[MOAB-dev] crash with clang compiler
Barry Smith
bsmith at mcs.anl.gov
Mon Jun 3 14:06:58 CDT 2013
This is with the nightly version of moab.
Do any of you guys build on the Mac with the clang compilers?
Barry
=============================================================================== Running make on MOAB; this may take several minutes =============================================================================== *******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
-------------------------------------------------------------------------------
Error running make; make install on MOAB: Could not execute "cd /Users/barrysmith/Src/PETSc/externalpackages/moab-4.7.0pre && make && make install":
make all-recursive
Making all in src
make all-recursive
Making all in parallel
make all-am
/bin/sh ../../libtool --tag=CXX --mode=compile /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ParallelComm.lo -MD -MP -MF .deps/ParallelComm.Tpo -c -o ParallelComm.lo ParallelComm.cpp
libtool: compile: /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ParallelComm.lo -MD -MP -MF .deps/ParallelComm.Tpo -c ParallelComm.cpp -fno-common -DPIC -o .libs/ParallelComm.o
libtool: compile: /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ParallelComm.lo -MD -MP -MF .deps/ParallelComm.Tpo -c ParallelComm.cpp -o ParallelComm.o >/dev/null 2>&1
mv -f .deps/ParallelComm.Tpo .deps/ParallelComm.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ProcConfig.lo -MD -MP -MF .deps/ProcConfig.Tpo -c -o ProcConfig.lo ProcConfig.cpp
libtool: compile: /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ProcConfig.lo -MD -MP -MF .deps/ProcConfig.Tpo -c ProcConfig.cpp -fno-common -DPIC -o .libs/ProcConfig.o
libtool: compile: /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ProcConfig.lo -MD -MP -MF .deps/ProcConfig.Tpo -c ProcConfig.cpp -o ProcConfig.o >/dev/null 2>&1
mv -f .deps/ProcConfig.Tpo .deps/ProcConfig.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ParallelData.lo -MD -MP -MF .deps/ParallelData.Tpo -c -o ParallelData.lo ParallelData.cpp
libtool: compile: /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ParallelData.lo -MD -MP -MF .deps/ParallelData.Tpo -c ParallelData.cpp -fno-common -DPIC -o .libs/ParallelData.o
libtool: compile: /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ParallelData.lo -MD -MP -MF .deps/ParallelData.Tpo -c ParallelData.cpp -o ParallelData.o >/dev/null 2>&1
mv -f .deps/ParallelData.Tpo .deps/ParallelData.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ParallelMergeMesh.lo -MD -MP -MF .deps/ParallelMergeMesh.Tpo -c -o ParallelMergeMesh.lo ParallelMergeMesh.cpp
libtool: compile: /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ParallelMergeMesh.lo -MD -MP -MF .deps/ParallelMergeMesh.Tpo -c ParallelMergeMesh.cpp -fno-common -DPIC -o .libs/ParallelMergeMesh.o
libtool: compile: /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ParallelMergeMesh.lo -MD -MP -MF .deps/ParallelMergeMesh.Tpo -c ParallelMergeMesh.cpp -o ParallelMergeMesh.o >/dev/null 2>&1
mv -f .deps/ParallelMergeMesh.Tpo .deps/ParallelMergeMesh.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ReadParallel.lo -MD -MP -MF .deps/ReadParallel.Tpo -c -o ReadParallel.lo ReadParallel.cpp
libtool: compile: /Users/barrysmith/Src/PETSc/arch-xolotl/bin/mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -I/Users/barrysmith/Src/PETSc/arch-xolotl/include -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -fPIC -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -MT ReadParallel.lo -MD -MP -MF .deps/ReadParallel.Tpo -c ReadParallel.cpp -fno-common -DPIC -o .libs/ReadParallel.o
