[MOAB-dev] problem with pcomm

Wed Dec 2 11:58:04 CST 2015

Hi Lorenzo,
This seems to be a problem on your system.
Maybe gdb is broken?

http://stackoverflow.com/questions/33159172/unable-to-step-into-a-class-method-gdb

Indeed, the message is not helpful in finding out what is the issue

Maybe Vijay or Rajeev can help more, they do compile on macs.

How did you configure hdf5? Did you use the same mpich version?

Thanks,
Iulian
________________________________
From: Lorenzo Alessio Botti [lorenzoalessiobotti at gmail.com]
Sent: Wednesday, December 02, 2015 11:33 AM
To: MOAB dev
Cc: Grindeanu, Iulian R.
Subject: Re: [MOAB-dev] problem with pcomm

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<mailto: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<mailto: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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/moab-dev/attachments/20151202/c9d306ef/attachment-0001.html>