This is alarming...Engine and mdserver linked with DB plugin libs!

[markcmiller86]

Go to build dir for engine and do a make clean; make VERBOSE=1 >& junk.out and then grep junk.out for hdf5. You will get hits. But, you should NOT get hits for hdf5. hdf5 is used only in a database plugin lib. If I look at a link of the libengine_ser.dylib, I get all the items listed below.

We are also getting hits for conduit, condiut_relay and blueprint. See below. Again, those are only used in DB plugins and should not be being linked into the engine.

I believe the reason this is happening is the use of MFEM in the engine. That is fine. But, we cannot use an MFEM in the engine that depends on I/O libs needed only in the plugins. We need to build MFEM differently for use in the engine.

Taggiging @iulian787 and @vijaysm because this is impacting MOAB plugin which uses HDF5 in either serial or parallel and the fact that engine is loading hdf5 serial prevents parallel MOAB plugin from operating correctly.

/usr/bin/clang++
-fno-common
-fexceptions
-g
-isysroot
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk
-dynamiclib
-Wl,-headerpad_max_install_names
-o
../../lib/libengine_ser.dylib
-install_name
@rpath/libengine_ser.dylib
CMakeFiles/engine_ser.dir/ProgrammableCompositer.C.o
CMakeFiles/engine_ser.dir/DataNetwork.C.o
CMakeFiles/engine_ser.dir/ClonedDataNetwork.C.o
CMakeFiles/engine_ser.dir/CumulativeQueryNamedSelectionExtension.C.o
CMakeFiles/engine_ser.dir/Engine.C.o
CMakeFiles/engine_ser.dir/EngineBase.C.o
CMakeFiles/engine_ser.dir/LoadBalancer.C.o
CMakeFiles/engine_ser.dir/MesaDisplay.C.o
CMakeFiles/engine_ser.dir/Netnodes.C.o
CMakeFiles/engine_ser.dir/NetworkManager.C.o
CMakeFiles/engine_ser.dir/VisItDisplay.C.o
-L/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/conduit/v0.9.1/darwin-x86_64/lib
-L/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/hdf5/1.8.14/darwin-x86_64/lib
-L/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/zlib/1.2.13/darwin-x86_64/lib
-L/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/mfem/4.6/darwin-x86_64/lib
-Wl,-rpath,/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/conduit/v0.9.1/darwin-x86_64/lib
-Wl,-rpath,/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/hdf5/1.8.14/darwin-x86_64/lib
-Wl,-rpath,/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/zlib/1.2.13/darwin-x86_64/lib
-Wl,-rpath,/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/mfem/4.6/darwin-x86_64/lib
-Wl,-rpath,/Users/miller86/visit/visit/34rc/build/lib
../../lib/libenginerpc.dylib
../../lib/libavtwriter_ser.dylib
../../lib/libavtquery_ser.dylib
../../lib/libavtviswindow_ser.dylib
-lmfem
-lhdf5
-lz
-lhdf5
-lz
-lz
-lz
../../lib/libavtblueprint.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkIOPLY.9.2.6.dylib
../../lib/libavtshapelets.dylib
../../lib/libavtexpressions_ser.dylib
../../lib/libavtdbin_ser.dylib
../../lib/libavtpythonfilters_ser.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/python/3.9.18/darwin-x86_64/lib/libpython3.9.dylib
../../lib/libavtplotter_ser.dylib
../../lib/libavtfilters_ser.dylib
../../lib/libavtview.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkRenderingFreeType.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkfreetype.9.2.6.dylib
../../lib/libavtdatabase_ser.dylib
../../lib/libavtmir_ser.dylib
../../lib/libavtpipeline_ser.dylib
../../lib/libavtdbatts.dylib
../../lib/libvisit_verdict.dylib
../../lib/libtess2.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkRenderingRayTracing.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkDomainsChemistry.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkRenderingSceneGraph.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkRenderingOpenGL2.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkRenderingHyperTreeGrid.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkFiltersHybrid.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkRenderingUI.9.2.6.dylib
-framework
Cocoa
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkglew.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkRenderingVolume.9.2.6.dylib
-Xlinker
-framework
-Xlinker
OpenGL
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkInteractionStyle.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkRenderingCore.9.2.6.dylib
../../lib/libvisit_vtk.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkFiltersExtraction.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkIOXMLParser.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkFiltersFlowPaths.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkFiltersGeometry.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkImagingHybrid.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkIOImage.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/zlib/1.2.13/darwin-x86_64/lib/libz.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtktiff.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkImagingCore.9.2.6.dylib
../../lib/libavtmath.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkFiltersModeling.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkFiltersSources.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkFiltersGeneral.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkCommonComputationalGeometry.9.2.6.dylib
-lmfem
../../lib/liblightweight_visit_vtk.dylib
../../lib/libvisitcommon.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/zlib/1.2.13/darwin-x86_64/lib/libz.dylib
-ldl
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkIOLegacy.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkIOCore.9.2.6.dylib
-lconduit
-lconduit_relay
-lconduit_blueprint
-lhdf5
-lz
-lhdf5
-lz
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkFiltersCore.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkCommonExecutionModel.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkCommonDataModel.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkCommonTransforms.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkCommonMisc.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkCommonMath.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkkissfft.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtkCommonCore.9.2.6.dylib
/Users/miller86/visit/visit/34rc/release/build-mb-3.4.1-darwin-21-x86_64-release/thirdparty_shared/third_party/vtk/9.2.6/darwin-x86_64/lib/libvtksys.9.2.6.dylib

