Commit 89fa076a authored by Gesa Meyer's avatar Gesa Meyer
Browse files

Merge branch 'container_update' into 'preReleaseV2' 

Container update

See merge request CanESM/CLASSIC!161
parents 0e504491 a4e92427

tools/apptainerContainerRecipe/CLASSIC_container.def

+4 −4
Original line number Diff line number Diff line
@@ -51,10 +51,10 @@ From:ubuntu:24.04 #noble or 24.04 gives 24.04 lts, which is 24.04.1 
  apt install -y libnetcdff7=4.6.0+really4.5.4+ds-3build2 libnetcdff-dev=4.6.0+really4.5.4+ds-3build2



  # Install other tools required by the CLASSIC ecosystem

  apt install -y vim=2:9.1.0016-1ubuntu7.8

  apt install -y vim=2:9.1.0016-1ubuntu7.9

  apt install -y make=4.3-4.1build2 

  apt install -y curl=8.5.0-2ubuntu10.6 

  apt install -y git=1:2.43.0-1ubuntu7.2 

  apt install -y git=1:2.43.0-1ubuntu7.3 

  apt install -y zip=3.0-13ubuntu0.2 

  apt install -y unzip=6.0-28ubuntu4.1 

  apt install -y python3=3.12.3-0ubuntu2
@@ -64,13 +64,13 @@ From:ubuntu:24.04 #noble or 24.04 gives 24.04 lts, which is 24.04.1 
  apt install -y zlib1g=1:1.3.dfsg-3.1ubuntu2.1 

  apt install -y mpich=4.2.0-5build3 

  apt install -y doxygen=1.9.8+ds-2build5 

  apt install -y python3-pip=24.0+dfsg-1ubuntu1.1 

  apt install -y python3-pip=24.0+dfsg-1ubuntu1.3 

  apt install -y nco=5.2.1-1build2 

  apt install -y libopenmpi-dev=4.1.6-7ubuntu2 

  apt install -y libgeos-dev=3.12.1-3build1 

  apt install -y libgdal-dev=3.8.4+dfsg-3ubuntu3

  apt install -y pandoc=3.1.3+ds-2 

  apt install -y poppler-utils=24.02.0-1ubuntu9.4

  apt install -y poppler-utils=24.02.0-1ubuntu9.7

  apt install -y texlive-latex-base=2023.20240207-1 

  apt install -y tree=2.1.1-2ubuntu3

tools/apptainerContainerRecipe/README.md

+25 −22

File changed.

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tools/siteLevelFLUXNET/prep_jobopts.sh

+8 −2
Original line number Diff line number Diff line
@@ -154,8 +154,11 @@ for f in $inputs/*; do 
    # Now we use sed (stream editor) to tailor the job options file with the info we gained from site_info.yaml and to have default site level behaviour

    echo "Preparing $jof"

    

    # Replace start year and end year

    sed -i "/readMetStartYear/s| = [0-9]* | = $start_year | ; /readMetEndYear/s| = [0-9]* | = $end_year | ; /metLoop/s| = [0-9]* | = 1 |" $jof

    # Replace run start year and end year

    sed -i "/runStartYear/s| = [0-9]*| = $start_year| ; /runEndYear/s| = [0-9]*| = $end_year|" $jof



    # Replace meteorological start year and end year

    sed -i "/actualMetStartYear/s| = [0-9]*| = $start_year| ; /actualMetEndYear/s| = [0-9]*| = $end_year|" $jof

    

    # Replace leap

    sed -i "/leap/s| = \..*\, | = $leap_flag |" $jof
@@ -218,6 +221,9 @@ for f in $inputs/*; do 
    # Turn Ksat scalar off

    sed -i "/KsatScalaron/s|=\s*\..*\.\s*,|= \.false\. ,|" $jof



    # Ensure specifiedSoilPermDepth is set to fill value

    sed -i "/specifiedSoilPermDepth/s|= [0-9\.]* |= -9999 |" $jof



    # Replace the IDISP, IZREF, ZRFH, and ZRFM

    sed -i "/IDISP/s|= [0-9\.]*\s*,|= 1 ,| ; /IZREF/s|= [0-9\.]*\s*,|= 1 ,| ; /ZRFH/s|= [0-9\.]*,|= $ZRFH ,| ; /ZRFM/s|= [0-9\.]*,|= $ZRFM ,|" $jof

tools/siteLevelFLUXNET/process_outputs.sh

+0 −1
Original line number Diff line number Diff line
@@ -26,7 +26,6 @@ fi 
# Report usage of this script in case of improper execution

if [[ ($# -eq 0) ]]; then

  echo ' Usage: process_outputs.sh runfolder(s)'

  echo ' Note: when running in the container (not on the HPC), only one runfolder can be handled at a time!!!'

  echo ' Note: the plots are placed into the first specified runfolder.'

  exit 2

fi