Octave with netcdf on linux

README.md

Octave on linux with netcdf4+statistics packages

https://octave.sourceforge.io/netcdf/

OS

Octave version too old.

Anaconda

Build octave-netcdf package

conda create -n bb conda-build
conda activate bb
mkdir octave-netcdf
# edit conda/octave-netcdf/recipe/meta.yaml
conda build octave-netcdf

Stuck at

Saving to: ‘netcdf.tar.gz’

netcdf.tar.gz                        100%[===================================================================>] 409.68K  1.88MB/s    in 0.2s    

2022-10-24 16:17:10 (1.88 MB/s) - ‘netcdf.tar.gz’ saved [419517/419517]

QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-verhoes'
mkdir (/tmp/oct-poACam)
untar (netcdf.tar.gz, /tmp/oct-poACam)
checking for gawk... gawk
checking whether the C++ compiler works... no
configure: error: in `/tmp/oct-poACam/netcdf-1.0.16/src':
configure: error: C++ compiler cannot create executables
See `config.log' for more details

error: pkg: error running the configure script for netcdf
error: called from
    configure_make at line 101 column 9
    install at line 202 column 7
    pkg at line 612 column 9
Traceback (most recent call last):

Snap

snap install octave
octave --version

Inject netcdf into existing octave snap

snap run --shell octave
curl https://downloads.unidata.ucar.edu/netcdf-c/4.9.0/netcdf-c-4.9.0.tar.gz > netcdf-c-4.9.0.tar.gz
curl https://downloads.unidata.ucar.edu/netcdf-cxx/4.3.1/netcdf-cxx4-4.3.1.tar.gz > netcdf-cxx4-4.3.1.tar.gz
tar -xf netcdf-c-4.9.0.tar.gz 
cd netcdf-c-4.9.0
./configure
checking for m4... no
configure: error: Cannot find m4 utility. Install m4 and try again.

snap run --shell octave
touch /lib/x86_64-linux-gnu/x
touch: cannot touch '/lib/x86_64-linux-gnu/x': Read-only file system

Create snap with netcdf4+statistics packages

sudo snap install --classic snapcraft
mkdir own
cd own
snapcraft init

Cannot use octave as base

New octave snap

Clone https://github.com/octave-snap/octave-snap

add netcdf-dev to octave-snap/snap/snapcraft.yaml

snapcraft

Failed with

  CXX      libinterp/corefcn/libinterp_corefcn_libcorefcn_la-input.lo
virtual memory exhausted: Cannot allocate memory
Makefile:17926: recipe for target 'libinterp/corefcn/libinterp_corefcn_libcorefcn_la-input.lo' failed
make[2]: *** [libinterp/corefcn/libinterp_corefcn_libcorefcn_la-input.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/root/parts/octave/build'
Makefile:26490: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/root/parts/octave/build'
Makefile:9865: recipe for target 'all' failed
make: *** [all] Error 2
Failed to run 'make -j2' for 'octave': Exited with code 2.
Verify that the part is using the correct parameters and try again.
Run the same command again with --debug to shell into the environment if you wish to introspect this failure.

meta.yaml

{% set version = "1.0.16" %}
package:
  name: octave-netcdf
  version: 1.0.16
build:
  number: 1
  script: | 
    wget -O netcdf.tar.gz https://octave.sourceforge.io/download.php?package=netcdf-{{ version }}.tar.gz && 
    octave --eval 'pkg install -verbose netcdf.tar.gz'
requirements:
  build:
    - octave
    - libnetcdf
    - gxx
  host:
    - octave
    - libnetcdf

snapcraft.yaml

name: octave
base: core18
summary: Interactive programming environment for numerical computations
description: |
  GNU Octave is a high-level interpreted language, primarily intended for
  numerical computations. It provides capabilities for the numerical
  solution of linear and nonlinear problems, and for performing other
  numerical experiments. It also provides extensive graphics capabilities
  for data visualization and manipulation. Octave is normally used through
  its interactive command line interface, but it can also be used to write
  non-interactive programs. The Octave language is quite similar to
  Matlab so that most programs are easily portable.
confinement: strict
adopt-info: octave

