Personal tools
You are here: Home Forum Install & build Installing medcoupling autonomously

Installing medcoupling autonomously

Up to Install & build

Installing medcoupling autonomously

Posted by pierre at October 22. 2019

Hello,

I have tried to install medcoupling 9-3-1 autonomously (without Salome)

I have started with medfile-4.0.0 and its installation seems OK.

Next I have tried to install medcoupling (medcoupling comes with 2 directories, CONFIGURATION_9.3.0 and MEDCOUPLING-9.3.0).

I have created a Build and a Install directory. In the Build directory I run CMAKE with these options :

DEST=$HOME/medcoupling/medcoupling_install
MEDFILE_INSTALL=$HOME/medfile/med-4.0.0/install
MED_COUPLING_SRC=$HOME/medcoupling/MEDCOUPLING-9.3.0
USE_MPI=ON
CONFIGURATION_SALOME=$HOME/medcoupling/CONFIGURATION_9.3.0

OPTIONS="
-DCMAKE_BUILD_TYPE=Release
-DMEDCOUPLING_USE_MPI=$USE_MPI
-DSALOME_USE_MPI=ON
-DCMAKE_INSTALL_PREFIX=$DEST
-DHDF5_ROOT_DIR=$HDF5_DIR
-DCONFIGURATION_ROOT_DIR=$CONFIGURATION_SALOME
-DMEDFILE_ROOT_DIR=$MEDFILE_INSTALL
-DMEDCOUPLING_BUILD_DOC=OFF
-DMEDCOUPLING_PARTITIONER_METIS=OFF
-DMEDCOUPLING_PARTITIONER_SCOTCH=OFF
-DMEDCOUPLING_ENABLE_RENUMBER=OFF
-DMEDCOUPLING_ENABLE_PARTITIONER=OFF
-DMEDCOUPLING_BUILD_TESTS=OFF
-DMEDCOUPLING_WITH_FILE_EXAMPLES=OFF
-DMEDCOUPLING_MEDLOADER_USE_XDR=OFF
-DMEDCOUPLING_PARTITIONER_PTSCOTCH=OFF
# -DMEDCOUPLING_BUILD_STATIC=ON
-DNO_CXX11_SUPPORT=ON "

cmake $OPTIONS $MED_COUPLING_SRC

 

And I obtain an error of CMAKE on hdf5 that is strange because it complains about a lack of the hdf5 TARGET during a GET_PROPERTY instruction, whereas the librairy hdf5 exists and has the right name...

The complete output of CMAKE is this:

-- The C compiler identification is GNU 6.3.0
-- The CXX compiler identification is GNU 6.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS_NO_OPERATOR_NAMES
-- Performing Test COMPILER_SUPPORTS_NO_OPERATOR_NAMES - Success
CMake Error at /home/XXXXXXX/medcoupling/CONFIGURATION_9.3.0/cmake/FindSalomeHDF5.cmake:73 (GET_PROPERTY):
  get_property could not find TARGET /home/XXXXXXX/hdf5/lib/libhdf5.so.
  Perhaps it has not yet been created.
Call Stack (most recent call first):
  CMakeLists.txt:110 (FIND_PACKAGE)


-- HDF5 was compiled with MPI:
-- Check for medfile ...
-- Variable MPI_ROOT_DIR was not explicitly defined. An installation was found anyway: /usr
-- Looking for MPI_Publish_name
-- Looking for MPI_Publish_name - found
-- Your mpi implementation is compatible with mpi2 ... adding -DHAVE_MPI2
-- Variable PYTHONINTERP_ROOT_DIR was not explicitly defined. An installation was found anyway: /usr/bin
-- Variable PYTHONLIBS_ROOT_DIR was not explicitly defined. An installation was found anyway: /usr
-- Python libs and interpreter versions are matching: 3.5.3
-- NumPy found : /usr/lib/python3/dist-packages/numpy/core/include
-- Scipy found : Version 0.18.1
-- Variable SWIG_ROOT_DIR was not explicitly defined. An installation was found anyway: /usr
-- Using Python 3
--
--   Optional packages - Detection report
--   ====================================
--
--   * PythonInterp             ->  Found
--   * PythonLibs               ->  Found
--   * SWIG                     ->  Found
--
--
-- Creation of /home/XXXXXXX/medcoupling/medcoupling_build/MEDCoupling_version.h
-- Found SWIG: /usr/bin/swig3.0 (found version "3.0.10")
-- Configuring incomplete, errors occurred!
See also "/home/XXXXXXX/medcoupling/medcoupling_build/CMakeFiles/CMakeOutput.log".

