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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Lorenzo,<br>
This seems to be a problem on your system.<br>
Maybe gdb is broken? <br>
<br>
<a href="http://stackoverflow.com/questions/33159172/unable-to-step-into-a-class-method-gdb" target="_blank">http://stackoverflow.com/questions/33159172/unable-to-step-into-a-class-method-gdb</a><br>
<br>
Indeed, the message is not helpful in finding out what is the issue <br>
<br>
Maybe Vijay or Rajeev can help more, they do compile on macs. <br>
<br>
How did you configure hdf5? Did you use the same mpich version? <br>
<br>
<br>
Thanks,<br>
Iulian<br>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF323257"><font size="2" color="#000000" face="Tahoma"><b>From:</b> Lorenzo Alessio Botti [lorenzoalessiobotti@gmail.com]<br>
<b>Sent:</b> Wednesday, December 02, 2015 11:33 AM<br>
<b>To:</b> MOAB dev<br>
<b>Cc:</b> Grindeanu, Iulian R.<br>
<b>Subject:</b> Re: [MOAB-dev] problem with pcomm<br>
</font><br>
</div>
<div></div>
<div>
<div class="">This is what I get with gdb</div>
<div class="">Not very informative, is it?</div>
<div class=""><br class="">
</div>
<div class="">moab is compiled with —enable-debug</div>
<div class="">Should I run with or compile with particular flags?</div>
<div class=""><br class="">
</div>
<div class="">
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Reading symbols for shared libraries ++++++++..............bfd_mach_o_scan_read_symtab_symbol: symbol "_bzero" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
bfd_mach_o_scan_read_symtab_symbol: symbol "_memccpy" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
bfd_mach_o_scan_read_symtab_symbol: symbol "_memchr" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
bfd_mach_o_scan_read_symtab_symbol: symbol "_memcmp" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
bfd_mach_o_scan_read_symtab_symbol: symbol "_memcpy" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
bfd_mach_o_scan_read_symtab_symbol: symbol "_memmove" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
bfd_mach_o_scan_read_symtab_symbol: symbol "_memset" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
bfd_mach_o_scan_read_symtab_symbol: symbol "_strchr" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
bfd_mach_o_scan_read_symtab_symbol: symbol "_strcmp" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
bfd_mach_o_scan_read_symtab_symbol: symbol "_strncmp" is unsupported 'indirect' reference: setting to undefined</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
...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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
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".</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
...................... done</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Program received signal EXC_BAD_ACCESS, Could not access memory.</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Reason: KERN_INVALID_ADDRESS at address: 0x0000000000001030</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
std::vector<char, std::allocator<char> >::begin (this=0x1030) at stl_vector.h:340</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
340<span class="Apple-tab-span" style="white-space:pre"> </span> { return const_iterator(this->_M_impl._M_start); }</p>
</div>
<div class=""><br class="">
</div>
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 02 Dec 2015, at 18:29, Grindeanu, Iulian R. <<a href="mailto:iulian@mcs.anl.gov" class="" target="_blank">iulian@mcs.anl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" style="font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; direction:ltr; font-family:Tahoma; font-size:10pt">
Dear Lorenzo,<br class="">
you just configure moab with --enable-debug<br class="">
<br class="">
something like this:<br class="">
<br class="">
./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<br class="">
<br class="">
I see now that you use hdf5 1.8.16, the make check error you see could be related to this<br class="">
(we test regularly with 1.8.12)<br class="">
<br class="">
Still, your crash with pcomm is unrelated to hdf5 version<br class="">
<br class="">
Iulian<br class="">
<br class="">
<div class="" style="font-family:'Times New Roman'; font-size:16px">
<hr tabindex="-1" class="">
<div id="divRpF280912" class="" style="direction:ltr"><font class="" size="2" face="Tahoma"><b class="">From:</b><span class="Apple-converted-space"> </span>Lorenzo Alessio Botti [<a href="mailto:lorenzoalessiobotti@gmail.com" class="" target="_blank">lorenzoalessiobotti@gmail.com</a>]<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, December 02, 2015 11:11 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>MOAB dev<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Grindeanu, Iulian R.<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [MOAB-dev] problem with pcomm<br class="">
</font><br class="">
</div>
<div class=""></div>
<div class="">
<div class="">Dear Iulian, how do I enable debug mode?</div>
