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

Mon Jul 25 21:19:00 EDT 2016

Excellent, thanks!  I’ll let you know if it works.

From: Chuck Atkins [mailto:chuck.atkins at kitware.com]
Sent: Monday, July 25, 2016 7:16 PM
To: Scott, W Alan <wascott at sandia.gov>
Cc: paraview-developers at paraview.org
Subject: [EXTERNAL] Re: [Paraview-developers] superbuild again on intel compilers on Linux cluster

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<mailto: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<tel:%28505%29%20284-0932>   FAX (505) 284-5619<tel:%28505%29%20284-5619>
---------------------------------------------------------

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