<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Sat, Feb 10, 2018 at 9:42 AM, Éric Chamberland <span dir="ltr"><<a href="mailto:Eric.Chamberland@giref.ulaval.ca" target="_blank">Eric.Chamberland@giref.ulaval.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>Hi,</p>
<p>we used to link our c++ code with PETSc using
PETSC_WITH_EXTERNAL_LIB variable defined in
$PETSC_DIR/lib/petsc/conf/<wbr>petscvariables and everything was fine
until this night.</p>
<p>It seems some libs have vanished from this variable, see the diff
here:</p>
<pre style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;word-wrap:break-word;white-space:pre-wrap"> -lptscotcherr
-lesmumps
-lscotch
-lscotcherr
-lm
-lX11
+-lstdc++
-ldl
-lmpi_usempi
-lmpi_mpifh
-lmpi
-lgfortran
-lm
-lgfortran
-lm
-lgcc_s
-lquadmath
-lpthread
--ldl
--lmpi_cxx
--lmpi
--lstdc++
--lm
--lgcc_s
--lpthread
-lrt
-lm
-lpthread
-lz
+-lstdc++
-ldl
causing these errors at link phase for us:
<font color="blue"> /pmi/cmpbib/compilation_BIB_<wbr>gcc_redhat_petsc-master_debug/<wbr>COMPILE_AUTO/GIREF/obj/dev/<wbr>StatistiqueMemoire.o: In function `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)': </font>
/opt/openmpi-1.10.2/include/<wbr>openmpi/ompi/mpi/cxx/op_inln.<wbr>h:122: undefined reference to `ompi_mpi_cxx_op_intercept'
<font color="blue"> /pmi/cmpbib/compilation_BIB_<wbr>gcc_redhat_petsc-master_debug/<wbr>COMPILE_AUTO/GIREF/obj/dev/<wbr>StatistiqueMemoire.o: In function `MPI::Intracomm::Create_graph(<wbr>int, int const*, int const*, bool) const': </font>
/opt/openmpi-1.10.2/include/<wbr>openmpi/ompi/mpi/cxx/<wbr>intracomm.h:25: undefined reference to `MPI::Comm::Comm()'
<font color="blue"> /pmi/cmpbib/compilation_BIB_<wbr>gcc_redhat_petsc-master_debug/<wbr>COMPILE_AUTO/GIREF/obj/dev/<wbr>StatistiqueMemoire.o: In function `MPI::Intercomm::Merge(bool) const': </font>
/opt/openmpi-1.10.2/include/<wbr>openmpi/ompi/mpi/cxx/<wbr>intracomm_inln.h:23: undefined reference to `MPI::Comm::Comm()'
<font color="blue"> /pmi/cmpbib/compilation_BIB_<wbr>gcc_redhat_petsc-master_debug/<wbr>COMPILE_AUTO/GIREF/obj/dev/<wbr>StatistiqueMemoire.o: In function `MPI::Intracomm::Split(int, int) const': </font>
/opt/openmpi-1.10.2/include/<wbr>openmpi/ompi/mpi/cxx/<wbr>intracomm_inln.h:23: undefined reference to `MPI::Comm::Comm()'
<font color="blue"> /pmi/cmpbib/compilation_BIB_<wbr>gcc_redhat_petsc-master_debug/<wbr>COMPILE_AUTO/GIREF/obj/dev/<wbr>StatistiqueMemoire.o: In function `MPI::Intracomm::Create(MPI::<wbr>Group const&) const': </font>
/opt/openmpi-1.10.2/include/<wbr>openmpi/ompi/mpi/cxx/<wbr>intracomm_inln.h:23: undefined reference to `MPI::Comm::Comm()'
<font color="blue"> /pmi/cmpbib/compilation_BIB_<wbr>gcc_redhat_petsc-master_debug/<wbr>COMPILE_AUTO/GIREF/obj/dev/<wbr>StatistiqueMemoire.o: In function `MPI::Intracomm::Clone() const': </font></pre></div></blockquote><div>Hi Eric,</div><div><br></div><div>These symbols are all coming from -lmpi_cxx. I would note that I believe the MPI Forum has deprecated the C++ interface, so it will</div><div>eventually go away. However, lets fix this. In the configure log, I see that mpicxx -show has that library in it, so it seems that the link</div><div>is not being done with the C++ compiler. Can you send the whole link line?</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#FFFFFF"><pre style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;word-wrap:break-word;white-space:pre-wrap"><font color="blue"></font></pre>
<p>Is this a normal and definitive change or an unwanted/unobserved
bug?</p>
<p>Thanks,</p>
<p>Eric</p>
<p>ps: here are the logs:</p>
<p>this night:</p>
<p>---------</p>
<pre style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;word-wrap:break-word;white-space:pre-wrap"><a class="m_1095262550823765165moz-txt-link-freetext" href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2018.02.10.02h00m01s_configure.log" target="_blank">http://www.giref.ulaval.ca/~<wbr>cmpgiref/petsc-master-debug/<wbr>2018.02.10.02h00m01s_<wbr>configure.log</a>
<a class="m_1095262550823765165moz-txt-link-freetext" href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2018.02.10.02h00m01s_make.log" target="_blank">http://www.giref.ulaval.ca/~<wbr>cmpgiref/petsc-master-debug/<wbr>2018.02.10.02h00m01s_make.log</a>
a day before:
------------
<a class="m_1095262550823765165moz-txt-link-freetext" href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2018.02.09.02h00m02s_configure.log" target="_blank">http://www.giref.ulaval.ca/~<wbr>cmpgiref/petsc-master-debug/<wbr>2018.02.09.02h00m02s_<wbr>configure.log</a>
<a class="m_1095262550823765165moz-txt-link-freetext" href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2018.02.09.02h00m02s_make.log" target="_blank">http://www.giref.ulaval.ca/~<wbr>cmpgiref/petsc-master-debug/<wbr>2018.02.09.02h00m02s_make.log</a>
</pre>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.caam.rice.edu/~mk51/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div>
</div></div>