Hi everyone,
I'm trying to install the latest version of dealII on a cluster now, got
another error unfortunately.
The output is below, and I attached the logs too. I would appreciate any
help with this.
> In file included from
>> /home/r/russ/lkaratun/aspect/dealii/include/deal.II/dofs/d
>>
>> of_handler.h:27:0,
>
> from
>> /home/r/russ/lkaratun/aspect/dealii/include/deal.II/dofs/d
>>
>> of_accessor.h:22,
>
> from
>> /home/r/russ/lkaratun/aspect/dealii/source/fe/fe_nedelec.c
>> c:23:
>
> /home/r/russ/lkaratun/aspect/dealii/include/deal.II/dofs/block_info.h:233:34:
>> in
>> ternal compiler error: Bus error
>
> types::global_dof_index BlockInfo::renumber (const unsigned int i) const
>
> ^
>
> 0x8d7a9f crash_signal
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/toplev.c:332
>
> 0x5d4dc0 pop_deferring_access_checks()
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/semantics.c:183
>
> 0x585848 cp_parser_parse_definitely
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:23820
>
> 0x59cc86 cp_parser_declarator
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:16227
>
> 0x5a28a0 cp_parser_init_declarator
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:15837
>
> 0x5a351e cp_parser_simple_declaration
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:10670
>
> 0x5a5020 cp_parser_block_declaration
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:10551
>
> 0x5acd6b cp_parser_declaration
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:10448
>
> 0x5abaad cp_parser_declaration_seq_opt
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:10334
>
> 0x5abcac cp_parser_namespace_body
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:15152
>
> 0x5abcac cp_parser_namespace_definition
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:15133
>
> 0x5accdd cp_parser_declaration
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:10436
>
> 0x5abaad cp_parser_declaration_seq_opt
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:10334
>
> 0x5ad2ba cp_parser_translation_unit
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:3813
>
> 0x5ad2ba c_parse_file()
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/cp/parser.c:28338
>
> 0x642a34 c_common_parse_file()
>
> /scinet/gpc/src/gcc/gcc-4.8.1/gcc/c-family/c-opts.c:1046
>
> Please submit a full bug report,
>
> with preprocessed source if appropriate.
>
> Please include the complete backtrace with any bug report.
>
> See <http://gcc.gnu.org/bugs.html> for instructions.
>
> make[2]: *** [source/fe/CMakeFiles/obj_fe_release.dir/fe_nedelec.cc.o]
>> Error 1
>
> make[1]: *** [source/fe/CMakeFiles/obj_fe_release.dir/all] Error 2
>
> make: *** [all] Error 2
>
>
>
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
https://groups.google.com/d/forum/dealii?hl=en
---
You received this message because you are subscribed to the Google Groups
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
###
#
# deal.II configuration:
# CMAKE_BUILD_TYPE: Release
# BUILD_SHARED_LIBS: ON
# CMAKE_INSTALL_PREFIX: /home/r/russ/lkaratun/aspect/dealii
# CMAKE_SOURCE_DIR: /home/r/russ/lkaratun/aspect/dealii
# (version 8.5.0-pre, shortrev f1284e9)
# CMAKE_BINARY_DIR: /home/r/russ/lkaratun/aspect/dealii/build
# CMAKE_CXX_COMPILER: GNU 4.8.1 on platform Linux x86_64
# /scinet/gpc/compilers/gcc-4.8.1/bin/g++
#
# Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION
= ON):
# ( DEAL_II_WITH_64BIT_INDICES = OFF )
# ( DEAL_II_WITH_ARPACK = OFF )
# DEAL_II_WITH_BOOST set up with bundled packages
# DEAL_II_WITH_BZIP2 set up with external dependencies
# ( DEAL_II_WITH_CUDA = OFF )
# DEAL_II_WITH_CXX11 = ON
# ( DEAL_II_WITH_CXX14 = OFF )
# ( DEAL_II_WITH_GSL = OFF )
# ( DEAL_II_WITH_HDF5 = OFF )
# ( DEAL_II_WITH_LAPACK = OFF )
# ( DEAL_II_WITH_METIS = OFF )
# DEAL_II_WITH_MPI set up with external dependencies
# DEAL_II_WITH_MUPARSER set up with bundled packages
# ( DEAL_II_WITH_NETCDF = OFF )
# ( DEAL_II_WITH_OPENCASCADE = OFF )
# DEAL_II_WITH_P4EST set up with external dependencies
# ( DEAL_II_WITH_PETSC = OFF )
# ( DEAL_II_WITH_SLEPC = OFF )
# DEAL_II_WITH_THREADS set up with bundled packages
# DEAL_II_WITH_TRILINOS set up with external dependencies
# ( DEAL_II_WITH_UMFPACK = OFF )
# DEAL_II_WITH_ZLIB set up with external dependencies
#
# Component configuration:
# ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
# DEAL_II_COMPONENT_EXAMPLES
# ( DEAL_II_COMPONENT_PACKAGE = OFF )
# ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
# Detailed information (compiler flags, feature configuration) can be found in
detailed.log
