[petsc-users] make check error
Manav Bhatia
bhatiamanav at gmail.com
Wed Mar 11 13:12:50 CDT 2015
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
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