apps:
  octave:
    command: bin/octave
    common-id: org.octave.Octave
    desktop: share/applications/org.octave.Octave.desktop
    environment:
      OCTAVE_HOME: "$SNAP"
      GNUPLOT_DRIVER_DIR: "$SNAP/usr/lib/gnuplot"
      GNUPLOT_LUA_DIR: "$SNAP/usr/share/gnuplot/gnuplot/5.2/lua"
      GNUPLOT_PS_DIR: "$SNAP/usr/share/gnuplot/gnuplot/5.2/PostScript"
      GS_LIB: "$SNAP/usr/share/ghostscript/9.26/Resource/Init:$SNAP/usr/share/ghostscript/9.26/lib:$SNAP/usr/share/ghostscript/9.26/Resource/Font:$SNAP/usr/share/ghostscript/fonts:$SNAP/usr/share/fonts"
      LD_LIBRARY_PATH: "$SNAP/lib/octave/$SNAPCRAFT_PROJECT_VERSION"
      LOCPATH: "$SNAP/usr/lib/locale"
      PKG_CONFIG_PATH: "$SNAP/lib/pkgconfig:$SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/pkgconfig:$SNAP/usr/share/pkgconfig"
      PKG_CONFIG_SYSROOT_DIR: "$SNAP"
      UNITSFILE: "$SNAP/usr/share/units/definitions.units"
    plugs:
      - desktop
      - desktop-legacy
      - home
      - network
      - opengl
      - pulseaudio
      - removable-media
      - unity7
      - wayland
      - x11
  octave-cli:
    command: bin/octave-cli
    environment:
      OCTAVE_HOME: "$SNAP"
      GNUPLOT_DRIVER_DIR: "$SNAP/usr/lib/gnuplot"
      GNUPLOT_LUA_DIR: "$SNAP/usr/share/gnuplot/gnuplot/5.2/lua"
      GNUPLOT_PS_DIR: "$SNAP/usr/share/gnuplot/gnuplot/5.2/PostScript"
      GS_LIB: "$SNAP/usr/share/ghostscript/9.26/Resource/Init:$SNAP/usr/share/ghostscript/9.26/lib:$SNAP/usr/share/ghostscript/9.26/Resource/Font:$SNAP/usr/share/ghostscript/fonts:$SNAP/usr/share/fonts"
      LD_LIBRARY_PATH: "$SNAP/lib/octave/$SNAPCRAFT_PROJECT_VERSION"
      LOCPATH: "$SNAP/usr/lib/locale"
      PKG_CONFIG_PATH: "$SNAP/lib/pkgconfig:$SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/pkgconfig:$SNAP/usr/share/pkgconfig"
      PKG_CONFIG_SYSROOT_DIR: "$SNAP"
      UNITSFILE: "$SNAP/usr/share/units/definitions.units"
    plugs:
      - desktop
      - desktop-legacy
      - home
      - network
      - opengl
      - pulseaudio
      - removable-media
      - unity7
      - wayland
      - x11

parts:
  alsa:
    plugin: nil
    source: https://github.com/diddledan/snapcraft-alsa.git
    override-pull: |
      cat > asound.conf <<EOF
      pcm.!default {
        type pulse
        fallback "sysdefault"
        hint {
          show on
          description "Default ALSA Output (currently PulseAudio Sound Server)"
        }
      }
      ctl.!default {
        type pulse
        fallback "sysdefault"
      }
      EOF
    override-build: |
      install -m644 -D -t $SNAPCRAFT_PART_INSTALL/etc asound.conf
    prime:
      - -usr/share/doc
      - -usr/share/man
    build-packages:
      - libasound2-dev
    stage-packages:
      - libasound2
      - libasound2-plugins

  octave:
    plugin: autotools
    source: https://hg.savannah.gnu.org/hgweb/octave
    source-type: hg
    source-commit: "@"
    build-environment:
      # Use a sensible default set of build flags, append flags from environment
      - CFLAGS: "-g -O2 -fexceptions -fstack-protector-strong${CFLAGS:+ $CFLAGS}"
      - CPPFLAGS: "-D_FORTIFY_SOURCE=2${CPPFLAGS:+ $CPPFLAGS}"
      - CXXFLAGS: "-g -O2 -fexceptions -fstack-protector-strong${CXXFLAGS:+ $CXXFLAGS}"
      - FFLAGS: "-g -O2${FFLAGS:+ $FFLAGS}"
      - FLIBS: "-lgfortran -lquadmath -lm"
      - LDFLAGS: "-Wl,-z,relro,-z,now -Wl,--as-needed${LDFLAGS:+ $LDFLAGS}"
      # Strip debug symbols from programs and libraries when installing
      - INSTALL_PROGRAM: "/usr/bin/install -s"
      - INSTALL_STRIP_FLAG: "-s"
      # Force Octave header files to be found before system header files
      # This override can be dropped after upgrading to snapcraft version 3.11
      - INCLUDES: "-Ilibinterp/corefcn"
    override-build: |
      # Parse octave version information and set snap grade and version
      sed -n '/^AC_INIT/{s/^[^,]*, *\[//;s/\],.*//;p}' configure.ac > ac-version.txt
      if test -d .hg; then
        # Construct a snapshot version string if we are building from mercurial
        hg log -r . -T "{node|short}" | cut -c1-8 > commit.txt
        date -u +%Y-%m-%d > date.txt
        echo "$(cat ac-version.txt)+hg$(cat commit.txt)" > version.txt
        echo "<release version=\"$(cat version.txt)\" type=\"development\" date=\"$(cat date.txt)\" />" > release.xml
        sed -i "/<releases>/a\    $(cat release.xml)" etc/icons/org.octave.Octave.appdata.xml
        sed -i "s/hg_safe.*||/hg_safe log -r . -T \"{node|short}\" ||/" build-aux/mk-hg-id.sh
        grade=devel
        version="$(cat version.txt)"
      else
        grade=stable
        version="$(cat ac-version.txt)"
      fi
      snapcraftctl set-grade "$grade"
      snapcraftctl set-version "$version"

