[O-MPI users] OpenMPI 1.0.1 with Torque 2.0
Hi, I am trying to install OpenMPI 1.0.1 on my Athlon X2 computer running SuSE10.0, the installation failed when I included --with-tm=/opt/torque option with the error message: ... gcc -shared .libs/pls_tm_component.o .libs/pls_tm_module.o -Wl,--rpath -Wl,/home/c00jsh00/openmpi-1.0.1/orte/.libs -Wl,--rpath -Wl,/home/c00jsh00/openmpi-1.0.1/opal/.libs -Wl,--rpath -Wl,/opt/openmpi/lib -L/opt/torque/lib -lpbs /home/c00jsh00/openmpi-1.0.1/orte/.libs/liborte.so -L/home/c00jsh00/openmpi-1.0.1/opal/.libs /home/c00jsh00/openmpi-1.0.1/opal/.libs/libopal.so -lm -lutil -lnsl -pthread -Wl,-soname -Wl,mca_pls_tm.so -o .libs/mca_pls_tm.so /usr/lib64/gcc/x86_64-suse-linux/4.0.2/../../../../x86_64-suse-linux/bin/ld: /opt/torque/lib/libpbs.a(tm.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC /opt/torque/lib/libpbs.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[4]: *** [mca_pls_tm.la] Error 1 make[4]: Leaving directory `/home/c00jsh00/openmpi-1.0.1/orte/mca/pls/tm' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/c00jsh00/openmpi-1.0.1/orte/dynamic-mca/pls' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/c00jsh00/openmpi-1.0.1/orte/dynamic-mca' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/c00jsh00/openmpi-1.0.1/orte' make: *** [all-recursive] Error 1 My TORQUE is 2.0.0p4, the latest version. Any hint? Jyh-Shyong Ho, Ph.D. Research Scientist National Center for High Performance Computing Hsinchu, Taiwan, ROC
Re: [O-MPI users] OpenMPI 1.0.1 with gcc-4.0.2
Hi, I have compiled OpenMPI with PGI and Intel comilers successfully on my Opteron computer running SuSE10.0, however, the compilation failed with gcc-4.0.2 compiler: make[3]: Leaving directory `/work/source/openmpi-1.0.1/ompi/mpi/f77' Making all in f90 make[3]: Entering directory `/work/source/openmpi-1.0.1/ompi/mpi/f90' make all-recursive make[4]: Entering directory `/work/source/openmpi-1.0.1/ompi/mpi/f90' Making all in scripts make[5]: Entering directory `/work/source/openmpi-1.0.1/ompi/mpi/f90/scripts' make[5]: Nothing to be done for `all'. make[5]: Leaving directory `/work/source/openmpi-1.0.1/ompi/mpi/f90/scripts' make[5]: Entering directory `/work/source/openmpi-1.0.1/ompi/mpi/f90' gfortran -I../../../include -I../../../include -I. -c -o mpi_address_f90.o mpi_address_f90.f90 In file mpi_address_f90.f90:83 real(kind=MPI_REAL16_KIND), intent(in) :: location 1 Error: Kind -1 not supported for type REAL at (1) In file mpi_address_f90.f90:107 complex(kind=MPI_REAL16_KIND), intent(in) :: location 1 Error: Kind -1 not supported for type COMPLEX at (1) In file mpi_address_f90.f90:195 real(kind=MPI_REAL16_KIND), dimension(:), intent(in) :: location 1 Error: Kind -1 not supported for type REAL at (1) In file mpi_address_f90.f90:219 complex(kind=MPI_REAL16_KIND), dimension(:), intent(in) :: location 1 Error: Kind -1 not supported for type COMPLEX at (1) In file mpi_address_f90.f90:307 real(kind=MPI_REAL16_KIND), dimension(:,:), intent(in) :: location 1 Error: Kind -1 not supported for type REAL at (1) In file mpi_address_f90.f90:331 complex(kind=MPI_REAL16_KIND), dimension(:,:), intent(in) :: location 1 Error: Kind -1 not supported for type COMPLEX at (1) In file mpi_address_f90.f90:419 real(kind=MPI_REAL16_KIND), dimension(:,:,:), intent(in) :: location 1 Error: Kind -1 not supported for type REAL at (1) In file mpi_address_f90.f90:443 complex(kind=MPI_REAL16_KIND), dimension(:,:,:), intent(in) :: location 1 Error: Kind -1 not supported for type COMPLEX at (1) In file mpi_address_f90.f90:531 real(kind=MPI_REAL16_KIND), dimension(:,:,:,:), intent(in) :: location 1 Error: Kind -1 not supported for type REAL at (1) In file mpi_address_f90.f90:555 complex(kind=MPI_REAL16_KIND), dimension(:,:,:,:), intent(in) :: location 1 Error: Kind -1 not supported for type COMPLEX at (1) make[5]: *** [mpi_address_f90.o] Error 1 make[5]: Leaving directory `/work/source/openmpi-1.0.1/ompi/mpi/f90' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/work/source/openmpi-1.0.1/ompi/mpi/f90' make[3]: *** [all] Error 2 make[3]: Leaving directory `/work/source/openmpi-1.0.1/ompi/mpi/f90' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/work/source/openmpi-1.0.1/ompi/mpi' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/work/source/openmpi-1.0.1/ompi' make: *** [all-recursive] Error 1 I used the following variables: FC=gfortran CC=gcc CXX=g++ F77=gfortran Any hint on how to solve this problem? Thanks. Jyh-Shyong Ho, Ph.D. Research Scientist National Center for High Performance Computing Hsinchu, Taiwan, ROC
Re: [O-MPI users] Open MPI and gfortran
