<div dir="ltr">Hong, <div><br></div><div>Would you mind sharing you CMakeCache (both at the superbuild and paraview sub build) with me?</div><div style><br></div><div style>I would like to fold your work into ParaViewSuperbuild so that the next zebra at this watering hole has an easier time of it.</div>
<div style><br></div><div style>thanks!</div></div><div class="gmail_extra"><br clear="all"><div>David E DeMarle<br>Kitware, Inc.<br>R&D Engineer<br>21 Corporate Drive<br>Clifton Park, NY 12065-8662<br>Phone: 518-881-4909</div>
<br><br><div class="gmail_quote">On Fri, Sep 6, 2013 at 5:27 PM, Hong Yi <span dir="ltr"><<a href="mailto:hongyi@renci.org" target="_blank">hongyi@renci.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Andy,
David,<br>
<br>
I used <span>GCC</span> to build both <span>ParaView</span> and simulation code. The problem is with ParaView's superbuild not being able to find MPI_Fortran on Titan. I got the following messages during superbuild:<br>
<br>
--------------<br>
Could NOT find MPI_Fortran (missing: MPI_Fortran_LIBRARIES MPI_Fortran_INCLUDE_PATH)<br>
</span>
<p style="margin-bottom:0in">No FortranCInterface mangling known for coprocessorinitialize</p>
<p style="margin-bottom:0in">...<br>
</p>
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">--------------<br>
<br>
I then tried to add "ftn" into FindMPI.cmake, but got the message "Unable to determine MPI from MPI driver /opt/cray/xt-asyncpe/5.17/bin/ftn" prior to those MPI_Fortran errors. I looked at ftn wrapper but could not determine the mpi Fortran executable, either.
Let me know if you have ideas on how to make superbuild to find MPI_Fortran. <br>
<br>
Many thanks,<br>
<br>
Hong<br>
</span><br>
<div style="font-size:16px;font-family:Times New Roman">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> David E DeMarle [<a href="mailto:dave.demarle@kitware.com" target="_blank">dave.demarle@kitware.com</a>]<br>
<b>Sent:</b> Friday, September 06, 2013 4:21 PM<br>
<b>To:</b> Andy Bauer<br>
<b>Cc:</b> Hong Yi; <a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a><div><div class="h5"><br>
<b>Subject:</b> Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1 to simulation code on Titan<br>
</div></div></font><br>
</div><div><div class="h5">
<div></div>
<div>
<div dir="ltr">
<div>The Superbuild on cray uses the backend flavor of the GCC compiler (xk7_gcc target). I haven't made an xk7_pgi target yet.</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>David E DeMarle<br>
Kitware, Inc.<br>
R&D Engineer<br>
21 Corporate Drive<br>
Clifton Park, NY 12065-8662<br>
Phone: <a href="tel:518-881-4909" value="+15188814909" target="_blank">518-881-4909</a></div>
<br>
<br>
<div class="gmail_quote">On Fri, Sep 6, 2013 at 4:07 PM, Andy Bauer <span dir="ltr">
<<a href="mailto:andy.bauer@kitware.com" target="_blank">andy.bauer@kitware.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">
<div>
<div>Hi Hong,<br>
<br>
</div>
This Fortran/C mangling issue is a bit tricky. It has to be done during the configuration process because the C and Fortran compilers won't necessarily know how to properly mangle the function names. The thing is that it the configuration process depends on
using the same compilers as any other code that links to the generated libraries. You can check out Bill Hoffman's blog at
<a href="http://www.kitware.com/blog/home/post/231" target="_blank">http://www.kitware.com/blog/home/post/231</a> which explains this issue and how CMake handles it. Now if ParaView Catalyst was built with GCC and you built your simulation code with PGI, for
example, then it wouldn't surprise me that this issue crops up. What compilers did you use for your ParaView build and your simulation code build? If they are consistent then it is a problem with CMake or ParaView's superbuild.<br>
<br>
</div>
Regards,<br>
Andy<br>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Fri, Sep 6, 2013 at 3:54 PM, Hong Yi <span dir="ltr">
<<a href="mailto:hongyi@renci.org" target="_blank">hongyi@renci.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-US">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Andy,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks for the useful info. You are exactly right – the problem is caused by C/Fortran mangling of the names. In the Fortran code, underbar trailing is not
there for all catalyst-related function calls, those underbar trailing to the function names as shown in the linking errors are automatically added by C/Fortran mangling in the final linking stage. I also pulled in the Fortran example in the github repo, and
got the similar undefined reference errors in the final linking stage when linking to the ParaView 4.0 built with superbuild. So the linking problem seems to be generic to Fortran code linking to Catalyst.
