[Paraview] Errors when linking catalyst in ParaView version 4.0.1 to simulation code on Titan

Fri Sep 6 16:21:44 EDT 2013

The Superbuild on cray uses the backend flavor of the GCC compiler (xk7_gcc
target). I haven't made an xk7_pgi target yet.

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Fri, Sep 6, 2013 at 4:07 PM, Andy Bauer <andy.bauer at kitware.com> wrote:

> Hi Hong,
>
> 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 http://www.kitware.com/blog/home/post/231 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.
>
> Regards,
> Andy
>
>
> On Fri, Sep 6, 2013 at 3:54 PM, Hong Yi <hongyi at renci.org> wrote:
>
>>  Hi Andy,****
>>
>> ** **
>>
>> 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. ****
>>
>> ** **
>>
>> 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:****
>>
>> ** **
>>
>> 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.****
>>
>> ** **
>>
>> Thanks,****
>>
>> ** **
>>
>> Hong****
>>
>> ** **
>>
>> ** **
>>
>> *From:* Andy Bauer [mailto:andy.bauer at kitware.com]
>> *Sent:* Friday, September 06, 2013 12:33 PM
>> *To:* Hong Yi
>> *Cc:* paraview at paraview.org
>> *Subject:* Re: [Paraview] Errors when linking catalyst in ParaView
>> version 4.0.1 to simulation code on Titan****
>>
>> ** **
>>
>> Hi Hong,****
>>
>> ** **
>>
>> 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:****
>>
>> Fortran -> call xyz()****
>>
>> C -> void xyz_() {...}.****
>>
>> 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.****
>>
>> ** **
>>
>> Regards,
>> And****
>>
>> ** **
>>
>> On Thu, Sep 5, 2013 at 5:52 PM, Hong Yi <hongyi at renci.org> wrote:****
>>
>> 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:
>>
>> -----------------
>> ../../lib/libincompressible.a(itrdrv.f.o): In function `itrdrv_':
>> itrdrv.f:(.text+0x2add): undefined reference to `coprocessorinitialize_'
>> itrdrv.f:(.text+0x6198): undefined reference to `coprocessorfinalize_'
>> itrdrv.f:(.text+0x973d): undefined reference to `coprocessorfinalize_'
>> ../../lib/libincompressible.a(phastaadaptor.f.o): In function
>> `phastacoprocessor_':
>> phastaadaptor.f:(.text+0x84): undefined reference to
>> `requestdatadescription_'
>> phastaadaptor.f:(.text+0x95): undefined reference to `needtocreategrid_'
>> phastaadaptor.f:(.text+0xba): undefined reference to `coprocess_'
>> /usr/bin/ld: link errors found, deleting executable
>> `../../bin/phastaIC.exe'
>> -----------------
>>
>> 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:
>> -------------------
>> if(USE_CATALYST)
>>        find_package(ParaView 3.98 REQUIRED COMPONENTS vtkPVPythonCatalyst)
>>         find_library(PHASTA_ADAPTOR_LIB PhastaAdaptorLib)
>>         include("${PARAVIEW_USE_FILE}")
>>         set(Adaptor_SRCS phastaadaptor.f)
>>         add_library(Adaptor ${Adaptor_SRCS})
>>         target_link_libraries(Adaptor ${PHASTA_ADAPTOR_LIB}
>> vtkPVPythonCatalyst)
>>         add_definitions("-DUSE_CATALYST")
>> endif()
>> -------------------
>>
>> Adaptor is then linked to the final executable.
>>
>> Please let me know if you have ideas on what I should do to resolve those
>> linking errors.
>>
>> Many thanks,
>>
>> Hong
>>
>>
>> ****
>>
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.paraview.org/mailman/listinfo/paraview****
>>
>> ** **
>>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://www.paraview.org/mailman/listinfo/paraview
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.paraview.org/pipermail/paraview/attachments/20130906/2061d5d3/attachment-0001.htm>