<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi all,</div><div class="">I’d like to discuss a problem I recently encountered compiling moab with intel compilers on a cluster at cineca (an Italian HPC facility)</div><div class=""><br class=""></div><div class="">When compiling my application linked to moab I got the following errors</div><div class=""><p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReaderWriterSet.o): In function `moab::ReaderWriterSet::get_file_extension_reader(std::string const&) const':</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">ReaderWriterSet.cpp:(.text+0xa22): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReaderWriterSet.o): In function `moab::ReaderWriterSet::get_file_extension_writer(std::string const&) const':</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">ReaderWriterSet.cpp:(.text+0xb72): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReaderWriterSet.o): In function `moab::ReaderWriterSet::extension_from_filename(std::string const&)':</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">ReaderWriterSet.cpp:(.text+0xcc7): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReadABAQUS.o): In function `moab::ReadABAQUS::get_keyword()':</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">ReadABAQUS.cpp:(.text+0x19c0): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">ReadABAQUS.cpp:(.text+0x19fb): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReadABAQUS.o):ReadABAQUS.cpp:(.text+0x285d): more undefined references to `std::__throw_out_of_range_fmt(char const*, ...)' follow</p></div><div class=""><br class=""></div><div class="">The problem seems to be related with <span style="color: rgb(195, 55, 32); font-family: Menlo; font-size: 14px; background-color: rgb(0, 0, 0);" class="">/cineca/prod/compilers/gnu/4.9.2/none/lib64/libstdc++.la</span></div><div class="">which is present in libMOAB.la but is missing in moab.make (see below) </div><div class=""><br class=""></div><div class="">(libMOAB.la)</div><div class=""><p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""><br class=""></p><p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># libMOAB.la - a libtool library file</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Generated by libtool (GNU libtool) 2.4.2</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class="">#</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Please DO NOT delete this file!</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># It is necessary for linking the library.</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># The name that we can dlopen(3).</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">dlname=<span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class="">''</span></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Names of this library.</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">library_names=<span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class="">''</span></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># The name of the static archive.</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">old_library=<span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class="">'libMOAB.a'</span></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Linker flags that can not go in dependency_libs.</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">inherited_linker_flags=<span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class="">''</span></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Libraries that this one depends upon.</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class="">dependency_libs=</span>' -L/galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/lib /galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/lib/libhdf5.la -lgpfs -lz /cineca/prod/compilers/gnu/4.9.2/none/lib64/libstdc++.la'</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Names of additional weak libraries provided by this library</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">weak_library_names=<span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class="">''</span></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Version information for libMOAB.</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">current=0</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">age=0</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">revision=0</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Is this an already installed library?</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">installed=no</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Should we warn about portability when linking against -modules?</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">shouldnotlink=no</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Files to dlopen/dlpreopen</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">dlopen=<span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class="">''</span></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">dlpreopen=<span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class="">''</span></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Directory that this library needs to be installed in:</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class="">libdir=</span>'/galileo/home/userexternal/lbotti00/moab/lib'</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(94, 52, 255); background-color: rgb(0, 0, 0);" class="">~ </p></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">(maob.make)</div><div class=""><p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># The values below are for an un-installed copy of MOAB used directly</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># from its build build directory. These values will be overridden below</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># for installed copies of MOAB.</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_LIBDIR = /galileo/home/userexternal/lbotti00/moab-4.6.3/src/.libs</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_INCLUDES = -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src \</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src \</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src/oldinc \</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src/parallel \</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src/parallel</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_INCLUDES +=</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_CPPFLAGS = -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -I/galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/include -isystem /galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_CXXFLAGS = -Wall -wd981 -wd279 -wd1418 -wd383 -wd1572 -wd2259 -O2 -DNDEBUG</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_CFLAGS = -Wall -wd981 -wd279 -wd1418 -wd383 -wd1572 -O2 -DNDEBUG</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_FFLAGS = -O2</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_FCFLAGS = -O2</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_LDFLAGS = -L/galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/lib</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR} -lMOAB -lm -lhdf5 -lgpfs -lz -ldl</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_CXX = /cineca/prod/compilers/intel/cs-xe-2015/binary/impi_5.0.2/intel64/bin/mpicxx</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_CC = /cineca/prod/compilers/intel/cs-xe-2015/binary/impi_5.0.2/intel64/bin/mpicc</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_FC = ifort</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">MOAB_F77 = ifort</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 16px;" class=""><br class=""></p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># Override MOAB_LIBDIR and MOAB_INCLUDES from above with the correct</p>
<p style="margin: 0px; font-size: 14px; font-family: Menlo; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""># values for the installed MOAB.</p><div class=""><br class=""></div></div><div class="">Adding the missing .la fixes the linking issue.</div><div class=""><br class=""></div><div class="">What do you guys think? I’m not an expert of this kind of problems...</div><div class=""><br class=""></div><div class="">Bests </div><div class="">Lorenzo</div><div class=""><br class=""></div><div class=""><br class=""></div></body></html>