moose tests won't build with vtk enabled

[Victor Koppejan]

I'm having some issues build moose with vtk support.

I'm getting the following error:

Compiling C++ (in dbg mode) /data/localhome/vwkoppejan/software/moose/vtk/test/build/unity_src/meshes_Unity.C...
Linking Library /data/localhome/vwkoppejan/software/moose/vtk/framework/libmoose-dbg.la...
Linking Executable /data/localhome/vwkoppejan/software/moose/vtk/framework/contrib/exodiff/exodiff...
Linking Library /data/localhome/vwkoppejan/software/moose/vtk/test/lib/libmoose_test-dbg.la...
Linking Executable /data/localhome/vwkoppejan/software/moose/vtk/test/moose_test-dbg...
/data/localhome/vwkoppejan/software/moose/vtk/framework/libmoose-dbg.so: error: undefined reference to 'vtkAlgorithm::GetOutputPort(int)'
/data/localhome/vwkoppejan/software/moose/vtk/framework/libmoose-dbg.so: error: undefined reference to 'vtkImageAlgorithm::GetOutput()'
collect2: error: ld returned 1 exit status
make: *** [/data/localhome/vwkoppejan/software/moose/vtk/test/moose_test-dbg] Error 1

Can anyone help me solve this?

Thanks in advance,

Victor

[Derek Gaston]

Do you need VTK support?  If not, try passing --disable-vtk to the update_and_rebuild_libmesh.sh script.  VTK is not critical for "normal" MOOSE usage.

Derek

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[Victor Koppejan]

Well need, need, no. It's just that many of my post processing scripts are based on vtk files. It's not so hard to change the input reader to exodus/nemesis.

I still find it a bit weird I can't get it to work. Can you guys share the cmake command you use for vtk with the moose rpms?

[Peterson, JW]

On Sat, May 5, 2018 at 1:19 PM, Victor Koppejan <victork...@gmail.com> wrote:

Well need, need, no. It's just that many of my post processing scripts are based on vtk files. It's not so hard to change the input reader to exodus/nemesis.

I still find it a bit weird I can't get it to work. Can you guys share the cmake command you use for vtk with the moose rpms?

Hmm... I see from your diagnostic log that you are using CentOS Linux and a VTK/7.1.1-gompi-2017b-Python-2.7.14 module. Is that VTK something you built yourself? 

It's possible that your VTK installation is slightly different from what we typically build, and requires different libraries to be linked against. We have seen this in the past, for example with the ArchLinux VTK binary distributions.

--

John

[Victor Koppejan]

Hi John,

I've used a vtk module I built using easybuild. How do you typically build vtk (I mean which cmake options do you use)?

[Miller, Jason M]

Victor,

Folks can view how we build all the software that goes into the moose-environment package from our package_builder repository: https://github.com/idaholab/package_builder/tree/master/build_from_source

To answer your question, we build VTK using the following configure:

# Assuming you can load a GNU MPI Wrapper of some sort

  module load cmake mpich-3.2-gcc

# Create an out-of-tree build location

  mkdir vtk-build; cd vtk-build

# Declare a installation base directory

  export PACKAGES_DIR=/opt/moose

# Assuming VTK-7.1.0 is up one directory where you extracted the tarball.

# Obviously you may want to change the directories a bit. For this example we are using gcc-7.3.0 as our compiler

cmake ../VTK-7.1.0 -DCMAKE_INSTALL_PREFIX=$PACKAGES_DIR/VTK-7.1.0/gcc-7.3.0 \

 -DCMAKE_INSTALL_RPATH:STRING=$PACKAGES_DIR/VTK-7.1.0/gcc-7.3.0/lib \

 -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON \

 -DCMAKE_INSTALL_NAME_DIR:STRING=$PACKAGES_DIR/VTK-7.1.0/gcc-7.3.0/lib \

 -DCMAKE_MACOSX_RPATH:BOOL=ON \

 -DVTK_WRAP_PYTHON=ON \

 -DVTK_Group_MPI:BOOL=ON -Wno-dev

The resulting module we create so VTK can be 'accessed' when needed:

#%Module1.0#####################################################################

##

## VTK-7.1.0 gcc-7.3.0 Module

##

##

##

set             BASE_PATH          "$PACKAGES_DIR"

if { [uname sysname] != "Darwin" } {

  prepend-path    LD_LIBRARY_PATH    "$BASE_PATH/VTK-7.1.0/gcc-7.3.0/lib"

}

setenv          VTKINCLUDE_DIR                "$BASE_PATH/VTK-7.1.0/gcc-7.3.0/include/vtk-7.1"

prepend-path    INCLUDE_PATH                  "$BASE_PATH/VTK-7.1.0/gcc-7.3.0/include/vtk-7.1"

setenv          VTKLIB_DIR                    "$BASE_PATH/VTK-7.1.0/gcc-7.3.0/lib"

setenv          VTK6_PYTHON_DIR               "$BASE_PATH/VTK-7.1.0/gcc-7.3.0/lib/python2.7/site-packages"

Cheers!

