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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Lorenzo,<br>
Your code works on my linux machine.<br>
It could be something specific to OSX, <br>
Sometimes we find that OSX uncovers bugs <br>
<br>
You mentioned that there is a seg fault at pcomm_tag(mbImpl, true)<br>
<br>
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>
<br>
Can you compile in debug mode and give more trace info?<br>
<br>
Thanks,<br>
Iulian<br>
<br>
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<div style="direction: ltr;" id="divRpF408631"><font size="2" color="#000000" face="Tahoma"><b>From:</b> Lorenzo Alessio Botti [lorenzoalessiobotti@gmail.com]<br>
<b>Sent:</b> Wednesday, December 02, 2015 10:20 AM<br>
<b>To:</b> MOAB dev<br>
<b>Cc:</b> Grindeanu, Iulian R.; Vijay S. Mahadevan<br>
<b>Subject:</b> Re: [MOAB-dev] problem with pcomm<br>
</font><br>
</div>
<div></div>
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<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
=====================================</p>
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MOAB 4.8.2: test/test-suite.log</p>
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=====================================</p>
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# TOTAL: 35</p>
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# PASS: 35</p>
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# SKIP: 0</p>
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# XFAIL: 0</p>
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# FAIL: 0</p>
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# XPASS: 0</p>
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# ERROR: 0</p>
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.. contents:: :depth: 2</p>
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<div class="">This is the sole failure.</div>
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==============================================</p>
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MOAB 4.8.2: test/parallel/test-suite.log</p>
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==============================================</p>
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# TOTAL: 11</p>
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# PASS: 10</p>
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# SKIP: 0</p>
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# XFAIL: 0</p>
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# FAIL: 1</p>
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# XPASS: 0</p>
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# ERROR: 0</p>
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.. contents:: :depth: 2</p>
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FAIL: parallel_hdf5_test</p>
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========================</p>
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Running test_write_elements ...</p>
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Running test_write_elements ...</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Warning: acis file has sequence numbers!</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Warning: acis file has sequence numbers!</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Warning: acis file has sequence numbers!</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Running test_write_shared_sets ...</p>
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Running test_write_shared_sets ...</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Warning: acis file has sequence numbers!</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Warning: acis file has sequence numbers!</p>
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Warning: acis file has sequence numbers!</p>
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Running test_var_length_parallel ...</p>
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Running test_var_length_parallel ...</p>
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Running test_read_elements ...</p>
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Running test_read_elements ...</p>
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Running test_read_elements_by_rank ...</p>
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Running test_read_elements_by_rank ...</p>
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Running test_read_tags ...</p>
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Running test_read_tags ...</p>
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Running test_read_global_tags ...</p>
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Running test_read_global_tags ...</p>
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Running test_read_sets ...</p>
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Running test_read_sets ...</p>
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Running test_read_sets_bcast_dups ...</p>
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Running test_read_sets_bcast_dups ...</p>
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Running test_read_sets_read_dups ...</p>
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Running test_read_sets_read_dups ...</p>
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Running test_read_bc_sets ...</p>
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Running test_read_bc_sets ...</p>
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Fatal error in MPI_Reduce: Invalid datatype, error stack:</p>
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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</p>
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MPI_Reduce(1168): Datatype for argument datatype is a null datatype</p>
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FAIL parallel_hdf5_test (exit status: 3)</p>
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</div>
<div class="">The whole code, without any MPI initialisation,</div>
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<span class="" style="color:#d53bd3">#include </span>"moab/ParallelComm.hpp"</p>
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<span class="" style="color:#d53bd3">#include </span>"MBParallelConventions.h"</p>
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<span class="" style="color:#d53bd3">#include </span>"MBTagConventions.hpp"</p>
<p 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:#d53bd3">#include </span>"moab/Core.hpp"</p>
<p 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:#d53bd3">#include </span>"moab_mpi.h"</p>
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<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,189,38); background-color:rgb(0,0,0)">
<span class="" style="color:#afad24">using</span><span class="" style="color:#f5f5f5">
</span>namespace<span class="" style="color:#f5f5f5"> moab;</span></p>
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<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)">
<span class="" style="color:#34bd26">int</span> main(<span class="" style="color:#34bd26">int</span> argc,
<span class="" style="color:#34bd26">char</span> **argv)</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