#
# Run $ make info to print a help message with a list of top level targets
#
###
###
#
# deal.II configuration:
# CMAKE_BUILD_TYPE: Release
# BUILD_SHARED_LIBS: ON
# CMAKE_INSTALL_PREFIX: /home/r/russ/lkaratun/aspect/dealii
# CMAKE_SOURCE_DIR: /home/r/russ/lkaratun/aspect/dealii
# (version 8.5.0-pre, shortrev f1284e9)
# CMAKE_BINARY_DIR: /home/r/russ/lkaratun/aspect/dealii/build
# CMAKE_CXX_COMPILER: GNU 4.8.1 on platform Linux x86_64
# /scinet/gpc/compilers/gcc-4.8.1/bin/g++
# CMAKE_C_COMPILER: /scinet/gpc/compilers/gcc-4.8.1/bin/gcc
# CMAKE_Fortran_COMPILER: /scinet/gpc/compilers/gcc-4.8.1/bin/gfortran
# CMAKE_GENERATOR: Unix Makefiles
#
# Base configuration (prior to feature configuration):
# DEAL_II_CXX_FLAGS: -pedantic -fPIC -Wall -Wextra
-Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch
-Woverloaded-virtual -Wno-long-long -Wno-deprecated-declarations
-Wno-literal-suffix -std=c++11 -g -O3
# DEAL_II_CXX_FLAGS_RELEASE: -O2 -funroll-loops -funroll-all-loops
-fstrict-aliasing -Wno-unused-local-typedefs
# DEAL_II_LINKER_FLAGS: -Wl,--as-needed -rdynamic
# DEAL_II_LINKER_FLAGS_RELEASE:
# DEAL_II_DEFINITIONS:
# DEAL_II_DEFINITIONS_RELEASE:
# DEAL_II_USER_DEFINITIONS:
# DEAL_II_USER_DEFINITIONS_REL:
# DEAL_II_INCLUDE_DIRS
# DEAL_II_USER_INCLUDE_DIRS:
# DEAL_II_BUNDLED_INCLUDE_DIRS:
# DEAL_II_LIBRARIES: m
# DEAL_II_LIBRARIES_RELEASE:
#
# Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION
= ON):
# ( DEAL_II_WITH_64BIT_INDICES = OFF )
# ( DEAL_II_WITH_ARPACK = OFF )
# DEAL_II_WITH_BOOST set up with bundled packages
# BOOST_CXX_FLAGS = -Wno-unused-local-typedefs
# BOOST_BUNDLED_INCLUDE_DIRS =
/home/r/russ/lkaratun/aspect/dealii/bundled/boost-1.62.0/include
# BOOST_LIBRARIES = rt
# DEAL_II_WITH_BZIP2 set up with external dependencies
# BZIP2_VERSION = 1.0.5
# BZIP2_INCLUDE_DIRS = /usr/include
# BZIP2_LIBRARIES = /usr/lib64/libbz2.so
# ( DEAL_II_WITH_CUDA = OFF )
# DEAL_II_WITH_CXX11 = ON
# ( DEAL_II_WITH_CXX14 = OFF )
# ( DEAL_II_WITH_GSL = OFF )
# ( DEAL_II_WITH_HDF5 = OFF )
# ( DEAL_II_WITH_LAPACK = OFF )
# ( DEAL_II_WITH_METIS = OFF )
# DEAL_II_WITH_MPI set up with external dependencies
# MPI_VERSION = 2.1
# OMPI_VERSION = 1.6.4
# MPI_C_COMPILER = /scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/bin/mpicc
# MPI_CXX_COMPILER =
/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/bin/mpicxx
# MPI_Fortran_COMPILER =
/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/bin/mpif90
# MPI_CXX_FLAGS =
# MPI_LINKER_FLAGS = -Wl,--rpath -Wl,/opt/torque/lib
-Wl,--export-dynamic
# MPI_INCLUDE_DIRS = /scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/include
# MPI_USER_INCLUDE_DIRS =
/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/include
# MPI_LIBRARIES =
/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/lib/libmpi_cxx.so;/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/lib/libmpi_f90.so;/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/lib/libmpi_f77.so;/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/lib/libmpi.so;/scinet/gpc/Libraries/MXM_1.5/lib/libosmcomp.so;/usr/lib64/librdmacm.so;/usr/lib64/libibverbs.so;/scinet/gpc/Libraries/MXM_1.5/lib/libmxm.so;/opt/torque/lib/libtorque.so;rt;nsl;/usr/lib64/libutil.so;m;dl
# DEAL_II_WITH_MUPARSER set up with bundled packages
# MUPARSER_BUNDLED_INCLUDE_DIRS =
/home/r/russ/lkaratun/aspect/dealii/bundled/muparser_v2_2_4//include
# ( DEAL_II_WITH_NETCDF = OFF )
# ( DEAL_II_WITH_OPENCASCADE = OFF )
# DEAL_II_WITH_P4EST set up with external dependencies
# P4EST_VERSION = 0.3.4.2
# P4EST_DIR = /home/r/russ/lkaratun/aspect/p4est/FAST
# P4EST_INCLUDE_DIRS =
/home/r/russ/lkaratun/aspect/p4est/FAST/include
# P4EST_USER_INCLUDE_DIRS =
/home/r/russ/lkaratun/aspect/p4est/FAST/include
# P4EST_LIBRARIES =
/home/r/russ/lkaratun/aspect/p4est/FAST/lib/libp4est.so;/home/r/russ/lkaratun/aspect/p4est/FAST/lib/libsc.so;/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/lib/libmpi.so;/scinet/gpc/Libraries/MXM_1.5/lib/libosmcomp.so;/usr/lib64/librdmacm.so;/usr/lib64/libibverbs.so;/scinet/gpc/Libraries/MXM_1.5/lib/libmxm.so;/opt/torque/lib/libtorque.so;rt;nsl;/usr/lib64/libutil.so;m;dl
