[Paraview] Still more trouble compiling VisitBridge with Paraview 3.10 on RHEL 5

Mon Apr 11 14:34:06 EDT 2011

Hello,
I don't know why or how I'm doing a static build and am not married to the idea -- it appears to be incidental to other choices I'm making.  I certainly never checked a box or set a variable explicitly requesting a static build that I recall.  I don't know if this list will allow me to attach the CMakeCache.txt file or if that would exceed a limit.
Clearly the executables are not statically linked, or else I would not need rpath, so I don't know in what sense I'm doing a static build.
The only libraries I'm statically linking are libsiloh5.a, libhdf5.a and libmili.a
Cheers and thank you
--Rich

On Apr 11, 2011, at 11:08 AM, Utkarsh Ayachit wrote:

> Rich,
>
> Dave just reminded me that you're doing a static build, I missed that.
> In that case you will no have the "wrapper" executable I was referring
> to and "shared forwarding" does not apply.
> Out of curiosity, what libraries are you linking in shared with this
> static build?
>
> Utkarsh
>
> On Mon, Apr 11, 2011 at 1:57 PM, Utkarsh Ayachit
> <utkarsh.ayachit at kitware.com> wrote:
>> I was hoping someone was going respond about the rpath stripping, but
>> alas I suppose I'll have to :).
>>
>> rpaths are stripped to ensure that installed executable don't depend
>> on anything that is not installed. To circumvent the LD_LIBRARY_PATH
>> issues, Paraview uses what we call "shared-forwarding". The paraview
>> executable that gets installed in "bin" directory is not the real
>> paraview executable instead it's a wrapper executable that sets up the
>> environment variables and the forks the real paraview executable
>> (which is trypically under lib/paraview-version/...).
>>
>> So to diagnose the missing path, run the installed paraview with
>> "--ldd" command line argument. What are the missing libraries and
>> where are they located?
>>
>> Utkarsh
>>
>> On Mon, Apr 11, 2011 at 1:40 PM, Cook, Rich <cook47 at llnl.gov> wrote:
>>> I also forgot to include the fact that IMO the installer stripping the rpath out of binaries without any way to prevent this breaks my install and is in my opinion a bug :-)  I have to install them by just copying them by hand.
>>> -- Rich
>>>
>>> On Apr 11, 2011, at 10:37 AM, Cook, Rich wrote:
>>>
>>>> Hi, thanks for replying.
>>>> I don't know what went wrong.  One thing is that paraview wants to
>>>> When I launch paraview, and then choose File->Open, then click on the "Files of Type" pull down menu in the File Open dialog, I see some Visit plugins, such as my ParaDIS reader, so I think some of the VisitBridge is "working" but I do not see a "Mili" file type option.  Also the user who requested it is not able to open his mili files yet.
>>>> Not sure what to check or how to proceed.  Thanks for any help!
>>>> -- Rich
>>>>
>>>> On Apr 11, 2011, at 5:28 AM, Robert Maynard wrote:
>>>>
>>>>> Hi Rich,
>>>>>
>>>>> Can you give me some more information on what went wrong on install
>>>>> time. I can spend some time this week making sure that static install
>>>>> work properly.
>>>>>
>>>>> On Fri, Apr 8, 2011 at 7:14 PM, Cook, Rich <cook47 at llnl.gov> wrote:
>>>>>> Sorry to speak up again.  I got MILI to compile but I think it did not install correctly.  Am I SOL for now?  The Mili support was the whole point of my trying to get this to work.  :-)
>>>>>> Thanks for all the support
>>>>>> -- Rich
>>>>>>
>>>>>> On Apr 8, 2011, at 12:06 PM, Robert Maynard wrote:
>>>>>>
>>>>>>> Hi Rich,
>>>>>>>
>>>>>>> I am currently working on fixing the issues with the MILI reader not
>>>>>>> compiling correctly.
>>>>>>>
>>>>>>> On Fri, Apr 8, 2011 at 1:15 PM, Cook, Rich <cook47 at llnl.gov> wrote:
>>>>>>>> Aha, it's the semicolon syntax that was unknown to me.  Thanks.
