Thanks a lot Ralph! I corrected the no_local to nolocal and now when I try to execute the script step1 (pls find it attached) [rchaud@helios amber10]$ ./step1 [helios.structure.uic.edu:16335] [0,0,0] ORTE_ERROR_LOG: Not available in file ras_bjs.c at line 247 -------------------------------------------------------------------------- There are no available nodes allocated to this job. This could be because no nodes were found or all the available nodes were already used.
Note that since the -nolocal option was given no processes can be launched on the local node. -------------------------------------------------------------------------- [helios.structure.uic.edu:16335] [0,0,0] ORTE_ERROR_LOG: Temporarily out of resource in file base/rmaps_base_support_fns.c at line 168 [helios.structure.uic.edu:16335] [0,0,0] ORTE_ERROR_LOG: Temporarily out of resource in file rmaps_rr.c at line 402 [helios.structure.uic.edu:16335] [0,0,0] ORTE_ERROR_LOG: Temporarily out of resource in file base/rmaps_base_map_job.c at line 210 [helios.structure.uic.edu:16335] [0,0,0] ORTE_ERROR_LOG: Temporarily out of resource in file rmgr_urm.c at line 372 [helios.structure.uic.edu:16335] mpirun: spawn failed with errno=-3 If I use the script without the --nolocal option, I get the following error: [helios.structure.uic.edu:20708] [0,0,0] ORTE_ERROR_LOG: Not available in file ras_bjs.c at line 247 thanks, On Mon, Nov 3, 2008 at 2:04 PM, <users-requ...@open-mpi.org> wrote: > Send users mailing list submissions to > us...@open-mpi.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.open-mpi.org/mailman/listinfo.cgi/users > or, via email, send a message with subject or body 'help' to > users-requ...@open-mpi.org > > You can reach the person managing the list at > users-ow...@open-mpi.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of users digest..." > > > Today's Topics: > > 1. Scyld Beowulf and openmpi (Rima Chaudhuri) > 2. Re: Scyld Beowulf and openmpi (Ralph Castain) > 3. Problems installing in Cygwin - Problem with GCC 3.4.4 > (Gustavo Seabra) > 4. Re: MPI + Mixed language coding(Fortran90 + C++) (Jeff Squyres) > 5. Re: Problems installing in Cygwin - Problem with GCC 3.4.4 > (Jeff Squyres) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 3 Nov 2008 11:30:01 -0600 > From: "Rima Chaudhuri" <rima.chaudh...@gmail.com> > Subject: [OMPI users] Scyld Beowulf and openmpi > To: us...@open-mpi.org > Message-ID: > <7503b17d0811030930i13acb974kc627983a1d481...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hello! > I am a new user of openmpi -- I've installed openmpi 1.2.6 for our > x86_64 linux scyld beowulf cluster inorder to make it run with amber10 > MD simulation package. > > The nodes can see the home directory i.e. a bpsh to the nodes works > fine and lists all the files in the home directory where I have both > openmpi and amber10 installed. > However if I try to run: > > $MPI_HOME/bin/mpirun -no_local=1 -np 4 $AMBERHOME/exe/sander.MPI ........ > > I get the following error: > [0,0,0] ORTE_ERROR_LOG: Not available in file ras_bjs.c at line 247 > -------------------------------------------------------------------------- > Failed to find the following executable: > > Host: helios.structure.uic.edu > Executable: -o > > Cannot continue. > -------------------------------------------------------------------------- > [helios.structure.uic.edu:23611] [0,0,0] ORTE_ERROR_LOG: Not found in > file rmgr_urm.c at line 462 > [helios.structure.uic.edu:23611] mpirun: spawn failed with errno=-13 > > any cues? > > > -- > -Rima > > > ------------------------------ > > Message: 2 > Date: Mon, 3 Nov 2008 12:08:36 -0700 > From: Ralph Castain <r...@lanl.gov> > Subject: Re: [OMPI users] Scyld Beowulf and openmpi > To: Open MPI Users <us...@open-mpi.org> > Message-ID: <91044a7e-ada5-4b94-aa11-b3c1d9843...@lanl.gov> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > For starters, there is no "-no_local" option to mpirun. You might want > to look at mpirun --help, or man mpirun. > > I suspect the option you wanted was --nolocal. Note that --nolocal > does not take an argument. > > Mpirun is confused by the incorrect option and looking for an > incorrectly named executable. > Ralph > > > On Nov 3, 2008, at 10:30 AM, Rima Chaudhuri wrote: > >> Hello! >> I am a new user of openmpi -- I've installed openmpi 1.2.6 for our >> x86_64 linux scyld beowulf cluster inorder to make it run with amber10 >> MD simulation package. >> >> The nodes can see the home directory i.e. a bpsh to the nodes works >> fine and lists all the files in the home directory where I have both >> openmpi and amber10 installed. >> However if I try to run: >> >> $MPI_HOME/bin/mpirun -no_local=1 -np 4 $AMBERHOME/exe/ >> sander.MPI ........ >> >> I get the following error: >> [0,0,0] ORTE_ERROR_LOG: Not available in file ras_bjs.c at line 247 >> -------------------------------------------------------------------------- >> Failed to find the following executable: >> >> Host: helios.structure.uic.edu >> Executable: -o >> >> Cannot continue. >> -------------------------------------------------------------------------- >> [helios.structure.uic.edu:23611] [0,0,0] ORTE_ERROR_LOG: Not found in >> file rmgr_urm.c at line 462 >> [helios.structure.uic.edu:23611] mpirun: spawn failed with errno=-13 >> >> any cues? >> >> >> -- >> -Rima >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > ------------------------------ > > Message: 3 > Date: Mon, 3 Nov 2008 14:53:55 -0500 > From: "Gustavo Seabra" <gustavo.sea...@gmail.com> > Subject: [OMPI users] Problems installing in Cygwin - Problem with GCC > 3.4.4 > To: "Open MPI Users" <us...@open-mpi.org> > Message-ID: > <f79359b60811031153l5591e0f8j49a7e4d9fb02e...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi everyone, > > Here's a "progress report"... more questions in the end :-) > > Finally, I was *almost* able to compile OpenMPI in Cygwin using the > following configure command: > > ./configure --prefix=/home/seabra/local/openmpi-1.3b1 \ > --with-mpi-param_check=always --with-threads=posix \ > --enable-mpi-threads --disable-io-romio \ > --enable-mca-no-build=memory_mallopt,maffinity,paffinity \ > --enable-contrib-no-build=vt \ > FC=g95 'FFLAGS=-O0 -fno-second-underscore' CXX=g++ > > I then had a very weird error during compilation of > ompi/tools/ompi_info/params.cc. (See below). > > The lines causing the compilation errors are: > > vector.tcc:307: const size_type __len = __old_size + > std::max(__old_size, __n); > vector.tcc:384: const size_type __len = __old_size + > std::max(__old_size, __n); > stl_bvector.h:522: const size_type __len = size() + std::max(size(), __n); > stl_bvector.h:823: const size_type __len = size() + std::max(size(), __n); > > (Notice that those are from the standard gcc libraries.) > > After googling it for a while, I could find that this error is caused > because, at come point, the source code being compiled redefined the > "max" function with a macro, g++ cannot recognize the "std::max" that > happens in those lines and only "sees" a (...), thus printing that > cryptic complaint. > > I looked in some places in the OpenMPI code, but I couldn't find > "max" being redefined anywhere, but I may be looking in the wrong > places. Anyways, the only way of found of compiling OpenMPI was a very > ugly hack: I have to go into those files and remove the "std::" before > the "max". With that, it all compiled cleanly. > > I did try running the tests in the 'tests' directory (with 'make > check'), and I didn't get any alarming message, except that in some > cases (class, threads, peruse) it printed "All 0 tests passed". I got > and "All (n) tests passed" (n>0) for asm and datatype. > > Can anybody comment on the meaning of those test results? Should I be > alarmed with the "All 0 tests passed" messages? > > Finally, in the absence of big red flags (that I noticed), I went > ahead and tried to compile my program. However, as soon as compilation > starts, I get the following: > > /local/openmpi/openmpi-1.3b1/bin/mpif90 -c -O3 -fno-second-underscore > -ffree-form -o constants.o _constants.f > -------------------------------------------------------------------------- > Unfortunately, this installation of Open MPI was not compiled with > Fortran 90 support. As such, the mpif90 compiler is non-functional. > -------------------------------------------------------------------------- > make[1]: *** [constants.o] Error 1 > make[1]: Leaving directory `/home/seabra/local/amber11/src/sander' > make: *** [parallel] Error 2 > > Notice that I compiled OpenMPI with g95, so there *should* be > Fortran95 support... Any ideas on what could