Merge branch 'magpiemodel:develop' into develop

magpiemodel · Aug 9, 2024 · e611cc7 · e611cc7
2 parents 141cc01 + e38329e
commit e611cc7
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Showing 24 changed files with 25 additions and 26 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **script** scripts/start_functions.R decide individually for demand and price whether they are read from a REMIND report.
 - **80_optimization** abort GAMS in case of execution errors
 - **script** updated EATLancet project start scripts
+- **script** replaced gdx package with gdx2 package calls
 
 ### added
 - **scripts** added output report `EU_report.R` that uses `EU_report.Rmd`

diff --git a/scripts/calibration/calc_calib.R b/scripts/calibration/calc_calib.R
@@ -39,7 +39,7 @@ calibration_run <- function(putfolder, calib_magpie_name, logoption = 3) {
 get_areacalib <- function(gdx_file) {
   require(magclass)
   require(magpie4)
-  require(gdx)
+  require(gdx2)
   data <- readGDX(gdx_file, "pm_land_start")[, , c("crop", "past")]
   data <- dimSums(data, dim = 1.2)
   magpie <- land(gdx_file)[, , c("crop", "past")]
@@ -54,7 +54,7 @@ get_areacalib <- function(gdx_file) {
 
 get_yieldcalib <- function(gdx_file) {
   require(magclass)
-  require(gdx)
+  require(gdx2)
   require(luscale)
 
   prep <- function(x) {
@@ -81,6 +81,7 @@ update_calib <- function(gdx_file, calib_accuracy = 0.1, calibrate_pasture = TRU
                          n_maxcalib = 20, best_calib = FALSE) {
   require(magclass)
   require(magpie4)
+  require(gdx2)
   if (!(modelstat(gdx_file)[1, 1, 1] %in% c(1, 2, 7))) stop("Calibration run infeasible")
 
   area_factor  <- get_areacalib(gdx_file)

diff --git a/scripts/calibration/landconversion_cost.R b/scripts/calibration/landconversion_cost.R
@@ -38,7 +38,7 @@ calibration_run <- function(putfolder, calib_magpie_name, logoption = 3, s_use_g
 getCalibFactor <- function(gdx_file, mode = "cost", calib_accuracy = 0.05, lowpass_filter = 1) {
   require(magclass)
   require(magpie4)
-  require(gdx)
+  require(gdx2)
   y <- readGDX(gdx_file,"t")
   magpie <- land(gdx_file)[, y, "crop"]
   hist <- dimSums(readGDX(gdx_file, "f10_land")[, , "crop"], dim = 1.2)
@@ -94,6 +94,7 @@ getHistCrop <- function() {
 update_calib <- function(gdx_file, calib_accuracy = 0.05, lowpass_filter = 1, calib_file, cost_max = 3, cost_min = 0.05, calibration_step = "", n_maxcalib = 40, best_calib = FALSE) {
   require(magclass)
   require(magpie4)
+  require(gdx2)
   if (!(modelstat(gdx_file)[1, 1, 1] %in% c(1, 2, 7))) stop("Calibration run infeasible")
 
   y <- readGDX(gdx_file,"t")

diff --git a/scripts/output/extra/disaggregation.R b/scripts/output/extra/disaggregation.R
@@ -16,6 +16,7 @@ library(luscale)
 library(madrat)
 library(dplyr)
 library(gms)
+library(gdx2)
 
 # =============================================
 # Basic configuration

diff --git a/scripts/output/extra/highres.R b/scripts/output/extra/highres.R
@@ -13,7 +13,7 @@
 # Author: Florian Humpenoeder
 
 library(magclass)
-library(gdx)
+library(gdx2)
 library(magpie4)
 library(lucode2)
 library(gms)

diff --git a/scripts/output/extra/out_of_bounds_check.R b/scripts/output/extra/out_of_bounds_check.R
@@ -15,7 +15,7 @@
 #########################
 # Version 1.0, Florian Humpenoeder
 #
-library(gdx)
+library(gdx2)
 library(lucode2)
 library(magclass)
 

diff --git a/scripts/output/extra/reportMAgPIE2SEALS.R b/scripts/output/extra/reportMAgPIE2SEALS.R
@@ -14,7 +14,7 @@
 # 1.00: first working version
 
 library(gms)
-library(gdx)
+library(gdx2)
 library(magpie4)
 
 message("Starting to report gridded MAgPIE land use for SEALS")

diff --git a/scripts/output/projects/FSDP_collect.R b/scripts/output/projects/FSDP_collect.R
@@ -17,7 +17,7 @@ library(magclass)
 library(gms)
 library(magpiesets)
 library(data.table)
-library(gdx)
+library(gdx2)
 library(quitte)
 library(m4fsdp)
 library(stringr)

diff --git a/scripts/output/projects/FSDP_collect2.R b/scripts/output/projects/FSDP_collect2.R
@@ -17,7 +17,7 @@ library(magclass)
 library(gms)
 library(magpiesets)
 library(data.table)
-library(gdx)
+library(gdx2)
 library(quitte)
 library(m4fsdp)
 library(stringr)

diff --git a/scripts/output/projects/peatland.R b/scripts/output/projects/peatland.R
@@ -18,7 +18,7 @@
 library(lucode2)
 library(magpie4)
 library(luscale)
-
+library(gdx2)
 library(luplot)
 library(ggplot2)
 library(luscale)

diff --git a/scripts/output/validation_cell.R b/scripts/output/validation_cell.R
@@ -15,6 +15,7 @@ library(luscale)
 library(luplot)
 library(lusweave)
 library(magpiesets)
+library(gdx2)
 
