Perhaps they have a different MPI install to go with "(GCC) 4.8.3" compilers - that you should look for.
Satish On Wed, 11 Mar 2015, Manav Bhatia wrote: > > > On Mar 11, 2015, at 1:47 PM, Satish Balay <[email protected]> wrote: > > > > Actually mumps is being used - so fortran is required [by mumps] > > > > The reason for the 'multiple' libgfortran messages is: openmpi is > > compiled with an older version of gcc/gfortran > > > > You are right about openmpi being build with an older version of the > compiler. I am trying to mix and match codes. > > > [and I suspect its harmless - as the binaries are created] > > > > The primary issue to check: is this openmpi install functional - if so > > how do you run mpi binaries? Perhaps its a cluster - and have to go > > through a scheduler.. [i.e make check is perhaps inappropriate for > > this case] > > This might be true. This is my first time working on this system, so I need > to find out the details. > > > > > Satish > > ---------- > > > > Python version: > > 2.4.2 (#1, Jan 10 2008, 17:43:47) > > [GCC 4.1.2 20070115 (prerelease) (SUSE Linux)] > > > > Executing: mpicc --version > > stdout: > > gcc (GCC) 4.8.3 > > > > Executing: mpicc -show > > stdout: gcc -I/usr/local/mpi/x86_64/openmpi-1.4.2/include -pthread > > -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib -lmpi -lopen-rte -lopen-pal -ldl > > -Wl,--export-dynamic -lnsl -lutil -lm -ldl > > > > Driving: /usr/local/gnu/gcc-4.8.3/bin/gfortran -o > > /tmp/petsc-X1bXQ9/config.compilers/conftest -v -Wall -Wno-unused-variable > > -ffree-line-length-0 -Wno-unused-dummy-argument -O > > /tmp/petsc-X1bXQ9/config.compilers/conftest.o > > -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib > > -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 > > -L/usr/local/s\ > > erver/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc > > -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64 > > -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -ldl -lmpi -lopen-rte > > -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl > > -I/usr/local/mpi/x86_64/openmpi-1.4.2/include -pthread > > -I/usr/local/mpi/x86_64/openmpi-1.4.2/lib > > -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib -lmpi_f90 -lmpi_f77 -lmpi > > -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -l gfortran > > -lm -ldl -l gfortran -l m -shared-libgcc > > -specs=/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64/libgfortran.spec > > > > > > /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, needed > > by /usr/local/mpi/x86_64/openmpi-1.4.2/lib/libmpi_f90.so, may conflict with > > libgfortran.so.3 > > > > > > > > On Wed, 11 Mar 2015, Barry Smith wrote: > > > >> > >> Since you are providing mpicc and mpicxx do not provide the > >> --with-mpi-include= --with-mpi-lib= > >> > >> I notice you have --with-fortran=0 if you do not want fortran than use > >> --with-fc=0 and do not provide --FC and this may solve the gfortran issue > >> > >> Barry > >> > >> > >> > >>> On Mar 11, 2015, at 1:24 PM, Manav Bhatia <[email protected]> wrote: > >>> > >>> I apologize for not sending these files along. Here they are for the two > >>> machines. > >>> > >>> Really appreciate your help. > >>> > >>> -Manav > >>> > >>> > >>>> On Mar 11, 2015, at 1:21 PM, Barry Smith <[email protected]> wrote: > >>>> > >>>> > >>>> Lots of problems with your system but the biggest is that it appears you > >>>> have two gfortran installs that interfere with each other. If you had > >>>> followed the instructions and sent configure.log and make.log we could > >>>> help you more. > >>>> > >>>> Barry > >>>> > >>>> > >>>>> On Mar 11, 2015, at 1:12 PM, Manav Bhatia <[email protected]> wrote: > >>>>> > >>>>> Greetings! > >>>>> > >>>>> I have come across the following error while running make check. I am > >>>>> not sure where to begin to sort this out. Any pointers would be greatly > >>>>> appreciated. > >>>>> > >>>>> Talon-login[114] bhatia$ make check > >>>>> gmake[1]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3' > >>>>> Running test examples to verify correct installation > >>>>> Using PETSC_DIR=/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3 and > >>>>> PETSC_ARCH=arch-linux2-cxx-opt > >>>>> gmake[2]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[2]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[2]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> *******************Error detected during compile or > >>>>> link!