Merge branch 'master' into JOSS

PIK-LPJmL · Sep 13, 2023 · 308286f · 308286f
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diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '2287233'
+ValidationKey: '2307608'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

diff --git a/CITATION.cff b/CITATION.cff
@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'lpjmlkit: Toolkit for Basic LPJmL Handling'
-version: 1.1.7
-date-released: '2023-07-11'
+version: 1.1.8
+date-released: '2023-07-18'
 abstract: A collection of basic functions to facilitate the work with the Dynamic
   Global Vegetation Model (DGVM) Lund-Potsdam-Jena managed Land (LPJmL) hosted at
   the Potsdam Institute for Climate Impact Research (PIK). It provides functions for

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: lpjmlkit
 Type: Package
 Title: Toolkit for Basic LPJmL Handling
-Version: 1.1.7
+Version: 1.1.8
 Authors@R: c(
     person("Jannes", "Breier", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9055-6904")),
     person("Sebastian","Ostberg", , "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-2368-7015")),
@@ -54,4 +54,4 @@ Suggests:
     sf
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Date: 2023-07-11
+Date: 2023-07-18
diff --git a/R/run_lpjml.R b/R/run_lpjml.R
@@ -312,19 +312,18 @@ do_sequential <- function(sim_names,
 
     # Check if slurm is available
     if (is_slurm_available() && Sys.getenv("SLURM_JOB_ID") == "") {
-      Sys.setenv(I_MPI_DAPL_UD = "disable", # nolint:undesirable_function_linter.
-                 I_MPI_FABRICS = "shm:shm",
-                 I_MPI_DAPL_FABRIC = "shm:sh")
+      mpi_var <- Sys.getenv("I_MPI_DAPL_UD_PROVIDER")
+      Sys.unsetenv("I_MPI_DAPL_UD_PROVIDER")# nolint:undesirable_function_linter.
+    } else {
+      mpi_var <- NULL
     }
     for (sim_name in sim_names) {
       do_run(sim_name, model_path, sim_path, write_stdout, raise_error)
     }
   }, finally = {
     # Check if slurm is available
-    if (is_slurm_available() && Sys.getenv("SLURM_JOB_ID") == "") {
-      Sys.setenv(I_MPI_DAPL_UD = "enable", # nolint:undesirable_function_linter.
-                 I_MPI_FABRICS = "shm:dapl")
-      Sys.unsetenv("I_MPI_DAPL_FABRIC")
+    if (!is.null(mpi_var)) {
+      Sys.setenv(I_MPI_DAPL_UD_PROVIDER = mpi_var) # nolint:undesirable_function_linter.
     }
   })
 }

