[MOAB-dev] problem with pcomm

Lorenzo Alessio Botti lorenzoalessiobotti at gmail.com
Wed Dec 2 11:33:44 CST 2015 

This is what I get with gdb
Not very informative, is it?

moab is compiled with —enable-debug
Should I run with or compile with particular flags?

Reading symbols for shared libraries ++++++++..............bfd_mach_o_scan_read_symtab_symbol: symbol "_bzero" is unsupported 'indirect' reference: setting to undefined
bfd_mach_o_scan_read_symtab_symbol: symbol "_memccpy" is unsupported 'indirect' reference: setting to undefined
bfd_mach_o_scan_read_symtab_symbol: symbol "_memchr" is unsupported 'indirect' reference: setting to undefined
bfd_mach_o_scan_read_symtab_symbol: symbol "_memcmp" is unsupported 'indirect' reference: setting to undefined
bfd_mach_o_scan_read_symtab_symbol: symbol "_memcpy" is unsupported 'indirect' reference: setting to undefined
bfd_mach_o_scan_read_symtab_symbol: symbol "_memmove" is unsupported 'indirect' reference: setting to undefined
bfd_mach_o_scan_read_symtab_symbol: symbol "_memset" is unsupported 'indirect' reference: setting to undefined
bfd_mach_o_scan_read_symtab_symbol: symbol "_strchr" is unsupported 'indirect' reference: setting to undefined
bfd_mach_o_scan_read_symtab_symbol: symbol "_strcmp" is unsupported 'indirect' reference: setting to undefined
bfd_mach_o_scan_read_symtab_symbol: symbol "_strncmp" is unsupported 'indirect' reference: setting to undefined
...warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Objects/coretls.build/coretls.build/Objects-normal/x86_64/system_coretls_vers.o" - no debug information available for "system_coretls_vers.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_ciphersuites.a(tls_ciphersuites.o)" - no debug information available for "tls_ciphersuites.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslSession.o)" - no debug information available for "sslSession.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslCipherSpecs.o)" - no debug information available for "sslCipherSpecs.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslDigests.o)" - no debug information available for "sslDigests.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslCrypto.o)" - no debug information available for "sslCrypto.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslChangeCipher.o)" - no debug information available for "sslChangeCipher.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslCert.o)" - no debug information available for "sslCert.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslKeyExchange.o)" - no debug information available for "sslKeyExchange.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslAlertMessage.o)" - no debug information available for "sslAlertMessage.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslHandshake.o)" - no debug information available for "sslHandshake.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslHandshakeFinish.o)" - no debug information available for "sslHandshakeFinish.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(tls1Callouts.o)" - no debug information available for "tls1Callouts.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(sslHandshakeHello.o)" - no debug information available for "sslHandshakeHello.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(tls_handshake.o)" - no debug information available for "tls_handshake.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_handshake.a(ssl3Callouts.o)" - no debug information available for "ssl3Callouts.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(tls1RecordCallouts.o)" - no debug information available for "tls1RecordCallouts.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(ssl3RecordCallouts.o)" - no debug information available for "ssl3RecordCallouts.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(tls_record.o)" - no debug information available for "tls_record.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(sslRc4Cipher.o)" - no debug information available for "sslRc4Cipher.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(sslMemory.o)" - no debug information available for "sslMemory.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(sslUtils.o)" - no debug information available for "sslUtils.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(symCipherParams.o)" - no debug information available for "symCipherParams.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(sslNullCipher.o)" - no debug information available for "sslNullCipher.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(symCipher.o)" - no debug information available for "symCipher.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(tls_digest.o)" - no debug information available for "tls_digest.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(tls_hashhmac.o)" - no debug information available for "tls_hashhmac.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_record.a(tls_hmac.o)" - no debug information available for "tls_hmac.c".

warning: Could not find object file "/BinaryCache/coreTLS/coreTLS-35.40.1~1/Symbols/BuiltProducts/libcoretls_stream_parser.a(tls_stream_parser.o)" - no debug information available for "tls_stream_parser.c".