Thank ou in advance for any help...

regards, Pierre

Re: Installing medcoupling autonomously

Posted by Nabil Ghodbane at December 23. 2019

Hi Pierre;

the most appropriate aproach here is to simply download the MEDCOUPLING archive at this link:

ftp://ftp.cea.fr/pub/salome/targz/MEDCOUPLING-9.4.0/

HTH

Re: Installing medcoupling autonomously

Posted by pierre at December 26. 2020

Previously Nabil Ghodbane wrote:

Hi Pierre;

the most appropriate aproach here is to simply download the MEDCOUPLING archive at this link:

ftp://ftp.cea.fr/pub/salome/targz/MEDCOUPLING-9.4.0/

HTH

Re: Installing medcoupling autonomously

Posted by pierre at December 26. 2020
Hello and thanks for this answer (I have just read it!). By the time, the version is 9.6.0 now  :)
 
I have started again, and I tried to install medcoupling autonomously, but it still doesnt work for me.
 
Please note that the README says the following: 
        
        In the following, $ROOT represents the directory where you have installed
        SALOME (the directory where this file is located).
 
Are you sure it is an autonomous distribution of medcoupling?
Nethertheless, I have tried to go through the 5 steps of the README:

a) $ROOT/sat prepare MEDCOUPLING-9.6.0. 
 
This seems to be OK and I obtain this: 
 
Creating environment files for MEDCOUPLING-9.6.0
  Target = /home/XXXXXX/medcoupling9.3/MEDCOUPLING-9.6.0-CO6-SRC/salomeTools/..
Create environment file env_launch.sh
Create environment file env_build.sh
    /home/XXXXXX/medcoupling9.3/MEDCOUPLING-9.6.0-CO6-SRC/salomeTools/../env_launch.sh
    /home/XXXXXX/medcoupling9.3/MEDCOUPLING-9.6.0-CO6-SRC/salomeTools/../env_build.sh

b)  ./sat launcher MEDCOUPLING-9.6.0

This second steps doesnt work:

***** salomeTools ERROR: sat launcher

Traceback (most recent call last):
  File "/home/XXXXXX/medcoupling9.3/MEDCOUPLING-9.6.0-CO6-SRC/salomeTools/src/salomeTools.py", line 478, in run_command
    res = __module__.run(argv, self, logger_command)
  File "/home/XXXXXX/medcoupling9.3/MEDCOUPLING-9.6.0-CO6-SRC/salomeTools/commands/launcher.py", line 346, in run
    no_path_init = no_path_initialisation )
  File "/home/v/medcoupling9.3/MEDCOUPLING-9.6.0-CO6-SRC/salomeTools/commands/launcher.py", line 111, in generate_launch_file
    kernel_cfg = src.product.get_product_config(config, "KERNEL")
  File "/home/XXXXXX/medcoupling9.3/MEDCOUPLING-9.6.0-CO6-SRC/salomeTools/src/product.py", line 51, in get_product_config
    version = config.APPLICATION.products[product_name]
  File "/home/XXXXXX/medcoupling9.3/MEDCOUPLING-9.6.0-CO6-SRC/salomeTools/src/pyconf.py", line 484, in __getitem__
    raise AttributeError("Unknown pyconf key: '%s'" % key)

AttributeError: Unknown pyconf key: 'KERNEL'
 
Do you have an idea of what is missing please ? 
 
My goal is precisely to run the example of medcoupling that is named ParaMEDMEMTest.zip without installing SALOME, could you help me for this please? 
 
Thanks again. 
 
