From e71ee647916322b6913b3247974371164df28569 Mon Sep 17 00:00:00 2001 From: Kasra Farmer Date: Thu, 25 Apr 2024 10:28:22 -0400 Subject: [PATCH] Temporary measure to have the tool work on DRAC Graham This commit is a temporary measure addressing issue #47 submitted to the GitHub repository of the tool. It assured the StdEnv/2020 module is loaded on Graham, so the module system works as before. Later on, this needs to change, to be able to use this tool on various clusters. Signed-off-by: Kasra Keshavarz --- depth_to_bedrock/depth_to_bedrock.sh | 15 ++++++++------- gsde/gsde.sh | 19 ++++++++++--------- landsat/landsat.sh | 1 + merit_hydro/merit_hydro.sh | 15 ++++++++------- modis/modis.sh | 1 + soil_class/soil_class.sh | 25 +++++++++++++------------ soil_grids/soil_grids_v1.sh | 15 ++++++++------- 7 files changed, 49 insertions(+), 42 deletions(-) diff --git a/depth_to_bedrock/depth_to_bedrock.sh b/depth_to_bedrock/depth_to_bedrock.sh index 5efc1f3..da7a9d2 100755 --- a/depth_to_bedrock/depth_to_bedrock.sh +++ b/depth_to_bedrock/depth_to_bedrock.sh @@ -135,13 +135,14 @@ renvPackagePath="${renvCache}/renv_0.16.0.tar.gz" # renv_0.16.0 source path # =================== # Modules below available on Compute Canada (CC) Graham Cluster Server load_core_modules () { - module -q purge - module -q load gcc/9.3.0 - module -q load r/4.1.2 - module -q load gdal/3.0.4 - module -q load udunits/2.2.28 - module -q load geos/3.10.2 - module -q load proj/9.0.0 + module -q purge + module -q load StdEnv/2020 + module -q load gcc/9.3.0 + module -q load r/4.1.2 + module -q load gdal/3.0.4 + module -q load udunits/2.2.28 + module -q load geos/3.10.2 + module -q load proj/9.0.0 } load_core_modules diff --git a/gsde/gsde.sh b/gsde/gsde.sh index ea489cb..4ab1638 100755 --- a/gsde/gsde.sh +++ b/gsde/gsde.sh @@ -139,15 +139,16 @@ lonVar="lon" # =================== # Modules below available on Compute Canada (CC) Graham Cluster Server load_core_modules () { - module -q purge - module -q load gcc/9.3.0 - module -q load r/4.1.2 - module -q load gdal/3.0.4 - module -q load udunits/2.2.28 - module -q load geos/3.10.2 - module -q load proj/9.0.0 - module -q load nco/5.0.6 - module -q load netcdf/4.7.4 + module -q purge + module -q load StdEnv/2020 + module -q load gcc/9.3.0 + module -q load r/4.1.2 + module -q load gdal/3.0.4 + module -q load udunits/2.2.28 + module -q load geos/3.10.2 + module -q load proj/9.0.0 + module -q load nco/5.0.6 + module -q load netcdf/4.7.4 } load_core_modules diff --git a/landsat/landsat.sh b/landsat/landsat.sh index 4ff8120..07c469b 100755 --- a/landsat/landsat.sh +++ b/landsat/landsat.sh @@ -148,6 +148,7 @@ landcoverchangeFile="land_change_2010v2_2015v2_30m_tif.zip" # Modules below available on Compute Canada (CC) Graham Cluster Server load_core_modules () { module -q purge + module -q load StdEnv/2020 module -q load gcc/9.3.0 module -q load r/4.1.2 module -q load gdal/3.0.4 diff --git a/merit_hydro/merit_hydro.sh b/merit_hydro/merit_hydro.sh index 112c6f9..3f8b32f 100755 --- a/merit_hydro/merit_hydro.sh +++ b/merit_hydro/merit_hydro.sh @@ -133,13 +133,14 @@ renvPackagePath="${renvCache}/renv_0.16.0.tar.gz" # renv_0.16.0 source path # =================== # Modules below available on Compute Canada (CC) Graham Cluster Server load_core_modules () { - module -q purge - module -q load gcc/9.3.0 - module -q load r/4.1.2 - module -q load gdal/3.0.4 - module -q load udunits/2.2.28 - module -q load geos/3.10.2 - module -q load proj/9.0.0 + module -q purge + module -q load StdEnv/2020 + module -q load