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Info

Detailed specification of the task, requirements and comments are here: https://trello.com/c/c5tyJ2ke

After task is finished, this page should contain step by step instruction for each and every installation

Table of Contents

 Installation of SPACK

  1. Load GCC 7.3.0:

    Code Block
    module load gnu/7.3.0


  2. Prepare directories:

    Code Block
    $: mkdir -p <ROOT_DIR>/{cache,libs,modules,spack,stage}-{<compiler_names>}
$: mkdir -p <ROOT_DIR>/cache-{<compiler_names>}/{cache,var,test}
$: tree <ROOT_DIR/
<ROOT_DIR>/
├── cache-compiler_x
│   ├── cache
│   ├── test
│   └── var
├── cache-compiler_y
│   ├── cache
│   ├── test
│   └── var
├── libs-compiler_x
├── libs-compiler_y
├── modules-compiler_x
├── modules-compiler_y
├── spack-compiler_x
├── spack-compiler_y
├── stage-compiler_x
└── stage-compiler_y


  3. Clone spack repository to spack-gcc :

    Code Block
    git clone https://github.com/spack/spack.git spack-compiler_name


  4. Go into spack-gcc directory:

    Code Block
    cd spack-compiler_name


  5. Checkout desired version of spack :

    Code Block
    git checkout v0.19.0


  6. Set-up spack configuration:

    1. Go to directory where default configuration files are stored (assuming you're still inside spack-compiler_name repository):

      Code Block
      cd etc/spack/defaults/


    2. Edit config.yaml :

      Code Block
      vim config.yaml

      You need to change the root of the install_tree, projections for all, build_stage dir, test_stage dir, source_cache dir and misc_cache dir.
      Example:

      1. root of the install_tree :

        Code Block
        config:
  # This is the path to the root of the Spack install tree.
  # You can use $spack here to refer to the root of the spack instance.
  install_tree:
    root: <path_prefix>/<ROOT_DIR>/libs-compiler_name


      2. projections :

        Code Block
        projections:
      all: "${PACKAGE}/${VERSION}/${COMPILERNAME}/${COMPILERVER}/${HASH}"


      3. build_stage :

        Code Block
          build_stage:
    - <path_prefix>/<ROOT_DIR>/stage-compiler_name


      4. test_stage :

        Code Block
          test_stage: <path_prefix>/<ROOT_DIR>/cache-compiler_name/test


      5. source_cache :

        Code Block
          source_cache: <path_prefix>/<ROOT_DIR>/cache-compiler_name/var/cache


      6. misc_cache :

        Code Block
          misc_cache: <path_prefix>/<ROOT_DIR>/cache-compiler_name/cache


    3. Edit modules.yaml :

      Code Block
      vim modules.yaml

      Change the roots for the tcl modules:

      1. Example: 

        Code Block
          # These are configurations for the module set named "default"
  default:
    # Where to install modules
    roots:
     tcl:    <path_prefix>/<ROOT_DIR>/modules-compiler_name


    4. Edit linux/modules.yaml :

      Code Block
      vim linux/modules.yaml

      Here you have to fill the whole body just to set the module structure projections:


      Code Block
      modules:
  default:
    arch_folder: false
    tcl:
      projections:
        all: '{name}/{version}/{compiler.name}/{compiler.version}/sha'
    prefix_inspections:
      lib:
        - LD_LIBRARY_PATH
      lib64:
        - LD_LIBRARY_PATH



  7. Change the directory to the top of the spack repository:

    Code Block
    cd ../../../


  8. Source spack :

    Code Block
    source share/spack/setup-env.sh


  9. Check the spack version - should be 0.19.0 :

    Code Block
    spack --version


Marconi + SPACK + GNU

This instruction covers all actions and commands from logging into the Marconi server to installing imasenv.

  1. Logging into the Marconi :

    Code Block
    ssh <USER_NAME>@login.marconi.cineca.it


  2. Change location to $WORK directory, which should point to /marconi_work/FUSIO_HLST :

    Code Block
    $: cd $WORK
$: pwd
/marconi_work/FUSIO_HLST


  3. Load GCC 7.3.0:

    Code Block
    module load gnu/7.3.0


  4. Prepare directories:

    Code Block
    $: mkdir -p IMAS_software/{cache,libs,modules,spack,stage}-{gcc,intel}
$: mkdir -p IMAS_software/cache-{gcc,intel}/{cache,var,test}
$: tree IMAS_software/
IMAS_software/
├── cache-gcc
│   ├── cache
│   ├── test
│   └── var
├── cache-intel
│   ├── cache
│   ├── test
│   └── var
├── libs-gcc
├── libs-intel
├── modules-gcc
├── modules-intel
├── spack-gcc
├── spack-intel
├── stage-gcc
└── stage-intel


  5. Go into IMAS_software directory:

    Code Block
    cd IMAS_software


  6. Clone spack repository to spack-gcc :

    Code Block
    git clone https://github.com/spack/spack.git spack-gcc


  7. Go into spack-gcc directory:

    Code Block
    cd spack-gcc


  8. Checkout desired version of spack :

    Code Block
    git checkout v0.19.0


  9. Set-up spack configuration:

    1. Go to directory where default configuration files are stored (assuming you're still inside spack-gcc repository):

      Code Block
      cd etc/spack/defaults/


    2. Edit config.yaml :

      Code Block
      vim config.yaml

      You need to change the root of the install_tree, projections for all, build_stage dir, test_stage dir, source_cache dir and misc_cache dir.
      Example:

      1. root of the install_tree :

        Code Block
        config:
  # This is the path to the root of the Spack install tree.
  # You can use $spack here to refer to the root of the spack instance.
  install_tree:
    root: /marconi_work/FUSIO_HLST/IMAS_software/libs-gcc


      2. projections :

        Code Block
        projections:
      all: "${PACKAGE}/${VERSION}/${COMPILERNAME}/${COMPILERVER}/${HASH}"


      3. build_stage :

