Merge branch 'master' into master

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -69,7 +69,6 @@ Suggests:
     rmarkdown,
     ggplot2,
     knitr,
-    sensitivity,
-    cowplot
+    sensitivity
 VignetteBuilder: knitr
 Encoding: UTF-8

R/run_biomee_f_bysite.R

@@ -500,7 +500,7 @@ run_biomee_f_bysite <- function(
   if (continue) {
 
     ## C wrapper call
-    lm3out <- .Call(
+    biomeeout <- .Call(
 
       'biomee_f_C',
 
@@ -569,14 +569,14 @@ run_biomee_f_bysite <- function(
       )
 
     # If simulation is very long, output gets massive.
-    # E.g., In a 3000 years-simulation 'lm3out' is 11.5 GB.
+    # E.g., In a 3000 years-simulation 'biomeeout' is 11.5 GB.
     # In such cases (here, more than 5 GB), ignore hourly and daily outputs at tile and cohort levels
     size_of_object_gb <- as.numeric(
       gsub(
         pattern = " Gb",
         replacement = "",
         format(
-          utils::object.size(lm3out), 
+          utils::object.size(biomeeout), 
           units = "GB"
           )
         )
@@ -587,28 +587,28 @@ run_biomee_f_bysite <- function(
         sprintf("Warning: Excessive size of output object (%s) for %s. 
                 Hourly and daily outputs at tile and cohort levels are not returned.",
                 format(
-                  utils::object.size(lm3out), 
+                  utils::object.size(biomeeout), 
                   units = "GB"
                 ), 
                 sitename))
     }
 
     #---- Single level output, one matrix ----
-    # hourly
-    if (size_of_object_gb < 5){
-      output_hourly_tile <- as.data.frame(lm3out[[1]], stringAsFactor = FALSE)
-      colnames(output_hourly_tile) <- c("year", "doy", "hour",
-                                        "rad", "Tair", "Prcp",
-                                        "GPP", "Resp", "Transp",
-                                        "Evap", "Runoff", "Soilwater",
-                                        "wcl", "FLDCAP", "WILTPT")
-    } else {
-      output_hourly_tile <- NA
-    }
+    # # hourly
+    # if (size_of_object_gb < 5){
+    #   output_hourly_tile <- as.data.frame(biomeeout[[1]], stringAsFactor = FALSE)
+    #   colnames(output_hourly_tile) <- c("year", "doy", "hour",
+    #                                     "rad", "Tair", "Prcp",
+    #                                     "GPP", "Resp", "Transp",
+    #                                     "Evap", "Runoff", "Soilwater",
+    #                                     "wcl", "FLDCAP", "WILTPT")
+    # } else {
+    #   output_hourly_tile <- NA
+    # }
 
     # daily_tile
     if (size_of_object_gb < 5){
-      output_daily_tile <- as.data.frame(lm3out[[2]], stringAsFactor = FALSE)
+      output_daily_tile <- as.data.frame(biomeeout[[1]], stringAsFactor = FALSE)
       colnames(output_daily_tile) <- c(
         "year", "doy", "Tc",
         "Prcp", "totWs", "Trsp",
@@ -627,7 +627,7 @@ run_biomee_f_bysite <- function(
     }
 
     # annual tile
-    output_annual_tile <- as.data.frame(lm3out[[30]], stringAsFactor = FALSE)
+    output_annual_tile <- as.data.frame(biomeeout[[29]], stringAsFactor = FALSE)
     colnames(output_annual_tile) <- c("year", "CAI", "LAI",
           "Density", "DBH", "Density12",
           "DBH12", "QMD", "NPP",
@@ -674,17 +674,17 @@ run_biomee_f_bysite <- function(
         "SW_N", "HW_N"
       )
       output_daily_cohorts <- lapply(1:length(daily_values), function(x){
-        loc <- 2 + x
+        loc <- 1 + x
         v <- data.frame(
-          as.vector(lm3out[[loc]]),
+          as.vector(biomeeout[[loc]]),
           stringsAsFactors = FALSE)
         names(v) <- daily_values[x]
         return(v)
       })
 
       output_daily_cohorts <- do.call("cbind", output_daily_cohorts)
 
