> On Mar 11, 2015, at 1:50 PM, Manav Bhatia <[email protected]> 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.
This is not a good idea. It is really really difficult for us to help you get things working when you have mixed and matched codes. Barry > >> [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> >>> >>> >