        Code Block
          build_stage:
    - /marconi_work/FUSIO_HLST/IMAS_software/stage-gcc


      4. test_stage :

        Code Block
          test_stage: /marconi_work/FUSIO_HLST/IMAS_software/cache-gcc/test


      5. source_cache :

        Code Block
          source_cache: /marconi_work/FUSIO_HLST/IMAS_software/cache-gcc/var/cache


      6. misc_cache :

        Code Block
          misc_cache: /marconi_work/FUSIO_HLST/IMAS_software/cache-gcc/cache


    3. Edit modules.yaml :

      Code Block
      vim modules.yaml

      Change the roots for the tcl modules:

      1. Example: 

        Code Block
          # These are configurations for the module set named "default"
  default:
    # Where to install modules
    roots:
     tcl:    /marconi_work/FUSIO_HLST/IMAS_software/modules-gcc


    4. Edit linux/modules.yaml :

      Code Block
      vim linux/modules.yaml

      Here you have to fill the whole body just to set the module structure projections:


      Code Block
      modules:
  default:
    arch_folder: false
    tcl:
      projections:
        all: '{name}/{version}/{compiler.name}/{compiler.version}/sha'
    prefix_inspections:
      lib:
        - LD_LIBRARY_PATH
      lib64:
        - LD_LIBRARY_PATH



  10. Change the directory to the top of the spack repository:

    Code Block
    cd ../../../


  11. Source spack :

    Code Block
    source share/spack/setup-env.sh


  12. Check the spack version - should be 0.19.0 :

    Code Block
    spack --version


  13. Install Lapack :

    Code Block
    spack install netlib-lapack %gcc@7.3.0 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  14. Install Blas :

    Code Block
    spack install -j 1 netlib-xblas %gcc@7.3.0 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  15. Install Python with tkinter support:

    Code Block
    spack install

...

  1. python +tkinter %gcc@7.3.0 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  2. Install py-scipy :

    Code Block
    spack install --fail-fast py-scipy %gcc@7.3.0 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  3. Install py-matplotlib :

    Code Block
    spack install --fail-fast py-matplotlib backend=tkagg %gcc@7.3.0 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  4. Install py-pyyaml :

    Code Block
    spack install --fail-fast py-pyyaml %gcc@7.3.0 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  5. Install hdf5 :

    Code Block
    spack install --fail-fast hdf5@1.12.2 %gcc@7.3.0 +threadsafe +cxx +fortran cflags="'-fPIC -pthread'" cxxflags="'-fPIC -pthread'" cppflags="'-fPIC -pthread'"


  6. Install boost :

    Code Block
    spack install --fail-fast boost %gcc@7.3.0 +python +numpy cflags="'-fPIC -pthread'" cxxflags="'-fPIC -pthread'" cppflags="'-fPIC -pthread'"


  7. Install blitz :

    Code Block
    spack install --fail-fast blitz@1.0.1 %gcc@7.3.0 cflags="'-fPIC -pthread'" cxxflags="'-fPIC -pthread'" cppflags="'-fPIC -pthread'"


  8. Install mdsplus :

    Code Block
    spack install --fail-fast mdsplus %gcc@7.3.0 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  9. Download Saxon :
    - it's required by IMAS, but Spack is missing proper recipe

    Code Block
    $: mkdir -p libs-gcc/saxon
$: cd libs-gcc/saxon
$: wget https://sourceforge.net/projects/saxon/files/Saxon-HE/9.9/SaxonHE9-9-1-5J.zip/download
$: unzip download

    Create two softlinks:

    Code Block
    $: ln -s saxon9-test.jar saxon9he-test.jar
$: ln -s saxon9-xqj.jar saxon9he-xqj.jar

    And set the saxon files available:

    Code Block
    chmod -R 777 .


  10. Prepare Saxon module:

    Code Block
    $: cd ../../
$: mkdir -p modules-gcc/saxon
$: vim modules-gcc/saxon/9.9

    And fill the created module with below content:

    Code Block
    #%Module
##
##      Modulefile for saxon
##	Maciej Smukowski 2022
##
set fpath	[file dirname $ModulesCurrentModulefile]
set VERSION	[file tail $ModulesCurrentModulefile]

module-whatis "Enable the usage of saxon $VERSION.
\tKeywords: math tool matlab"


proc ModulesDisplay {} {
}

conflict saxon

set SAXON_HOME /marconi_work/FUSIO_HLST/IMAS_software/libs-gcc/saxon
prepend-path SAXON_HOME /marconi_work/FUSIO_HLST/IMAS_software/libs-gcc/saxon

prepend-path    CLASSPATH $SAXON_HOME/saxon9he.jar
prepend-path    CLASSPATH $SAXON_HOME/saxon9-test.jar
prepend-path    CLASSPATH $SAXON_HOME/saxon9-xqj.jar
prepend-path    CLASSPATH $SAXON_HOME/saxon9he-test.jar
prepend-path    CLASSPATH $SAXON_HOME/saxon9he-xqj.jar

...


  2. Prepare spack-imasenv module prototype:
     Code Block
    $: mkdir -p modules/spack-imasenv/3.37.0/gcc
$: vim modules/spack-imasenv/3.37.0/gcc/7.3.0
    And fill the created module with below content:
     Code Block
    #%Module
##
##      Modulefile for imasenv
##	Maciej Smukowski 2022
##

module-whatis "One IMASENV module to rule them all"