-      cohort <- sort(rep(1:ncol(lm3out[[3]]),nrow(lm3out[[3]])))
+      cohort <- sort(rep(1:ncol(biomeeout[[3]]),nrow(biomeeout[[3]])))
       output_daily_cohorts <- cbind(cohort, output_daily_cohorts)
 
       # drop rows (cohorts) with no values
@@ -711,9 +711,9 @@ run_biomee_f_bysite <- function(
     )
 
     output_annual_cohorts <- lapply(1:length(annual_values), function(x){
-      loc <- 30 + x
+      loc <- 29 + x
       v <- data.frame(
-        as.vector(lm3out[[loc]]),
+        as.vector(biomeeout[[loc]]),
         stringsAsFactors = FALSE)
       names(v) <- annual_values[x]
       return(v)
@@ -733,7 +733,7 @@ run_biomee_f_bysite <- function(
 
     # format the output in a structured list
     out <- list(
-      output_hourly_tile = output_hourly_tile,
+      # output_hourly_tile = output_hourly_tile,
       output_daily_tile = output_daily_tile,
       output_daily_cohorts = output_daily_cohorts,
       output_annual_tile = output_annual_tile,

README.md

@@ -119,4 +119,5 @@ Weng, E. S., Malyshev, S., Lichstein, J. W., Farrior, C. E., Dybzinski, R., Zhan
 
 ## Acknowledgements
 
-The {rsofun} is part of the LEMONTREE project and funded by Schmidt Futures and under the umbrella of the Virtual Earth System Research Institute (VESRI).
+The {rsofun} is part of the LEMONTREE project and funded by Schmidt Futures and under the umbrella of the Virtual Earth System Research Institute (VESRI). 
+

src/Makevars.in

@@ -1,6 +1,13 @@
 # PKG_FFLAGS = -ffree-line-length-0 -fbacktrace -ffpe-trap=invalid,zero,overflow -O1 -Wall -Wextra -pedantic -fbacktrace -fPIC -fmax-errors=1 -ggdb -fcheck=all
 # PKG_FFLAGS = -fbounds-check
 
+# Add package flags:
+# -frecursive: to avoid "Warning: Array 'out_biosphere' at (1) is larger than limit ..."
+# -fbounds-check: https://scicomp.stackexchange.com/questions/36045/ifort-everithing-ok-but-with-gfortran-segmentation-fault
+# -Wall -Wextra -Wpedantic: to get more warnings
+# -fsanitize=address: Using the Address Sanitizer https://rstudio.github.io/r-manuals/r-exts/Debugging.html#using-the-address-sanitizer
+# PKG_FFLAGS = -frecursive -fbounds-check -Wall -Wextra -Wpedantic -g -O0 -fsanitize=address
+
 # C objects
 C_OBJS = wrappersc.o
 

src/biosphere_biomee.mod.f90

@@ -33,13 +33,13 @@ subroutine biosphere_annual(out_biosphere)
     ! ! local variables
     integer :: dm, moy, doy
     logical, save :: init = .true.   ! is true only on the first day of the simulation 
-    logical, parameter :: verbose = .false.       ! change by hand for debugging etc.
+    ! logical, parameter :: verbose = .false.       ! change by hand for debugging etc.
 
     !----------------------------------------------------------------
     ! Biome-E stuff
     !----------------------------------------------------------------
-    integer, parameter :: rand_seed = 86456
-    integer, parameter :: totalyears = 10
+    ! integer, parameter :: rand_seed = 86456
+    ! integer, parameter :: totalyears = 10
     integer, parameter :: nCohorts = 1
     real    :: tsoil, soil_theta
     integer :: year0
@@ -119,7 +119,7 @@ subroutine biosphere_annual(out_biosphere)
           !----------------------------------------------------------------
           call vegn_CNW_budget( vegn, myinterface%climate(idata), init )
 
-          call hourly_diagnostics( vegn, myinterface%climate(idata), iyears, idoy, i , out_biosphere%hourly_tile(idata))
+          call hourly_diagnostics( vegn, myinterface%climate(idata) )  !, iyears, idoy, i, out_biosphere%hourly_tile(idata)
 
           init = .false.
 