 

Re: Installing medcoupling autonomously

Posted by Nabil Ghodbane at December 27. 2020

Hi,

it seems that the README file is not correct.. Assuming you downloaded the latest stable MEDCOUPLING archive from the download section: https://www.salome-platform.org/downloads/current-version

, here is what you have to do:

tar zxvf MEDCOUPLING-9.6.0-CO6-SRC-.tar.gz

cd MEDCOUPLING-9.6.0-CO6-SRC

source env_launch.sh

python

import medcoupling as mc

 

In case you want to compile everything from scratch you need to do: (for CentOS 6, you need to have at hand a more modern gcc compiler, you can for instance install devtoolset)

cd MEDCOUPLING-9.6.0-CO6-SRC

./install_bin.sh

./sat prepare MEDCOUPLIGN-9.6.0

./sat compile MEDCOUPLING-9.6.0

./sat environ MEDCOUPLING-9.6.0

then to run MEDCOUPLING, you have to source the env_launch.sh script to consistently define PYTHONPATH, LD_LIBRARY_PATH, etc.. and launch python

python -i

import medcoupling as mc

or/

python my_medcoupling.py script.

HTH.

Note, that if you compile everything from scratch,openssl-devel needs to be installed on your workstation

 

 

Re: Installing medcoupling autonomously

Posted by pierre at January 04. 2021

Hello Nabil,

Thanks for your answer I discover... and happy new year 2021 !

I am going to check this rapidly and let you know if it works for me...

Regards, Pierre

Re: Installing medcoupling autonomously

Posted by pierre at January 04. 2021
...Hello again.
 
I have attempted to install by compiling everything from scratch but it doesn't work.
 
I have made sure that openssl-devel is installed on my machine (Debian GNU/Linux 9.13 (stretch)) . 
 
The first command (./sat prepare MEDCOUPLIGN-9.6.0) seems OK.
The second (compilation) gives a KO at the final step (the 41 first steps are OK as shows the attached log file). 

Would you have an idea of the problem ?
Thanks in advance, 
Pierre
Attachments

Re: Installing medcoupling autonomously

Posted by Nabil Ghodbane at January 04. 2021

can you share these two files which will help to figure out what is missing:

MEDCOUPLING-9.6.0-DB09-SRC/LOGS/MEDCOUPLING/cmake

MEDCOUPLING-9.6.0-DB09-SRC/LOGS/MEDCOUPLING/make



Re: Installing medcoupling autonomously

Posted by Gregor Simic at January 04. 2021
Dear Pierre,
 
in the LOGS you have the file LOGS/MEDCOUPLING/make which contain the output of the make command for MEDCOUPLING. Can you attach or check the contants of that file? Usually searching for strings "error" or "Error" is enough to locate the line with error.

 

 
Best regards,
Gregor Simic

Re: Installing medcoupling autonomously

Posted by pierre at January 04. 2021
Surprisingly, the upload doesn't work (when I click on "Choisir un fichier", that doesn't load the selected file, and yet, both are smaller than 100 Kb).
 
I can send them if you give me a mail adress or you can read them hereafter (sorry for the presentation).
 
Thanks again, 
 
First is CMAKE : 
 
build_dir   = /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../BUILD/MEDCOUPLING
install_dir = /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../INSTALL/MEDCOUPLING
 
