmět: Re: [OMPI users] OpenMPI-ROMIO-OrangeFS
> >
> >
> > Edgar hasn't had a chance to find the necessary patch - he was on
> > travel, returning soon.
> >
> >
> > On Feb 26, 2014, at 9:27 AM, vithanousek
> <vithanousek_at_[hidden]> wrote:
> >
> > > Hello,
> > >
> > > I have still problems with compiling OpenMPI 1.6.5 with OrangeFS
> > 2.8.7 support.
> > >
> > > I compiled OrangeFS by this:
> > >
> > > ./configure --prefix=/usr/local/orangefs2
> > --with-kernel=/usr/src/kernels/2.6.32-431.5.1.el6.x86_64
> > --with-openib=/usr --without-bmi-tcp
> > > make -j 32
> > > make -j 32 kmod
> > > make install
> > > make kmod_install
> > >
> > > this works.
> > > than I tried to compile OpenMPI (with fixed convert_named
> function
> > in ad_pvfs2_io_dtype.c) by this:
> > >
> > > ./configure --prefix=/usr/local/openmpi_1.6.5_romio2
> > --with-io-romio-flags='--with-pvfs2=/usr/local/orangefs2'
> > > (...)
> > > make -j32
> > > (...)
> > > CCLD mca_io_romio.la
> > > /usr/bin/ld:
> /usr/local/orangefs2/lib/libpvfs2.a(errno-mapping.o):
> > relocation R_X86_64_32S against `PINT_errno_mapping' can not
> be used
> > when making a shared object; recompile with -fPIC
> > > /usr/local/orangefs2/lib/libpvfs2.a: could not read symbols:
> Bad value
> > > collect2: ld returned 1 exit status
> > > make[3]: *** [mca_io_romio.la] Error 1
> > >
> > > So I tried recompile OrangeFS by this:
> > >
> > > export CFLAGS="-fPIC"
> > > ./configure --prefix=/usr/local/orangefs2
> > --with-kernel=/usr/src/kernels/2.6.32-431.5.1.el6.x86_64
> > --with-openib=/usr --without-bmi-tcp
> > > make -j 32
> > > make -j 32 kmod
> > > make install
> > > make kmod_install
> > >
> > > (there was errors with current->fsuid =>
> current->cred->fsuid, in
> > multiple files. I hardcoded this in files, bad idea I know )
> > > Then compilation of OpenMPI works.
> > >
> > > ./configure --prefix=/usr/local/openmpi_1.6.5_romio2
> > --with-io-romio-flags='--with-pvfs2=/usr/local/orangefs2'
> > > make -j32
> > > make install
> > >
> > > but when i created simple program which is using MPIIO, it
> failed
> > when i run it:
> > >
> > > mpirun -np 1 -host node18 mpiio
> > > [node18:01696] mca: base: component_find: unable to open
> > /usr/local/openmpi_1.6.5_romio/lib/openmpi/mca_io_romio:
> > /usr/local/openmpi_1.6.5_romio/lib/openmpi/mca_io_romio.so:
> > undefined symbol: ADIOI_PVFS2_IReadContig (ignored)
> > >
> > > Because I got message form OrangeFS mailing list about -fPIC
> > errors, i tryed to recompile OrangeFS withou this flag and compile
> > OpenMPI (static linked) by this:
> > >
> > > ./congure --prefix=/usr/local/openmpi_1.6.5_romio2
> > --with-io-romio-flags='--with-pvfs2=/usr/local/orangefs2'
> > --enable-static --disable-shared
> > > (...)
> > > make -j 32
> > > (...)
> > > CCLD otfmerge-mpi
> > >
> >
> /root/openmpi-1.6.5/ompi/contrib/vt/vt/../../../.libs/libmpi.a(ad_pvfs2.o):(.data+0x60):
> > undefined reference to `ADIOI_PVFS2_IReadContig'
> > >
> >
> /root/openmpi-1.6.5/ompi/contrib/vt/vt/../../../.libs/libmpi.a(ad_pvfs2.o):(.data+0x68):
> > undefined reference to `ADIOI_PVFS2_IWriteContig'
> > > collect2: ld returned 1 exit status
> > > make[10]: *** [otfmerge-mpi] Error 1
> > > (...)
> > >
> > > Now I realy dont know, what is wrong.
> > > Is there Anybody ho has OpenMPI working with OrangeFS?
> > >
> > > Thanks for replies
> > > HanousekVít
> > > _______________________________________________
> > > 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
> >
>
> --
> Edgar Gabriel
> Associate Professor
> Parallel Software Technologies Lab http://pstl.cs.uh.edu
> Department of Computer Science University of Houston
> Philip G. Hoffman Hall, Room 524 Houston, TX-77204, USA
> Tel: +1 (713) 743-3857 Fax: +1 (713)
> 743-3335_______________________________________________
> 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
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>

-- 
Edgar Gabriel
Associate Professor
Parallel Software Technologies Lab      http://pstl.cs.uh.edu
Department of Computer Science          University of Houston
Philip G. Hoffman Hall, Room 524        Houston, TX-77204, USA
Tel: +1 (713) 743-3857                  Fax: +1 (713) 743-3335