<div class="">I want to be sure compile with the right flags…</div>
<div class=""><br class="">
</div>
<div class="">Thanks </div>
<div class="">Lorenzo</div>
<div class=""><br class="">
</div>
<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 02 Dec 2015, at 18:03, Grindeanu, Iulian R. <<a href="mailto:iulian@mcs.anl.gov" class="" target="_blank">iulian@mcs.anl.gov</a>> wrote:</div>
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Hi Lorenzo,<br class="">
Your code works on my linux machine.<br class="">
It could be something specific to OSX,<span class="Apple-converted-space"> </span><br class="">
Sometimes we find that OSX uncovers bugs<span class="Apple-converted-space"> </span><br class="">
<br class="">
You mentioned that there is a seg fault at pcomm_tag(mbImpl, true)<br class="">
<br class="">
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)<br class="">
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Can you compile in debug mode and give more trace info?<br class="">
<br class="">
Thanks,<br class="">
Iulian<br class="">
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<div id="divRpF408631" class="" style="direction:ltr"><font class="" size="2" face="Tahoma"><b class="">From:</b><span class="Apple-converted-space"> </span>Lorenzo Alessio Botti [<a href="mailto:lorenzoalessiobotti@gmail.com" class="" target="_blank">lorenzoalessiobotti@gmail.com</a>]<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, December 02, 2015 10:20 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>MOAB dev<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Grindeanu, Iulian R.; Vijay S. Mahadevan<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [MOAB-dev] problem with pcomm<br class="">
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=====================================</div>
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MOAB 4.8.2: test/test-suite.log</div>
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=====================================</div>
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# TOTAL: 35</div>
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# PASS: 35</div>
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# SKIP: 0</div>
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# XFAIL: 0</div>
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# FAIL: 0</div>
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# XPASS: 0</div>
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# ERROR: 0</div>
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.. contents:: :depth: 2</div>
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<div class="">This is the sole failure.</div>
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==============================================</div>
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MOAB 4.8.2: test/parallel/test-suite.log</div>
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==============================================</div>
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# TOTAL: 11</div>
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# PASS: 10</div>
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# SKIP: 0</div>
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# XFAIL: 0</div>
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# FAIL: 1</div>
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# XPASS: 0</div>
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# ERROR: 0</div>
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.. contents:: :depth: 2</div>
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FAIL: parallel_hdf5_test</div>
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========================</div>
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Running test_write_elements ...</div>
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Running test_write_elements ...</div>
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Warning: acis file has sequence numbers!</div>
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Warning: acis file has sequence numbers!</div>
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Warning: acis file has sequence numbers!</div>
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Running test_write_shared_sets ...</div>
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Running test_write_shared_sets ...</div>
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Warning: acis file has sequence numbers!</div>
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Warning: acis file has sequence numbers!</div>
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Warning: acis file has sequence numbers!</div>
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Running test_var_length_parallel ...</div>
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Running test_var_length_parallel ...</div>
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Running test_read_elements ...</div>
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Running test_read_elements ...</div>