Jason

On Tue, May 8, 2018 at 10:49 PM, Victor Koppejan <victork...@gmail.com> wrote:

Hi John,

I've used a vtk module I built using easybuild. How do you typically build vtk (I mean which cmake options do you use)?

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[Peterson, JW]

On Wed, May 9, 2018 at 6:40 AM, Miller, Jason M <jason....@inl.gov> wrote:

Victor,

Folks can view how we build all the software that goes into the moose-environment package from our package_builder repository: https://github.com/idaholab/package_builder/tree/master/build_from_source

To answer your question, we build VTK using the following configure:

# Assuming you can load a GNU MPI Wrapper of some sort

  module load cmake mpich-3.2-gcc

# Create an out-of-tree build location

  mkdir vtk-build; cd vtk-build

# Declare a installation base directory

  export PACKAGES_DIR=/opt/moose

# Assuming VTK-7.1.0 is up one directory where you extracted the tarball.

# Obviously you may want to change the directories a bit. For this example we are using gcc-7.3.0 as our compiler

cmake ../VTK-7.1.0 -DCMAKE_INSTALL_PREFIX=$PACKAGES_DIR/VTK-7.1.0/gcc-7.3.0 \

 -DCMAKE_INSTALL_RPATH:STRING=$PACKAGES_DIR/VTK-7.1.0/gcc-7.3.0/lib \

 -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON \

 -DCMAKE_INSTALL_NAME_DIR:STRING=$PACKAGES_DIR/VTK-7.1.0/gcc-7.3.0/lib \

 -DCMAKE_MACOSX_RPATH:BOOL=ON \

 -DVTK_WRAP_PYTHON=ON \

 -DVTK_Group_MPI:BOOL=ON -Wno-dev

An important option that we are using is the -DVTK_Group_MPI:BOOL=ON option. That option seems to be missing from the easybuild config I randomly found at:

https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb

This could be related to the linking error you are getting, not 100% sure though.

In our VTK builds, the symbol in question is found (using the nm utility) in the following dylib on MacOS:

./libvtkCommonExecutionModel-7.1.1.dylib

000000000000b700 T __ZN12vtkAlgorithm13GetOutputPortEi

Could you check if there is something similar on your system (the exact name mangling may be slightly different)?

--

John

[Victor Koppejan]

Hi Jason and John,

Thanks for looking into this. I have the -DVTK_Group_MPI:BOOL=ON option in my easyconfig file, the problem could be the -DVTK_WRAP_PYTHON=ON.

I have the libvtkCommonExecutionModel-7.1.so present in my VTK lib dir.

I'll recompile tomorrow and see if it I can get it to work.

Op woensdag 9 mei 2018 16:36:50 UTC+2 schreef jw.peterson:

[Victor Koppejan]

sorry, forgot the nm output, the symbol is found.

Op woensdag 9 mei 2018 16:48:37 UTC+2 schreef Victor Koppejan:

[Peterson, JW]

On Wed, May 9, 2018 at 8:51 AM, Victor Koppejan <victork...@gmail.com> wrote:

sorry, forgot the nm output, the symbol is found.

I agree, as I see 

0000000000059160 T _ZN12vtkAlgorithm13GetOutputPortEi

in your output. Now, MOOSE does not link against libvtkCommonExecutionModel-7.1.so directly, it links against the following libs

libvtkCommonCore-7.1.so

libvtkIOCore-7.1.so

libvtkCommonDataModel-7.1.so

libvtkFiltersCore-7.1.so

libvtkIOXML-7.1.so

libvtkImagingCore-7.1.so

libvtkIOImage-7.1.so

libvtkImagingMath-7.1.so

libvtkIOParallelXML-7.1.so

libvtkParallelMPI-7.1.so

libvtkParallelCore-7.1.so

one or more of which links against libvtkCommonExecutionModel-7.1.so, so we end up pulling in the required symbols indirectly.

On my system, I can run "otool -L" on dynamic libraries to see what they are linked against. I'm not sure what the corresponding command is on Linux, but it would be good to verify that one of the libraries in the list above links to libvtkCommonExecutionModel-7.1.so on your system... 

Another potential issue that could arise is if a different compiler was used to compile VTK than you are now using to compile MOOSE as they could have different name manglings...

