Open MPI logo

Open MPI User's Mailing List Archives

  |   Home   |   Support   |   FAQ   |   all Open MPI User's mailing list

Subject: Re: [OMPI users] OpenMPI-ROMIO-OrangeFS
From: vithanousek (vithanousek_at_[hidden])
Date: 2014-02-26 15:05:00


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 PÅ™edmÄ›t: 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 PÅ™edmÄ›t: 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 > PÅ™edmÄ›t: 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"--=_5f04d18520bec3f7003adf7cª8dba96-fcaa-5da1-a4d4-c455285ba8e2_Content-Type: text/html;
        charset=utf-8
Content-Transfer-Encoding: quoted-printable

<html><body>Now I compiled by doing this:<br>OrangeFS (original, withou editing):<br><br>./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<br>make <br>make kmod<br>make install<br>make kmod_install<br><br>Without error.<br>OpenMPI (with edited switch to ifs):<br><br>./configure --prefix=/usr/local/openmpi_1.6.5_romio --with-io-romio-flags='--with-pvfs2=/usr/local/orangefs'<br>make <br>make install<br><br>Without error.<br>parallel FS mount work. But I still cant use MPIIO. <br>I compiled simple MPIIO program and run it by this:<br><br>mpicc -o mpiio mpiio.c<br>mpirun -np 1 -host node18 mpiio<br>[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)<br><br>And no file is created.<br>I tried compile it with:<br>mpicc -o mpiio mpiio.c -lpvfs2 -L/usr/local/orangefs/lib<br><br>but i got the same results, have You any idea?<br><br>Thank for reply<br>Hanousek Vít<br><br><br><br><br><br><p>---------- Původní zpráva ----------<br>Od: vithanousek &lt;vithanousek_at_[hidden]&gt;<br>Komu: Open MPI Users &lt;users_at_[hidden]&gt;<br>Datum: 26. 2. 2014 20:30:17<br>PÅ™edmÄ›t: Re: [OMPI users] OpenMPI-ROMIO-OrangeFS</p><br><blockquote><div>Thanks for your Time,<br><br>I'm little bit confused, what is diferent between pvfs2 and orangefs. I was thinking, that only project changes name.<br><br>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 =&gt;ifs" in ROMIO).<br><br>I will test if it is working in next hour (some configuration steps is needed).<br><br>Thanks.<br>Hanousek Vít<br><br><p>---------- Původní zpráva ----------<br>Od: Edgar Gabriel &lt;gabriel_at_[hidden]&gt;<br>Komu: Open MPI Users &lt;users_at_[hidden]&gt;<br>Datum: 26. 2. 2014 20:18:03<br>PÅ™edmÄ›t: Re: [OMPI users] OpenMPI-ROMIO-OrangeFS</p><br><blockquote>so we had ROMIO working with PVFS2 (not OrangeFS, which is however<br>registered as PVFS2 internally). We have one cluster which uses<br>OrangeFS, on that machine however we used OMPIO, not ROMIO. I am<br>currently compiling the 1.6 version of Open MPI to see whether I can<br>reproduce your problem.<br><br>Thanks<br>Edgar<br><br>On 2/26/2014 12:23 PM, vithanousek wrote:<br>&gt; Thanks for reply,<br>&gt; <br>&gt; Is it possible that the patch solvs all this problems, not only "switch<br>&gt; =&gt; ifs" problem?<br>&gt; I realy dont know, wher the problem is now (OpenMPI, ROMIO, OrangeFS).<br>&gt; <br>&gt; Thanks<br>&gt; Hanousek Vít<br>&gt; <br>&gt; ---------- Původní zpráva ----------<br>&gt; Od: Ralph Castain &lt;rhc_at_[hidden]&gt;<br>&gt; Komu: Open MPI Users &lt;users_at_[hidden]&gt;<br>&gt; Datum: 26. 2. 2014 19:16:36<br>&gt; PÅ™edmÄ›t: Re: [OMPI users] OpenMPI-ROMIO-OrangeFS<br>&gt; <br>&gt; <br>&gt; Edgar hasn't had a chance to find the necessary patch - he was on<br>&gt; travel, returning soon.<br>&gt; <br>&gt; <br>&gt; On Feb 26, 2014, at 9:27 AM, vithanousek &lt;vithanousek_at_[hidden]&gt; wrote:<br>&gt; <br>&gt; &gt; Hello,<br>&gt; &gt;<br>&gt; &gt; I have still problems with compiling OpenMPI 1.6.5 with OrangeFS<br>&gt; 2.8.7 support.<br>&gt; &gt;<br>&gt; &gt; I compiled OrangeFS by this:<br>&gt; &gt;<br>&gt; &gt; ./configure --prefix=/usr/local/orangefs2<br>&gt; --with-kernel=/usr/src/kernels/2.6.32-431.5.1.el6.x86_64<br>&gt; --with-openib=/usr --without-bmi-tcp<br>&gt; &gt; make -j 32<br>&gt; &gt; make -j 32 kmod<br>&gt; &gt; make install<br>&gt; &gt; make kmod_install<br>&gt; &gt;<br>&gt; &gt; this works.<br>&gt; &gt; than I tried to compile OpenMPI (with fixed convert_named function<br>&gt; in ad_pvfs2_io_dtype.c) by this:<br>&gt; &gt;<br>&gt; &gt; ./configure --prefix=/usr/local/openmpi_1.6.5_romio2<br>&gt; --with-io-romio-flags='--with-pvfs2=/usr/local/orangefs2'<br>&gt; &gt; (...)