<div dir="ltr">Ok, I deactivated mpich and have run <span style="font-size:12.8000001907349px">simfactory/bin/sim build --optionlist=osx-macports.cfg >build2.log 2>&1 and get similar errors. I have pasted the contents of build2.log to <a href="http://pastebin.com/kcua0vKQ">http://pastebin.com/kcua0vKQ</a>. It does not seem that the deactivation of mpich had the desired effect.</span><div><span style="font-size:12.8000001907349px"><br></span></div><div><span style="font-size:12.8000001907349px">Thanks.</span></div><div><span style="font-size:12.8000001907349px"><br></span></div><div><span style="font-size:12.8000001907349px">Comer</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, May 20, 2015 at 12:24 PM, Comer Duncan <span dir="ltr"><<a href="mailto:comer.duncan@gmail.com" target="_blank">comer.duncan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Erik,<div><br></div><div>Thanks. I think I had mpich first and then added openmpi. I will deactivate mpich-default. The question is do I need to run simfactory/bin/sim build --optionlist=osx-macports.cfg >build.log 2>&1 with build2.log instead of build.log so I get a new log file? Will it do just what is necessary relative to openmpi libs or do the whole business from scratch?</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Comer</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, May 20, 2015 at 12:13 PM, Erik Schnetter <span dir="ltr"><<a href="mailto:schnetter@cct.lsu.edu" target="_blank">schnetter@cct.lsu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Comer<div><br></div><div>I would have only one MPI implementation active. I assume you had mpich active, and then added openmpi when you followed our instructions. You can try to deactivate mpich: "sudo port deactivate mpich-default". Alternatively, you can deactivate openmpi. After this, you would need to configure and build from scratch.</div><span><font color="#888888"><div><br></div><div>-erik</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, May 20, 2015 at 12:04 PM, Comer Duncan <span dir="ltr"><<a href="mailto:comer.duncan@gmail.com" target="_blank">comer.duncan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Erik,<div><br></div><div>Here is what I find:</div><div><br></div><div><div>ComerMacProRetina:Cactus comerduncan$ /opt/local/bin/mpiCC -showme</div><div>/usr/bin/clang -I/opt/local/include/openmpi-mp -Wl,-flat_namespace -L/opt/local/lib/openmpi-mp -lmpi</div><div>ComerMacProRetina:Cactus comerduncan$ port installed | grep mpi</div><div> mpi-doc @3.1.3_0</div><div> mpi-doc @3.1.4_0 (active)</div><div> mpi_select @0.0_3 (active)</div><div> mpich-default @3.1.3_0+gcc49</div><div> mpich-default @3.1.4_0+gcc49 (active)</div><div> openmpi @1.7.5_3 (active)</div><div> openmpi-default @1.7.5_3+gcc47 (active)</div><div> petsc @3.5.3_1+accelerate+hwloc+mpich</div><div> petsc @3.5.3_1+accelerate+hwloc+openmpi (active)</div></div><div><br></div><div>Any recommendations for changes?</div><div><br></div><div>Thanks.</div><span><font color="#888888"><div><br></div><div>Comer</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, May 20, 2015 at 9:26 AM, Erik Schnetter <span dir="ltr"><<a href="mailto:schnetter@cct.lsu.edu" target="_blank">schnetter@cct.lsu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Comer<div><br></div><div>Maybe you have two different MPI implementations installed. What is the output of "/opt/local/bin/mpiCC -showme"? What is the output of "port installed | grep mpi"?</div><div><br></div><div>-erik</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Wed, May 20, 2015 at 9:20 AM, Comer Duncan <span dir="ltr"><<a href="mailto:comer.duncan@gmail.com" target="_blank">comer.duncan@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">Hi Ian,<div><br></div><div>I did make sure that all ports mentioned in the osx-macports.cfg file were done before attempting a build. I've followed your suggestion on rebuilding and have pasted the build log to <a href="http://pastebin.com/ka7c3QT5" target="_blank">http://pastebin.com/ka7c3QT5</a> </div><div><br></div><div>Thanks for your help.</div><span><font color="#888888"><div><br></div><div>Comer</div><div><br></div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 19, 2015 at 6:27 PM, Ian Hinder <span dir="ltr"><<a href="mailto:ian.hinder@aei.mpg.de" target="_blank">ian.hinder@aei.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><br><div><div><div><div>On 19 May 2015, at 21:03, Comer Duncan <<a href="mailto:comer.duncan@gmail.com" target="_blank">comer.duncan@gmail.com</a>> wrote:</div><br><blockquote type="cite"><div dir="ltr">I have tried to build the new release on my local macbook. I am running Yosemite and am using the optionlist for macports. Here is the part of the make which chokes:<div>.</div><div>.</div><div>.