>>>>>>>> I do want to reiterate that turning on the MILI reader did not result in a
>>>>>>>> successful reader build, because the include and library settings do not get
>>>>>>>> placed in the right makefiles.  I have to manually hack the link.txt and
>>>>>>>> make.flags files or otherwise do workarounds for that.  As long as I'm doing
>>>>>>>> that anyhow, I can just place the deeper dependencies there as well.
>>>>>>>> On Apr 8, 2011, at 6:26 AM, David Partyka wrote:
>>>>>>>>
>>>>>>>> Hi Rich,
>>>>>>>> Because you're building static you need to tell CMake what your
>>>>>>>> Silo/Mili/HDF5 dependencies are because it has no way of knowing. To do
>>>>>>>> this, in ccmake/cmake-gui you can list them in the same variables where you
>>>>>>>> specified SILO_LIBRARY,MILI_LIBRARY, HDF5_LIBRARY/HDF5_LIBRARIES. This
>>>>>>>> should give CMake enough information to compute the correct link line.
>>>>>>>> For example, you should be able to set these in ccmake/cmake-gui like so:
>>>>>>>> SILO_LIBRARY /usr/gapps/visit/silo/4.8/linux-x86_64_gcc-4.1/lib/libsiloh5.a;/usr/gapps/visit/szip/2.1/linux-x86_64_gcc-4.1/lib/libsz.a
>>>>>>>> On Thu, Apr 7, 2011 at 7:19 PM, Cook, Rich <cook47 at llnl.gov> wrote:
>>>>>>>>>
>>>>>>>>> OK, I just solved this by hacking into all the link.txt files I found
>>>>>>>>> laying around.  This has been one ugly build process!
>>>>>>>>> -- Rich
>>>>>>>>>
>>>>>>>>> On Apr 7, 2011, at 4:00 PM, Cook, Rich wrote:
>>>>>>>>>
>>>>>>>>>> So, our libmili.a, libsiloh5.a and libhdf5.a libraries have dependencies
>>>>>>>>>> on another library, libsz.  I've tried adding  -lz
>>>>>>>>>> /usr/gapps/visit/szip/2.1/linux-x86_64_gcc-4.1/lib/libsz.a  to every STRING
>>>>>>>>>> I can in the CMakeCache.txt file, but I'm stuck on this error.  How can I
>>>>>>>>>> append linker flags to what cmake is doing here?  You can see that the -lz
>>>>>>>>>> and libsz.a are being inserted here, but it needs to come at the end of the
>>>>>>>>>> link line to resolve the symbols.  I might resort to sed and grep if this
>>>>>>>>>> keeps up, but I hope I don't have to.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Linking CXX executable ../../../../bin/ServerManagerStateLoader
>>>>>>>>>> cd
>>>>>>>>>> /nfs/tmp2/rcook/Paraview/3.10/build/ParaView-3.10.0/build/Servers/ServerManager/Testing/Cxx
>>>>>>>>>> && /usr/gapps/visit/cmake/2.8.3/linux-x86_64_gcc-4.1/bin/cmake -E
>>>>>>>>>> cmake_link_script CMakeFiles/ServerManagerStateLoader.dir/link.txt
>>>>>>>>>> --verbose=1
>>>>>>>>>> /usr/local/bin/g++
>>>>>>>>>> -I/usr/global/tools/Kitware/Paraview/3.10/chaos_4_x86_64_ib/include
>>>>>>>>>> -I/usr/gapps/visit/mili/1.10.0/linux-x86_64_gcc-4.1/include
>>>>>>>>>> -Wno-deprecated -g
>>>>>>>>>> -L/usr/global/tools/Kitware/Paraview/3.10/chaos_4_x86_64_ib/lib
>>>>>>>>>> -L/usr/gapps/visit/mili/1.10.0/linux-x86_64_gcc-4.1/lib -lmili
>>>>>>>>>> /usr/gapps/visit/hdf5/1.8.4/linux-x86_64_gcc-4.1/lib/libhdf5.a -lz
