[Paraview] Building on Titan using ParaViewSuperbuild

Hong Yi hongyi at renci.org
Thu Sep 5 17:36:49 EDT 2013 

Many thanks, David. I am able to modify ParaViewDefaults.cmake to add options to build my new plugin and PhastaAdaptor with superbuild on Titan. I now have linking errors when linking Catalyst in ParaView version 4.0.1 with our simulation code. Will start a new thread on the problem.

Thanks again for all the useful information!

Best regards,
Hong

________________________________
From: David E DeMarle [dave.demarle at kitware.com]
Sent: Thursday, September 05, 2013 12:29 PM
To: Hong Yi
Cc: Vanmoer, Mark W; paraview at paraview.org
Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild

Probably easiest to set them in CMake/cross_compile/bgp_xlc/ParaViewDefaults.cmake.

That is what defined the initial CMakeCache for ParaView itself (as opposed to the CMakeCache of the outer super build project).


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


On Thu, Sep 5, 2013 at 12:12 PM, Hong Yi <hongyi at renci.org<mailto:hongyi at renci.org>> wrote:
Thanks very much for the info, David. Turning off MPI4PY for version 3.98 as you suggested works for me to build version 3.98 on Titan also with SuperBuild.

I do want to stick with 4.0, but built 3.98 also just in case since my new plugin works well on version 3.98. After some further examination, it looks like my plugin should work on version 4.0 also. Have put my plugin code into 4.0 source directory under both tools and cross subdirectories and hope it can be built and work for version 4.0 also.

Have spent this morning trying to figure out how to turn on some additional flags in superbuild such as my new filter plugin, Fortran coprocessing adaptor, and Phasta adaptor, but cannot succeed. Hope to get some hint on how to do so. Apparently, passing those flags in by adding corresponding –D to configuretools only resulted in CMake warning indicating those manually-specified variables were not used. Have tried to change some cmake files in superbuild, but does not seem to have any effect. Really appreciate any suggestions you can offer here to turn on those additional flags which are important for our coprocessing purposes.

Thanks,

Hong


From: David E DeMarle [mailto:dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>]
Sent: Sunday, September 01, 2013 1:56 PM

To: Hong Yi
Cc: Vanmoer, Mark W; paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild

Between 3.98 and 4.0 the syntax of the option to turn off MPI4PY changes like so:
I recommend staying with 4.0, but try reverting this change if you need 3.98 for some reason.

-------------- CMake/crosscompile/xk7_gnu/ParaViewDefaults.cmake --------------
index 5835693..68c2bea 100644
@@ -3,7 +3,8 @@ list(APPEND PARAVIEW_OPTIONS "-DBUILD_SHARED_LIBS:BOOL=OFF")
 list(APPEND PARAVIEW_OPTIONS "-DBUILD_TESTING:BOOL=OFF")
 list(APPEND PARAVIEW_OPTIONS "-DPARAVIEW_BUILD_QT_GUI:BOOL=OFF")
 #
-list(APPEND PARAVIEW_OPTIONS "-DENABLE_MPI4PY:BOOL=OFF")
+list(APPEND PARAVIEW_OPTIONS "-DPARAVIEW_USE_SYSTEM_MPI4PY:BOOL=ON")
+#
 list(APPEND PARAVIEW_OPTIONS "-DPARAVIEW_USE_MPI:BOOL=ON")
 #/opt/cray/mpt/5.5.5/gni/mpich2-gnu/47/lib/
 #libmpich.a


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

On Sat, Aug 31, 2013 at 4:10 PM, Hong Yi <hongyi at renci.org<mailto:hongyi at renci.org>> wrote:
Just a quick update. Like Mark, I can build ParaView 4.0.1 with Superbuild successfully without issues using CMake 2.8.11.2 on Titan. However, I cannot build Paraview 3.98.1 with Superbuild using the same CMake version. I still got the same linking error from mpi4py.MPI.c in the final stage of linking after 100% built for the cross stage (see below for details) if I built version 3.98.1 using superbuild. Perhaps the latest version of Superbuild has some sort of incompatibility with the older version of ParaView for xk7_gnu target? Anyway, looks like we have to go with the latest ParaView version for in-situ visualization on Titan since superbuild does not work with older 3.98.1 version for us, which may very well prove a good thing for us in the long run due to a lot of improvement made on Catalyst in the latest ParaView version.

Thanks,
Hong

________________________________
From: paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org> [paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>] on behalf of Hong Yi [hongyi at renci.org<mailto:hongyi at renci.org>]
Sent: Friday, August 30, 2013 5:43 PM
To: Vanmoer, Mark W; David E DeMarle
Cc: paraview at paraview.org<mailto:paraview at paraview.org>

Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild

Thanks for the info, Mark. Looks like it is sensible for me to try newer version of CMake 2.8.11.2 and see how it goes.

