[Paraview] RHEL6 Superbuild error (UNCLASSIFIED)

Angelini, Richard C (Rick) CIV USARMY ARL (US) richard.c.angelini.civ at mail.mil
Thu May 9 08:02:04 EDT 2013 

Turns out that I can't get past this on the RHEL6 cluster --- I looked in Source/Projects/qt.cmake and these were already being set:

                      -nomake demos
                      -nomake examples

I added
                      -nomake tests

but it wasn't a workaround for the errors.    It's clearly some interaction between the webkit and libgstreamer.     I'd take an option to not build the webkit and eliminate the help-subsystem if that'll get me a clean build.

$ make qt
[ 13%] Built target libxml2
[ 33%] Built target zlib
[ 50%] Built target freetype
[ 66%] Built target fontconfig
[ 83%] Built target png
[ 83%] Performing build step for 'qt'
LD_LIBRARY_PATH = /u/home/angelini/PV/Build/install/lib:/app/openmpi/gnu/1.6.3/lib:/app/openmpi/gnu/1.6.3/lib
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlOutputBufferCreateFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNodeGetContent at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewChild at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDocNode at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseCharEncoding at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSearchNsByHref at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFindCharEncodingHandler at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSaveFormatFileTo at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseMemory at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFree at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlDocGetRootElement at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFreeDoc at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewNs at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDoc at LIBXML2_2.4.30'
collect2: ld returned 1 exit status
gmake[7]: *** [tst_qwebhistoryinterface] Error 1
gmake[6]: *** [sub-qwebhistoryinterface-make_default] Error 2
gmake[6]: *** Waiting for unfinished jobs....
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlOutputBufferCreateFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNodeGetContent at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewChild at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDocNode at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseCharEncoding at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSearchNsByHref at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFindCharEncodingHandler at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSaveFormatFileTo at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseMemory at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFree at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlDocGetRootElement at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFreeDoc at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewNs at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDoc at LIBXML2_2.4.30'
collect2: ld returned 1 exit status
gmake[7]: *** [tst_qwebelement] Error 1
gmake[6]: *** [sub-qwebelement-make_default] Error 2
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlOutputBufferCreateFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNodeGetContent at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewChild at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDocNode at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseCharEncoding at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSearchNsByHref at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFindCharEncodingHandler at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSaveFormatFileTo at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseMemory at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFree at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlDocGetRootElement at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFreeDoc at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewNs at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDoc at LIBXML2_2.4.30'
collect2: ld returned 1 exit status
gmake[7]: *** [tst_qgraphicswebview] Error 1
gmake[6]: *** [sub-qgraphicswebview-make_default] Error 2
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlOutputBufferCreateFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNodeGetContent at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewChild at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDocNode at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseCharEncoding at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSearchNsByHref at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFindCharEncodingHandler at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSaveFormatFileTo at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseMemory at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFree at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlDocGetRootElement at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFreeDoc at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewNs at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDoc at LIBXML2_2.4.30'
collect2: ld returned 1 exit status
gmake[7]: *** [tst_qwebframe] Error 1
gmake[6]: *** [sub-qwebframe-make_default] Error 2
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlOutputBufferCreateFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNodeGetContent at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewChild at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDocNode at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseCharEncoding at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseFile at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSearchNsByHref at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFindCharEncodingHandler at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlSaveFormatFileTo at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlParseMemory at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFree at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlDocGetRootElement at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlFreeDoc at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewNs at LIBXML2_2.4.30'
/usr/lib64/libgstreamer-0.10.so.0: undefined reference to `xmlNewDoc at LIBXML2_2.4.30'
collect2: ld returned 1 exit status
gmake[7]: *** [tst_qwebpage] Error 1
gmake[6]: *** [sub-qwebpage-make_default] Error 2
gmake[5]: *** [sub-WebKit-qt-tests-make_default-ordered] Error 2
gmake[4]: *** [sub-webkit-make_default-ordered] Error 2
CMake Error at /u/home/angelini/PV/Build/pv-qt-build.cmake:26 (message):
  Failed!!!


make[3]: *** [qt/src/qt-stamp/qt-build] Error 1
make[2]: *** [CMakeFiles/qt.dir/all] Error 2
make[1]: *** [CMakeFiles/qt.dir/rule] Error 2
make: *** [qt] Error 2


________________________________
Rick Angelini

USArmy Research Laboratory
CISD/HPC Architectures Team
Building 120 Cube 315
Phone:  410-278-6266

________________________________________
From: paraview-bounces at paraview.org [paraview-bounces at paraview.org] on behalf of Utkarsh Ayachit [utkarsh.ayachit at kitware.com]
Sent: Wednesday, May 08, 2013 2:11 PM
To: Angelini, Richard C (Rick) CIV USARMY ARL (US)
Cc: paraview at paraview.org
Subject: Re: [Paraview] RHEL6 Superbuild error (UNCLASSIFIED)

Rick,

You cannot avoid building WebKit for ParaView (the tests/examples sure
can be skipped). ParaView currently needs WebKit. I've been thinking
of making that optional and not build the help-subsystem if WebKit is
unavailable, but that hasn't happened yet.