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I checked the Catalyst static lib built with superbuild and found the lib only includes function symbols without the trailing underbar such as coprocessorinitialize,
which explains why those undefined reference errors result. I also tried to build ParaView 3.98 with superbuild which included FortranAdaptor lib, and found the FortranAdatpor lib built with superbuild does not include the trailing underbar for coprocessor-related
functions, while the FortranAdaptor lib built from source does include the trailing underbar, which explains why I can link our simulation code to Catalyst 3.98 built from source, but cannot successfully link to Catalyst 3.98 built with superbuild. So here
is my question:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Should Catalyst libs built with superbuild contain those coprocessing function symbols with trailing underbar in addition to those corresponding function
symbols without trailing underbar? Specifically, for example, I am wondering whether both coprocessorinitialize and coprocessorinitialize_ need to present so these coprocessing functions can be called from different languages including Fortran? Could you confirm
whether this is the case? If so, I need to check my superbuild to see why those trailing underbar functions are not created in the Catalyst libs. Let me know if you, David, or anybody else can confirm whether this is the case, or offer any ideas/suggestions.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hong<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Andy Bauer [mailto:<a href="mailto:andy.bauer@kitware.com" target="_blank">andy.bauer@kitware.com</a>]
<br>
<b>Sent:</b> Friday, September 06, 2013 12:33 PM<br>
<b>To:</b> Hong Yi<br>
<b>Cc:</b> <a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a><br>
<b>Subject:</b> Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1 to simulation code on Titan<u></u><u></u></span></p>
<div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Hong,<u></u><u></u></p>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal">I think it's the Fortran mangling of the names. Try taking out the underscore on the Fortran subroutine calls. Let me know if that doesn't help. Otherwise it may be an issue with how C/Fortran mangles things. The GCC behavior should be
the following:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Fortran -> call xyz()<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">C -> void xyz_() {...}.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">All of these methods should be available in the vtkPVCatalyst module. If you can't get it to work, try to see what you can do with the Fortran example in the github repo.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal">Regards,<br>
And<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Thu, Sep 5, 2013 at 5:52 PM, Hong Yi <<a href="mailto:hongyi@renci.org" target="_blank">hongyi@renci.org</a>> wrote:<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">When linking our simulation code (a variant of phasta) to Catalyst in ParaView version 4.0.1 built on Titan with superbuild, I got the following
linking errors:<br>
<br>
-----------------<br>
../../lib/libincompressible.a(itrdrv.f.o): In function `itrdrv_':<br>
itrdrv.f:(.text+0x2add): undefined reference to `coprocessorinitialize_'<br>
itrdrv.f:(.text+0x6198): undefined reference to `coprocessorfinalize_'<br>
itrdrv.f:(.text+0x973d): undefined reference to `coprocessorfinalize_'<br>
../../lib/libincompressible.a(phastaadaptor.f.o): In function `phastacoprocessor_':<br>
phastaadaptor.f:(.text+0x84): undefined reference to `requestdatadescription_'<br>
phastaadaptor.f:(.text+0x95): undefined reference to `needtocreategrid_'<br>
phastaadaptor.f:(.text+0xba): undefined reference to `coprocess_'<br>
/usr/bin/ld: link errors found, deleting executable `../../bin/phastaIC.exe'<br>
-----------------<br>
<br>
I use CMake to link Catalyst to our simulation code. I was able to resolve those linking errors when linking to ParaView version 3.98.1 by adding "find_package(ParaView 3.98 REQUIRED COMPONENTS FortranAdaptor)" in addition to find_package for vtkCoProcessorImplementation
and then link both to the final executable. However, for ParaView version 4.0.1, it seems FortranAdaptor does not exist any more which defines those functions such as coprocessorinitialize, etc. Here is the corresponding excerpt in my CMakeLists.txt related
to linking Catalyst in ParaView version 4.0.1:<br>
-------------------<br>
if(USE_CATALYST)<br>
find_package(ParaView 3.98 REQUIRED COMPONENTS vtkPVPythonCatalyst)<br>
find_library(PHASTA_ADAPTOR_LIB PhastaAdaptorLib)<br>
include("${PARAVIEW_USE_FILE}")<br>
set(Adaptor_SRCS phastaadaptor.f)<br>
add_library(Adaptor ${Adaptor_SRCS})<br>
target_link_libraries(Adaptor ${PHASTA_ADAPTOR_LIB} vtkPVPythonCatalyst)<br>
add_definitions("-DUSE_CATALYST")<br>
endif()<br>
-------------------<br>
<br>
Adaptor is then linked to the final executable. <br>
<br>
Please let me know if you have ideas on what I should do to resolve those linking errors.<br>
<br>
Many thanks,<br>
<br>
Hong<br>
<br>
<br>
<u></u><u></u></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
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