...................... done

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x0000000000001030
std::vector<char, std::allocator<char> >::begin (this=0x1030) at stl_vector.h:340
340	      { return const_iterator(this->_M_impl._M_start); }


> On 02 Dec 2015, at 18:29, Grindeanu, Iulian R. <iulian at mcs.anl.gov> wrote:
> 
> Dear Lorenzo,
> you just configure moab with --enable-debug
> 
> something like this:
> 
> ./configure --disable-fortran --disable-imesh --with-mpi=/Users/ihabia/src2/mpich-3.2/mpich3/ --with-hdf5=/Users/ihabia/src2/hdf5-1.8.16/hdf5/ --prefix=/Users/ihabia/src2/moab-4.8.2/moab  --enable-debug
> 
> I see now that you use hdf5 1.8.16, the make check error you see could be related to this
> (we test regularly with 1.8.12)
> 
> Still, your crash with pcomm is unrelated to hdf5 version
> 
> Iulian
> 
> From: Lorenzo Alessio Botti [lorenzoalessiobotti at gmail.com]
> Sent: Wednesday, December 02, 2015 11:11 AM
> To: MOAB dev
> Cc: Grindeanu, Iulian R.
> Subject: Re: [MOAB-dev] problem with pcomm
> 
> Dear Iulian, how do I enable debug mode?
> I want to be sure compile with the right flags…
> 
> Thanks 
> Lorenzo
> 
> 
>> On 02 Dec 2015, at 18:03, Grindeanu, Iulian R. <iulian at mcs.anl.gov <mailto:iulian at mcs.anl.gov>> wrote:
>> 
>> Hi Lorenzo,
>> Your code works on my linux machine.
>> It could be something specific to OSX, 
>> Sometimes we find that OSX uncovers bugs 
>> 
>> You mentioned that there is a seg fault at pcomm_tag(mbImpl, true)
>> 
>> It just creates there a sparse tag with name __PARALLEL_COMM, which will be used to store ParallelComm objects on the root (entity handle = 0)
>> 
>> Can you compile in debug mode and give more trace info?
>> 
>> Thanks,
>> Iulian
>> 
>> From: Lorenzo Alessio Botti [lorenzoalessiobotti at gmail.com <mailto:lorenzoalessiobotti at gmail.com>]
>> Sent: Wednesday, December 02, 2015 10:20 AM
>> To: MOAB dev
>> Cc: Grindeanu, Iulian R.; Vijay S. Mahadevan
>> Subject: Re: [MOAB-dev] problem with pcomm
>> 
>> 
>> 
>> =====================================
>>    MOAB 4.8.2: test/test-suite.log
>> =====================================
>> 
>> # TOTAL: 35
>> # PASS:  35
>> # SKIP:  0
>> # XFAIL: 0
>> # FAIL:  0
>> # XPASS: 0
>> # ERROR: 0
>> 
>> .. contents:: :depth: 2
>> 
>> This is the sole failure.
>> 
>> ==============================================
>>    MOAB 4.8.2: test/parallel/test-suite.log
>> ==============================================
>> 
>> # TOTAL: 11
>> # PASS:  10
>> # SKIP:  0
>> # XFAIL: 0
>> # FAIL:  1
>> # XPASS: 0
>> # ERROR: 0
>> 
>> .. contents:: :depth: 2
>> 
>> FAIL: parallel_hdf5_test
>> ========================
>> 
>> Running test_write_elements ...
>> Running test_write_elements ...
>> Warning: acis file has sequence numbers!
>> Warning: acis file has sequence numbers!
>> Warning: acis file has sequence numbers!
>> Running test_write_shared_sets ...
>> Running test_write_shared_sets ...
>> Warning: acis file has sequence numbers!
>> Warning: acis file has sequence numbers!
