[Paraview-developers] superbuild again on intel compilers on Linux cluster

[Chuck Atkins]

Hi Alan,

This is a known problem with C++11 compatibility and the Intel compiler.
Intel's C++ compiler provides the necessary language features for C++ 11
but does not provide any of the standard C++ library headers for it.
Instead it pulls headers from an available g++.  If a new enough g++ is not
used for the headers then you end up with a very strange situation of half
broken C++11 support with language support but no library support.  To make
matters worse, different versions of icpc are (in)compatible with different
versions of g++ headers.

You can fix it by changing which g++ icpc is using to get the correct C++11
support using the GCCROOT, GXX_INCLUDE, and GXX_ROOT environment
variables.  If none of the variables are specified then it will be pulling
C++ headers from your available system compiler, which on EL6 is gcc 4.4
which definitely does not have the necessary C++11 support.  Intel <=
16.0.2 should work correctly with g++ 4.8.x and 4.9.x headers while >=
16.0.3 should work with g++ 4.8.x all the way through 5.x.

This will also be an issue for anybody else trying to use C++11 and icpc to
get complete support.

----------
Chuck Atkins
Staff R&D Engineer, Scientific Computing
Kitware, Inc.
(518) 881-1183

On Mon, Jul 25, 2016 at 7:54 PM, Scott, W Alan <wascott at sandia.gov> wrote:

> I am also trying to do Intel superbuilds on a Linux, Intel compiler, as we
> will have to do for Trinity.  We are failing trying to find libatomic – a
> gnu library!  That shouldn’t happen, I would figure.  Anyway, here is where
> I ended up:
>
>
>
> cMakeVars =
> -DCMAKE_INSTALL_PREFIX:PATH=/projects/viz/paraview/ParaView/5.1.1-sbi-mesa/Linux-chama-x86_64
> -DBUILD_TESTING:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release
> -DParaView_FROM_GIT:BOOL=OFF -DParaView_FROM_SOURCE_DIR:BOOL=ON
> -DPARAVIEW_SOURCE_DIR:PATH=/projects/viz/paraview/src/ParaView/5.1.1-sbi/ParaView5
> -DPARAVIEW_ALWAYS_SECURE_CONNECTION:BOOL=ON -DENABLE_paraview:BOOL=ON
> -DENABLE_ffmpeg:BOOL=ON -DENABLE_python:BOOL=ON -DENABLE_numpy:BOOL=ON
> -DENABLE_png:BOOL=ON -DENABLE_osmesa:BOOL=ON -DENABLE_cgns:BOOL=ON
> -DENABLE_silo:BOOL=ON -DENABLE_visitbridge:BOOL=ON
> -DMPI_COMPILER:FILEPATH=/opt/openmpi-1.8-intel//bin/mpicxx
> -DPARAVIEW_ALWAYS_SECURE_CONNECTION:BOOL=ON -DENABLE_mpi:BOOL=ON
> -DPARAVIEW_USE_MPI:BOOL=ON
> -DMPI_INCLUDE_PATH:PATH=/opt/openmpi-1.8-intel//include/
>
>
>
> -- Using git-describe to determine ParaView version
>
> -- Could not use git to determine source version, using version
>
> -- Using ParaView Version: 5.1.0 (5|1|0|)
>
> -- Using system EGL. Pick correct python based on your deployment target
>
> -- Enabling zlib since needed by: boost;cgns;ffmpeg;hdf5;png;python;silo
>
> -- Enabling szip since needed by: hdf5
>
> -- Enabling hdf5 since needed by: cgns;silo
>
> -- Enabling cgns as requested.
>
> -- Enabling ffmpeg as requested.
>
> -- Enabling mpi as requested.
>
> -- Enabling bzip2 since needed by: python
>
> -- Enabling png as requested.
>
> -- Enabling python as requested.
>
> -- Enabling numpy as requested.
>
> -- Enabling llvm since needed by: osmesa
>
> -- Enabling osmesa as requested.
>
> -- Enabling boost since needed by: visitbridge
>
> -- Enabling silo as requested.
>
> -- Enabling visitbridge as requested.
>
> -- Enabling paraview as requested.
>
> -- PROJECTS_ENABLED
> zlib;szip;hdf5;cgns;ffmpeg;mpi;bzip2;png;python;numpy;llvm;osmesa;boost;silo;visitbridge;paraview
>
> -- Configuring done
>
> -- Generating done
>
> -- Build files have been written to:
> /projects/viz/paraview/ParaView/5.1.1-sbi-mesa/Linux-chama-x86_64/Build
>
> [  7%] Built target zlib
>
> [ 14%] Built target szip
>
> [ 20%] Built target hdf5
>
> [ 27%] Built target cgns
>
> [ 33%] Built target boost
>
> [ 39%] Built target ffmpeg
>
> [ 45%] Built target silo
>
> [ 51%] Built target visitbridge
>
> [ 57%] Built target png
>
> [ 63%] Built target bzip2
>
> [ 70%] Built target python
>
> [ 76%] Built target mpi
>
> [ 82%] Built target numpy
>
> [ 83%] Performing configure step for 'llvm'
>
> CMake Error at cmake/modules/CheckAtomic.cmake:36 (message):
>
>   Host compiler appears to require libatomic, but cannot find it.
>
> Call Stack (most recent call first):
>
>   cmake/config-ix.cmake:296 (include)
>
>   CMakeLists.txt:407 (include)
>
>
>
>
>
> -- Configuring incomplete, errors occurred!
>
> See also
> "/projects/viz/paraview/ParaView/5.1.1-sbi-mesa/Linux-chama-x86_64/Build/llvm/src/llvm-build/CMakeFiles/CMakeOutput.log".
>
> See also
> "/projects/viz/paraview/ParaView/5.1.1-sbi-mesa/Linux-chama-x86_64/Build/llvm/src/llvm-build/CMakeFiles/CMakeError.log".
>
> make[2]: *** [llvm/src/llvm-stamp/llvm-configure] Error 1
>
> make[1]: *** [CMakeFiles/llvm.dir/all] Error 2
>
>
>
>
>
> Thanks for any help,
>
>
>
> Alan
>
>
>
> --------------------------------------------------------
>
> W. Alan Scott
>
> ParaView Support Manager
>
>
>
> SAIC
>
> Sandia National Laboratories, MS 0822
>
> Org 9326 - Building 880 A1-K
>
> (505) 284-0932   FAX (505) 284-5619
>
> ---------------------------------------------------------
>
>
>
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