be going wrong? > > Thank you very much, > Gustavo. > > ====================================== > Error in the compilation of params.cc > ====================================== > $ g++ -DHAVE_CONFIG_H -I. -I../../../opal/include > -I../../../orte/include -I../../../ompi/include > -I../../../opal/mca/paffinity/linux/plpa/src/libplpa > -DOMPI_CONFIGURE_USER="\"seabra\"" -DOMPI_CONFIGURE_HOST="\"ACS02\"" > -DOMPI_CONFIGURE_DATE="\"Sat Nov 1 20:44:32 EDT 2008\"" > -DOMPI_BUILD_USER="\"$USER\"" -DOMPI_BUILD_HOST="\"`hostname`\"" > -DOMPI_BUILD_DATE="\"`date`\"" -DOMPI_BUILD_CFLAGS="\"-O3 -DNDEBUG > -finline-functions -fno-strict-aliasing \"" > -DOMPI_BUILD_CPPFLAGS="\"-I../../.. -D_REENTRANT\"" > -DOMPI_BUILD_CXXFLAGS="\"-O3 -DNDEBUG -finline-functions \"" > -DOMPI_BUILD_CXXCPPFLAGS="\"-I../../.. -D_REENTRANT\"" > -DOMPI_BUILD_FFLAGS="\"-O0 -fno-second-underscore\"" > -DOMPI_BUILD_FCFLAGS="\"\"" -DOMPI_BUILD_LDFLAGS="\"-export-dynamic > \"" -DOMPI_BUILD_LIBS="\"-lutil \"" > -DOMPI_CC_ABSOLUTE="\"/usr/bin/gcc\"" > -DOMPI_CXX_ABSOLUTE="\"/usr/bin/g++\"" > -DOMPI_F77_ABSOLUTE="\"/usr/bin/g77\"" > -DOMPI_F90_ABSOLUTE="\"/usr/local/bin/g95\"" > -DOMPI_F90_BUILD_SIZE="\"small\"" -I../../.. -D_REENTRANT -O3 > -DNDEBUG -finline-functions -MT param.o -MD -MP -MF $depbase.Tpo -c > -o param.o param.cc > In file included from /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/vector:72, > from ../../../ompi/tools/ompi_info/ompi_info.h:24, > from param.cc:43: > /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_bvector.h: In > member function `void std::vector<bool, > _Alloc>::_M_insert_range(std::_Bit_iterator, _ForwardIterator, > _ForwardIterator, std::forward_iterator_tag)': > /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_bvector.h:522: > error: expected unqualified-id before '(' token > /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_bvector.h: In > member function `void std::vector<bool, > _Alloc>::_M_fill_insert(std::_Bit_iterator, size_t, bool)': > /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_bvector.h:823: > error: expected unqualified-id before '(' token > In file included from /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/vector:75, > from ../../../ompi/tools/ompi_info/ompi_info.h:24, > from param.cc:43: > /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/vector.tcc: In > member function `void std::vector<_Tp, > _Alloc>::_M_fill_insert(__gnu_cxx::__normal_iterator<typename > _Alloc::pointer, std::vector<_Tp, _Alloc> >, size_t, const _Tp&)': > /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/vector.tcc:307: > error: expected unqualified-id before '(' token > /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/vector.tcc: In > member function `void std::vector<_Tp, > _Alloc>::_M_range_insert(__gnu_cxx::__normal_iterator<typename > _Alloc::pointer, std::vector<_Tp, _Alloc> >, _ForwardIterator, > _ForwardIterator, std::forward_iterator_tag)': > /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/vector.tcc:384: > error: expected unqualified-id before '(' token > > > -- > Gustavo Seabra > Postdoctoral Associate > Quantum Theory Project - University of Florida > Gainesville - Florida - USA > > > ------------------------------ > > Message: 4 > Date: Mon, 3 Nov 2008 14:54:25 -0500 > From: Jeff Squyres <jsquy...@cisco.com> > Subject: Re: [OMPI users] MPI + Mixed language coding(Fortran90 + C++) > To: Open MPI Users <us...@open-mpi.org> > Message-ID: <45698801-0857-466f-a19d-c529f72d4...@cisco.com> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Can you replicate the scenario in smaller / different cases? > > - write a sample plugin in C instead of C++ > - write a non-MPI Fortran application that loads your C++ application > - ...? > > In short, *MPI* shouldn't be interfering with Fortran/C++ common > blocks. Try taking MPI out of the picture and see if that makes the > problem go away. > > Those are pretty much shots in the dark, but I don't know where to go, > either -- try random things until you find what you want. > > > On Nov 3, 2008, at 3:51 AM, Rajesh Ramaya wrote: > >> Helllo Jeff, Gustavo, Mi >> Thank for the advice. I am familiar with the difference in the >> compiler code generation for C, C++ & FORTRAN. I even tried to look >> at some of the common block symbols. The name of the symbol remains >> the same. The only difference that I observe is in FORTRAN compiled >> *.o 0000000000515bc0 B aux7loc_ and the C++ compiled code U >> aux7loc_ the memory is not allocated as it has been declared as >> extern in C++. When the executable loads the shared library it finds >> all the undefined symbols. Atleast if it did not manage to find a >> single symbol it prints undefined symbol error. >> I am completely stuck up and do not know how to continue further. >> >> Thanks, >> Rajesh >> >> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] >> On Behalf Of Mi Yan >> Sent: samedi 1 novembre 2008 23:26 >> To: Open MPI Users >> Cc: 'Open MPI Users'; users-boun...@open-mpi.org >> Subject: Re: [OMPI users] MPI + Mixed language coding(Fortran90 + C++) >> >> So your tests show: >> 1. "Shared library in FORTRAN + MPI executable in FORTRAN" works. >> 2. "Shared library in C++ + MPI executable in FORTRAN " does not work. >> >> It seems to me that the symbols in C library are not really >> recognized by FORTRAN executable as you thought. What compilers did >> yo use to built OpenMPI? >> >> Different compiler has different convention to handle symbols. E.g. >> if there is a variable "var_foo" in your FORTRAN code, some FORTRN >> compiler will save "var_foo_" in the object file by default; if you >> want to access "var_foo" in C code, you actually need to refer >> "var_foo_" in C code. If you define "var_foo" in a module in the >> FORTAN compiler, some FORTRAN compiler may append the module name to >> "var_foo". >> So I suggest to check the symbols in the object files generated by >> your FORTAN and C compiler to see the difference. >> >> Mi >> <image001.gif>"Rajesh Ramaya" <rajesh.ram...@e-xstream.com> >> >> >> "Rajesh Ramaya" <rajesh.ram...@e-xstream.com> >> Sent by: users-boun...@open-mpi.org >> 10/31/2008 03:07 PM >> >> Please respond to >> Open MPI Users <us...@open-mpi.org> >> <image002.gif> >> To >> <image003.gif> >> "'Open MPI Users'" <us...@open-mpi.org>, "'Jeff Squyres'" <jsquy...@cisco.com >> > >> <image002.gif> >> cc >> <image003.gif> >> <image002.gif> >> Subject >> <image003.gif> >> Re: [OMPI users] MPI + Mixed language coding(Fortran90 + C++) >> >> <image003.gif> >> <image003.gif> >> >> Hello Jeff Squyres, >> Thank you very much for the immediate reply. I am able to >> successfully >> access the data from the common block but the values are zero. In my >> algorithm I even update a common block but the update made by the >> shared >> library is not taken in to account by the executable. Can you please >> be very >> specific how to make the parallel algorithm aware of the data? >> Actually I am >> not writing any MPI code inside? It's the executable (third party >> software) >> who does that part. All that I am doing is to compile my code with >> MPI c >> compiler and add it in the LD_LIBIRARY_PATH. >> In fact I did a simple test by creating a shared library using a >> FORTRAN >> code and the update made to the common block is taken in to account >> by the >> executable. Is there any flag or pragma that need to be activated >> for mixed >> language MPI? >> Thank you once again for the reply. >> >> Rajesh >> >> -----Original Message----- >> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] >> On >> Behalf Of Jeff Squyres >> Sent: vendredi 31 octobre 2008 18:53 >> To: Open MPI Users >> Subject: Re: [OMPI users] MPI + Mixed language coding(Fortran90 + C++) >> >> On Oct 31, 2008, at 11:57 AM, Rajesh Ramaya wrote: >> >> > I am completely new to MPI. I have a basic question concerning >> > MPI and mixed language coding. I hope any of you could help me out. >> > Is it possible to access FORTRAN common blocks in C++ in a MPI >> > compiled code. It works without MPI but as soon I switch to MPI the >> > access of common block does not work anymore. >> > I have a Linux MPI executable which loads a shared library at >> > runtime and resolves all undefined symbols etc The shared library >> > is written in C++ and the MPI executable in written in FORTRAN. Some >> > of the input that the shared library looking for are in the Fortran >> > common blocks. As I access those common blocks during runtime the >> > values are not initialized. I would like to know if what I am >> > doing is possible ?I hope that my problem is clear...... >> >> >> Generally, MPI should not