<br>&gt; &gt; make -j32<br>&gt; &gt; (...)<br>&gt; &gt; CCLD mca_io_romio.la<br>&gt; &gt; /usr/bin/ld: /usr/local/orangefs2/lib/libpvfs2.a(errno-mapping.o):<br>&gt; relocation R_X86_64_32S against `PINT_errno_mapping' can not be used<br>&gt; when making a shared object; recompile with -fPIC<br>&gt; &gt; /usr/local/orangefs2/lib/libpvfs2.a: could not read symbols: Bad value<br>&gt; &gt; collect2: ld returned 1 exit status<br>&gt; &gt; make[3]: *** [mca_io_romio.la] Error 1<br>&gt; &gt;<br>&gt; &gt; So I tried recompile OrangeFS by this:<br>&gt; &gt;<br>&gt; &gt; export CFLAGS="-fPIC"<br>&gt; &gt; ./configure --prefix=/usr/local/orangefs2<br>&gt; --with-kernel=/usr/src/kernels/2.6.32-431.5.1.el6.x86_64<br>&gt; --with-openib=/usr --without-bmi-tcp<br>&gt; &gt; make -j 32<br>&gt; &gt; make -j 32 kmod<br>&gt; &gt; make install<br>&gt; &gt; make kmod_install<br>&gt; &gt;<br>&gt; &gt; (there was errors with current-&gt;fsuid =&gt; current-&gt;cred-&gt;fsuid, in<br>&gt; multiple files. I hardcoded this in files, bad idea I know )<br>&gt; &gt; Then compilation of OpenMPI works.<br>&gt; &gt;<br>&gt; &gt; ./configure --prefix=/usr/local/openmpi_1.6.5_romio2<br>&gt; --with-io-romio-flags='--with-pvfs2=/usr/local/orangefs2'<br>&gt; &gt; make -j32<br>&gt; &gt; make install<br>&gt; &gt;<br>&gt; &gt; but when i created simple program which is using MPIIO, it failed<br>&gt; when i run it:<br>&gt; &gt;<br>&gt; &gt; mpirun -np 1 -host node18 mpiio<br>&gt; &gt; [node18:01696] mca: base: component_find: unable to open<br>&gt; /usr/local/openmpi_1.6.5_romio/lib/openmpi/mca_io_romio:<br>&gt; /usr/local/openmpi_1.6.5_romio/lib/openmpi/mca_io_romio.so:<br>&gt; undefined symbol: ADIOI_PVFS2_IReadContig (ignored)<br>&gt; &gt;<br>&gt; &gt; Because I got message form OrangeFS mailing list about -fPIC<br>&gt; errors, i tryed to recompile OrangeFS withou this flag and compile<br>&gt; OpenMPI (static linked) by this:<br>&gt; &gt;<br>&gt; &gt; ./congure --prefix=/usr/local/openmpi_1.6.5_romio2<br>&gt; --with-io-romio-flags='--with-pvfs2=/usr/local/orangefs2'<br>&gt; --enable-static --disable-shared<br>&gt; &gt; (...)<br>&gt; &gt; make -j 32<br>&gt; &gt; (...)<br>&gt; &gt; CCLD otfmerge-mpi<br>&gt; &gt;<br>&gt; /root/openmpi-1.6.5/ompi/contrib/vt/vt/../../../.libs/libmpi.a(ad_pvfs2.o):(.data+0x60):<br>&gt; undefined reference to `ADIOI_PVFS2_IReadContig'<br>&gt; &gt;<br>&gt; /root/openmpi-1.6.5/ompi/contrib/vt/vt/../../../.libs/libmpi.a(ad_pvfs2.o):(.data+0x68):<br>&gt; undefined reference to `ADIOI_PVFS2_IWriteContig'<br>&gt; &gt; collect2: ld returned 1 exit status<br>&gt; &gt; make[10]: *** [otfmerge-mpi] Error 1<br>&gt; &gt; (...)<br>&gt; &gt;<br>&gt; &gt; Now I realy dont know, what is wrong.<br>&gt; &gt; Is there Anybody ho has OpenMPI working with OrangeFS?<br>&gt; &gt;<br>&gt; &gt; Thanks for replies<br>&gt; &gt; HanousekVít<br>&gt; &gt; _______________________________________________<br>&gt; &gt; users mailing list<br>&gt; &gt; users_at_[hidden]<br>&gt; &gt; http://www.open-mpi.org/mailman/listinfo.cgi/users>&gt; <br>&gt; _______________________________________________<br>&gt; users mailing list<br>&gt; users_at_[hidden]<br>&gt; http://www.open-mpi.org/mailman/listinfo.cgi/users>&gt; <br>&gt; <br>&gt; <br>&gt; _______________________________________________<br>&gt; users mailing list<br>&gt; users_at_[hidden]<br>&gt; http://www.open-mpi.org/mailman/listinfo.cgi/users>&gt; <br><br>-- <br>Edgar Gabriel<br>Associate Professor<br>Parallel Software Technologies Lab http://pstl.cs.uh.edu>Department of Computer Science University of Houston<br>Philip G. Hoffman Hall, Room 524 Houston, TX-77204, USA<br>Tel: +1 (713) 743-3857 Fax: +1 (713) 743-3335_______________________________________________<br>users mailing list<br>users_at_[hidden]<br>http://www.open-mpi.org/mailman/listinfo.cgi/users></div>_______________________________________________<br>users mailing list<br>users_at_[hidden]<br>http://www.open-mpi.org/mailman/listinfo.cgi/users></body></html>--=_5f04d18520bec3f7003adf7cª8dba96-fcaa-5da1-a4d4-c455285ba8e2_=--