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>