> cmake  -DMEDCOUPLING_ENABLE_PYTHON=ON -DMEDCOUPLING_ENABLE_PARTITIONER=ON -DMEDCOUPLING_ENABLE_RENUMBER=ON -DMEDCOUPLING_PARTITIONER_METIS=ON -DMEDCOUPLING_PARTITIONER_SCOTCH=ON -DMEDCOUPLING_PARTITIONER_PARMETIS=OFF -DMEDCOUPLING_MICROMED=OFF -DMEDCOUPLING_USE_MPI=OFF -DMEDCOUPLING_USE_64BIT_IDS=ON  -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../INSTALL/MEDCOUPLING /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../SOURCES/MEDCOUPLING
-- The C compiler identification is GNU 6.3.0
-- The CXX compiler identification is GNU 6.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS_NO_OPERATOR_NAMES
-- Performing Test COMPILER_SUPPORTS_NO_OPERATOR_NAMES - Success
-- Performing Test COMPILER_SUPPORTS_CXX11
-- Performing Test COMPILER_SUPPORTS_CXX11 - Success
-- Enable C++11 support
-- Found HDF5 in CONFIG mode!
-- HDF5 found directory matches what was specified in the HDF5_ROOT_DIR variable, all good!
-- Check for medfile ...
-- MEDFile found directory matches what was specified in the MEDFILE_ROOT_DIR variable, all good!
-- MEDFile: size of med_int is 8
-- Check for XDR ...
-- Could not find XDR libraries ...
-- Variable XDR_ROOT_DIR was not explicitly defined. An installation was found anyway: /usr
-- LibXml2 found directory matches what was specified in the LIBXML2_ROOT_DIR variable, all good!
-- Check for metis ...
-- Metis maj version 5 detected.
-- Metis found directory matches what was specified in the METIS_ROOT_DIR variable, all good!
-- Check for scotch ...
-- Scotch found directory matches what was specified in the SCOTCH_ROOT_DIR variable, all good!
-- Checking for one of the modules 'cppunit'
-- CppUnit found directory matches what was specified in the CPPUNIT_ROOT_DIR variable, all good!
-- Boost found directory matches what was specified in the BOOST_ROOT_DIR variable, all good!
-- Boost include dirs is: /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/INSTALL/boost/include
-- Setting PYTHONINTERP_ROOT_DIR to: /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../INSTALL/Python
-- Setting PYTHONLIBS_ROOT_DIR to: /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../INSTALL/Python
-- Python libs and interpreter versions are matching: 3.6.5
-- NumPy found : /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BINARIES-DB09/Python/lib/python3.6/site-packages/numpy/core/include
-- Scipy found : Version 0.19.1
-- SWIG found directory matches what was specified in the SWIG_ROOT_DIR variable, all good!
-- Using Python 3
-- Doxygen found directory matches what was specified in the DOXYGEN_ROOT_DIR variable, all good!
-- Graphviz found directory matches what was specified in the GRAPHVIZ_ROOT_DIR variable, all good!
CMake Warning at /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/SOURCES/CONFIGURATION/cmake/SalomeMacros.cmake:605 (MESSAGE):
  Sphinx was found, but not at the path given by the environment
  SPHINX_ROOT_DIR! Is the variable correctly set? The two paths are:
  /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BINARIES-DB09/Python and:
  /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../INSTALL/Python
Call Stack (most recent call first):
  /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/SOURCES/CONFIGURATION/cmake/FindSalomeSphinx.cmake:25 (SALOME_FIND_PACKAGE_AND_DETECT_CONFLICTS)
  CMakeLists.txt:214 (FIND_PACKAGE)
 
 
-- 
--   Optional packages - Detection report 
--   ==================================== 
-- 
--   * LibXml2                  ->  Found
--   * Metis                    ->  Found
--   * Scotch                   ->  Found
--   * CppUnit                  ->  Found
--   * Boost                    ->  Found
--   * PythonInterp             ->  Found
--   * PythonLibs               ->  Found
--   * SWIG                     ->  Found
--   * Doxygen                  ->  Found
--   * Graphviz                 ->  Found
--   * Sphinx                   ->  Found
-- 
-- 
-- Creation of /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BUILD/MEDCOUPLING/MEDCoupling_version.h
-- Found SWIG: /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/INSTALL/swig/bin/swig (found version "3.0.12") 
-- Creation of /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BUILD/MEDCOUPLING/doc/developer/doxygen/Doxyfile_med_dev
-- Creation of /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BUILD/MEDCOUPLING/doc/developer/doxygen/static/header.html
-- Creation of /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BUILD/MEDCOUPLING/doc/tutorial/conf.py
-- Creation of /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BUILD/MEDCOUPLING/doc/user/conf.py
-- Creation of /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BUILD/MEDCOUPLING/doc/user/static/switchers.js
-- Configuring done
-- Generating done
-- Build files have been written to: /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BUILD/MEDCOUPLING
 