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Running test_read_elements_by_rank ...</div>
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Running test_read_elements_by_rank ...</div>
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Running test_read_tags ...</div>
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Running test_read_tags ...</div>
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Running test_read_global_tags ...</div>
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Running test_read_global_tags ...</div>
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Running test_read_sets ...</div>
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Running test_read_sets ...</div>
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Running test_read_sets_bcast_dups ...</div>
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Running test_read_sets_bcast_dups ...</div>
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Running test_read_sets_read_dups ...</div>
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Running test_read_sets_read_dups ...</div>
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Running test_read_bc_sets ...</div>
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Running test_read_bc_sets ...</div>
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Fatal error in MPI_Reduce: Invalid datatype, error stack:</div>
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MPI_Reduce(1258): MPI_Reduce(sbuf=0x7fff533896d4, rbuf=0x7fff533896c8, count=3, MPI_DATATYPE_NULL, MPI_SUM, root=0, MPI_COMM_WORLD) failed</div>
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MPI_Reduce(1168): Datatype for argument datatype is a null datatype</div>
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FAIL parallel_hdf5_test (exit status: 3)</div>
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<div class="">The whole code, without any MPI initialisation,</div>
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<span class="" style="color:rgb(213,59,211)">#include<span class="Apple-converted-space"> </span></span>"moab/ParallelComm.hpp"</div>
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<span class="" style="color:rgb(213,59,211)">#include<span class="Apple-converted-space"> </span></span>"MBParallelConventions.h"</div>
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<span class="" style="color:rgb(213,59,211)">#include<span class="Apple-converted-space"> </span></span>"MBTagConventions.hpp"</div>
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<span class="" style="color:rgb(213,59,211)">#include<span class="Apple-converted-space"> </span></span>"moab/Core.hpp"</div>
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<span class="" style="color:rgb(213,59,211)">#include<span class="Apple-converted-space"> </span></span>"moab_mpi.h"</div>
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</div>
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<span class="" style="color:rgb(175,173,36)">using</span><span class="" style="color:rgb(245,245,245)"> </span>namespace<span class="" style="color:rgb(245,245,245)"><span class="Apple-converted-space"> </span>moab;</span></div>
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<br class="">
</div>
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<span class="" style="color:rgb(52,189,38)">int</span><span class="Apple-converted-space"> </span>main(<span class="" style="color:rgb(52,189,38)">int</span><span class="Apple-converted-space"> </span>argc,<span class="Apple-converted-space"> </span><span class="" style="color:rgb(52,189,38)">char</span><span class="Apple-converted-space"> </span>**argv)</div>
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{</div>
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Core moab;</div>
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Interface& imoab = moab;</div>
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ParallelComm* pcomm = ParallelComm::get_pcomm(&moab,<span class="Apple-converted-space"> </span><span class="" style="color:rgb(206,121,36)">0</span>);</div>
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<span class="Apple-converted-space"> </span><span class="" style="color:rgb(175,173,36)">if</span><span class="Apple-converted-space"> </span>(<span class="" style="color:rgb(206,121,36)">0</span><span class="Apple-converted-space"> </span>== pcomm)</div>
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{</div>
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pcomm =<span class="Apple-converted-space"> </span><span class="" style="color:rgb(175,173,36)">new</span><span class="Apple-converted-space"> </span>ParallelComm(&imoab, MPI_COMM_WORLD);</div>
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}</div>
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<span class="Apple-converted-space"> </span><span class="" style="color:rgb(175,173,36)">delete</span><span class="Apple-converted-space"> </span>pcomm;</div>