>> Warning: acis file has sequence numbers!
>> Running test_var_length_parallel ...
>> Running test_var_length_parallel ...
>> Running test_read_elements ...
>> Running test_read_elements ...
>> Running test_read_elements_by_rank ...
>> Running test_read_elements_by_rank ...
>> Running test_read_tags ...
>> Running test_read_tags ...
>> Running test_read_global_tags ...
>> Running test_read_global_tags ...
>> Running test_read_sets ...
>> Running test_read_sets ...
>> Running test_read_sets_bcast_dups ...
>> Running test_read_sets_bcast_dups ...
>> Running test_read_sets_read_dups ...
>> Running test_read_sets_read_dups ...
>> Running test_read_bc_sets ...
>> Running test_read_bc_sets ...
>> Fatal error in MPI_Reduce: Invalid datatype, error stack:
>> MPI_Reduce(1258): MPI_Reduce(sbuf=0x7fff533896d4, rbuf=0x7fff533896c8, count=3, MPI_DATATYPE_NULL, MPI_SUM, root=0, MPI_COMM_WORLD) failed
>> MPI_Reduce(1168): Datatype for argument datatype is a null datatype
>> FAIL parallel_hdf5_test (exit status: 3)
>> 
>> 
>> The whole code, without any MPI initialisation,
>> 
>> #include "moab/ParallelComm.hpp"
>> #include "MBParallelConventions.h"
>> #include "MBTagConventions.hpp"
>> #include "moab/Core.hpp"
>> #include "moab_mpi.h"
>> 
>> using namespace moab;
>> 
>> int main(int argc, char **argv)
>> {
>>   Core moab;
>>   Interface& imoab = moab;
>> 
>>   ParallelComm* pcomm = ParallelComm::get_pcomm(&moab, 0);
>>   if (0 == pcomm)
>>   {
>>     pcomm = new ParallelComm(&imoab, MPI_COMM_WORLD);
>>   }
>>   delete pcomm;
>>   return EXIT_SUCCESS;
>> };
>> 
>> ~         
>> 
>> This is the Makefile
>> MOAB_LIB_DIR = /Users/ihabia/src2/moab-4.8.2/moab/
>> include $(MOAB_LIB_DIR)/lib/moab.make
>> 
>> %.o : %.cpp
>>         @echo "Compiling ("$(CXX)") "$<" "
>>         @$(CXX) ${MOAB_INCLUDES} -c $< -o $@
>> 
>> CXX = mpicxx -O2 -DNDEBUG
>> 
>> objects := $(patsubst %.cpp,%.o,$(wildcard ./*.cpp))
>> 
>> mbtestrun : $(objects)
>>         @echo "Linking "$(CURDIR)"/"$@
>>         @$(CXX) $(objects) -o $@ $(MOAB_LIBS_LINK) 
>> 
>> .PHONY : clean 
>> 
>> clean :
>>         @rm $(objects)
>> 
>> 
>> and this is mob.make
>> 
>> # The values below are for an un-installed copy of MOAB used directly
>> # from its build build directory.  These values will be overridden below
>> # for installed copies of MOAB.
>> MOAB_LIBDIR = /Users/ihabia/src2/moab-4.8.2/src/.libs
>> MOAB_INCLUDES = -I/Users/ihabia/src2/moab-4.8.2/src \
>>                 -I/Users/ihabia/src2/moab-4.8.2/src \
>>                 -I/Users/ihabia/src2/moab-4.8.2/src/oldinc \
>>                 -I/Users/ihabia/src2/moab-4.8.2/src/parallel \
>>                 -I/Users/ihabia/src2/moab-4.8.2/src/parallel
>> 
>> MOAB_INCLUDES +=
>> 
>> MOAB_CPPFLAGS =        -I/Users/ihabia/src2/hdf5-1.8.16/hdf5//include -isystem /Users/ihabia/src2/hdf5-1.8.16/hdf5//include
>> MOAB_CXXFLAGS =  -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align  -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -stdlib=libstdc++ -O2 -DNDEBUG