 
 
SECOND IS MAKE
 
 
 
  build_dir   = /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../BUILD/MEDCOUPLING
  install_dir = /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../INSTALL/MEDCOUPLING
 
> make -j32 
Scanning dependencies of target tutorial_doc
Scanning dependencies of target PYCOMPILE_v8_work_0
/usr/bin/env: « /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BINARIES-DB09/Python/bin/sphinx-build »: Aucun fichier ou dossier de ce type
doc/tutorial/CMakeFiles/tutorial_doc.dir/build.make:57 : la recette pour la cible « doc/tutorial/CMakeFiles/tutorial_doc » a échouée
make[2]: *** [doc/tutorial/CMakeFiles/tutorial_doc] Erreur 127
CMakeFiles/Makefile2:2323 : la recette pour la cible « doc/tutorial/CMakeFiles/tutorial_doc.dir/all » a échouée
make[1]: *** [doc/tutorial/CMakeFiles/tutorial_doc.dir/all] Erreur 2
make[1]: *** Attente des tâches non terminées....
[  0%] Generating medcoup7to8.cpython-36.pyc, medcoup7to8.cpython-36.opt-1.pyc
Scanning dependencies of target MEDPartitioner_swig_compilation
Scanning dependencies of target MEDCouplingRemapper_swig_compilation
Scanning dependencies of target MEDRenumber_swig_compilation
[  1%] Swig source
[  2%] Swig source
[  2%] Swig source
Scanning dependencies of target interpkernel
Scanning dependencies of target medcoupling_swig_compilation
[  2%] Built target PYCOMPILE_v8_work_0
[  2%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/TransformedTriangleIntersect.cxx.o
[  3%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/TransformedTriangle.cxx.o
[  3%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/TranslationRotationMatrix.cxx.o
[  4%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/BoundingBox.cxx.o
[  4%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/TransformedTriangleMath.cxx.o
[  4%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/CellModel.cxx.o
[  4%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/OrientationInverter.cxx.o
[  4%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/InterpolationOptions.cxx.o
[  4%] Swig source
[  5%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/TetraAffineTransform.cxx.o
[  6%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/DiameterCalculator.cxx.o
[  7%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/DirectedBoundingBox.cxx.o
[  8%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/UnitTetraIntersectionBary.cxx.o
[  8%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/BoxSplittingOptions.cxx.o
[  8%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/InterpKernelCellSimplify.cxx.o
[  9%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DBounds.cxx.o
[  9%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Interpolation3D1D.cxx.o
[ 10%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Interpolation3DSurf.cxx.o
[ 10%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Interpolation3D.cxx.o
[ 10%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Interpolation2DCurve.cxx.o
[ 11%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/VolSurfUser.cxx.o
[ 11%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/SplitterTetra.cxx.o
[ 11%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/InterpKernelMatrixTools.cxx.o
[ 11%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/MeshElement.cxx.o
[ 12%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Interpolation2D3D.cxx.o
[ 14%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Interpolation1D0D.cxx.o
[ 14%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/InterpKernelMeshQuality.cxx.o
[ 15%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Bases/InterpKernelException.cxx.o
[ 15%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DAbstractEdge.cxx.o
[ 15%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DPrecision.cxx.o
[ 16%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DComposedEdge.cxx.o
[ 16%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DEdgeArcCircle.cxx.o
[ 16%] Built target MEDPartitioner_swig_compilation
[ 17%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DEdge.cxx.o
[ 17%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DEdgeInfLin.cxx.o
[ 18%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DEdgeLin.cxx.o
[ 18%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DElementaryEdge.cxx.o
[ 18%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DNode.cxx.o
[ 19%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/Geometric2D/InterpKernelGeo2DQuadraticPolygon.cxx.o
[ 19%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/ExprEval/InterpKernelExprParser.cxx.o
[ 20%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/ExprEval/InterpKernelFunction.cxx.o
[ 20%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/ExprEval/InterpKernelUnit.cxx.o
[ 21%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/ExprEval/InterpKernelValue.cxx.o
[ 21%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/ExprEval/InterpKernelAsmX86.cxx.o
[ 22%] Building CXX object src/INTERP_KERNEL/CMakeFiles/interpkernel.dir/GaussPoints/InterpKernelGaussCoords.cxx.o
/home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/SOURCES/MEDCOUPLING/src/RENUMBER_Swig/MEDRenumberCommon.i:35: Warning 302: Identifier 'ivec' redefined (ignored) (Renamed from 'vector< int >'),
/home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/SOURCES/MEDCOUPLING/src/RENUMBER_Swig/../MEDCoupling_Swig/MEDCouplingCommon.i:83: Warning 302: previous definition of 'ivec' (Renamed from 'vector< long >').
/home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/SOURCES/MEDCOUPLING/src/RENUMBER_Swig/MEDRenumberCommon.i:36: Warning 302: Identifier 'dvec' redefined (ignored) (Renamed from 'vector< double >'),
/home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/SOURCES/MEDCOUPLING/src/RENUMBER_Swig/../MEDCoupling_Swig/MEDCouplingCommon.i:65: Warning 302: previous definition of 'dvec' (Renamed from 'vector< double >').
/home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/SOURCES/MEDCOUPLING/src/RENUMBER_Swig/MEDRenumberCommon.i:37: Warning 302: Identifier 'svec' redefined (ignored) (Renamed from 'vector< std::string >'),
/home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/SOURCES/MEDCOUPLING/src/RENUMBER_Swig/../MEDCoupling_Swig/MEDCouplingCommon.i:66: Warning 302: previous definition of 'svec' (Renamed from 'vector< std::string >').
[ 22%] Linking CXX shared library libinterpkernel.so
[ 22%] Built target interpkernel
[ 22%] Built target MEDRenumber_swig_compilation
[ 22%] Built target MEDCouplingRemapper_swig_compilation
[ 22%] Built target medcoupling_swig_compilation
Makefile:140 : la recette pour la cible « all » a échouée
make: *** [all] Erreur 2
 