proc ModulesDisplay {} {
}

conflict imasenv

# Add spack modules to MODULEPATH
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-gcc

module load gnu/7.3.0
module load cmake/3.25.0/gcc/7.3.0/sha-a4xv7cs
module load pkgconf/1.8.0/gcc/7.3.0/sha-haasdgy
module load netlib-lapack/3.10.1/gcc/7.3.0/sha-qyarwjw
module load netlib-xblas/1.0.248/gcc/7.3.0/sha-7hrl4sf
module load python/3.10.8/gcc/7.3.0/sha-ns7dn4v
module load py-pip/22.2.2/gcc/7.3.0/sha-a3eh27l
module load py-setuptools/59.4.0/gcc/7.3.0/sha-6ufe5bh
module load py-wheel/0.37.1/gcc/7.3.0/sha-lw533jd
module load py-cython/0.29.32/gcc/7.3.0/sha-ucdjw62
module load py-pyyaml/6.0/gcc/7.3.0/sha-s7dm72x
module load py-numpy/1.23.4/gcc/7.3.0/sha-4nr26mj
module load py-scipy/1.8.1/gcc/7.3.0/sha-c5puafq
module load py-matplotlib/3.6.2/gcc/7.3.0/sha-2sxscln
module load hdf5/1.12.2/gcc/7.3.0/sha-hxkrksx
module load openjdk/11.0.17_8/gcc/7.3.0/sha-impa6zh
module load git
module load blitz/1.0.1/gcc/7.3.0/sha-5jpnc3r
module load boost/1.80.0/gcc/7.3.0/sha-nwvpbv4
module load mdsplus/stable_release-7-96-17/gcc/7.3.0/sha-zwraez5
module load libxml2/2.10.3/gcc/7.3.0/sha-p5tucjm
    DISCLAIMER!: If you're doing your spack installation from scratch be cautious about module names. The pattern is "sha-{hash}" , where hash is generated during installation, therefore your hashes will be different than mine.
  3. Load spack-imasenv module:
     Code Block
    $: module use /marconi_work/FUSIO_HLST/IMAS_software/modules
$: module load spack-imasenv/3.37.0/gcc/7.3.0

  4. Load Saxon module:
     Code Block
    module load saxon/9.9

  5. Clone IMAS Installer :
     Code Block
    git clone ssh://git@git.iter.org/imas/installer.git imas-installer-gcc
    for convenience, let's loosen the read and write permissions for all files:
     Code Block
    chmod -R 777 .
    The top directory should look somewhat like this:
     Code Block
    drwxrwxrwx   6 interactive  4096 Dec  7 14:00 cache-gcc
drwxrwxrwx   3 interactive  4096 Nov 16 13:47 cache-intel
drwxrwxrwx   7 interactive  4096 Dec  8 12:19 imas-installer-gcc
drwxrwxrwx 132 interactive 32768 Dec  8 11:50 libs-gcc
drwxrwxrwx 120 interactive 32768 Nov 16 13:56 libs-intel
drwxrwxrwx   3 interactive  4096 Dec  8 11:45 modules
drwxrwxrwx 130 interactive 32768 Dec  8 12:19 modules-gcc
drwxrwxrwx 120 interactive 32768 Nov 16 13:48 modules-intel
drwxrwxrwx   3 interactive  4096 Nov 16 13:47 spack
drwxrwxrwx   9 interactive  4096 Dec  7 23:44 spack-gcc
drwxrwxrwx   3 interactive  4096 Dec  7 14:31 stage-gcc
drwxrwxrwx   3 interactive  4096 Nov 16 13:43 stage-intel

  6. Create IMAS configuration script:
     Code Block
    vim imas-installer-gcc/3.37.0_4.11.0.sh
    and fill it with below content:
     Code Block
    export TAG_DD=3.37.0

export TAG_AL=4.11.0
# make sure these branches exist

export VER_DD=$TAG_DD
export VER_AL=$TAG_AL
export IMAS_VERSION=$TAG_DD
export UAL_VERSION=$TAG_AL
export MODULE_FULL_VERSION=$VER_DD/AL/$VER_AL


export IMAS_HOME=/marconi_work/FUSIO_HLST/IMAS_software/libs-gcc/IMAS

export IMAS_UDA=fat
export IMAS_HDC=no

export IMAS_CPP=yes

export IMAS_FORTRAN=yes
export IMAS_G95=no
export IMAS_PGI=no
export IMAS_IFORT=no
export IMAS_GFORTRAN=yes
export IMAS_NAGFOR=no

export IMAS_JAVA=yes

export IMAS_MATLAB=no
export IMAS_PYTHON=yes
export IMAS_PYTHON2=no
export IMAS_PYTHON3=yes


# After Installation Environment
eval `./tools/imasdb.in test`

export UAL=$(realpath ./src/$IMAS_VERSION/ual/$UAL_VERSION)
export MY_INSTALL=$IMAS_HOME/core/IMAS/${VER_DD}/AL/${VER_AL}
export IMAS_INSTALL_DIR=$MY_INSTALL
export PYTHONPATH=$MY_INSTALL/python/lib/:$PYTHONPATH
export CLASSPATH=$UAL/javainterface/build/:$CLASSPATH
export IMAS_PREFIX=$MY_INSTALL/
export ids_path="$MDSPLUS_TREE_BASE_0;$MY_INSTALL/models/mdsplus/;$ids_path"
export LD_LIBRARY_PATH=$MY_INSTALL/lib:$LD_LIBRARY_PATH
export TOKAMAKNAME=test
export DATAVERSION=3
    Note that there are at least 3 places that should be customized:
    1. export TAG_DD=<desired_data_dictionary_tag>
    2. export TAG_AL=<desired_access_layer_tag>
    3. export IMAS_HOME=<your_IMAS_HOME_path>

  7. Go inside imas-installer-gcc directory:
     Code Block
    cd imas-installer-gcc

  8. Source IMAS configuration script:
     Code Block
    source 3.37.0_4.11.0.sh

  9. Download build files:
     Code Block
    make cache

  10. Check if everything is set-up correctly:
     Code Block
    make help

  11. Build and install IMAS :
     Code Block
    make install

  12. Leave the imas-installer-gcc directory:
     Code Block
    cd ..

  13. Extend spack-imasenv modulefile:
     Code Block
    vim modules/spack-imasenv/3.37.0/gcc/7.3.0

    1. Add path to IMAS module:
       Code Block
      module use /marconi_work/FUSIO_HLST/IMAS_software/libs-gcc/IMAS/etc/modulefiles