{</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Core moab;</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
Interface& imoab = moab;</p>
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<br class="">
</p>
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ParallelComm* pcomm = ParallelComm::get_pcomm(&moab, <span class="" style="color:#ce7924">
0</span>);</p>
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<span class="" style="color:#afad24">if</span> (<span class="" style="color:#ce7924">0</span> == pcomm)</p>
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{</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
pcomm = <span class="" style="color:#afad24">new</span> ParallelComm(&imoab, MPI_COMM_WORLD);</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
}</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
<span class="" style="color:#afad24">delete</span> pcomm;</p>
<p 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:#f5f5f5"> </span><span class="" style="color:#afad24">return</span><span class="" style="color:#f5f5f5">
</span>EXIT_SUCCESS<span class="" style="color:#f5f5f5">;</span></p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
};</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(83,48,225); background-color:rgb(0,0,0)">
<b class="">~ </b></p>
</div>
<div><br class="">
</div>
<div>This is the Makefile</div>
<div>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
<span class="" style="color:#34bbc7"><b class="">MOAB_LIB_DIR </b></span>= /Users/ihabia/src2/moab-4.8.2/moab/</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
<span class="" style="color:#d53bd3">include</span> <span class="" style="color:#34bbc7">
<b class="">$(MOAB_LIB_DIR)</b></span>/lib/moab.make</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
<b class="">%.o :</b><span class="" style="color:#f5f5f5"> </span><b class="">%</b><span class="" style="color:#f5f5f5">.cpp</span></p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(206,121,36); background-color:rgb(0,0,0)">
<span class="" style="color:#d53bd3"> @</span>echo "Compiling ("<span class="" style="color:#34bbc7"><b class="">$(CXX)</b></span>") "<span class="" style="color:#34bbc7"><b class="">$<</b></span>" "</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
<span class="" style="color:#d53bd3"> @</span><b class="">$(CXX)</b><span class="" style="color:#ce7924">
</span><b class="">${MOAB_INCLUDES}</b><span class="" style="color:#ce7924"> -c </span>
<b class="">$<</b><span class="" style="color:#ce7924"> -o </span><b class="">$@</b></p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
<span class="" style="color:#34bbc7"><b class="">CXX </b></span>= mpicxx -O2 -DNDEBUG</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
<b class="">objects </b><span class="" style="color:#f5f5f5">:= </span><b class="">$(</b><span class="" style="color:#afad24">patsubst</span><b class=""> %.cpp,%.o,$(</b><span class="" style="color:#afad24">wildcard</span><b class=""> ./*.cpp))</b></p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0); min-height:16px">
<br class="">
</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(52,187,199); background-color:rgb(0,0,0)">
<b class="">mbtestrun :</b><span class="" style="color:#f5f5f5"> </span><b class="">$(objects)</b></p>
<p 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:#d53bd3"> @</span>echo "Linking "<span class="" style="color:#34bbc7"><b class="">$(CURDIR)</b></span>"/"<span class="" style="color:#34bbc7"><b class="">$@</b></span></p>
<p 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:#d53bd3"> @</span><b class="">$(CXX)</b><span class="" style="color:#ce7924">
</span><b class="">$(objects)</b><span class="" style="color:#ce7924"> -o </span>
<b class="">$@</b><span class="" style="color:#ce7924"> </span><b class="">$(MOAB_LIBS_LINK)</b><span class="" style="color:#ce7924"> </span></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(175,173,36); background-color:rgb(0,0,0)">
.PHONY :<span class="" style="color:#f5f5f5"> clean </span></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(52,187,199); background-color:rgb(0,0,0)">
<b class="">clean :</b></p>
<p 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:#d53bd3"> @</span><span class="" style="color:#ce7924">rm
</span><b class="">$(objects)</b></p>
<div class=""><b class=""><br class="">
</b></div>
</div>
<div><br class="">
</div>
<div>and this is mob.make</div>
<div><br class="">
</div>
<div>
<p 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</p>
<p 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</p>
<p 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.</p>
<p 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</p>
<p 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 \</p>
<p 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 \</p>
<p 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 \</p>
<p 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 \</p>
<p 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</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)">
MOAB_INCLUDES +=</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)">
MOAB_CPPFLAGS = -I/Users/ihabia/src2/hdf5-1.8.16/hdf5//include -isystem /Users/ihabia/src2/hdf5-1.8.16/hdf5//include</p>
<p 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</p>
<p 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</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_FFLAGS =</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_FCFLAGS =</p>
<p 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++</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); 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)">
MOAB_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR} -lMOAB -lhdf5 -lc++ -lz -ldl -lm -lc++ -lz -ldl -lm</p>
<p 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</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)">
MOAB_CXX = /Users/ihabia/src2/mpich-3.2/mpich3//bin/mpicxx</p>
<p 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</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_FC =</p>
<p class="" style="margin:0px; font-size:14px; font-family:Menlo; color:rgb(245,245,245); background-color:rgb(0,0,0)">
MOAB_F77 =</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(52,187,199); background-color:rgb(0,0,0)">
# Override MOAB_LIBDIR and MOAB_INCLUDES from above with the correct</p>
<p 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.</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)">
MOAB_LIBDIR=/Users/ihabia/src2/moab-4.8.2/moab/lib</p>
<p 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</p>
</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div><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? <br class="">
<br class="">
<br class="">
Iulian<br class="">
<br class="">
________________________________________<br class="">
From: <a href="mailto:moab-dev-bounces@mcs.anl.gov" class="" target="_blank">moab-dev-bounces@mcs.anl.gov</a> [<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<br class="">
<br class="">
<br class="">
</blockquote>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</body>
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