Re: Installing medcoupling autonomously

Posted by Gregor Simic at January 04. 2021

Right, it seems that sphinx is missing, which makes the documentation build fail and exits with error.

You can solve it by installing sphinx (Shouldn't that be in the MEDCOUPLING directory as dependency? I am downloading the archive and will check) or pass the CMake option "MEDCOUPLING_BUILD_DOC:bool=Off" to the CMake options of MEDCOUPLING.

 

To pass the CMake option, find the MEDCOUPLING.pyconf file. There is an entry there cmake_options and in it, add the "MEDCOUPLING_BUILD_DOC:bool=Off"

 

Best regards,

Gregor Simic

Re: Installing medcoupling autonomously

Posted by Gregor Simic at January 04. 2021

So I downloaded the ftp://ftp.cea.fr/pub/salome/targz/MEDCOUPLING-9.6.0/MEDCOUPLING-9.6.0-DB10-SRC.tar.gz archive and did the following:

tar xzf ../MEDCOUPLING-9.6.0-DB10-SRC.tar.gz

cd MEDCOUPLING-9.6.0-DB10-SRC

./install_bin.sh

./sat prepare MEDCOUPLING-9.6.0

rm -rf INSTALL/MEDCOUPLING # Re-compiling only MEDCOUPLING

./sat compile MEDCOUPLING-9.6.0 -p MEDCOUPLING


And I had no problems. Why would you want to recompile MEDCOUPLING again, if you already have provided MEDCOUPLING stand-alone at the FTP?

Re: Installing medcoupling autonomously

Posted by pierre at January 04. 2021

Thanks Gregor for your help...

I have added the option (MEDCOUPLING_BUILD_DOC=OFF) in the file ./PROJECT/products/MEDCOUPLING.pyconf. I have also installed Sphinx by doing a "pip3 install -U Sphinx", but in both cases (with the option OFF or after having installed Sphinx) it still gives the same thing, that is the "sat prepare" command works fine and the "sat compile" command fails.

I feel lost when you ask "Why would you want to recompile MEDCOUPLING again, if you already have provided MEDCOUPLING stand-alone at the FTP"  ?