 ############################# BASIC CONFIGURATION ##############################
 if (!file.exists(paste0(outputdir, "/LUH2_croparea_0.5.mz"))) stop("Cell validation is not possible. LUH2_croparea_0.5.mz and MAPSPAM_croparea_0.5.mz files are missing")

diff --git a/scripts/run_submit/submit_priority.sh b/scripts/run_submit/submit_priority.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 
 #SBATCH --qos=priority
-#SBATCH --partition=priority
 #SBATCH --job-name=mag-run
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL

diff --git a/scripts/run_submit/submit_priority_maxMem.sh b/scripts/run_submit/submit_priority_maxMem.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 
 #SBATCH --qos=priority
-#SBATCH --partition=priority
 #SBATCH --job-name=mag-run
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL

diff --git a/scripts/run_submit/submit_standby.sh b/scripts/run_submit/submit_standby.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 
 #SBATCH --qos=standby
-#SBATCH --partition=priority
 #SBATCH --job-name=mag-run
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL

diff --git a/scripts/run_submit/submit_standby_dayMax.sh b/scripts/run_submit/submit_standby_dayMax.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 
 #SBATCH --qos=standby
-#SBATCH --partition=priority
 #SBATCH --job-name=mag-run
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL

diff --git a/scripts/run_submit/submit_standby_maxMem.sh b/scripts/run_submit/submit_standby_maxMem.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 
 #SBATCH --qos=standby
-#SBATCH --partition=priority
 #SBATCH --job-name=mag-run
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL

diff --git a/scripts/run_submit/submit_standby_maxMem_dayMax.sh b/scripts/run_submit/submit_standby_maxMem_dayMax.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 
 #SBATCH --qos=standby
-#SBATCH --partition=priority
 #SBATCH --job-name=mag-run
 #SBATCH --output=slurm.log
 #SBATCH --mail-type=END,FAIL

diff --git a/scripts/slurmOutput.yml b/scripts/slurmOutput.yml
@@ -1,5 +1,5 @@
 slurmjobs:
-  SLURM standby: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=standby --partition=priority --time=24:00:00"
-  SLURM standby maxMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=standby --partition=priority --time=24:00:00 --mem-per-cpu=0 --cpus-per-task=16"
-  SLURM priority: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=priority --partition=priority"
-  SLURM priority maxMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=priority --partition=priority --mem-per-cpu=0 --cpus-per-task=16"
+  SLURM standby: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=standby --time=24:00:00"
+  SLURM standby maxMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=standby --time=24:00:00 --mem-per-cpu=0 --cpus-per-task=16"
+  SLURM priority: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=priority"
+  SLURM priority maxMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --mem-per-cpu=8000 --wrap=\"Rscript %SCRIPT\" --qos=priority --mem-per-cpu=0 --cpus-per-task=16"
diff --git a/scripts/slurmStart.yml b/scripts/slurmStart.yml
@@ -1,4 +1,4 @@
 slurmjobs:
-  SLURM priority: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=priority --partition=priority --cpus-per-task=3"
-  SLURM standby: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=standby --partition=priority --cpus-per-task=3"
+  SLURM priority: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=priority --cpus-per-task=3"
+  SLURM standby: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=standby --cpus-per-task=3"
   SLURM medium: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=medium --cpus-per-task=3"
diff --git a/scripts/start/extra/input_REMIND.R b/scripts/start/extra/input_REMIND.R
@@ -12,7 +12,7 @@
 
 library(gms)
 library(magclass)
-library(gdx)
+library(gdx2)
 
 # Load start_run(cfg) function which is needed to start MAgPIE runs
 source("scripts/start_functions.R")

diff --git a/scripts/start/projects/paper_peatland.R b/scripts/start/projects/paper_peatland.R
@@ -12,7 +12,7 @@
 
 library(gms)
 library(magclass)
-library(gdx)
+library(gdx2)
 library(luscale)
 library(magpie4)
 

diff --git a/scripts/start/projects/project_ABCDR.R b/scripts/start/projects/project_ABCDR.R
@@ -7,7 +7,7 @@
 library(lucode2)
 library(gms)
 library(magclass)
-library(gdx)
+library(gdx2)
 
 # Load start_run(cfg) function which is needed to start MAgPIE runs
 source("scripts/start_functions.R")

diff --git a/scripts/start/projects/project_BEST.R b/scripts/start/projects/project_BEST.R
@@ -17,7 +17,7 @@ version <- "V13"
 
 library(lucode2)
 library(magclass)
-library(gdx)
+library(gdx2)
 library(magpie4)
 library(gms)
 

diff --git a/scripts/start/projects/project_LAMACLIMA_WP4.R b/scripts/start/projects/project_LAMACLIMA_WP4.R
@@ -16,7 +16,7 @@
 
 library(gms)
 library(magclass)
-library(gdx)
+library(gdx2)
 
 # Load start_run(cfg) function which is needed to start MAgPIE runs
 source("scripts/start_functions.R")