>>>>>>>>>> /usr/gapps/visit/szip/2.1/linux-x86_64_gcc-4.1/lib/libsz.a
>>>>>>>>>> CMakeFiles/ServerManagerStateLoader.dir/ServerManagerStateLoader.cxx.o
>>>>>>>>>> CMakeFiles/ServerManagerStateLoader.dir/vtkTestingProcessModuleGUIHelper.cxx.o
>>>>>>>>>> CMakeFiles/ServerManagerStateLoader.dir/vtkTestingOptions.cxx.o  -o
>>>>>>>>>> ../../../../bin/ServerManagerStateLoader -rdynamic
>>>>>>>>>> ../../../../bin/libvtkPVServerManager.a ../../../../bin/libvtkPVFiltersCS.a
>>>>>>>>>> ../../../../bin/libvtkPVFilters.a ../../../../bin/libvtkPVServerCommonCS.a
>>>>>>>>>> ../../../../bin/libvtkPVServerCommon.a
>>>>>>>>>> ../../../../bin/libvtkPVCommandOptions.a ../../../../bin/libvtkChartsCS.a
>>>>>>>>>> ../../../../bin/libvtkViewsCS.a ../../../../bin/libvtkInfovisCS.a
>>>>>>>>>> ../../../../bin/libQVTK.a
>>>>>>>>>> /usr/global/tools/Kitware/Paraview/3.10/chaos_4_x86_64_ib/lib/libQtWebKit.so
>>>>>>>>>> /usr/global/tools/Kitware/Paraview/3.10/chaos_4_x86_64_ib/lib/libQtXmlPatterns.so
>>>>>>>>>> /usr/global/tools/Kitware/Paraview/3.10/chaos_4_x86_64_ib/lib/libQtNetwork.so
>>>>>>>>>> ../../../../bin/libIceTMPI.a ../../../../bin/libIceTGL.a
>>>>>>>>>> ../../../../bin/libIceTCore.a -lGLU
>>>>>>>>>> ../../../../bin/libvtkVolumeRenderingCS.a
>>>>>>>>>> ../../../../bin/libvtkVolumeRendering.a ../../../../bin/libvtkWidgetsCS.a
>>>>>>>>>> ../../../../bin/libKWCommon.a ../../../../bin/libvtkCharts.a
>>>>>>>>>> ../../../../bin/libvtkViews.a ../../../../bin/libvtkInfovis.a
>>>>>>>>>> ../../../../bin/libvtkWidgets.a ../../../../bin/libvtkalglib.a
>>>>>>>>>> ../../../../bin/libvtkXdmfCS.a ../../../../bin/libvtkXdmf.a
>>>>>>>>>> ../../../../bin/libXdmf.a ../../../../bin/libvtklibxml2.a -lm
>>>>>>>>>> ../../../../bin/libvtkVisItDatabasesCS.a
>>>>>>>>>> ../../../../bin/libvtkVisItAVTAlgorithmsCS.a
>>>>>>>>>> ../../../../bin/libvtkHybridCS.a ../../../../bin/libvtkParallelCS.a
>>>>>>>>>> ../../../../bin/libvtkHybrid.a ../../../../bin/libvtkParallel.a
>>>>>>>>>> ../../../../bin/libVPIC.a ../../../../bin/libCosmo.a
>>>>>>>>>> /usr/local/tools/mvapich-gnu/lib/shared/libmpich.so
>>>>>>>>>> ../../../../bin/libvtkexoIIc.a ../../../../bin/libvtkRenderingCS.a
>>>>>>>>>> ../../../../bin/libvtkRendering.a ../../../../bin/libvtkftgl.a
>>>>>>>>>> /usr/global/tools/Kitware/Paraview/3.10/chaos_4_x86_64_ib/lib/libQtGui.so
>>>>>>>>>> /usr/global/tools/Kitware/Paraview/3.10/chaos_4_x86_64_ib/lib/libQtSql.so
>>>>>>>>>> /usr/global/tools/Kitware/Paraview/3.10/chaos_4_x86_64_ib/lib/libQtCore.so
>>>>>>>>>> -lGL ../../../../bin/libvtkfreetype.a -lXt -lSM -lICE -lX11 -lXext
>>>>>>>>>> ../../../../bin/libvtkGenericFilteringCS.a
>>>>>>>>>> ../../../../bin/libvtkGenericFiltering.a ../../../../bin/libvtkGraphicsCS.a
>>>>>>>>>> ../../../../bin/libvtkImagingCS.a ../../../../bin/libvtkIOCS.a
>>>>>>>>>> ../../../../bin/libvtkFilteringCS.a ../../../../bin/libvtkCommonCS.a