I have downloaded the SOURCE files (MEDCOUPLING-9.6.0-DB09-SRC.tar.gz) and it seemed to me that the ./sat prepare MEDCOUPLING command was installing the source files, whereas the ./sat compile MEDCOUPLING-9.6.0  command was compiling them.    Is this correct ? 

If so, I don't understand why you say I want ro recompile again, as I have only done the "sat prepare" command (the "sat compile" has failed).

Sorry for my confusions...


Re: Installing medcoupling autonomously

Posted by Gregor Simic at January 04. 2021

No problem pierre,

 

the MEDCOUPLING-9.6.0 archives, that are available for individual OS on  ftp://ftp.cea.fr/pub/salome/targz/MEDCOUPLING-9.6.0/ contains both the source code and compiled libraries.  So MEDCOUPLING library is already compiled and you can use it as a standalone package.

 

If you perform the steps written by Nabil Ghodbane:

First open a new terminal and download the appropriate archive:

tar zxvf MEDCOUPLING-9.6.0-DB09-SRC.tar.gz

cd MEDCOUPLING-9.6.0-DB09-SRC

source env_launch.sh

python

import medcoupling as mc

Do these steps work? If I extract the archive then I get:

$: pwd

~/Downloads/tmp/MEDCOUPLING-9.6.0-DB10-SRC # I use Debian 10

$: source env_launch.sh
$: which python
  ~/Downloads/tmp/MEDCOUPLING-9.6.0-DB10-SRC/salomeTools/../INSTALL/Python/bin/python
$:python
Python 3.6.5 (default, Nov 20 2020, 05:49:52)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import medcoupling
>>> medcoupling
<module 'medcoupling' from '~/Downloads/tmp/MEDCOUPLING-9.6.0-DB10-SRC/INSTALL/MEDCOUPLING/lib/python3.6/site-packages/medcoupling.py'>
>>>

 

And finally, I think I see the problem you have, from your environment I see that you have the path loaded from the BINARIES-XYZK. The original env_launch.sh file does not properly set the environment for me and probably the same happens to you.

Can you re-generate the env_launch.sh file? The command for that is

./sat environ MEDCOUPLING-9.6.0

Afterwards, clean your shell environment or open a new terminal.

Now try to compile MEDCOUPLING again.

 

Hope that helps and best regards,

Gregor Simic

Re: Installing medcoupling autonomously

Posted by Nabil Ghodbane at January 04. 2021

Hi Pierre,

I did not manage to reproduce the issue on our Debian 9 node nor on CentOS 7, starting from a MEDCOUPLING 9.6.0 archive:

 

Looking at the log error message, it seems that you did not start from a fresh environment, since one can see  that you have the following message:

SPHINX_ROOT_DIR! Is the variable correctly set? The two paths are:
  /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/BINARIES-DB09/Python
and:
  /home/XXXXXX/MEDCOUPLING-9.6.0-DB09-SRC/salomeTools/../INSTALL/Python
 
 
To compile the archive, you need to do in a terminal (without sourcing any env_*.sh script):
 tar zxf MEDCOUPLING-9.6.0-DB09-SRC.tar.gz
 cd MEDCOUPLING-9.6.0-DB09-SRC
 # prepare all sources
 ./sat prepare MEDCOUPLING-9.6.0
 # compile everything
 ./sat compile MEDCOUPLING-9.6.0 --clean_all
 # generate environment files
 ./sat environ MEDCOUPLING-9.6.0
 
in case it still does not work, we can investigate it further.
HTH.

 

 

 
 

Re: Installing medcoupling autonomously

Posted by pierre at January 04. 2021

You got it Gregor!   

I have re-generated the env_launch.sh file with this ./sat environ MEDCOUPLING-9.6.0 command and now the whole process works.

The command ./sat compile MEDCOUPLING-9.6.0  returns this:

......
Compilation of numpy ......................... Already installed
Compilation of scipy ......................... Already installed
Compilation of doxygen ....................... Already installed
Compilation of MEDCOUPLING ................... Already installed

Compilation: OK (42/42)
 
Also, an "import medcoupling" command in python works as well...
 