In file included from ParallelComm.cpp:2:
./moab/ParallelComm.hpp:737:33: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
void set_stored_size() {*((int*)mem_ptr) = (int)(buff_ptr - mem_ptr);}
^~~~~~~~~~~~~
./moab/ParallelComm.hpp:738:39: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
int get_stored_size() {return *((int*)mem_ptr);}
^~~~~~~~~~~~~
ParallelComm.cpp:605:11: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
*((int*)(buff.mem_ptr + prev_size)) = buff_size;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ParallelComm.cpp:692:26: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
(int*)(remoteOwnedBuffs[ind]->mem_ptr),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ParallelComm.cpp:1137:30: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
(int*)(localOwnedBuffs[ind2/2]->mem_ptr),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ParallelComm.cpp:3734:53: warning: cast from 'int *' to 'long *' increases required alignment from 4 to 8 [-Wcast-align]
result = gsd->initialize(skin_ents[0].size(), (long*)&gid_data[0],
^~~~~~~~~~~~~~~~~~~
ParallelComm.cpp:5469:27: warning: argument type 'int *' doesn't match specified 'MPI' type tag that requires 'unsigned char *' [-Wtype-safety]
success = MPI_Irecv(ack_buff, sizeof(int),
^~~~~~~~
ParallelComm.cpp:5561:16: warning: cast from 'unsigned char *' to 'size_t *' (aka 'unsigned long *') increases required alignment from 1 to 8 [-Wcast-align]
assert(*((size_t*)send_buff->mem_ptr) > INITIAL_BUFF_SIZE);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/assert.h:93:25: note: expanded from macro 'assert'
(__builtin_expect(!(e), 0) ? __assert_rtn(__func__, __FILE__, __LINE__, #e) : (void)0)
^
ParallelComm.cpp:8183:25: warning: argument type 'moab::ParallelComm::SharedEntityData *' doesn't match specified 'MPI' type tag that requires 'unsigned char *' [-Wtype-safety]
ierr = MPI_Irecv( &result[i][0],
^~~~~~~~~~~~~
ParallelComm.cpp:8193:25: warning: argument type 'moab::ParallelComm::SharedEntityData *' doesn't match specified 'MPI' type tag that requires 'unsigned char *' [-Wtype-safety]
ierr = MPI_Isend( &send_data[i][0],
^~~~~~~~~~~~~~~~
ParallelComm.cpp:8588:17: warning: cast from 'char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
int numents = *(int*)(((char*)recvbuf)+displs[i]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ParallelComm.cpp:8589:16: warning: cast from 'char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
int* id_ptr = (int*)(((char*)recvbuf)+displs[i]+sizeof(int));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ParallelComm.cpp:8715:70: warning: cast from 'unsigned char *' to 'double *' increases required alignment from 1 to 8 [-Wcast-align]
result = mbImpl->get_coords(&intx_nodes[0], intx_nodes.size(), (double*)buff->buff_ptr);
^~~~~~~~~~~~~~~~~~~~~~~
13 warnings generated.
In file included from ParallelData.cpp:2:
./moab/ParallelComm.hpp:737:33: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
void set_stored_size() {*((int*)mem_ptr) = (int)(buff_ptr - mem_ptr);}
^~~~~~~~~~~~~
./moab/ParallelComm.hpp:738:39: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
int get_stored_size() {return *((int*)mem_ptr);}
^~~~~~~~~~~~~
2 warnings generated.
In file included from ParallelMergeMesh.cpp:1:
In file included from ./moab/ParallelMergeMesh.hpp:7:
./moab/ParallelComm.hpp:737:33: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
void set_stored_size() {*((int*)mem_ptr) = (int)(buff_ptr - mem_ptr);}
^~~~~~~~~~~~~
./moab/ParallelComm.hpp:738:39: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
int get_stored_size() {return *((int*)mem_ptr);}
^~~~~~~~~~~~~
2 warnings generated.