@@ -205,6 +205,12 @@ subroutine biosphere_annual(out_biosphere)
 
     !if (iyears == 700 .or. iyears == 800) &
     !     call reset_vegn_initial(vegn) 
+
+    if (myinterface%steering%finalize) then
+      !----------------------------------------------------------------
+      ! Finazlize run: deallocating memory
+      !----------------------------------------------------------------
+      deallocate( vegn )
 
     if(myinterface%params_siml%do_reset_veg) then
 

src/biosphere_pmodel.mod.f90

@@ -10,7 +10,7 @@ module md_biosphere_pmodel
   use md_gpp_pmodel, only: getpar_modl_gpp, gpp
   use md_vegdynamics_pmodel, only: vegdynamics
   use md_tile_pmodel, only: tile_type, tile_fluxes_type, initglobal_tile, initdaily_tile_fluxes, &
-    getpar_modl_tile, diag_daily, diag_annual, init_annual
+    getpar_modl_tile, diag_daily !, init_annual
   use md_plant_pmodel, only: getpar_modl_plant
   use md_sofunutils, only: calc_patm
   use md_soiltemp, only: soiltemp
@@ -41,7 +41,7 @@ function biosphere_annual() result( out_biosphere )
     ! local variables
     integer :: dm, moy, doy
     logical, save           :: init_daily            ! is true only on the first day of the simulation 
-    logical, parameter      :: verbose = .false.     ! change by hand for debugging etc.
+    ! logical, parameter      :: verbose = .false.     ! change by hand for debugging etc.
 
     !----------------------------------------------------------------
     ! INITIALISATIONS
@@ -71,10 +71,10 @@ function biosphere_annual() result( out_biosphere )
 
     endif 
 
-    !----------------------------------------------------------------
-    ! Set annual sums to zero
-    !----------------------------------------------------------------
-    call init_annual( tile_fluxes(:) )
+    ! !----------------------------------------------------------------
+    ! ! Set annual sums to zero
+    ! !----------------------------------------------------------------
+    ! call init_annual( tile_fluxes(:) )
 
     !----------------------------------------------------------------
     ! LOOP THROUGH MONTHS
@@ -111,8 +111,8 @@ function biosphere_annual() result( out_biosphere )
         call solar( tile_fluxes(:), &
                     myinterface%grid, & 
                     myinterface%climate(doy),  &
-                    doy, &
-                    myinterface%params_siml%in_netrad &
+                    doy &
+                    ! myinterface%params_siml%in_netrad &
                     )
         ! if (verbose) print*,'... done'
 
@@ -135,12 +135,10 @@ function biosphere_annual() result( out_biosphere )
                   tile_fluxes(:), &
                   myinterface%pco2, &
                   myinterface%climate(doy), &
-                  myinterface%vegcover(doy), &
                   myinterface%grid, &
                   init_daily, &
                   myinterface%params_siml%in_ppfd &
                   )
-
         ! if (verbose) print*,'... done'
 
         !----------------------------------------------------------------
@@ -202,12 +200,11 @@ function biosphere_annual() result( out_biosphere )
 
     end do monthloop
 
-    !----------------------------------------------------------------
-    ! annual diagnostics
-    !----------------------------------------------------------------
-    call diag_annual( tile(:), tile_fluxes(:) )
+    ! !----------------------------------------------------------------
+    ! ! annual diagnostics
+    ! !----------------------------------------------------------------
+    ! call diag_annual( tile(:), tile_fluxes(:) )
 
-
     ! if (verbose) print*,'Done with biosphere for this year. Guete Rutsch!'
 
   end function biosphere_annual