</div><div><div>Undefined symbols for architecture x86_64:</div><div> "MPI::Win::Free()", referenced from:</div><div> vtable for MPI::Win in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> vtable for MPI::Win in libthorn_Carpet.a(helpers.cc.o)</div><div> vtable for MPI::Win in libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o)</div><div> vtable for MPI::Win in libthorn_CarpetIOASCII.a(ioascii.cc.o)</div><div> vtable for MPI::Win in libthorn_CarpetIOBasic.a(iobasic.cc.o)</div><div> vtable for MPI::Win in libthorn_CarpetIOHDF5.a(Input.cc.o)</div><div> vtable for MPI::Win in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o)</div><div> ...</div><div> "MPI::Comm::Comm()", referenced from:</div><div> MPI::Intercomm::Merge(bool) const in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> MPI::Intracomm::Split(int, int) const in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> MPI::Intracomm::Create(MPI::Group const&) const in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> MPI::Graphcomm::Clone() const in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> MPI::Cartcomm::Clone() const in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> MPI::Intracomm::Clone() const in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> ...</div><div> "MPI::Datatype::Free()", referenced from:</div><div> vtable for MPI::Datatype in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> vtable for MPI::Datatype in libthorn_Carpet.a(helpers.cc.o)</div><div> vtable for MPI::Datatype in libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o)</div><div> vtable for MPI::Datatype in libthorn_CarpetIOASCII.a(ioascii.cc.o)</div><div> vtable for MPI::Datatype in libthorn_CarpetIOBasic.a(iobasic.cc.o)</div><div> vtable for MPI::Datatype in libthorn_CarpetIOHDF5.a(Input.cc.o)</div><div> vtable for MPI::Datatype in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o)</div><div> ...</div><div> "_ompi_mpi_cxx_op_intercept", referenced from:</div><div> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_PeriodicCarpet.a(periodic.cc.o)</div><div> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_Carpet.a(helpers.cc.o)</div><div> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o)</div><div> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetIOASCII.a(ioascii.cc.o)</div><div> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetIOBasic.a(iobasic.cc.o)</div><div> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetIOHDF5.a(Input.cc.o)</div><div> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o)</div><div> ...</div><div>ld: symbol(s) not found for architecture x86_64</div><div>collect2: error: ld returned 1 exit status</div><div>make[1]: *** [/Users/comerduncan/Cactus/exe/cactus_sim] Error 1</div><div>make: *** [sim] Error 2</div></div><div><br></div><div>Here is the build I did:</div><div><br></div><div>simfactory/bin/sim build --optionlist=/Users/comerduncan/Cactus/simfactory/mdb/optionlists/osx-macports.cfg<br></div><div><br></div><div>Can you please help me figure out what went wrong?</div></div></blockquote><div><br></div></div></div><div>Hi Comer,</div><div><br></div><div>My guess would be that there might be more than one version of MPI installed, or something in the MPI configuration script didn't work quite right. Did you install all the ports recommended in the comment in the os-macports.cfg optionlist? Can you post the output from the full build? I suggest to remove the configuration</div><div><br></div><div><span style="white-space:pre-wrap"> </span>rm -rf configs/sim</div><div><br></div><div>and then build, keeping all output:</div><div><br></div><div><span style="white-space:pre-wrap"> </span>simfactory/bin/sim build --optionlist=osx-macports.cfg >build.log 2>&1</div><div><br></div><div>You could then copy and paste build.log into <a href="http://pastebin.com" target="_blank">http://pastebin.com</a> and include the link in your reply (to avoid having a large attachment on the mailing list).</div><span><font color="#888888"><div><br></div></font></span></div><span><font color="#888888"><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div>-- </div><div>Ian Hinder</div><div><a href="http://members.aei.mpg.de/ianhin" target="_blank">http://members.aei.mpg.de/ianhin</a></div></div></div></div></div>
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<br></blockquote></div><span><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div>Erik Schnetter <<a href="mailto:schnetter@cct.lsu.edu" target="_blank">schnetter@cct.lsu.edu</a>><br><a href="http://www.perimeterinstitute.ca/personal/eschnetter/" target="_blank">http://www.perimeterinstitute.ca/personal/eschnetter/</a></div>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div>Erik Schnetter <<a href="mailto:schnetter@cct.lsu.edu" target="_blank">schnetter@cct.lsu.edu</a>><br><a href="http://www.perimeterinstitute.ca/personal/eschnetter/" target="_blank">http://www.perimeterinstitute.ca/personal/eschnetter/</a></div>
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