>>>>>>>>>> ../../../../bin/libvtkClientServer.a ../../../../bin/libvtkVisItDatabases.a
>>>>>>>>>> ../../../../bin/libvtkVisItAVTAlgorithms.a
>>>>>>>>>> ../../../../bin/libavtdatabase_par.a ../../../../bin/libavtpipeline_par.a
>>>>>>>>>> ../../../../bin/libavtdbatts.a ../../../../bin/libavtivp.a
>>>>>>>>>> ../../../../bin/libvisit_vtk.a ../../../../bin/libvtkGraphics.a
>>>>>>>>>> ../../../../bin/libvtkverdict.a ../../../../bin/libvtkImaging.a
>>>>>>>>>> ../../../../bin/liblightweight_visit_vtk.a ../../../../bin/libvtkIO.a
>>>>>>>>>> ../../../../bin/libvtkDICOMParser.a ../../../../bin/libvtkNetCDF_cxx.a
>>>>>>>>>> ../../../../bin/libvtkmetaio.a ../../../../bin/libvtksqlite.a
>>>>>>>>>> ../../../../bin/libvtkpng.a ../../../../bin/libvtktiff.a
>>>>>>>>>> ../../../../bin/libvtkzlib.a ../../../../bin/libvtkjpeg.a
>>>>>>>>>> ../../../../bin/libvtkexpat.a ../../../../bin/libvtkFiltering.a
>>>>>>>>>> ../../../../bin/libavtmath.a ../../../../bin/libvtkCommon.a
>>>>>>>>>> ../../../../bin/libvtksys.a -lm -lpthread -lz
>>>>>>>>>> /usr/gapps/visit/szip/2.1/linux-x86_64_gcc-4.1/lib/libsz.a -ldl
>>>>>>>>>> ../../../../bin/libvisitcommon.a ../../../../bin/libvtkNetCDF.a
>>>>>>>>>> /usr/gapps/visit/hdf5/1.8.4/linux-x86_64_gcc-4.1/lib/libhdf5.a
>>>>>>>>>> /usr/gapps/visit/silo/4.8/linux-x86_64_gcc-4.1/lib/libsiloh5.a
>>>>>>>>>> /usr/gapps/visit/cgns/3.0.8/linux-x86_64_gcc-4.1/lib/libcgns.a
>>>>>>>>>> /usr/gapps/visit/mili/1.10.0/linux-x86_64_gcc-4.1/lib/libmili.a
>>>>>>>>>> -Wl,-rpath,/usr/global/tools/Kitware/Paraview/3.10/chaos_4_x86_64_ib/lib:/usr/local/tools/mvapich-gnu/lib/shared
>>>>>>>>>> /usr/gapps/visit/hdf5/1.8.4/linux-x86_64_gcc-4.1/lib/libhdf5.a(H5Z.o):
>>>>>>>>>> In function `H5Z_init_interface':
>>>>>>>>>> H5Z.c:(.text+0x27d): undefined reference to `SZ_encoder_enabled'
>>>>>>>>>>
>>>>>>>>>> /usr/gapps/visit/hdf5/1.8.4/linux-x86_64_gcc-4.1/lib/libhdf5.a(H5Zszip.o):
>>>>>>>>>> In function `H5Z_filter_szip':
>>>>>>>>>> H5Zszip.c:(.text+0x121): undefined reference to
>>>>>>>>>> `SZ_BufftoBuffDecompress'
>>>>>>>>>> H5Zszip.c:(.text+0x1ce): undefined reference to `SZ_BufftoBuffCompress'
>>>>>>>>>>
>>>>>>>>>> /usr/gapps/visit/silo/4.8/linux-x86_64_gcc-4.1/lib/libsiloh5.a(silo_hdf5.o):
>>>>>>>>>> In function `db_hdf5_InqMeshName':
>>>>>>>>>> silo_hdf5.c:(.text+0x839e): undefined reference to `H5Topen1'
>>>>>>>>>>
>>>>>>>>>> /usr/gapps/visit/silo/4.8/linux-x86_64_gcc-4.1/lib/libsiloh5.a(silo_hdf5.o):
>>>>>>>>>> In function `db_hdf5_hdrwr':
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> ✐Richard Cook
>>>>>>>>>> ✇ Lawrence Livermore National Laboratory
>>>>>>>>>> Bldg-453 Rm-4024, Mail Stop L-557
>>>>>>>>>> 7000 East Avenue,  Livermore, CA, 94550, USA
>>>>>>>>>> ☎ (office) (925) 423-9605
>>>>>>>>>> ☎ (fax) (925) 423-6961
>>>>>>>>>> ---
>>>>>>>>>> Information Management & Graphics Grp., Services & Development Div.,
>>>>>>>>>> Integrated Computing & Communications Dept.