      # Patch RapidJSON header files with upstream fixes that haven't been
      # incorporated into the Ubuntu distributed version of the library
      if test -d /usr/include/rapidjson/.orig; then
        cp -a /usr/include/rapidjson/.orig/*.h /usr/include/rapidjson
      fi
      patch -p3 -N -d /usr/include/rapidjson -b -B .orig/ < $SNAPCRAFT_PROJECT_DIR/patches/rapidjson-issue-905.patch
      patch -p3 -N -d /usr/include/rapidjson -b -B .orig/ < $SNAPCRAFT_PROJECT_DIR/patches/rapidjson-issue-1718.patch

      # Patch build_env and mkoctfile to record the original build flags from
      # above, so that additional flags from snapcraft build setup aren't leaked
      sed -i "s|%OCTAVE_CONF_CFLAGS%|\"-g -O2 -fexceptions -fstack-protector-strong\"|" libinterp/build-env.in.cc src/mkoctfile.in.cc
      sed -i "s|%OCTAVE_CONF_CPPFLAGS%|\"-D_FORTIFY_SOURCE=2\"|" libinterp/build-env.in.cc src/mkoctfile.in.cc
      sed -i "s|%OCTAVE_CONF_CXXFLAGS%|\"-g -O2 -fexceptions -fstack-protector-strong\"|" libinterp/build-env.in.cc src/mkoctfile.in.cc
      sed -i "s|%OCTAVE_CONF_LDFLAGS%|\"-Wl,-z,relro,-z,now -Wl,--as-needed\"|" libinterp/build-env.in.cc src/mkoctfile.in.cc
      sed -i "s|%OCTAVE_CONF_OCT_LINK_OPTS%|\"-Wl,-z,relro,-z,now -Wl,--as-needed\"|" libinterp/build-env.in.cc src/mkoctfile.in.cc
      snapcraftctl build
    override-prime: |
      snapcraftctl prime
      sed -i 's|^Icon=octave|Icon=/share/icons/hicolor/scalable/apps/octave.svg|' share/applications/org.octave.Octave.desktop
      sed -i 's|^prefix=.*|prefix=/usr|' usr/lib/$SNAPCRAFT_ARCH_TRIPLET/pkgconfig/*.pc
      rm -f usr/lib/$SNAPCRAFT_ARCH_TRIPLET/pkgconfig/hdf5.pc
      ln -s hdf5-serial.pc usr/lib/$SNAPCRAFT_ARCH_TRIPLET/pkgconfig/hdf5.pc
      rm -f usr/bin/gnuplot
      ln -s gnuplot-qt usr/bin/gnuplot
    prime:
      - -share/man
      - -usr/share/doc
      - -usr/share/doc-base
      - -usr/share/man
      - -usr/share/texmf/ls-R
    organize:
      usr/lib/$SNAPCRAFT_ARCH_TRIPLET/openblas: usr/lib/$SNAPCRAFT_ARCH_TRIPLET
    after: [alsa]

    build-packages:
      - bison
      - epstool
      - flex
      - gfortran
      - ghostscript
      - gnuplot-nox
      - gperf
      - icoutils
      - less
      - libarpack2-dev
      - libcurl4-gnutls-dev
      - libfftw3-dev
      - libfltk1.3-dev
      - libfontconfig1-dev
      - libgl2ps-dev
      - libglpk-dev
      - libglu1-mesa-dev
      - libgraphicsmagick++1-dev
      - libhdf5-dev
      - libnetcdf-dev
      - libncurses5-dev
      - libopenblas-dev
      - libpcre3-dev
      - libqhull-dev
      - libqrupdate-dev
      - libqscintilla2-qt5-dev
      - libqt5opengl5-dev
      - libreadline-dev
      - librsvg2-bin
      - libsndfile1-dev
      - libsuitesparse-dev
      - pkg-config
      - portaudio19-dev
      - qtbase5-dev
      - qttools5-dev
      - qttools5-dev-tools
      - rapidjson-dev
      - texinfo
      - texlive-fonts-recommended
      - texlive-latex-base
      - texlive-plain-generic