    2. Add loading of the IMAS module:
       Code Block
      module load IMAS/3.37.0/AL/4.11.0

    3. Final spack-imasenv module:
       Code Block
      #%Module
##
##      Modulefile for imasenv
##	Maciej Smukowski 2022
##

module-whatis "One IMASENV module to rule them all"


proc ModulesDisplay {} {
}

conflict imasenv

# Add spack modules to MODULEPATH
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-gcc
module use /marconi_work/FUSIO_HLST/IMAS_software/libs-gcc/IMAS/etc/modulefiles

module load gnu/7.3.0
module load cmake/3.25.0/gcc/7.3.0/sha-a4xv7cs
module load pkgconf/1.8.0/gcc/7.3.0/sha-haasdgy
module load netlib-lapack/3.10.1/gcc/7.3.0/sha-qyarwjw
module load netlib-xblas/1.0.248/gcc/7.3.0/sha-7hrl4sf
module load python/3.10.8/gcc/7.3.0/sha-ns7dn4v
module load py-pip/22.2.2/gcc/7.3.0/sha-a3eh27l
module load py-setuptools/59.4.0/gcc/7.3.0/sha-6ufe5bh
module load py-wheel/0.37.1/gcc/7.3.0/sha-lw533jd
module load py-cython/0.29.32/gcc/7.3.0/sha-ucdjw62
module load py-pyyaml/6.0/gcc/7.3.0/sha-s7dm72x
module load py-numpy/1.23.4/gcc/7.3.0/sha-c5ljmas
module load py-scipy/1.8.1/gcc/7.3.0/sha-c5puafq
module load py-matplotlib/3.6.2/gcc/7.3.0/sha-2sxscln
module load hdf5/1.12.2/gcc/7.3.0/sha-hxkrksx
module load openjdk/11.0.17_8/gcc/7.3.0/sha-impa6zh
module load git
module load blitz/1.0.1/gcc/7.3.0/sha-5jpnc3r
module load boost/1.80.0/gcc/7.3.0/sha-nwvpbv4
module load mdsplus/stable_release-7-96-17/gcc/7.3.0/sha-zwraez5
module load libxml2/2.10.3/gcc/7.3.0/sha-p5tucjm

module load IMAS/3.37.0/AL/4.11.0

Marconi + SPACK + INTEL
This instruction covers all actions and commands from logging into the Marconi server to installing imasenv.
  1. Logging into the Marconi :
     Code Block
    ssh <USER_NAME>@login.marconi.cineca.it

  2. Change location to $WORK directory, which should point to /marconi_work/FUSIO_HLST :
     Code Block
    $: cd $WORK
$: pwd
/marconi_work/FUSIO_HLST

  3. Load GCC 7.3.0 and then INTEL 2020:
     Code Block
    $: module load gnu/7.3.0
$: module load intel/pe-xe-2020--binary

  4. Prepare directories:
     Code Block
    $: mkdir -p IMAS_software/{cache,libs,modules,spack,stage}-{gcc,intel}
$: mkdir -p IMAS_software/cache-{gcc,intel}/{cache,var,test}
$: tree IMAS_software/
IMAS_software/
├── cache-gcc
│   ├── cache
│   ├── test
│   └── var
├── cache-intel
│   ├── cache
│   ├── test
│   └── var
├── libs-gcc
├── libs-intel
├── modules-gcc
├── modules-intel
├── spack-gcc
├── spack-intel
├── stage-gcc
└── stage-intel

  5. Go into IMAS_software directory:
     Code Block
    cd IMAS_software

  6. Clone spack repository to spack-intel :
     Code Block
    git clone https://github.com/spack/spack.git spack-intel

  7. Go into spack-intel directory:
     Code Block
    cd spack-intel

  8. Checkout desired version of spack :
     Code Block
    git checkout v0.19.0

  9. Set-up spack configuration:
    1. Go to directory where default configuration files are stored (assuming you're still inside spack-intel repository):
       Code Block
      cd etc/spack/defaults/

    2. Edit config.yaml :
       Code Block
      vim config.yaml
      You need to change the root of the install_tree, projections for all, build_stage dir, test_stage dir, source_cache dir and misc_cache dir.
      Example:
      1. root of the install_tree :
         Code Block
        config:
  # This is the path to the root of the Spack install tree.
  # You can use $spack here to refer to the root of the spack instance.
  install_tree:
    root: /marconi_work/FUSIO_HLST/IMAS_software/libs-intel

      2. projections :
         Code Block
        projections:
      all: "${PACKAGE}/${VERSION}/${COMPILERNAME}/${COMPILERVER}/${HASH}"

      3. build_stage :
         Code Block
          build_stage:
    - /marconi_work/FUSIO_HLST/IMAS_software/stage-intel

      4. test_stage :
         Code Block
          test_stage: /marconi_work/FUSIO_HLST/IMAS_software/cache-intel/test

      5. source_cache :
         Code Block
          source_cache: /marconi_work/FUSIO_HLST/IMAS_software/cache-intel/var/cache

      6. misc_cache :
         Code Block
          misc_cache: /marconi_work/FUSIO_HLST/IMAS_software/cache-intel/cache

    3. Edit modules.yaml :
       Code Block
      vim modules.yaml
      Change the roots for the tcl modules:
      1. Example: 
         Code Block
          # These are configurations for the module set named "default"
  default:
    # Where to install modules
    roots:
     tcl:    /marconi_work/FUSIO_HLST/IMAS_software/modules-intel

    4. Edit linux/modules.yaml :
       Code Block
      vim linux/modules.yaml
      Here you have to fill the whole body just to set the module structure projections:

       Code Block
      modules:
  default:
    arch_folder: false
    tcl:
      projections:
        all: '{name}/{version}/{compiler.name}/{compiler.version}/sha'
    prefix_inspections:
      lib:
        - LD_LIBRARY_PATH
      lib64:
        - LD_LIBRARY_PATH