>>>>>>>>>> (opinions expressed herein are mine and not those of LLNL)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> ✐Richard Cook
>>>>>>>>> ✇ Lawrence Livermore National Laboratory
>>>>>>>>> Bldg-453 Rm-4024, Mail Stop L-557
>>>>>>>>> 7000 East Avenue,  Livermore, CA, 94550, USA
>>>>>>>>> ☎ (office) (925) 423-9605
>>>>>>>>> ☎ (fax) (925) 423-6961
>>>>>>>>> ---
>>>>>>>>> Information Management & Graphics Grp., Services & Development Div.,
>>>>>>>>> Integrated Computing & Communications Dept.
>>>>>>>>> (opinions expressed herein are mine and not those of LLNL)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ✐Richard Cook
>>>>>>>> ✇ Lawrence Livermore National Laboratory
>>>>>>>> Bldg-453 Rm-4024, Mail Stop L-557
>>>>>>>> 7000 East Avenue,  Livermore, CA, 94550, USA
>>>>>>>> ☎ (office) (925) 423-9605
>>>>>>>> ☎ (fax) (925) 423-6961
>>>>>>>> ---
>>>>>>>> Information Management & Graphics Grp., Services & Development Div.,
>>>>>>>> Integrated Computing & Communications Dept.
>>>>>>>> (opinions expressed herein are mine and not those of LLNL)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Robert Maynard
>>>>>>
>>>>>> --
>>>>>> ✐Richard Cook
>>>>>> ✇ Lawrence Livermore National Laboratory
>>>>>> Bldg-453 Rm-4024, Mail Stop L-557
>>>>>> 7000 East Avenue,  Livermore, CA, 94550, USA
>>>>>> ☎ (office) (925) 423-9605
>>>>>> ☎ (fax) (925) 423-6961
>>>>>> ---
>>>>>> Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.
>>>>>> (opinions expressed herein are mine and not those of LLNL)
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Robert Maynard
>>>>
>>>> --
>>>> ✐Richard Cook
>>>> ✇ Lawrence Livermore National Laboratory
>>>> Bldg-453 Rm-4024, Mail Stop L-557
>>>> 7000 East Avenue,  Livermore, CA, 94550, USA
>>>> ☎ (office) (925) 423-9605
>>>> ☎ (fax) (925) 423-6961
>>>> ---
>>>> Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.
>>>> (opinions expressed herein are mine and not those of LLNL)
>>>>
>>>>
>>>>
>>>
>>> --
>>> ✐Richard Cook
>>> ✇ Lawrence Livermore National Laboratory
>>> Bldg-453 Rm-4024, Mail Stop L-557
>>> 7000 East Avenue,  Livermore, CA, 94550, USA
>>> ☎ (office) (925) 423-9605
>>> ☎ (fax) (925) 423-6961
>>> ---
>>> Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.
>>> (opinions expressed herein are mine and not those of LLNL)
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>>>
>>

--
✐Richard Cook
✇ Lawrence Livermore National Laboratory
Bldg-453 Rm-4024, Mail Stop L-557
7000 East Avenue,  Livermore, CA, 94550, USA
☎ (office) (925) 423-9605
☎ (fax) (925) 423-6961
---
Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.
(opinions expressed herein are mine and not those of LLNL)