gcc/9.3.0 + module -q load r/4.1.2 + module -q load gdal/3.0.4 + module -q load udunits/2.2.28 + module -q load geos/3.10.2 + module -q load proj/9.0.0 } load_core_modules diff --git a/modis/modis.sh b/modis/modis.sh index 21c39f0..b222737 100755 --- a/modis/modis.sh +++ b/modis/modis.sh @@ -133,6 +133,7 @@ renvPackagePath="${renvCache}/renv_0.16.0.tar.gz" # renv_0.16.0 source path # Modules below available on Compute Canada (CC) Graham Cluster Server load_core_modules () { module -q purge + module -q load StdEnv/2020 module -q load gcc/9.3.0 module -q load r/4.1.2 module -q load gdal/3.0.4 diff --git a/soil_class/soil_class.sh b/soil_class/soil_class.sh index 1c217ec..0d410d3 100755 --- a/soil_class/soil_class.sh +++ b/soil_class/soil_class.sh @@ -67,7 +67,7 @@ do -i | --dataset-dir) geotiffDir="$2" ; shift 2 ;; # required -o | --output-dir) outputDir="$2" ; shift 2 ;; # required -v | --variable) variables="$2" ; shift 2 ;; # required - -r | --crs) crs="$2" ; shift 2 ;; # required + -r | --crs) crs="$2" ; shift 2 ;; # required -s | --start-date) startDate="$2" ; shift 2 ;; # redundant - added for compatibility -e | --end-date) endDate="$2" ; shift 2 ;; # redundant - added for compatibility -l | --lat-lims) latLims="$2" ; shift 2 ;; # required - could be redundant @@ -75,11 +75,11 @@ do -f | --shape-file) shapefile="$2" ; shift 2 ;; # required - could be redundant -F | --fid) fid="$2" ; shift 2 ;; # optional -t | --print-geotiff) printGeotiff="$2" ; shift 2 ;; # required - -a | --stat) stats="$2" ; shift 2 ;; # optional + -a | --stat) stats="$2" ; shift 2 ;; # optional -u | --include-na) includeNA="$2" ; shift 2 ;; # required - -q | --quantile) quantiles="$2" ; shift 2 ;; # optional - -p | --prefix) prefix="$2" ; shift 2 ;; # optional - -c | --cache) cache="$2" ; shift 2 ;; # required + -q | --quantile) quantiles="$2" ; shift 2 ;; # optional + -p | --prefix) prefix="$2" ; shift 2 ;; # optional + -c | --cache) cache="$2" ; shift 2 ;; # required -L | --lib-path) renvCache="$2" ; shift 2 ;; # required # -- means the end of the arguments; drop this, and break out of the while loop @@ -135,13 +135,14 @@ renvPackagePath="${renvCache}/renv_0.16.0.tar.gz" # renv_0.16.0 source path # =================== # Modules below available on Compute Canada (CC) Graham Cluster Server load_core_modules () { - module -q purge - module -q load gcc/9.3.0 - module -q load r/4.1.2 - module -q load gdal/3.0.4 - module -q load udunits/2.2.28 - module -q load geos/3.10.2 - module -q load proj/9.0.0 + module -q purge + module -q load StdEnv/2020 + module -q load gcc/9.3.0 + module -q load r/4.1.2 + module -q load gdal/3.0.4 + module -q load udunits/2.2.28 + module -q load geos/3.10.2 + module -q load proj/9.0.0 } load_core_modules diff --git a/soil_grids/soil_grids_v1.sh b/soil_grids/soil_grids_v1.sh index 0c3a0ae..0b77c07 100755 --- a/soil_grids/soil_grids_v1.sh +++ b/soil_grids/soil_grids_v1.sh @@ -135,13 +135,14 @@ renvPackagePath="${renvCache}/renv_0.16.0.tar.gz" # renv_0.16.0 source path # =================== # Modules below available on Compute Canada (CC) Graham Cluster Server load_core_modules () { - module -q purge - module -q load gcc/9.3.0 - module -q load r/4.1.2 - module -q load gdal/3.0.4 - module -q load udunits/2.2.28 - module -q load geos/3.10.2 - module -q load proj/9.0.0 + module -q purge + module -q load StdEnv/2020 + module -q load gcc/9.3.0 + module -q load r/4.1.2 + module -q load gdal/3.0.4 + module -q load udunits/2.2.28 + module -q load geos/3.10.2 + module -q load proj/9.0.0 } load_core_modules