  10. Change the directory to the top of the spack repository:
     Code Block
    cd ../../../


  11. Source spack :
     Code Block
    source share/spack/setup-env.sh

  12. Check the spack version - should be 0.19.0 :
     Code Block
    spack --version

  13. Install Lapack :
     Code Block
    spack install netlib-lapack %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"

  14. Install Blas :
     Code Block
    spack install -j 1 netlib-xblas %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"

  15. Install Python with tkinter support:
     Code Block
    spack install python +tkinter %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"

  16. Install py-scipy :
     Code Block
    spack install --fail-fast py-scipy %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"

  17. Install py-matplotlib :
     Code Block
    spack install --fail-fast py-matplotlib backend=tkagg %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"

  18. Install py-pyyaml :
     Code Block
    spack install --fail-fast py-pyyaml %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"

  19. Install hdf5 :
     Code Block
    spack install --fail-fast hdf5@1.12.2 %intel@19.1.3.304 +threadsafe +cxx +fortran cflags="'-fPIC -pthread'" cxxflags="'-fPIC -pthread'" cppflags="'-fPIC -pthread'"

  20. Install boost :
     Code Block
    spack install --fail-fast boost %intel@19.1.3.304 +python +numpy cflags="'-fPIC -pthread'" cxxflags="'-fPIC -pthread'" cppflags="'-fPIC -pthread'"

  21. Install blitz :
     Code Block
    spack install --fail-fast blitz@1.0.1 %intel@19.1.3.304 cflags="'-fPIC -pthread'" cxxflags="'-fPIC -pthread'" cppflags="'-fPIC -pthread'"

  22. Install mdsplus :
     Code Block
    spack install --fail-fast mdsplus %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"

  23. Download Saxon :
    - it's required by IMAS, but Spack is missing proper recipe
     Code Block
    $: mkdir -p libs-intel/saxon
$: cd libs-intel/saxon
$: wget https://sourceforge.net/projects/saxon/files/Saxon-HE/9.9/SaxonHE9-9-1-5J.zip/download
$: unzip download
    Create two softlinks:
     Code Block
    $: ln -s saxon9-test.jar saxon9he-test.jar
$: ln -s saxon9-xqj.jar saxon9he-xqj.jar
    And set the saxon files available:
     Code Block
    chmod -R 777 .

  24. Prepare Saxon module:
     Code Block
    $: cd ../../
$: mkdir -p modules-intel/saxon
$: vim modules-intel/saxon/9.9
    And fill the created module with below content:
     Code Block
    #%Module
##
##      Modulefile for saxon
##	Maciej Smukowski 2022
##
set fpath	[file dirname $ModulesCurrentModulefile]
set VERSION	[file tail $ModulesCurrentModulefile]

module-whatis "Enable the usage of saxon $VERSION.
\tKeywords: math tool matlab"


proc ModulesDisplay {} {
}

conflict saxon

set SAXON_HOME /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/saxon
prepend-path SAXON_HOME /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/saxon

prepend-path    CLASSPATH $SAXON_HOME/saxon9he.jar
prepend-path    CLASSPATH $SAXON_HOME/saxon9-test.jar
prepend-path    CLASSPATH $SAXON_HOME/saxon9-xqj.jar
prepend-path    CLASSPATH $SAXON_HOME/saxon9he-test.jar
prepend-path    CLASSPATH $SAXON_HOME/saxon9he-xqj.jar

  25. Prepare spack-imasenv module prototype:
     Code Block
    $: mkdir -p modules/spack-imasenv/3.37.0/intel
$: vim modules/spack-imasenv/3.37.0/intel/2020
    And fill the created module with below content:
     Code Block
    #%Module
##
##      Modulefile for imasenv
##  Maciej Smukowski 2022
##

module-whatis "One IMASENV module to rule them all"


proc ModulesDisplay {} {
}

conflict imasenv

# Add spack modules to MODULEPATH
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-gcc
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-intel

module load gnu/7.3.0
module load intel/pe-xe-2020--binary
module load intelmpi/2020--binary
module load cmake/3.25.0/gcc/7.3.0/sha-a4xv7cs
module load pkgconf/1.8.0/intel/19.1.3.304/sha-fbevp5q
module load netlib-lapack/3.10.1/intel/19.1.3.304/sha-g4e3xak
module load netlib-xblas/1.0.248/intel/19.1.3.304/sha-zp4t7zq
module load python/3.10.8/intel/19.1.3.304/sha-ufy2r2o
module load py-pip/22.2.2/intel/19.1.3.304/sha-ksiszmp
module load py-setuptools/59.4.0/intel/19.1.3.304/sha-p6m2okz
module load py-wheel/0.37.1/intel/19.1.3.304/sha-h5qnby4
module load py-cython/0.29.32/intel/19.1.3.304/sha-ekt45in
module load py-pyyaml/6.0/intel/19.1.3.304/sha-e7pj6rd
module load py-numpy/1.22.4/intel/19.1.3.304/sha-vtkr2zd
module load py-scipy/1.8.1/intel/19.1.3.304/sha-j7sstl3
module load py-matplotlib/3.6.2/intel/19.1.3.304/sha-wbwigpl
module load hdf5/1.12.2/intel/19.1.3.304/sha-lpavud5
module load openjdk/11.0.17_8/intel/19.1.3.304/sha-nwh5yaq
module load git
module load blitz/1.0.1/intel/19.1.3.304/sha-gpct7uz
module load boost/1.80.0/intel/19.1.3.304/sha-6erl3nf
module load mdsplus/stable_release-7-96-17/intel/19.1.3.304/sha-jiasz6w
module load libxml2/2.10.1/intel/19.1.3.304/sha-3te5l7z
    DISCLAIMER!: If you're doing your spack installation from scratch be cautious about module names. The pattern is "sha-{hash}" , where hash is generated during installation, therefore your hashes will be different than mine.
  26. Load spack-imasenv module:
     Code Block
    $: module use /marconi_work/FUSIO_HLST/IMAS_software/modules
$: module load spack-imasenv/3.37.0/intel/2020