Utkarsh

On Wed, May 8, 2013 at 1:49 PM, Angelini, Richard C (Rick) CIV USARMY
ARL (US) <richard.c.angelini.civ at mail.mil> wrote:
> Classification: UNCLASSIFIED
> Caveats: NONE
>
> I'll try modifying the files as you suggest.  I've used Superbuild on
> numerous systems to build 3.98.1 and I have not run into this particular QT
> issue.  This is also one of the first (the first?) RHEL6 cluster that I've
> tried to build on.
>
> Given the error messages, I thought that the easiest workaround would be to
> throw some flags at the configuration script to avoid building WebKit,
> examples and tests.    HOWEVER, it may be worth someone's effort to try to
> figure out where the error messages are coming from and what's the correct
> fix, rather than giggling the configuration command!   8-)
>
>
>
> -----Original Message-----
> From: Utkarsh Ayachit [mailto:utkarsh.ayachit at kitware.com]
> Sent: Wednesday, May 08, 2013 12:56 PM
> To: Angelini, Richard C (Rick) CIV USARMY ARL (US)
> Cc: paraview at paraview.org
> Subject: Re: [Paraview] RHEL6 Superbuild error
>
> Try changing the flags in Source/Prohects/qt.cmake instead. For my info,
> what are the flags that you're setting. Maybe we can change the default
> setup itself.
>
> Utkarsh
>
> On Wed, May 8, 2013 at 11:34 AM, Angelini, Richard C (Rick) CIV USARMY ARL
> (US) <richard.c.angelini.civ at mail.mil> wrote:
>> I'm trying to build ParaView 3.98.1 on a RHEL6 cluster and I'm getting
> stuck
>> in Qt.    The errors look like they are related to Webkit and the
>> tests/examples.     Does it need to build with Webkit?     Or better yet,
>> how to I get the Superbuild to not build Webkit, examples and tests?
>> There's a file pv-qt-configure.cmake where I can set some flags, but it
>> keeps getting overwritten if I make changes to this file.    There must be
> a
>> better way to do this!   8-)
>>
>>
>> FYI - here is the error I seen on my RHEL6 cluster build:
>>
>> make[2]: Entering directory
>>
> `/u/US_HOME1/angelini/PV/Build/qt/src/qt-build/src/3rdparty/webkit/Source/We
> bKit/qt/tests'
>> cd qwebframe/ && make -f Makefile.WebKit
>> make[3]: Entering directory
>>
> `/u/US_HOME1/angelini/PV/Build/qt/src/qt-build/src/3rdparty/webkit/Source/We
> bKit/qt/tests/qwebframe'
>> g++ -L/u/home/angelini/PV/Build/install/lib -Wl,-O1
>> -Wl,-rpath,/u/US_HOME1/angelini/PV/Build/qt/src/qt/src/3rdparty/webkit
>> /Source/lib -Wl,-rpath,/u/home/angelini/PV/Build/install/lib
>> -Wl,-rpath,/u/home/angelini/PV/Build/install/lib -o tst_qwebframe
>> .obj/release-shared/tst_qwebframe.o
>> .obj/release-shared/qrc_tst_qwebframe.o
>> -L/u/home/angelini/PV/Build/install/lib
>> -L/u/US_HOME1/angelini/PV/Build/qt/src/qt-build/lib -L/usr/X11R6/lib64
>> -L/u/home/angelini/PV/Build/install/lib
>> -L/u/US_HOME1/angelini/PV/Build/qt/src/qt-build/lib -lQtDeclarative
>> -lQtScript -lQtSql -lQtXmlPatterns -L/usr/X11R6/lib64 -lQtWebKit
>> -lQtTest -lQtGui -lQtNetwork -lQtCore -lpthread -lXrender -lfontconfig
>> -lfreetype -lXext -lX11 -lm
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlOutputBufferCreateFile at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlNodeGetContent at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlNewChild at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlNewDocNode at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlParseCharEncoding at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlParseFile at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlSearchNsByHref at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlFindCharEncodingHandler at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlSaveFormatFileTo at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlParseMemory at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlFree at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlDocGetRootElement at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlFreeDoc at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlNewNs at LIBXML2_2.4.30'
>> /usr/lib64/libgstreamer-0.10.so.0: undefined reference to
>> `xmlNewDoc at LIBXML2_2.4.30'
>> collect2: ld returned 1 exit status
>> make[3]: *** [tst_qwebframe] Error 1
>> make[3]: Leaving directory
>>
> `/u/US_HOME1/angelini/PV/Build/qt/src/qt-build/src/3rdparty/webkit/Source/We
> bKit/qt/tests/qwebframe'
>> make[2]: *** [sub-qwebframe-make_default] Error 2
>> make[2]: Leaving directory
>>
> `/u/US_HOME1/angelini/PV/Build/qt/src/qt-build/src/3rdparty/webkit/Source/We
> bKit/qt/tests'
>> make[1]: *** [sub-WebKit-qt-tests-make_default-ordered] Error 2
>> make[1]: Leaving directory
>> `/u/US_HOME1/angelini/PV/Build/qt/src/qt-build/src/3rdparty/webkit/Source'
>> make: *** [sub-webkit-make_default-ordered] Error 2
>>
>>
>> ________________________________
>> Rick Angelini
>>
>> USArmy Research Laboratory
>> CISD/HPC Architectures Team
>> Building 120 Cube 315
>> Phone:  410-278-6266
>>
>> _______________________________________________
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>>
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>> Please keep messages on-topic and check the ParaView Wiki at:
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>
> Classification: UNCLASSIFIED
> Caveats: NONE
>
>
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