get in the way of sharing common blocks >> between Fortran and C/C++. Indeed, in Open MPI itself, we share a few >> common blocks between Fortran and the main C Open MPI implementation. >> >> What is the exact symptom that you are seeing? Is the application >> failing to resolve symbols at run-time, possibly indicating that >> something hasn't instantiated a common block? Or are you able to >> successfully access the data from the common block, but it doesn't >> have the values you expect (e.g., perhaps you're seeing all zeros)? >> >> If the former, you might want to check your build procedure. You >> *should* be able to simply replace your C++ / F90 compilers with >> mpicxx and mpif90, respectively, and be able to build an MPI version >> of your app. If the latter, you might need to make your parallel >> algorithm aware of what data is available in which MPI process -- >> perhaps not all the data is filled in on each MPI process...? >> >> -- >> Jeff Squyres >> Cisco Systems >> >> >> _______________________________________________ >> 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 > > > -- > Jeff Squyres > Cisco Systems > > > > ------------------------------ > > Message: 5 > Date: Mon, 3 Nov 2008 15:04:47 -0500 > From: Jeff Squyres <jsquy...@cisco.com> > Subject: Re: [OMPI users] Problems installing in Cygwin - Problem with > GCC 3.4.4 > To: Open MPI Users <us...@open-mpi.org> > Message-ID: <8e364b51-6726-4533-ade2-aea266380...@cisco.com> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > On Nov 3, 2008, at 2:53 PM, Gustavo Seabra wrote: > >> Finally, I was *almost* able to compile OpenMPI in Cygwin using the >> following configure command: >> >> ./configure --prefix=/home/seabra/local/openmpi-1.3b1 \ >> --with-mpi-param_check=always --with-threads=posix \ >> --enable-mpi-threads --disable-io-romio \ >> --enable-mca-no- >> build=memory_mallopt,maffinity,paffinity \ >> --enable-contrib-no-build=vt \ >> FC=g95 'FFLAGS=-O0 -fno-second-underscore' CXX=g++ > > For your fortran issue, the Fortran 90 interface needs the Fortran 77 > interface. So you need to supply an F77 as well (the output from > configure should indicate that the F90 interface was disabled because > the F77 interface was disabled). > >> I then had a very weird error during compilation of >> ompi/tools/ompi_info/params.cc. (See below). >> >> The lines causing the compilation errors are: >> >> vector.tcc:307: const size_type __len = __old_size + >> std::max(__old_size, __n); >> vector.tcc:384: const size_type __len = __old_size + >> std::max(__old_size, __n); >> stl_bvector.h:522: const size_type __len = size() + >> std::max(size(), __n); >> stl_bvector.h:823: const size_type __len = size() + >> std::max(size(), __n); >> >> (Notice that those are from the standard gcc libraries.) >> >> After googling it for a while, I could find that this error is caused >> because, at come point, the source code being compiled redefined the >> "max" function with a macro, g++ cannot recognize the "std::max" that >> happens in those lines and only "sees" a (...), thus printing that >> cryptic complaint. >> >> I looked in some places in the OpenMPI code, but I couldn't find >> "max" being redefined anywhere, but I may be looking in the wrong >> places. Anyways, the only way of found of compiling OpenMPI was a very >> ugly hack: I have to go into those files and remove the "std::" before >> the "max". With that, it all compiled cleanly. > > I'm not sure I follow -- I don't see anywhere in OMPI where we use > std::max. What areas did you find that you needed to change? > >> I did try running the tests in the 'tests' directory (with 'make >> check'), and I didn't get any alarming message, except that in some >> cases (class, threads, peruse) it printed "All 0 tests passed". I got >> and "All (n) tests passed" (n>0) for asm and datatype. >> >> Can anybody comment on the meaning of those test results? Should I be >> alarmed with the "All 0 tests passed" messages? > > No. We don't really maintain the "make check" stuff too well. > > -- > Jeff Squyres > Cisco Systems > > > > ------------------------------ > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > > End of users Digest, Vol 1055, Issue 2 > ************************************** > -- -Rima
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