  27. Load Saxon module:
     Code Block
    module load saxon/9.9

  28. Clone IMAS Installer :
     Code Block
    git clone ssh://git@git.iter.org/imas/installer.git imas-installer-intel
    for convenience, let's loosen the read and write permissions for all files:
     Code Block
    chmod -R 777 .
    The top directory should look somewhat like this:
     Code Block
    drwxrwxrwx   6 interactive  4096 Dec  7 14:00 cache-gcc
drwxrwxrwx   4 interactive  4096 Dec 10 16:45 cache-intel
drwxrwxrwx  10 interactive  4096 Dec  8 15:42 imas-installer-gcc
drwxrwxrwx   7 interactive  4096 Dec 11 22:43 imas-installer-intel
drwxrwxrwx 135 interactive 32768 Dec 10 16:28 libs-gcc
drwxrwxrwx 118 interactive 32768 Dec 11 22:29 libs-intel
drwxrwxrwx   3 interactive  4096 Dec  8 11:45 modules
drwxrwxrwx 132 interactive 32768 Dec 10 16:28 modules-gcc
drwxrwxrwx 124 interactive 32768 Dec 11 22:30 modules-intel
drwxrwxrwx   9 interactive  4096 Dec  7 23:44 spack-gcc
drwxr-xr-x   9 interactive  4096 Dec 10 16:38 spack-intel
drwxrwxrwx   3 interactive  4096 Dec  7 14:31 stage-gcc
drwxrwxrwx   3 interactive  4096 Dec 10 16:44 stage-intel

  29. Create IMAS configuration script:
     Code Block
    vim imas-installer-intel/3.37.0_4.11.0.sh
    and fill it with below content:
     Code Block
    export TAG_DD=3.37.0

export TAG_AL=4.11.0
# make sure these branches exist

export VER_DD=$TAG_DD
export VER_AL=$TAG_AL
export IMAS_VERSION=$TAG_DD
export UAL_VERSION=$TAG_AL
export MODULE_FULL_VERSION=$VER_DD/AL/$VER_AL


export IMAS_HOME=/marconi_work/FUSIO_HLST/IMAS_software/libs-intel/IMAS

export IMAS_UDA=fat
export IMAS_HDC=no

export IMAS_CPP=yes

export IMAS_FORTRAN=yes
export IMAS_G95=no
export IMAS_PGI=no
export IMAS_IFORT=yes
export IMAS_GFORTRAN=no
export IMAS_NAGFOR=no

export IMAS_JAVA=yes

export IMAS_MATLAB=no
export IMAS_PYTHON=yes
export IMAS_PYTHON2=no
export IMAS_PYTHON3=yes


# After Installation Environment
eval `./tools/imasdb.in test`

export UAL=$(realpath ./src/$IMAS_VERSION/ual/$UAL_VERSION)
export MY_INSTALL=$IMAS_HOME/core/IMAS/${VER_DD}/AL/${VER_AL}
export IMAS_INSTALL_DIR=$MY_INSTALL
export PYTHONPATH=$MY_INSTALL/python/lib/:$PYTHONPATH
export CLASSPATH=$UAL/javainterface/build/:$CLASSPATH
export IMAS_PREFIX=$MY_INSTALL/
export ids_path="$MDSPLUS_TREE_BASE_0;$MY_INSTALL/models/mdsplus/;$ids_path"
export LD_LIBRARY_PATH=$MY_INSTALL/lib:$LD_LIBRARY_PATH
export TOKAMAKNAME=test
export DATAVERSION=3
    Note that there are at least 3 places that should be customized:
    1. export TAG_DD=<desired_data_dictionary_tag>
    2. export TAG_AL=<desired_access_layer_tag>
    3. export IMAS_HOME=<your_IMAS_HOME_path>

  30. Go inside imas-installer-intel directory:
     Code Block
    cd imas-installer-intel

  31. Source IMAS configuration script:
     Code Block
    source 3.37.0_4.11.0.sh

  32. Download build files:
     Code Block
    make cache

  33. Edit Makefile.common file to not use GNU compilers by default:
     Code Block
    src/3.37.0/ual/4.11.0/Makefile.common

    1. Line 105 change to:
       Code Block
      CC ?= gcc

    2. Line 106 change to: 
       Code Block
      CXX ?= g++

  34. Check if everything is set-up correctly:
     Code Block
    make help

  35. Build and install IMAS :
     Code Block
    make install

    1. Caution!
      During IMAS installation under INTEL-2020 compiler you may encounter following error:
       Code Block
      #error Blitz is configured with --enable-threadsafe, but no compiler thread support is found. Did you forget, e.g., "--pthread"?
      Issue description: Known issues - Intel 2020#BLITZandmissing-pthreadflag

      FIX:
      1. Edit Blitz pkgconfig:
         Code Block
        vim /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/blitz/1.0.1/intel/19.1.3.304/gpct7uzeeiprapilq7oygmwdthhvcw24/lib/pkgconfig/blitz.pc

      2. Set 12 line to use pthread Cflag:
         Code Block
        Cflags: -I${includedir} -pthread

  36. Leave the imas-installer-intel directory:
     Code Block
    cd ..

  37. Extend spack-imasenv modulefile:
     Code Block
    vim modules/spack-imasenv/3.37.0/intel/2020

    1. Add path to IMAS module:
       Code Block
      module use /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/IMAS/etc/modulefiles