On a somewhat related question: I am trying to pass in some CMake flags to make it build my new filter plugin as well as FortranAdaptor for coprocessing (yes, I discovered also that coprocessing/catalyst is built by default by superbuild, but FortranAdaptor is turned off by default). I tried to pass it in by adding corresponding –D to configuretools, but got CMake warning as well indicating those manually-specified variables were not used. I am wondering whether I can do it by directly changing CMakeCache.txt under paraview/src/paraview-build to force the corresponding flags to be on…

Thanks,
Hong

From: Vanmoer, Mark W [mailto:mvanmoer at illinois.edu<mailto:mvanmoer at illinois.edu>]
Sent: Friday, August 30, 2013 5:34 PM
To: Hong Yi; David E DeMarle
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

Hi Hong,
I was able to get David’s instructions to work using CMake 2.8.11.2 and ParaView 4.0.1. The build process seems to be sensitive to versions.
Mark

From: Hong Yi [mailto:hongyi at renci.org]
Sent: Friday, August 30, 2013 3:52 PM
To: David E DeMarle; Vanmoer, Mark W
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

I tried to follow the instructions and the configuration scripts to build ParaView for compute nodes on Titan. It built successfully without issues for the TOOLS stage, but when doing final linking for paraview in the CROSS stage, I got numerous similar linking error from different lines such as the following:

----------------
/....../ParaView/ParaViewSuperbuild/cross/paraview/src/paraview/Utilities/mpi4py/src/mpi4py.MPI.c: In function '__pyx_pf_6mpi4py_3MPI_4File_54Sync':
/....../ParaView/ParaViewSuperbuild/cross/paraview/src/paraview/Utilities/mpi4py/src/mpi4py.MPI.c:89682:7: error: '_save' undeclared (first use in this function)
----------------

The same error message were raised from the same file mpi4py.MPI.c from different lines.

I am using CMake version 2.8.10.2 which is provided by Titan, and using the ParaView source tree version 3.98 with one additional filter I have developed.

Any idea on what could cause the linking error?

Thanks,
Hong
________________________________
From: David E DeMarle [dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>]
Sent: Thursday, August 29, 2013 4:08 PM
To: Vanmoer, Mark W
Cc: Hong Yi; paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild
On Thu, Aug 29, 2013 at 3:51 PM, Vanmoer, Mark W <mvanmoer at illinois.edu<mailto:mvanmoer at illinois.edu>> wrote:
So coprocessing will not be built using the below instructions? I would have mentioned that, but coprocessing appears to
still be part of a regular, non-cross-compile build, so I figured it was part of ENABLE_paraview

The coprocessing plugin, which adds things to the GUI to make it easy to record coprocessing pipeline setups doesn't need to be turned on since that lives in the client only. (It is like python trace or state recording, but tailored to recording in-situ setups).

Catalyst (the stripped down version of ParaView server that a simulation code can link to and use to run those recorded pipelines quickly) is not yet an option in ParaViewSuperbuild. To cross compile Catalyst a bit more work will be required. It will follow the same plan as how the ParaView server is compiled, but I just haven't tried it. When I did cross compile Catalyst last year at this time I did the same steps that ParaViewSuperbuild's TOOLS and CROSS build passes did, just by hand.
Also, for the below configcross.sh, do we need to pass in a CMake variable telling it where the tools build dir is located?

That should be an option that you can easily set, but it isn't sorry.

 CMake/CrossCompilationMacros.cmake assumes it can find it one directory up and over like so:
macro(find_hosttools)
  set(PARAVIEW_HOSTTOOLS_DIR ${CMAKE_BINARY_DIR}/../tools/paraview/src/paraview-build/ CACHE PATH
    "Location of host built paraview compile tools directory")
  set(PYTHON_HOST_EXE ${CMAKE_BINARY_DIR}/../tools/install/bin/python CACHE PATH
    "Location of host built python executable")
  set(PYTHON_HOST_LIBDIR ${CMAKE_BINARY_DIR}/../tools/install/lib CACHE PATH
    "Location of host built python libraries")
  set(BOOST_HOST_INCLUDEDIR ${CMAKE_BINARY_DIR}/../tools/install/include CACHE PATH
    "Location of host built boost headers")
endmacro()

You could predefine all four of those if you like.

Thanks,
Mark

From: David E DeMarle [mailto:dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>]
Sent: Thursday, August 29, 2013 1:41 PM
To: Hong Yi
Cc: Vanmoer, Mark W; paraview at paraview.org<mailto:paraview at paraview.org>

Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild

On Thu, Aug 29, 2013 at 2:13 PM, Hong Yi <hongyi at renci.org<mailto:hongyi at renci.org>> wrote:
Hi David,

I just started to try superbuild on Titan also. I don't see you set ENABLE_MPI to be true in your configure script. Could you confirm whether ENABLE_MPI needs to be set to TRUE in order for ParaView to run on Titan in parallel? Since my purpose is to link our

The ENABLE_MPI flag at the Superbuild level is unrelated. It has a purpose only when CROSS_BUILD_STAGE=HOST, that is when making ParaView binary installers for desktops from Superbuild.