>> MOAB_CFLAGS =  -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align  -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG
>> MOAB_FFLAGS =
>> MOAB_FCFLAGS =
>> MOAB_LDFLAGS =          -L/Users/ihabia/src2/hdf5-1.8.16/hdf5//lib  -stdlib=libstdc++
>> 
>> 
>> MOAB_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR} -lMOAB    -lhdf5    -lc++ -lz -ldl -lm       -lc++ -lz -ldl -lm
>> DAGMC_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR}  -lMOAB    -lhdf5    -lc++ -lz -ldl -lm       -lc++ -lz -ldl -lm
>> 
>> MOAB_CXX = /Users/ihabia/src2/mpich-3.2/mpich3//bin/mpicxx
>> MOAB_CC  = /Users/ihabia/src2/mpich-3.2/mpich3//bin/mpicc
>> MOAB_FC  =
>> MOAB_F77  =
>> 
>> # Override MOAB_LIBDIR and MOAB_INCLUDES from above with the correct
>> # values for the installed MOAB.
>> 
>> MOAB_LIBDIR=/Users/ihabia/src2/moab-4.8.2/moab/lib
>> MOAB_INCLUDES=-I/Users/ihabia/src2/moab-4.8.2/moab/include
>> 
>> 
>> 
>> 
>>> On 02 Dec 2015, at 16:17, Grindeanu, Iulian R. <iulian at mcs.anl.gov <mailto:iulian at mcs.anl.gov>> wrote:
>>> 
>>> Hi Lorenzo,
>>> 
>>> Do you initialize MPI before using moab? 
>>> 
>>> 
>>> Iulian
>>> 
>>> ________________________________________
>>> From: moab-dev-bounces at mcs.anl.gov <mailto:moab-dev-bounces at mcs.anl.gov> [moab-dev-bounces at mcs.anl.gov <mailto:moab-dev-bounces at mcs.anl.gov>] on behalf of Vijay S. Mahadevan [vijay.m at gmail.com <mailto:vijay.m at gmail.com>]
>>> Sent: Wednesday, December 02, 2015 9:08 AM
>>> To: Lorenzo Alessio Botti
>>> Cc: MOAB dev
>>> Subject: Re: [MOAB-dev] problem with pcomm
>>> 
>>> Lorenzo, we test your configuration very regularly (on buildbot and on
>>> linux machines) and I haven't seen any issues with ParallelComm. Does
>>> "make check" pass cleanly ?
>>> 
>>> I'll see if I can replicate this on my Mac.
>>> 
>>> Vijay
>>> 
>>> On Wed, Dec 2, 2015 at 8:49 AM, Lorenzo Alessio Botti
>>> <lorenzoalessiobotti at gmail.com <mailto:lorenzoalessiobotti at gmail.com>> wrote:
>>>> Dear All,
>>>> I have a problem with the latest moab builds (both 4.8.2 and 4.9)…
>>>> I cannot run the following code in an application linked to moab
>>>> 
>>>>  Core moab;
>>>> 
>>>>  Interface& imoab = moab;
>>>> 
>>>> 
>>>>  ParallelComm* pcomm = ParallelComm::get_pcomm(&moab, 0);
>>>> 
>>>>  if (0 == pcomm)
>>>> 
>>>>  {
>>>> 
>>>>    pcomm = new ParallelComm(&imoab, MPI_COMM_WORLD);
>>>> 
>>>>  }
>>>> 
>>>>  delete pcomm;
>>>> 
>>>> 
>>>> It seems that a segmentation fault is triggered during the initialization of
>>>> the pcomm in particular in this function
>>>> 
>>>>  Tag ParallelComm::pcomm_tag(Interface *impl,
>>>> 
>>>>                              bool create_if_missing)
>>>> 
>>>> 
>>>> with create_if_missing = true.
>>>> 
>>>> I’m building on OS X.
>>>> Have you ever experienced this issue? What can I do?
>>>> 
>>>> I attach the config.log below
>>>> 
>>>> 
>>>> 
>>>> Bests
>>>> Lorenzo

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