Now, I can (maybe) check the ParaMEDMEMTest that is provided in 
~/MEDCOUPLING-9.6.0-DB09-SRC/SOURCES/MEDCOUPLING/src/
(my first objective was precisely to run this test!)
 
At the risk of abusing your help a little more, would you mind giving me the command to run a test like this one?
 
In any case, I thank you again for your efficient help ! 
Regards, Pierre
 
 
 

Re: Installing medcoupling autonomously

Posted by Gregor Simic at January 04. 2021

Hello Pierre,

 

others will know more, check the INSTALL/MEDCOUPLING/bin directory. There are some Test  binaries and python test scripts, which can be run if you first load the envionment with:

$ # Open new terminal and go to where you extracted MEDCOUPLING archive

$ source env_launch.sh

$ <Name of the test binary>

Otherwise if you wish to change the sources of MEDCOUPLING, then you have to re-compile MEDCOUPLING, using sat command:

 

# Open a new terminal

cd /path/to/where/you/extracted/MEDCOUPLING

./sat compile MEDCOUPLING-9.6.0 -p MEDCOUPLING --clean_all

If your setup is now a-Okay, then MEDCOUPLING should build fine. In BUILD/MEDCOUPLING you can run the tests by invoking make test.

Example output:

➜  MEDCOUPLING-9.6.0-DB10-SRC pwd
~/Downloads/tmp/MEDCOUPLING-9.6.0-DB10-SRC
➜  MEDCOUPLING-9.6.0-DB10-SRC cd BUILD/MEDCOUPLING
➜  MEDCOUPLING make test
Running tests...
Test project ~/Downloads/tmp/MEDCOUPLING-9.6.0-DB10-SRC/BUILD/MEDCOUPLING
      Start  1: TestINTERP_KERNEL
 1/31 Test  #1: TestINTERP_KERNEL ..................   Passed    1.28 sec
      Start  2: TestMEDCoupling
 2/31 Test  #2: TestMEDCoupling ....................   Passed    0.44 sec
      Start  3: TestMEDCouplingRemapper
 3/31 Test  #3: TestMEDCouplingRemapper ............   Passed    0.02 sec
      Start  4: TestMEDCouplingExamples
 4/31 Test  #4: TestMEDCouplingExamples ............   Passed    0.01 sec
...

 

Best regards,

Gregor Simic

Re: Installing medcoupling autonomously

Posted by pierre at January 04. 2021

Hello Gregor...the 31 tests are OK.

I noticed that the command " ./sat compile MEDCOUPLING-9.6.0 -p MEDCOUPLING --clean_all " turned out to be necessary (there were 3 failed tests before I run this 'clean' command).  

Also, It seems that the test I was interested in (that is the ParaMEDMEMTest test) is not processed by the " make test " command...I guess that a CMakefile somewhere probably needs to be updated...(I work on it).
 
Anyway, the initial issue that concerned the installation of MEDCOUPLING is solved thanks to you, and my post can be tagged as such.
 
If required, I can open a new post for the remaining question that concerns the ParaMEDMEMTest...
 
Best regards, Pierre

Re: Installing medcoupling autonomously

Posted by Nabil Ghodbane at January 05. 2021

I understand that you are interested in  the MEDCOUPLING MPI version which is indeed available in the download area as well:

https://files.salome-platform.org/Salome/Salome9.6.0/MEDCOUPLING-9.6.0-MPI-CO7-SRC.tar.gz

Since you're on Debian, you need to compile it as follows:

tar zxf MEDCOUPLING-9.6.0-MPI-CO7-SRC.tar.gz

mv MEDCOUPLING-9.6.0-MPI-CO7-SRC MEDCOUPLING-9.6.0-MPI-DB09-SRC

cd MEDCOUPLING-9.6.0-MPI-DB09-SRC

./sat prepare MEDCOUPLING-9.6.0-MPI

./sat compile MEDCOUPLING-9.6.0-MPI --clean_all

and run your TestParaMEDMEM tests.

Powered by Ploneboard
Document Actions