    2. Add loading of the IMAS module:
       Code Block
      module load IMAS/3.37.0/AL/4.11.0

    3. Final spack-imasenv module:
       Code Block
      #%Module
##
##      Modulefile for imasenv
##  Maciej Smukowski 2022
##

module-whatis "One IMASENV module to rule them all"


proc ModulesDisplay {} {
}

conflict imasenv

# Add spack modules to MODULEPATH
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-gcc
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-intel
module use /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/IMAS/etc/modulefiles

module load gnu/7.3.0
module load intel/pe-xe-2020--binary
module load intelmpi/2020--binary
module load cmake/3.25.0/gcc/7.3.0/sha-a4xv7cs
module load pkgconf/1.8.0/intel/19.1.3.304/sha-fbevp5q
module load netlib-lapack/3.10.1/intel/19.1.3.304/sha-g4e3xak
module load netlib-xblas/1.0.248/intel/19.1.3.304/sha-zp4t7zq
module load python/3.10.8/intel/19.1.3.304/sha-ufy2r2o
module load py-pip/22.2.2/intel/19.1.3.304/sha-ksiszmp
module load py-setuptools/59.4.0/intel/19.1.3.304/sha-p6m2okz
module load py-wheel/0.37.1/intel/19.1.3.304/sha-h5qnby4
module load py-cython/0.29.32/intel/19.1.3.304/sha-ekt45in
module load py-pyyaml/6.0/intel/19.1.3.304/sha-e7pj6rd
module load py-numpy/1.22.4/intel/19.1.3.304/sha-vtkr2zd
module load py-scipy/1.8.1/intel/19.1.3.304/sha-j7sstl3
module load py-matplotlib/3.6.2/intel/19.1.3.304/sha-wbwigpl
module load hdf5/1.12.2/intel/19.1.3.304/sha-lpavud5
module load openjdk/11.0.17_8/intel/19.1.3.304/sha-nwh5yaq
module load git
module load blitz/1.0.1/intel/19.1.3.304/sha-gpct7uz
module load boost/1.80.0/intel/19.1.3.304/sha-6erl3nf
module load mdsplus/stable_release-7-96-17/intel/19.1.3.304/sha-jiasz6w
module load libxml2/2.10.1/intel/19.1.3.304/sha-3te5l7z

module load IMAS/3.37.0/AL/4.11.0

  38. Create temp-intel  directory:
     Code Block
    mkdir temp-intel

  39. Go inside temp-intel directory:
     Code Block
    cd temp-intel

  40. Clone IDStools :
     Code Block
    git clone ssh://git@git.iter.org/imas/idstools.git

  41. Go into IDStools directory:
     Code Block
    cd idstools

  42. Build IDStools :
     Code Block
    make all

  43. Install IDStools :
     Code Block
    make install

  44. Leave temp directory:
     Code Block
    cd ../..

  45. Update spack-imasenv/3.37.0/intel/2020 module to use IDStools :
     Code Block
    vim modules/spack-imasenv/3.37.0/intel/2020

    1. Use path to IDStools module:
       Code Block
      module use /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/IMAS/etc/modulefiles

    2. Load IDStools modules:
       Code Block
      module load idstools/1.13.1

    3. Updated spack-imasenv/3.37.0/intel/2020 module:
       Code Block
      #%Module
##
##      Modulefile for imasenv
##  Maciej Smukowski 2022
##

module-whatis "One IMASENV module to rule them all"


proc ModulesDisplay {} {
}

conflict imasenv

# Add spack modules to MODULEPATH
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-gcc
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-intel
module use /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/IMAS/etc/modulefiles

module load gnu/7.3.0
module load intel/pe-xe-2020--binary
module load intelmpi/2020--binary
module load cmake/3.25.0/gcc/7.3.0/sha-a4xv7cs
module load pkgconf/1.8.0/intel/19.1.3.304/sha-fbevp5q
module load netlib-lapack/3.10.1/intel/19.1.3.304/sha-g4e3xak
module load netlib-xblas/1.0.248/intel/19.1.3.304/sha-zp4t7zq
module load python/3.10.8/intel/19.1.3.304/sha-ufy2r2o
module load py-pip/22.2.2/intel/19.1.3.304/sha-ksiszmp
module load py-setuptools/59.4.0/intel/19.1.3.304/sha-p6m2okz
module load py-wheel/0.37.1/intel/19.1.3.304/sha-h5qnby4
module load py-cython/0.29.32/intel/19.1.3.304/sha-ekt45in
module load py-pyyaml/6.0/intel/19.1.3.304/sha-e7pj6rd
module load py-numpy/1.22.4/intel/19.1.3.304/sha-vtkr2zd
module load py-scipy/1.8.1/intel/19.1.3.304/sha-j7sstl3
module load py-matplotlib/3.6.2/intel/19.1.3.304/sha-wbwigpl
module load hdf5/1.12.2/intel/19.1.3.304/sha-lpavud5
module load openjdk/11.0.17_8/intel/19.1.3.304/sha-nwh5yaq
module load git
module load blitz/1.0.1/intel/19.1.3.304/sha-gpct7uz
module load boost/1.80.0/intel/19.1.3.304/sha-6erl3nf
module load mdsplus/stable_release-7-96-17/intel/19.1.3.304/sha-jiasz6w
module load libxml2/2.10.1/intel/19.1.3.304/sha-3te5l7z

module load IMAS/3.37.0/AL/4.11.0
module load idstools/1.13.1

  46. Reaload the spack-imasenv/3.37.0/intel/2020 and check the idsdump command to verify IDStools installation:
     Code Block
    $: module purge
$: module load spack-imasenv/3.37.0/intel/2020
$: idsdump --help

    1. If normal help manual is printed then the installation is correct.
    2. In case of the following error:
       Code Block
      -bash: /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/IMAS/core/idstools/1.13.1/bin/idsdump: /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/python/3.10.8/intel/19.1.3.3: bad interpreter: No such file or directory
      The shebang line with python interpreter is longer than 128 characters which is usually a limit set by the kernel. Workaround:
      1. Go to the python installation directory, under the compiler name directory:
         Code Block
        cd /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/python/3.10.8/intel/