# ( DEAL_II_WITH_PETSC = OFF )
# ( DEAL_II_WITH_SLEPC = OFF )
# DEAL_II_WITH_THREADS set up with bundled packages
# THREADS_CXX_FLAGS = -Wno-parentheses
# THREADS_LINKER_FLAGS = -pthread
# THREADS_BUNDLED_INCLUDE_DIRS =
/home/r/russ/lkaratun/aspect/dealii/bundled/tbb41_20130401oss/include
# THREADS_LIBRARIES = dl
# DEAL_II_WITH_TRILINOS set up with external dependencies
# TRILINOS_VERSION = 11.4.3
# TRILINOS_DIR = /home/r/russ/lkaratun/aspect/trilinos
# TRILINOS_INCLUDE_DIRS =
/home/r/russ/lkaratun/aspect/trilinos/include
# TRILINOS_USER_INCLUDE_DIRS =
/home/r/russ/lkaratun/aspect/trilinos/include
# TRILINOS_LIBRARIES =
/home/r/russ/lkaratun/aspect/trilinos/lib/libstratimikos.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libstratimikosbelos.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libstratimikosaztecoo.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libstratimikosamesos.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libstratimikosml.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libstratimikosifpack.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libbelostpetra.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libbelosepetra.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libbelos.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libml.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libifpack.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libamesos.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libgaleri-xpetra.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libgaleri.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libaztecoo.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libisorropia.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libthyraepetra.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libthyracore.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libxpetra-sup.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libxpetra-ext.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libxpetra.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libepetraext.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libtpetraext.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libtpetrainout.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libtpetra.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libtriutils.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libzoltan.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libepetra.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libkokkosdisttsqr.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libkokkosnodetsqr.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libkokkoslinalg.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libkokkosnodeapi.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libkokkos.so;/home/r/russ/lkaratun/aspect/trilinos/lib/librtop.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libsacado.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libtpi.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libteuchosremainder.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libteuchosnumerics.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libteuchoscomm.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libteuchosparameterlist.so;/home/r/russ/lkaratun/aspect/trilinos/lib/libteuchoscore.so;/scinet/gpc/intel/ics/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_rt.so;/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/lib/libmpi_cxx.so;/scinet/gpc/mpi/openmpi/1.6.4-gcc-v4.7.2/lib/libmpi.so;/scinet/gpc/Libraries/MXM_1.5/lib/libosmcomp.so;/usr/lib64/librdmacm.so;/usr/lib64/libibverbs.so;/scinet/gpc/Libraries/MXM_1.5/lib/libmxm.so;/opt/torque/lib/libtorque.so;rt;nsl;/usr/lib64/libutil.so;m;dl
# ( DEAL_II_WITH_UMFPACK = OFF )
# DEAL_II_WITH_ZLIB set up with external dependencies
# ZLIB_VERSION = 1.2.3
# ZLIB_INCLUDE_DIRS = /usr/include
# ZLIB_LIBRARIES = /usr/lib64/libz.so
#
# Component configuration:
# ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
# DEAL_II_COMPONENT_EXAMPLES
# ( DEAL_II_COMPONENT_PACKAGE = OFF )
# ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
###