******************* > >>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>> /cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials > >>>>> ex19 > >>>>> ********************************************************************************* > >>>>> gmake[3]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[4]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[4]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> mpicxx -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing > >>>>> -Wno-unknown-pragmas -O > >>>>> -I/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/include > >>>>> -I/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/include > >>>>> -I/usr/local/openssl/x86_64/include > >>>>> -I/usr/local/mpi/x86_64/openmpi/include > >>>>> -I/usr/local/mpi/x86_64/openmpi-1.4.2/include `pwd`/ex19.c > >>>>> mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>>> -O -o ex19 ex19.o > >>>>> -L/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/lib > >>>>> -lpetsc > >>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/lib > >>>>> -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack > >>>>> -lsuperlu_4.3 -lsuperlu_dist_3.3 > >>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/lapack > >>>>> -L/cavs/projects/sams/codes/raptor/lapack -llapack > >>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/blas > >>>>> -L/cavs/projects/sams/codes/raptor/blas -lblas -lparmetis -lmetis > >>>>> -lpthread -Wl,-rpath,/usr/local/openssl/x86_64/lib > >>>>> -L/usr/local/openssl/x86_64/lib -lssl -lcrypto > >>>>> -Wl,-rpath,/usr/local/mpi/x86_64/openmpi/lib > >>>>> -L/usr/local/mpi/x86_64/openmpi/lib -lmpi_cxx -lmpi > >>>>> -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64 > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -lmpi_f90 -lmpi_f77 > >>>>> -lgfortran -lm -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpi_cxx > >>>>> -lstdc++ -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64 > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -ldl -lmpi > >>>>> -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl > >>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, > >>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict > >>>>> with libgfortran.so.3 > >>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, > >>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict > >>>>> with libgfortran.so.3 > >>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, > >>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict > >>>>> with libgfortran.so.3 > >>>>> /bin/rm -f ex19.o > >>>>> gmake[3]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 > >>>>> MPI process > >>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. > >>>>> This will severely limit memory registrations. > >>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. > >>>>> libibverbs: Warning: no userspace device-specific driver found for > >>>>> /sys/class/infiniband_verbs/uverbs0 > >>>>> CMA: unable to open /dev/infiniband/rdma_cm > >>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. > >>>>> This will severely limit memory registrations. > >>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. > >>>>> [Talon-login:18281] *** Process received signal *** > >>>>> [Talon-login:18281] Signal: Segmentation fault (11) > >>>>> [Talon-login:18281] Signal code: Address not mapped (1) > >>>>> [Talon-login:18281] Failing at address: 0x100002990 > >>>>> [Talon-login:18281] [ 0] /lib64/libpthread.so.0 [0x2b8e9cbc6c00] > >>>>> [Talon-login:18281] [ 1] /usr/ofed/lib64/libibverbs.so.1 > >>>>> [0x2b8e9fcad4ce] > >>>>> [Talon-login:18281] [ 2] > >>>>> /usr/ofed/lib64/libibverbs.so.1(ibv_get_device_list+0x9e) > >>>>> [0x2b8e9fcac49e] > >>>>> [Talon-login:18281] [ 3] > >>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_btl_openib.so > >>>>> [0x2b8e9fdbe15a] > >>>>> [Talon-login:18281] [ 4] > >>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_btl_base_select+0x156) > >>>>> [0x2b8e9d223166] > >>>>> [Talon-login:18281] [ 5] > >>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_bml_r2.so > >>>>> [0x2b8e9f997821] > >>>>> [Talon-login:18281] [ 6] > >>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_bml_base_init+0x72) > >>>>> [0x2b8e9d222972] > >>>>> [Talon-login:18281] [ 7] > >>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_pml_ob1.so > >>>>> [0x2b8e9f77fc8f] > >>>>> [Talon-login:18281] [ 8] > >>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_pml_base_select+0x383) > >>>>> [0x2b8e9d22c743] > >>>>> [Talon-login:18281] [ 9] /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0 > >>>>> [0x2b8e9d1f0050] > >>>>> [Talon-login:18281] [10] > >>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(PMPI_Init_thread+0xc1) > >>>>> [0x2b8e9d20db41] > >>>>> [Talon-login:18281] [11] ./ex19(PetscInitialize+0x1bd) [0x4990fe] > >>>>> [Talon-login:18281] [12] ./ex19(main+0x2a) [0x48471e] > >>>>> [Talon-login:18281] [13] /lib64/libc.so.6(__libc_start_main+0xf4) > >>>>> [0x2b8e9e331164] > >>>>> [Talon-login:18281] [14] ./ex19 [0x482639] > >>>>> [Talon-login:18281] *** End of error message *** > >>>>> -------------------------------------------------------------------------- > >>>>> mpirun noticed that process rank 0 with PID 18281 on node > >>>>> Talon-login.HPC.MsState.Edu exited on signal 11 (Segmentation fault). > >>>>> -------------------------------------------------------------------------- > >>>>> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 > >>>>> MPI processes > >>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. > >>>>> This will severely limit memory registrations. > >>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. > >>>>> libibverbs: Warning: no userspace device-specific driver found for > >>>>> /sys/class/infiniband_verbs/uverbs0 > >>>>> CMA: unable to open /dev/infiniband/rdma_cm > >>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. > >>>>> This will severely limit memory registrations. > >>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. > >>>>> [Talon-login:18286] *** Process received signal *** > >>>>> [Talon-login:18286] Signal: Segmentation fault (11) > >>>>> [Talon-login:18286] Signal code: Address not mapped (1) > >>>>> [Talon-login:18286] Failing at address: 0x100002990 > >>>>> [Talon-login:18286] [ 0] /lib64/libpthread.so.0 [0x2acc0604ec00] > >>>>> [Talon-login:18286] [ 1] /usr/ofed/lib64/libibverbs.so.1 > >>>>> [0x2acc091354ce] > >>>>> [Talon-login:18286] [ 2] > >>>>> /usr/ofed/lib64/libibverbs.so.1(ibv_get_device_list+0x9e) > >>>>> [0x2acc0913449e] > >>>>> [Talon-login:18286] [ 3] > >>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_btl_openib.so > >>>>> [0x2acc0924615a] > >>>>> [Talon-login:18286] [ 4] > >>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_btl_base_select+0x156) > >>>>> [0x2acc066ab166] > >>>>> [Talon-login:18286] [ 5] > >>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_bml_r2.so > >>>>> [0x2acc08e1f821] > >>>>> [Talon-login:18286] [ 6] > >>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_bml_base_init+0x72) > >>>>> [0x2acc066aa972] > >>>>> [Talon-login:18286] [ 7] > >>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_pml_ob1.so > >>>>> [0x2acc08c07c8f] > >>>>> [Talon-login:18286] [ 8] > >>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_pml_base_select+0x383) > >>>>> [0x2acc066b4743] > >>>>> [Talon-login:18286] [ 9] /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0 > >>>>> [0x2acc06678050] > >>>>> [Talon-login:18286] [10] > >>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(PMPI_Init_thread+0xc1) > >>>>> [0x2acc06695b41] > >>>>> [Talon-login:18286] [11] ./ex19(PetscInitialize+0x1bd) [0x4990fe] > >>>>> [Talon-login:18286] [12] ./ex19(main+0x2a) [0x48471e] > >>>>> [Talon-login:18286] [13] /lib64/libc.so.6(__libc_start_main+0xf4) > >>>>> [0x2acc077b9164] > >>>>> [Talon-login:18286] [14] ./ex19 [0x482639] > >>>>> [Talon-login:18286] *** End of error message *** > >>>>> -------------------------------------------------------------------------- > >>>>> mpirun noticed that process rank 0 with PID 18286 on node > >>>>> Talon-login.HPC.MsState.Edu exited on signal 11 (Segmentation fault). > >>>>> -------------------------------------------------------------------------- > >>>>> gmake[3]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[3]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[2]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[2]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> *******************Error detected during compile or > >>>>> link!******************* > >>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>> /cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials > >>>>> ex5f > >>>>> ********************************************************* > >>>>> gmake[3]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> mpif90 -c -Wall -Wno-unused-variable -ffree-line-length-0 > >>>>> -Wno-unused-dummy-argument -O > >>>>> -I/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/include > >>>>> -I/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/include > >>>>> -I/usr/local/openssl/x86_64/include > >>>>> -I/usr/local/mpi/x86_64/openmpi/include > >>>>> -I/usr/local/mpi/x86_64/openmpi-1.4.2/include -o ex5f.o ex5f.F > >>>>> mpif90 -Wall -Wno-unused-variable -ffree-line-length-0 > >>>>> -Wno-unused-dummy-argument -O -o ex5f ex5f.o > >>>>> -L/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/lib > >>>>> -lpetsc > >>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/lib > >>>>> -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack > >>>>> -lsuperlu_4.3 -lsuperlu_dist_3.3 > >>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/lapack > >>>>> -L/cavs/projects/sams/codes/raptor/lapack -llapack > >>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/blas > >>>>> -L/cavs/projects/sams/codes/raptor/blas -lblas -lparmetis -lmetis > >>>>> -lpthread -Wl,-rpath,/usr/local/openssl/x86_64/lib > >>>>> -L/usr/local/openssl/x86_64/lib -lssl -lcrypto > >>>>> -Wl,-rpath,/usr/local/mpi/x86_64/openmpi/lib > >>>>> -L/usr/local/mpi/x86_64/openmpi/lib -lmpi_cxx -lmpi > >>>>> -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4..8.3/lib64 > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -lmpi_f90 -lmpi_f77 > >>>>> -lgfortran -lm -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpi_cxx > >>>>> -lstdc++ -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64 > >>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -ldl -lmpi > >>>>> -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl > >>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, > >>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict > >>>>> with libgfortran.so.3 > >>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, > >>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict > >>>>> with libgfortran.so.3 > >>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, > >>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict > >>>>> with libgfortran.so.3 > >>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, > >>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict > >>>>> with libgfortran.so.3 > >>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, > >>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict > >>>>> with libgfortran.so.3 > >>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, > >>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict > >>>>> with libgfortran.so.3 > >>>>> /bin/rm -f ex5f.o > >>>>> gmake[3]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> Possible error running Fortran example src/snes/examples/tutorials/ex5f > >>>>> with 1 MPI process > >>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. > >>>>> This will severely limit memory registrations. > >>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. > >>>>> libibverbs: Warning: no userspace device-specific driver found for > >>>>> /sys/class/infiniband_verbs/uverbs0 > >>>>> CMA: unable to open /dev/infiniband/rdma_cm > >>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. > >>>>> This will severely limit memory registrations. > >>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. > >>>>> > >>>>> Program received signal SIGSEGV: Segmentation fault - invalid memory > >>>>> reference. > >>>>> > >>>>> Backtrace for this error: > >>>>> #0 0x2B6CD4A6F4D7 > >>>>> #1 0x2B6CD4A6FADE > >>>>> #2 0x2B6CD5805E1F > >>>>> #3 0x2B6CD716F4CE > >>>>> #4 0x2B6CD716E49D > >>>>> #5 0x2B6CD7280159 > >>>>> #6 0x2B6CD46E5165 > >>>>> #7 0x2B6CD6E59820 > >>>>> #8 0x2B6CD46E4971 > >>>>> #9 0x2B6CD6C41C8E > >>>>> #10 0x2B6CD46EE742 > >>>>> #11 0x2B6CD46B204F > >>>>> #12 0x2B6CD46CF99F > >>>>> #13 0x2B6CD494AA84 > >>>>> #14 0x489A6D in petscinitialize_ > >>>>> #15 0x487CEC in MAIN__ at ex5f.F:? > >>>>> -------------------------------------------------------------------------- > >>>>> mpirun noticed that process rank 0 with PID 18354 on node > >>>>> Talon-login.HPC.MsState.Edu exited on signal 11 (Segmentation fault). > >>>>> -------------------------------------------------------------------------- > >>>>> gmake[3]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[3]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[2]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[2]: Entering directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> gmake[2]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' > >>>>> Completed test examples > >>>>> gmake[1]: Leaving directory > >>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3' > >>>>> ========================================= > >>>>> Now to evaluate the computer systems you plan use - do: > >>>>> make PETSC_DIR=/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3 > >>>>> PETSC_ARCH=arch-linux2-cxx-opt streams NPMAX=<number of MPI processes > >>>>> you intend to use> > >>>>> Talon-login[115] bhatia$ > >>>>> > >>>>> > >>>>> Thanks, > >>>>> Manav > >>>>> > >>>> > >>> > >>> <configure_shadow.log><configure_talon.log><make_shadow.log><make_talon.log> > >> > >> > >