You shouldn't turn it on in the TOOLS or CROSS stages. Instead let the CROSS stage use the system installed MPI. It does that by turning PARAVIEW_USE_MPI=ON when it configures the ParaView sub-build. See CMake/crosscompile/xk7_gnu to see where it does that, and to see the other flags it uses.

simulation code (already built statically with CMake on Titan) to ParaView CoProcessing libraries (I am using version 3.98.1) for in-situ visualization on Titan, so in this case, do I have to set ENABLE_paraview to true and do I need to enable OSMesa for ParaView to resort to off-screen rendering for in-situ visualization?

The CROSS stage turns on Python, Mesa and ParaView. Titan's accelerators don't really run X11, so Mesa is the only option for rendering there.

Although I can build ParaView from source on Titan login nodes, I am not able to run it on compute nodes, so I am starting to try superbuild hoping to be able to cross build ParaView libraries to run in-situ visualization on Titan.

I've cross compiled Catalyst itself before on a bluegene. I did it manually before SuperBuild existed. I will see if I can dig up my config scripts. Cross compiling Catalyst should be more or less that same thing as cross compiling ParaView, but a bit faster and easier because their is less code involved.

Thanks,
Hong
________________________________
From: paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org> [paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>] on behalf of David E DeMarle [dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>]
Sent: Thursday, August 29, 2013 1:21 PM

To: Vanmoer, Mark W
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild

Your tools build is pointing to the compiler wrapper that you normally would use to make code for the back end.
The tools build should just use plain old local gcc since we only build things at that point that run on the login node.

Try these setup scripts:
I source configtools.sh to set up my environment before I build the compile tools, and configcross.sh before before I cross compile ParaView.

configtools.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for front end
module unload PrgEnv-pgi
module load gcc
#configure settings for to build compile tools only
cmake \
  -DCROSS_BUILD_STAGE:STRING=TOOLS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DBUILD_TESTING:BOOL=FALSE \
  -DParaView_FROM_GIT:BOOL=OFF \
  -DENABLE_paraview:BOOL=TRUE \
  -DENABLE_boost:BOOL=TRUE \
  -DENABLE_python:BOOL=TRUE \
  -DENABLE_portfwd:BOOL=FALSE \
  ../../ParaViewSuperbuild


then make

configcross.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for back end
module unload PrgEnv-pgi
module unload gcc
module load PrgEnv-gnu
#not sure why module load wasn't sufficient, but ended up needing to force
#cmake to choose the right compiler
setenv CC /opt/cray/xt-asyncpe/5.17/bin/cc
setenv CXX /opt/cray/xt-asyncpe/5.17/bin/CC
#configure settings to cross compile python, (mesa - implied), and paraview
cmake \
  -DCROSS_BUILD_STAGE:STRING=CROSS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DBUILD_TESTING:BOOL=TRUE \
  -DParaView_FROM_GIT:BOOL=OFF \
  -DENABLE_paraview:BOOL=TRUE \
  -DENABLE_python:BOOL=TRUE \
  ../../ParaViewSuperbuild

then make again


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

On Tue, Aug 27, 2013 at 4:26 PM, Vanmoer, Mark W <mvanmoer at illinois.edu<mailto:mvanmoer at illinois.edu>> wrote:
Hi, I'm trying to follow the advice on building ParaView on Titan using the ParaViewSuperbuild method from an earlier discussion in June.

When I run make in the "TOOLS" directory I get the following error:

[ 66%] Building CXX object Utilities/ProcessXML/CMakeFiles/kwProcessXML.dir/ProcessXML.cxx.o
Linking CXX executable ../../bin/vtkkwProcessXML-pv4.0
/usr/bin/ld: attempted static link of dynamic object `../../lib/libvtkCommonCore-pv4.0.so.1'
collect2: error: ld returned 1 exit status
make[6]: *** [bin/vtkkwProcessXML-pv4.0] Error 1
make[5]: *** [Utilities/ProcessXML/CMakeFiles/kwProcessXML.dir/all] Error 2
make[4]: *** [CMakeFiles/pvCompileTools.dir/rule] Error 2
make[3]: *** [pvCompileTools] Error 2
CMake Error at /ccs/home/vanmoer/builds/superbuild/tools-build/pv-paraview-build.cmake:26 (message):
  Failed!!!


make[2]: *** [paraview/src/paraview-stamp/paraview-build] Error 1

I don't see a BUILD_SHARED that I can toggle. All of the CMAKE_SHARED_LINKER_FLAGS* vars are empty, if those are related.

Any suggestions?

Thanks,
Mark



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