[petsc-users] make check error

Wed Mar 11 13:21:17 CDT 2015

  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 <bhatiamanav at gmail.com> 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
> 