In file included from ReadParallel.cpp:8:
./moab/ParallelComm.hpp:737:33: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
void set_stored_size() {*((int*)mem_ptr) = (int)(buff_ptr - mem_ptr);}
^~~~~~~~~~~~~
./moab/ParallelComm.hpp:738:39: warning: cast from 'unsigned char *' to 'int *' increases required alignment from 1 to 4 [-Wcast-align]
int get_stored_size() {return *((int*)mem_ptr);}
^~~~~~~~~~~~~
0 clang 0x0000000100c57bb2 main + 12932498
Stack dump:
0. Program arguments: /usr/bin/clang -cc1 -triple x86_64-apple-macosx10.8.0 -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name ReadParallel.cpp -pic-level 2 -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 136 -g -coverage-file /Users/barrysmith/Src/PETSc/externalpackages/moab-4.7.0pre/src/parallel/.libs/ReadParallel.o -resource-dir /usr/bin/../lib/clang/4.2 -dependency-file .deps/ReadParallel.Tpo -sys-header-deps -MP -MT ReadParallel.lo -isystem /Users/barrysmith/Src/PETSc/arch-xolotl/include -D HAVE_CONFIG_H -D TEMPLATE_SPECIALIZATION -D TEMPLATE_FUNC_SPECIALIZATION -D HAVE_VSNPRINTF -D _FILE_OFFSET_BITS=64 -D USE_MPI -D HDF5_FILE -D HDF5_PARALLEL -D NETCDF_FILE -D IS_BUILDING_MB -D SRCDIR=. -D UNORDERED_MAP_NS=std::tr1 -D HAVE_UNORDERED_MAP=tr1/unordered_map -D HAVE_UNORDERED_SET=tr1/unordered_set -D PIC -I . -I ../.. -I ../../src/moab -I ../../src -I /Users/barrysmith/Src/PETSc/arch-xolotl/include -I /Users/barrysmith/Src/PETSc/arch-xolotl/include -I ./.. -I .. -I ./../io -I ./../io/mhdf/include -I /Users/barrysmith/Src/PETSc/arch-xolotl/include -fmodule-cache-path /var/folders/c1/ldz_dt8n2r3dtwv_chp5pfr40000gq/T/clang-module-cache -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wall -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -pedantic -fconst-strings -fdeprecated-macro -fdebug-compilation-dir /Users/barrysmith/Src/PETSc/externalpackages/moab-4.7.0pre/src/parallel -ferror-limit 19 -fmessage-length 0 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime=macosx-10.8.0 -fobjc-dispatch-method=mixed -fobjc-default-synthesize-properties -fcxx-exceptions -fexceptions -fno-common -fdiagnostics-show-option -o .libs/ReadParallel.o -x c++ ReadParallel.cpp
1. ReadParallel.cpp:549:56: current parser token ')'
2. ReadParallel.cpp:18:1: parsing namespace 'moab'
3. ReadParallel.cpp:264:1: parsing function body 'load_file'
4. ReadParallel.cpp:264:1: in compound statement ('{}')
5. ReadParallel.cpp:540:16: in compound statement ('{}')
6. ReadParallel.cpp:547:50: in compound statement ('{}')
clang: error: unable to execute command: Segmentation fault: 11
clang: error: clang frontend command failed due to signal (use -v to see invocation)
Apple LLVM version 4.2 (clang-425.0.28) (based on LLVM 3.2svn)
Target: x86_64-apple-darwin12.3.0
Thread model: posix
clang: note: diagnostic msg: PLEASE submit a bug report to http://developer.apple.com/bugreporter/ and include the crash backtrace, preprocessed source, and associated run script.
clang: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang: note: diagnostic msg: /var/folders/c1/ldz_dt8n2r3dtwv_chp5pfr40000gq/T/ReadParallel-EE94m9.cpp
clang: note: diagnostic msg: /var/folders/c1/ldz_dt8n2r3dtwv_chp5pfr40000gq/T/ReadParallel-EE94m9.sh
clang: note: diagnostic msg:
********************
make[5]: *** [ReadParallel.lo] Error 1
make[4]: *** [all] Error 2
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
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