      2. Create a symlink with shorter name than 19.1.3.304, e.g. 2020 :
         Code Block
        ln -s 19.1.3.304 2020

      3. Now you have to edit each IDStools command script and replace the shebang line with symlink line:
         Code Block
        vim /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/IMAS/core/idstools/1.13.1/bin/idsdump
        Delete line:
         Code Block
        DEL: #!/marconi_work/FUSIO_HLST/IMAS_software/libs-intel/python/3.10.8/intel/19.1.3.304/ufy2r2oat5k6zgn7w5ci26pillyjqtfd/./bin/python
        Insert line:
         Code Block
        INSERT: #!/marconi_work/FUSIO_HLST/IMAS_software/libs-intel/python/3.10.8/intel/2020/ufy2r2oat5k6zgn7w5ci26pillyjqtfd/./bin/python
        The two actions above has to be repeated for each IDStools command that fails to use the Intel-Python interpreter!
  47. Get back to the IMAS_software directory:
     Code Block
    cd /marconi_work/FUSIO_HLST/IMAS_software/

  48. Create directory for XMLLIB - INTEL installation:
     Code Block
    mkdir -p libs-intel/xmllib/3.3.1/intel/19.1.3.304

  49. Go to the temp-intel directory:
     Code Block
    cd temp-intel

  50. Clone XMLLIB :
     Code Block
    git clone ssh://git@git.iter.org/lib/xmllib.git

  51. Change directory to xmllib :
     Code Block
    cd xmllib

  52. Checkout 3.3.1 version:
     Code Block
    git checkout 3.3.1

  53. Clean up all:
     Code Block
    git clean -f -x -d

  54. Optionally launch bootsrap:
     Code Block
    ./bootstrap

  55. Run configure :
     Code Block
    ./configure --prefix=/marconi_work/FUSIO_HLST/IMAS_software/libs-intel/xmllib/3.3.1/intel/19.1.3.304 FC=ifort CC=icc

  56. Build XMLLIB :
     Code Block
    make all

  57. Check XMLLIB build:
     Code Block
    make check

  58. Install XMLLIB :
     Code Block
    make install

  59. Leave directory:
     Code Block
    cd ../..

  60. Create modulefile for XMLLIB :

    1. Create module directory:
       Code Block
      mkdir -p modules-intel/xmllib/3.3.1/intel/

    2. Create modulefile:
       Code Block
      vim modules-intel/xmllib/3.3.1/intel/19.1.3.304

    3. Fill it with below content:
       Code Block
      #%Module1.0#####################################################################
##
## xmllib modulefile
##
set ver 3.3.1
set name xmllib
set loading [module-info mode load]
set desc "Library to assist parsing of XML data"
proc ModulesHelp { } {
puts stderr "\tThis module sets the environment for $name v$ver"
}
conflict $name

prereq   intel/pe-xe-2020--binary


module-whatis "$desc (v$ver)"
set prefix /marconi_work/FUSIO_HLST/IMAS_software/libs-gcc/xmllib/3.3.1/intel/19.1.3.304
set exec_prefix ${prefix}
prepend-path CPATH ${prefix}/include
prepend-path LD_LIBRARY_PATH ${exec_prefix}/lib
prepend-path PKG_CONFIG_PATH ${exec_prefix}/lib/pkgconfig

  61. Update spack-imasenv/3.37.0/intel/2020 :
     Code Block
    vim modules/spack-imasenv/3.37.0/intel/2020

    1. Add load of the XMLLIB  module:
       Code Block
      module load xmllib/3.3.1/intel/19.1.3.304

    2. Full module:
       Code Block
      #%Module
##
##      Modulefile for imasenv
##  Maciej Smukowski 2022
##

module-whatis "One IMASENV module to rule them all"


proc ModulesDisplay {} {
}

conflict imasenv

# Add spack modules to MODULEPATH
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-gcc
module use /marconi_work/FUSIO_HLST/IMAS_software/modules-intel
module use /marconi_work/FUSIO_HLST/IMAS_software/libs-intel/IMAS/etc/modulefiles

module load gnu/7.3.0
module load intel/pe-xe-2020--binary
module load intelmpi/2020--binary
module load cmake/3.25.0/gcc/7.3.0/sha-a4xv7cs
module load pkgconf/1.8.0/intel/19.1.3.304/sha-fbevp5q
module load netlib-lapack/3.10.1/intel/19.1.3.304/sha-g4e3xak
module load netlib-xblas/1.0.248/intel/19.1.3.304/sha-zp4t7zq
module load python/3.10.8/intel/19.1.3.304/sha-ufy2r2o
module load py-pip/22.2.2/intel/19.1.3.304/sha-ksiszmp
module load py-setuptools/59.4.0/intel/19.1.3.304/sha-p6m2okz
module load py-wheel/0.37.1/intel/19.1.3.304/sha-h5qnby4
module load py-cython/0.29.32/intel/19.1.3.304/sha-ekt45in
module load py-pyyaml/6.0/intel/19.1.3.304/sha-e7pj6rd
module load py-numpy/1.22.4/intel/19.1.3.304/sha-vtkr2zd
module load py-scipy/1.8.1/intel/19.1.3.304/sha-j7sstl3
module load py-matplotlib/3.6.2/intel/19.1.3.304/sha-wbwigpl
module load hdf5/1.12.2/intel/19.1.3.304/sha-lpavud5
module load openjdk/11.0.17_8/intel/19.1.3.304/sha-nwh5yaq
module load git
module load blitz/1.0.1/intel/19.1.3.304/sha-gpct7uz
module load boost/1.80.0/intel/19.1.3.304/sha-6erl3nf
module load mdsplus/stable_release-7-96-17/intel/19.1.3.304/sha-jiasz6w
module load libxml2/2.10.1/intel/19.1.3.304/sha-3te5l7z

module load IMAS/3.37.0/AL/4.11.0
module load idstools/1.13.1

module load xmllib/3.3.1/intel/19.1.3.304

Gateway + SPACK + GNU
Gateway + SPACK + INTEL
 
This work has been carried out within the framework of the EUROfusion Consortium, funded by the European Union via the Euratom Research and Training Programme (Grant Agreement No. 101052200—EUROfusion).  Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those  of the European Union or the European Commission. Neither the European Union nor the European Commission can be held responsible for them. The project activities are co-financed by Polish Ministry of Science and Higher Education from financial resources of the programme entitled "PMW" in 2021, 2022.
Marconi + SPACK + INTEL
Gateway + SPACK + GNU
...