--

John

[Alexander Lindsay]

ldd

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[Victor Koppejan]

I compiled vtk-7.1.1 myself using

cmake .. -DCMAKE_INSTALL_PREFIX=/data/localhome/vwkoppejan/software/VTK/7.1.1/deb -DCMAKE_INSTALL_RPATH:STRING=/data/software/VTK/7.1.1/deb/lib -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON -DCMAKE_INSTALL_NAME_DIR:STRING=/data/software/VTK/7.1.1/deb/lib -DCMAKE_BUILD_TYPE=Debug -DCMAKE_MACOSX_RPATH:BOOL=ON -DVTK_WRAP_PYTHON=ON -DVTK_Group_MPI:BOOL=ON -Wno-dev

Using the same toolchain I compiled moose using the update/rebuild script. The configure command finds vtk versions,  just as I showed earlier. Tests give t he same problem. Using ldd I can see the the vtk shared libs arer properly linked against  libvtkCommonExecutionModel-7.1.so.

not sure where to look next

Op woensdag 9 mei 2018 20:18:20 UTC+2 schreef Alexander Lindsay:

ldd

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[Miller, Jason M]

Did you set your environment up to include the following after installing VTK? For us, we need to export the following in order for libMesh to detect and link to it:

setenv          VTKINCLUDE_DIR                "/opt/moose/VTK-7.1.0/gcc-7.3.0/include/vtk-7.1"

prepend-path    INCLUDE_PATH                  "/opt/moose/VTK-7.1.0/gcc-7.3.0/include/vtk-7.1"

setenv          VTKLIB_DIR                    "/opt/moose/VTK-7.1.0/gcc-7.3.0/lib"

setenv          VTK6_PYTHON_DIR               "/opt/moose/VTK-7.1.0/gcc-7.3.0/lib/python2.7/site-packages"

Of course, your paths will be different than ours. According to your cmake configure line, I think it should look like:

export VTKINCLUDE_DIR="/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/include/vtk-7.1"

export INCLUDE_PATH="/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/include/vtk-7.1:$INCLUDE_PATH"

export VTKLIB_DIR="/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/lib"

export VTK6_PYTHON_DIR="/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/lib/python2.7/site-packages"

Once the above is set, you will want to rebuild libMesh within the same terminal... After you do, can you submit the new libmesh_diagnostic.log generated?

Thanks!

Jason

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[Peterson, JW]

The configure command finds vtk versions,  just as I showed earlier.

But not _exactly_ as you showed earlier, since your hand-built VTK is now in a different location, right?

Other than that, it sounds like you are doing everything correctly/consistently so I don't understand how you would still get undefined symbols while linking.

--

John

[Victor Koppejan]

Apologies, I ment that the configure command in the update/build script recognizes and approves the vtk installation.

I went through Jason´s steps, but the problem´s still there. I´ve added the log file and the module file for moose (vtk.lua)

bash history

module load moose/vtk 

export VTKINCLUDE_DIR="/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/include/vtk-7.1"

export INCLUDE_PATH="/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/include/vtk-7.1:$INCLUDE_PATH"

export VTKLIB_DIR="/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/lib"

export VTK6_PYTHON_DIR="/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/lib/python2.7/site-packages"

cd software/moose/vtk/

cd scripts/

./update_and_rebuild_libmesh.sh 

cd ../test/

make -j8

Op donderdag 10 mei 2018 16:26:58 UTC+2 schreef jw.peterson:

[Peterson, JW]

On Thu, May 10, 2018 at 8:55 AM, Victor Koppejan <victork...@gmail.com> wrote:

Apologies, I ment that the configure command in the update/build script recognizes and approves the vtk installation.

Could you write a simple main program program that makes a dummy call to one or both of the offending functions

vtkAlgorithm::GetOutputPort(int)

vtkImageAlgorithm::GetOutput()

and then attempt to compile/link it with the command:

mpicxx -o foo -I/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/include/vtk-7.1 foo.cpp -ldl -Wl,-rpath,/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/lib \

-L/data/localhome/vwkoppejan/software/VTK/7.1.1/deb/lib -lvtkIOCore-7.1 -lvtkCommonCore-7.1 -lvtkCommonDataModel-7.1 -lvtkFiltersCore-7.1 -lvtkIOXML-7.1 -lvtkImagingCore-7.1 -lvtkIOImage-7.1 -lvtkImagingMath-7.1 -lvtkIOParallelXML-7.1 -lvtkParallelMPI-7.1 -lvtkParallelCore-7.1

(assuming your source file is called foo.cpp). If that works, then I'm still stumped, but it if fails, we may be able to play with different linker libraries etc. until we get it working.

--

John