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<span class="" style="color:rgb(245,245,245)"> <span class="Apple-converted-space"> </span></span><span class="" style="color:rgb(175,173,36)">return</span><span class="" style="color:rgb(245,245,245)"> </span>EXIT_SUCCESS<span class="" style="color:rgb(245,245,245)">;</span></div>
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};</div>
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<b class="">~ </b></div>
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<div class="">This is the Makefile</div>
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<span class="" style="color:rgb(52,187,199)"><b class="">MOAB_LIB_DIR<span class="Apple-converted-space"> </span></b></span>= /Users/ihabia/src2/moab-4.8.2/moab/</div>
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<span class="" style="color:rgb(213,59,211)">include</span><span class="Apple-converted-space"> </span><span class="" style="color:rgb(52,187,199)"><b class="">$(MOAB_LIB_DIR)</b></span>/lib/moab.make</div>
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<b class="">%.o :</b><span class="" style="color:rgb(245,245,245)"> </span><b class="">%</b><span class="" style="color:rgb(245,245,245)">.cpp</span></div>
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<span class="" style="color:rgb(213,59,211)"> @</span>echo "Compiling ("<span class="" style="color:rgb(52,187,199)"><b class="">$(CXX)</b></span>") "<span class="" style="color:rgb(52,187,199)"><b class="">$<</b></span>" "</div>
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<span class="" style="color:rgb(213,59,211)"> @</span><b class="">$(CXX)</b><span class="" style="color:rgb(206,121,36)"> </span><b class="">${MOAB_INCLUDES}</b><span class="" style="color:rgb(206,121,36)"><span class="Apple-converted-space"> </span>-c<span class="Apple-converted-space"> </span></span><b class="">$<</b><span class="" style="color:rgb(206,121,36)"><span class="Apple-converted-space"> </span>-o<span class="Apple-converted-space"> </span></span><b class="">$@</b></div>
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<span class="" style="color:rgb(52,187,199)"><b class="">CXX<span class="Apple-converted-space"> </span></b></span>= mpicxx -O2 -DNDEBUG</div>
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</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
<b class="">objects<span class="Apple-converted-space"> </span></b><span class="" style="color:rgb(245,245,245)">:=<span class="Apple-converted-space"> </span></span><b class="">$(</b><span class="" style="color:rgb(175,173,36)">patsubst</span><b class=""><span class="Apple-converted-space"> </span>%.cpp,%.o,$(</b><span class="" style="color:rgb(175,173,36)">wildcard</span><b class=""><span class="Apple-converted-space"> </span>./*.cpp))</b></div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
<b class="">mbtestrun :</b><span class="" style="color:rgb(245,245,245)"> </span><b class="">$(objects)</b></div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(206,121,36); background-color:rgb(0,0,0)">
<span class="" style="color:rgb(213,59,211)"> @</span>echo "Linking "<span class="" style="color:rgb(52,187,199)"><b class="">$(CURDIR)</b></span>"/"<span class="" style="color:rgb(52,187,199)"><b class="">$@</b></span></div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
<span class="" style="color:rgb(213,59,211)"> @</span><b class="">$(CXX)</b><span class="" style="color:rgb(206,121,36)"> </span><b class="">$(objects)</b><span class="" style="color:rgb(206,121,36)"><span class="Apple-converted-space"> </span>-o<span class="Apple-converted-space"> </span></span><b class="">$@</b><span class="" style="color:rgb(206,121,36)"> </span><b class="">$(MOAB_LIBS_LINK)</b><span class="" style="color:rgb(206,121,36)"> </span></div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(175,173,36); background-color:rgb(0,0,0)">
.PHONY :<span class="" style="color:rgb(245,245,245)"><span class="Apple-converted-space"> </span>clean </span></div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
<b class="">clean :</b></div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
<span class="" style="color:rgb(213,59,211)"> @</span><span class="" style="color:rgb(206,121,36)">rm<span class="Apple-converted-space"> </span></span><b class="">$(objects)</b></div>
<div class=""><b class=""><br class="">
</b></div>
</div>
<div class=""><br class="">
</div>
<div class="">and this is mob.make</div>
<div class=""><br class="">
</div>
<div class="">
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
# The values below are for an un-installed copy of MOAB used directly</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
# from its build build directory. These values will be overridden below</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
# for installed copies of MOAB.</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_LIBDIR = /Users/ihabia/src2/moab-4.8.2/src/.libs</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_INCLUDES = -I/Users/ihabia/src2/moab-4.8.2/src \</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
-I/Users/ihabia/src2/moab-4.8.2/src \</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
