At first Thank you very much for your time. "--with-file-system=pvfs2+ufs+nfs" didnt help.
But if find (by google) some part of orangefs test. I dont know what is this exactly doing, but when I edited source code of OpenMPI like doing this line, all seems that it is working now. (changing ADIOI_PVFS2_IReadContig and ADIOI_PVFS2_IWriteContig to NULL in file ad_pvfs2.c) http://www.orangefs.org/trac/orangefs/browser/branches/OFSTest-dev/OFSTest/ OFSTestNode.py?rev=10645#L1328 Other tests I will do tomorrow. Thanks Hanousek Vít ---------- Původní zpráva ---------- Od: Edgar Gabriel <gabr...@cs.uh.edu> Komu: us...@open-mpi.org Datum: 26. 2. 2014 21:08:07 Předmět: Re: [OMPI users] OpenMPI-ROMIO-OrangeFS "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 <vithanou...@seznam.cz> > Komu: Open MPI Users <us...@open-mpi.org> > 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 <gabr...@cs.uh.edu> > Komu: Open MPI Users <us...@open-mpi.org> > 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 <r...@open-mpi.org> > > Komu: Open MPI Users <us...@open-mpi.org> > > 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 > <vithanou...@seznam.cz> 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 > > > us...@open-mpi.org > > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > _______________________________________________ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > > > _______________________________________________ > > users mailing list > > us...@open-mpi.org > > 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 > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > _______________________________________________ > users mailing list > us...@open-mpi.org > 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 us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users";