    stage-packages:
      - build-essential
      - curl
      - epstool
      - gfortran
      - ghostscript
      - gnuplot-qt
      - info
      - libamd2
      - libarpack2
      - libcamd2
      - libccolamd2
      - libcholmod3
      - libcolamd2
      - libcurl3-gnutls
      - libcxsparse3
      - libfftw3-double3
      - libfftw3-single3
      - libfltk-gl1.3
      - libfltk1.3
      - libfontconfig1
      - libgl2ps1.4
      - libglpk40
      - libglu1-mesa
      - libgraphicsmagick++-q16-12
      - libhdf5-dev
      - libnetcdf-dev
      - libncurses5-dev
      - libopenblas-dev
      - libpcre3-dev
      - libportaudio2
      - libpython3-dev
      - libqhull-r7
      - libqrupdate1
      - libqscintilla2-qt5-13
      - libqt5core5a
      - libqt5gui5
      - libqt5help5
      - libqt5network5
      - libqt5opengl5
      - libqt5printsupport5
      - libqt5sql5
      - libqt5sql5-sqlite
      - libqt5widgets5
      - libqt5xml5
      - libsndfile1
      - libspqr2
      - libumfpack5
      - locales-all
      - pkg-config
      - python3-venv
      - texinfo
      - units
      - unzip
      - zip

  python-packages:
    plugin: python
    python-packages:
      - mpmath==1.1.0
      - sympy==1.5.1
    prime:
      - -bin/isympy
      - -share/man
      - -usr/share/doc
      - -usr/share/man


layout:
  /usr/lib/$SNAPCRAFT_ARCH_TRIPLET/alsa-lib:
    bind: $SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/alsa-lib
  /etc/asound.conf:
    bind-file: $SNAP/etc/asound.conf
  /usr/share/alsa/alsa.conf:
    bind-file: $SNAP/etc/asound.conf

  # Make staged dri and pulseaudio modules available in expected locations
  /usr/lib/$SNAPCRAFT_ARCH_TRIPLET/dri:
    symlink: $SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/dri
  /usr/lib/$SNAPCRAFT_ARCH_TRIPLET/pulseaudio:
    symlink: $SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/pulseaudio

  # Make staged perl modules available in expected perl path directories
  /usr/lib/$SNAPCRAFT_ARCH_TRIPLET/perl/5.26:
    symlink: $SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/perl/5.26
  /usr/lib/$SNAPCRAFT_ARCH_TRIPLET/perl5:
    symlink: $SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/perl5
  /usr/share/perl:
    symlink: $SNAP/usr/share/perl
  /usr/share/perl5/Text:
    symlink: $SNAP/usr/share/perl5/Text
  /usr/share/perl5/XML:
    symlink: $SNAP/usr/share/perl5/XML

  # Make staged qt plugins available in expected locations
  /usr/lib/$SNAPCRAFT_ARCH_TRIPLET/qt5:
    symlink: $SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/qt5

  # Make xkb configuration files available in expected locations, required
  # by qt in 18.04, may not be needed in 20.04
  /usr/share/X11:
    symlink: $SNAP/usr/share/X11

  # Make all system and staged development library header files available in
  # standard /usr/include location, to allow compiling oct files and packages
  /usr/include:
    bind: $SNAP/usr/include

  # Make certain libc static library fragments available in expected locations,
  # to allow linking oct files and packages
  /usr/lib/$SNAPCRAFT_ARCH_TRIPLET/libc_nonshared.a:
    symlink: $SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/libc_nonshared.a
  /usr/lib/$SNAPCRAFT_ARCH_TRIPLET/libmvec_nonshared.a:
    symlink: $SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/libmvec_nonshared.a
  /usr/lib/$SNAPCRAFT_ARCH_TRIPLET/libpthread_nonshared.a:
    symlink: $SNAP/usr/lib/$SNAPCRAFT_ARCH_TRIPLET/libpthread_nonshared.a

  # Make staged Python wheels available in expected system directory
  /usr/share/python-wheels:
    symlink: $SNAP/usr/share/python-wheels