[markcmiller86]

If I disable mfem, I get the same problem with conduit. The engine includes and links with conduit so any dependencies for conduit get linked into the engine.

[markcmiller86]

@iulian787 and @vijaysm if I disable conduit, mfem and fsm in my build, I can get the engine to run and use MOAB in parallel correctly...

[vijaysm]

That is excellent news! Thanks for checking this thoroughly @markcmiller86

When you say MOAB parallel engine is working correctly, I assume this means there are no HDF5 property table errors that we were seeing before? I am still puzzled as to why the Ubuntu 22 version of engine_par is still failing (eventhough ldd verification showed that it was not linked against HDF5-serial).

[markcmiller86]

When you say MOAB parallel engine is working correctly, I assume this means there are no HDF5 property table errors that we were seeing before?

Yes, correct.

I am still puzzled as to why the Ubuntu 22 version of engine_par is still failing (eventhough ldd verification showed that it was not linked against HDF5-serial).

I am too but I believe linux is more lenient about shared lib dependencies and so think the engine is still loading the serial hdf5 library. An strace would confirm that.

[markcmiller86]

Was chatting with @brugger1 about this. One idea he has...build engine_par against hdf5_mpi instead of hdf5. That would fix the collision with MOAB parallel database plugin.

But, it would mean we continue to link the engine (and mdsever) against hdf5 and that would mean nobody would be allowed to build a custom plugin using a different version of hdf5 than what VisIt was built with.

If VisIt was not on such an ancient version of hdf5, that is probably ok. But, because we are on such an ancient version of hdf5, it would likely conflict with any plugin developer using many of the newer features in newer versions of hdf5.

So, we would need to upgrade hdf5 in VisIt.

That said, I still think it would be best to get hdf5 out of the engine and mdserver if possible.

[biagas]

@markcmiller86 conduit and mfem were added as dependencies when avt/Blueprint and avt/MFEM were added.
With those additions, we also get whatever dependencies conduit and mfem have.

[markcmiller86]

@markcmiller86 conduit and mfem were added as dependencies when avt/Blueprint and avt/MFEM were added.
With those additions, we also get whatever dependencies conduit and mfem have.

Yes, that is right. So, it may mean we have to build those libs two different ways...one way for VisIt components and another way for database plugins...only the latter of which can depend on things like hdf5, netcdf, etc.

[cyrush]

@markcmiller86 Both Conduit and MFEM are used outside of the database plugins.
We have avt libs that provide MFEM to VTK and Conduit to VTK as a general service for the engine.

While Conduit's I/O that uses HDF5 does not need to link HDF5, I think that MFEM actually links Conduit relay, which does link HDF5.

In general unless we have a fully name mangled serial hdf5 and mpi hdf5, I think we have an issue regardless if it's DB only vs in the engine. Yes we can disable plugins, but that approach won't work for an install that can be widely used

[markcmiller86]

Both Conduit and MFEM are used outside of the database plugins.

Sure...but I guess my question is...what do conduit and MFEM need to do in the way of I/O with HDF5 in the engine and mdserver? I don't think the engine or mdserver need to do any I/O with or without HDF5 and so the question remains...why do business this way? It can't be for the convenience of a 3rd party lib dependency that isn't designed to build without HDF5?

As an aside, as things are designed now, no one building a custom HDF5 plugin would be able to build against an hdf5 version other than 1.8.XX (1.8.14 is over 10 years old now). So, someone wishing to use newer features in HDF5 would simply not be able to use a newer HDF5. That paricular issue is solved, of course, by updating to newer HDF5 in VisIt. But, that only minimizes that particular issue. It doesn't fix it.

[cyrush]

The answer is simple: MFEM does not have multiple libraries that partition features based on dependencies.

Those features are either on or off for a build of mfem.

Conduit has multiple libraries - (relay is the one with all the i/o deps), but if MFEM is using Conduit, it will also link those I/O libs.

[cyrush]

We are going to explore building MPI enabled HDF5 will work for all cases (engine_ser and engine_par)