Dear Jeff, Thanks for yor reply. I checked and confirmed that my gfortran is version 4.0.2, so the test program failed since it does not support real(16). The log files for configure and make are attached. It is strange since I am able to use the same configuration and build OpenMPI successfully on another SuSE10/AMD 64 computer. Something must be missing. Best regards Jyh-Shyong Ho, Ph.D. Research Scientist National Center for High Performance Computing Hsinchu, Taiwan, ROC Jeff Squyres wrote: What concerns me, though, is that Open MPI shouldn't have tried to compile support for real(16) in the first place -- our configure script should have detected that the compiler didn't support real(16) (which, it at least partially did, because the constants seem to have a value of -1) and then the generated F90 bindings should not have included support for it. This is why I'd like to see the configure output (etc.) and see what happened. On Jan 5, 2006, at 12:59 PM, rod mach wrote: Hi. To my knowledge you must be using gfortran 4.1 not 4.0 to get access to large kind support like real(16) You can verify by trying to compile the following code with gfortran. This compiles under gfortran 4.1, but I don't believe it will work under 4.0 since this support was added in 4.1. program test real(16) :: x, y y = 4.0_16 x = sqrt(y) print *, x end --Rod -- Rod Mach Absoft HPC Technical Director www.absoft.com Error: Kind -1 not supported for type REAL at (1) In file mpi_address_f90.f90:331 make[2]: Leaving directory `/work/source/openmpi-1.0.1/ompi/mpi' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/work/source/openmpi-1.0.1/ompi' make: *** [all-recursive] Error 1 I used the following variables: FC=gfortran CC=gcc CXX=g++ F77=gfortran Any hint on how to solve this problem? Thanks. Jyh-Shyong Ho, Ph.D. Research Scientist National Center for High Performance Computing Hsinchu, Taiwan, ROC ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users -- {+} Jeff Squyres {+} The Open MPI Project {+} http://www.open-mpi.org/ ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users config.log.tgz Description: Binary data make.log.tgz Description: Binary data
Re: [O-MPI users] Open MPI and gfortran
Sorry, here are the files again. Something went wrong when I compressed these files. Jyh-Shyong Ho Jeff Squyres wrote: It looks like the files you sent were corrupted -- I didn't see the information that I needed to see. Were you working on a case- insensitive filesystem, perchance? I notice that our instructions on the web page would probably result in this kind of corruption for case-insensitive filesystems. I've updated the web page to make the instructions work on case-insensitive filesystems -- can you go check the instructions, do it again and re-send? Sorry about that. :-\ Specifically, your config.log file had a big chunk of the beginning missing -- it was overlaid with the output of configure (which our instructions previously had you write to config.LOG, and could create this kind of problem on a case-insensitive filesystem). FWIW, I just built Open MPI 1.0.1 on a RHEL4U2 machine with gfortran 4.0.2; it correctly identified that there was no real(16) support and didn't run into the problems that you are seeing (i.e., it didn't try to make MPI F90 bindings with real(16) parameters). So I'm curious to see your full logs to figure out why it's failing for you. On Jan 5, 2006, at 7:49 PM, Jyh-Shyong Ho wrote: Dear Jeff, Thanks for yor reply. I checked and confirmed that my gfortran is version 4.0.2, so the test program failed since it does not support real(16). The log files for configure and make are attached. It is strange since I am able to use the same configuration and build OpenMPI successfully on another SuSE10/AMD 64 computer. Something must be missing. Best regards Jyh-Shyong Ho, Ph.D. Research Scientist National Center for High Performance Computing Hsinchu, Taiwan, ROC Jeff Squyres wrote: What concerns me, though, is that Open MPI shouldn't have tried to compile support for real(16) in the first place -- our configure script should have detected that the compiler didn't support real (16) (which, it at least partially did, because the constants seem to have a value of -1) and then the generated F90 bindings should not have included support for it. This is why I'd like to see the configure output (etc.) and see what happened. On Jan 5, 2006, at 12:59 PM, rod mach wrote: Hi. To my knowledge you must be using gfortran 4.1 not 4.0 to get access to large kind support like real(16) You can verify by trying to compile the following code with gfortran. This compiles under gfortran 4.1, but I don't believe it will work under 4.0 since this support was added in 4.1. program test real(16) :: x, y y = 4.0_16 x = sqrt(y) print *, x end --Rod -- Rod Mach Absoft HPC Technical Director www.absoft.com Error: Kind -1 not supported for type REAL at (1) In file mpi_address_f90.f90:331 make[2]: Leaving directory `/work/source/ openmpi-1.0.1/ompi/mpi' make[1]: *** [all-recursive] Error 1 make [1]: Leaving directory `/work/source/openmpi-1.0.1/ompi' make: *** [all-recursive] Error 1 I used the following variables: FC=gfortran CC=gcc CXX=g++ F77=gfortran Any hint on how to solve this problem? Thanks. Jyh-Shyong Ho, Ph.D. Research Scientist National Center for High Performance Computing Hsinchu, Taiwan, ROC ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/ listinfo.cgi/users -- {+} Jeff Squyres {+} The Open MPI Project {+} http://www.open- mpi.org/ ___ 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 {+} The Open MPI Project {+} http://www.open-mpi.org/ ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users config.log.tar.bz2 Description: Binary data make.log.tar.bz2 Description: Binary data