-I/Users/ihabia/src2/moab-4.8.2/src/oldinc \</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
-I/Users/ihabia/src2/moab-4.8.2/src/parallel \</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
-I/Users/ihabia/src2/moab-4.8.2/src/parallel</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_INCLUDES +=</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_CPPFLAGS = -I/Users/ihabia/src2/hdf5-1.8.16/hdf5//include -isystem /Users/ihabia/src2/hdf5-1.8.16/hdf5//include</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_CXXFLAGS = -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -stdlib=libstdc++ -O2 -DNDEBUG</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_CFLAGS = -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_FFLAGS =</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_FCFLAGS =</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_LDFLAGS = -L/Users/ihabia/src2/hdf5-1.8.16/hdf5//lib -stdlib=libstdc++</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR} -lMOAB -lhdf5 -lc++ -lz -ldl -lm -lc++ -lz -ldl -lm</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
DAGMC_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR} -lMOAB -lhdf5 -lc++ -lz -ldl -lm -lc++ -lz -ldl -lm</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_CXX = /Users/ihabia/src2/mpich-3.2/mpich3//bin/mpicxx</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_CC = /Users/ihabia/src2/mpich-3.2/mpich3//bin/mpicc</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_FC =</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_F77 =</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
# Override MOAB_LIBDIR and MOAB_INCLUDES from above with the correct</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
# values for the installed MOAB.</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_LIBDIR=/Users/ihabia/src2/moab-4.8.2/moab/lib</div>
<div class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_INCLUDES=-I/Users/ihabia/src2/moab-4.8.2/moab/include</div>
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 02 Dec 2015, at 16:17, Grindeanu, Iulian R. <<a href="mailto:iulian@mcs.anl.gov" class="" target="_blank">iulian@mcs.anl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi Lorenzo,<br class="">
<br class="">
Do you initialize MPI before using moab?<span class="Apple-converted-space"> </span><br class="">
<br class="">
<br class="">
Iulian<br class="">
<br class="">
________________________________________<br class="">
From:<span class="Apple-converted-space"> </span><a href="mailto:moab-dev-bounces@mcs.anl.gov" class="" target="_blank">moab-dev-bounces@mcs.anl.gov</a><span class="Apple-converted-space"> </span>[<a href="mailto:moab-dev-bounces@mcs.anl.gov" class="" target="_blank">moab-dev-bounces@mcs.anl.gov</a>]
on behalf of Vijay S. Mahadevan [<a href="mailto:vijay.m@gmail.com" class="" target="_blank">vijay.m@gmail.com</a>]<br class="">
Sent: Wednesday, December 02, 2015 9:08 AM<br class="">
To: Lorenzo Alessio Botti<br class="">
Cc: MOAB dev<br class="">
Subject: Re: [MOAB-dev] problem with pcomm<br class="">
<br class="">
Lorenzo, we test your configuration very regularly (on buildbot and on<br class="">
linux machines) and I haven't seen any issues with ParallelComm. Does<br class="">
"make check" pass cleanly ?<br class="">
<br class="">
I'll see if I can replicate this on my Mac.<br class="">
<br class="">
Vijay<br class="">
<br class="">
On Wed, Dec 2, 2015 at 8:49 AM, Lorenzo Alessio Botti<br class="">
<<a href="mailto:lorenzoalessiobotti@gmail.com" class="" target="_blank">lorenzoalessiobotti@gmail.com</a>> wrote:<br class="">
<blockquote type="cite" class="">Dear All,<br class="">
I have a problem with the latest moab builds (both 4.8.2 and 4.9)…<br class="">
I cannot run the following code in an application linked to moab<br class="">
<br class="">
Core moab;<br class="">
<br class="">
Interface& imoab = moab;<br class="">
<br class="">
<br class="">
ParallelComm* pcomm = ParallelComm::get_pcomm(&moab, 0);<br class="">
<br class="">
if (0 == pcomm)<br class="">
<br class="">
{<br class="">
<br class="">
pcomm = new ParallelComm(&imoab, MPI_COMM_WORLD);<br class="">
<br class="">
}<br class="">
<br class="">
delete pcomm;<br class="">
<br class="">
<br class="">
It seems that a segmentation fault is triggered during the initialization of<br class="">
the pcomm in particular in this function<br class="">
<br class="">
Tag ParallelComm::pcomm_tag(Interface *impl,<br class="">
<br class="">
bool create_if_missing)<br class="">
<br class="">
<br class="">
with create_if_missing = true.<br class="">
<br class="">
I’m building on OS X.<br class="">
Have you ever experienced this issue? What can I do?<br class="">
<br class="">
I attach the config.log below<br class="">
<br class="">
<br class="">
<br class="">
Bests<br class="">
Lorenzo</blockquote>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
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