diff --git a/R/submit_lpjml.R b/R/submit_lpjml.R
@@ -27,17 +27,32 @@
 #'   More information at <https://www.pik-potsdam.de/en>. Defaults to `"short"`.
 #'
 #' @param ntasks Integer defining the number of tasks/threads. More information
-#'   at <https://www.pik-potsdam.de/en> and <https://slurm.schedmd.com>.
-#'   Defaults to `256`.
+#'   at <https://www.pik-potsdam.de/en> and
+#'   <https://slurm.schedmd.com/sbatch.html>. Defaults to `256`.
 #'
 #' @param wtime Character string defining the time limit. Setting a lower time
 #'   limit than the maximum runtime for `sclass` can reduce the wait time in the
 #'   SLURM job queue. More information at <https://www.pik-potsdam.de/en> and
-#'   <https://slurm.schedmd.com>.
+#'   <https://slurm.schedmd.com/sbatch.html>.
 #'
 #' @param blocking Integer defining the number of cores to be blocked. More
 #'   information at <https://www.pik-potsdam.de/en> and
-#'   <https://slurm.schedmd.com>.
+#'   <https://slurm.schedmd.com/sbatch.html>.
+#'
+#' @param constraint Character string defining constraints for node selection.
+#'   Use `constraint = "haswell"` to request nodes of the type haswell with 16
+#'   cores per node, `constraint = "broadwell"` to request nodes of the type
+#'   broadwell CPUs with 32 cores per node or `constraint = "exclusive"` to
+#'   reserve all CPUs of assigned nodes even if less are requested by `ntasks`.
+#'   Using `exclusive` should prevent interference of other batch jobs with
+#'   LPJmL. More information at <https://www.pik-potsdam.de> and
+#'   <https://slurm.schedmd.com/sbatch.html>.
+
+#'
+#' @param slurm_options A named list of further arguments to be passed to sbatch.
+#'   E.g. list(`mail-user` = "[email protected]")
+#'   More information at <https://www.pik-potsdam.de> and
+#'   <https://slurm.schedmd.com/sbatch.html>
 #'
 #' @param no_submit Logical. Set to `TRUE` to test if `x` set correctly or
 #'   `FALSE` to actually submit job to SLURM.
@@ -67,11 +82,11 @@
 #' | scen2_transient | scen1 _spinup  |
 #'
 #' To use different SLURM settings for each run the optional SLURM options
-#' `"sclass"`, `"ntask"`, `"wtime"` or `"blocking"` can also be supplied to the
-#' initial \link[tibble]{tibble} supplied as `param` to
+#' `"sclass"`, `"ntasks"`, `"wtime"`, "blocking"` or `constraint` can also be
+#' supplied to the initial \link[tibble]{tibble} supplied as `param` to
 #' [`write_config()`]. These overwrite the (default) SLURM
-#' arguments (`sclass`, `ntask`, `wtime` or `blocking`) supplied to
-#' `submit_lpjml`.
+#' arguments (`sclass`, `ntasks`, `wtime`, `blocking` or ` `constraint`)
+#' supplied to `submit_lpjml`.
 #'
 #' | **sim_name**    | **dependency** | **wtime** |
 #' |:--------------- |:-------------- |----------:|
@@ -175,6 +190,8 @@ submit_lpjml <- function(x, # nolint:cyclocomp_linter.
                          ntasks = 256,
                          wtime = "",
                          blocking = "",
+                         constraint = "",
+                         slurm_options = list(),
                          no_submit = FALSE,
                          output_path = NULL) {
 
@@ -213,7 +230,9 @@ submit_lpjml <- function(x, # nolint:cyclocomp_linter.
   x$type <- "simulation"
   x$job_id <- NA
   x$status <- "failed"
-  slurm_args <- c("sclass", "ntask", "wtime", "blocking")
+  slurm_args <- c(
+    "sclass", "ntasks", "wtime", "blocking", "constraint", "slurm_options"
+  )
 
   if ("order" %in% colnames(x)) {
 
@@ -258,7 +277,9 @@ submit_lpjml <- function(x, # nolint:cyclocomp_linter.
                             ntasks,
                             wtime,
                             blocking,
-                            dependency)
+                            constraint,
+                            dependency,
+                            slurm_options)
 
           if (job$status == 0) {
             x$job_id[sim_idx] <- strsplit(
@@ -307,7 +328,9 @@ submit_lpjml <- function(x, # nolint:cyclocomp_linter.
                           ntasks,
                           wtime,
                           blocking,
-                          dependency = NA)
+                          constraint,
+                          dependency = NA,
+                          slurm_options)
 
         if (job$status == 0) {
           x$job_id[sim_idx] <- strsplit(
@@ -341,7 +364,9 @@ submit_run <- function(sim_name,
                        ntasks,
                        wtime,
                        blocking,
-                       dependency) {
+                       constraint,
+                       dependency,
+                       slurm_options) {
 
   config_file <- paste0("config_",
                         sim_name,
@@ -373,6 +398,14 @@ submit_run <- function(sim_name,
                   timestamp,
                   ".json")
 
+  if (is.list(slurm_options) && length(slurm_options) > 0) {
+    further_slurm_options <- paste0(
+      " -option ", names(slurm_options), "=", slurm_options, collapse = " "
+    )
+  } else {
+    further_slurm_options <- ""
+  }
+
   inner_command <-  paste0(model_path, "/bin/lpjsubmit", # nolint:absolute_path_linter.
                            " -nocheck",
                            " -class ", sclass,
@@ -383,9 +416,13 @@ submit_run <- function(sim_name,
                            ifelse(blocking != "",
                                   paste0(" -blocking ", blocking),
                                   ""),
+                           ifelse(constraint != "",
+                                  paste0(" -constraint ", constraint),
+                                  ""),
                            ifelse(!is.na(dependency),
                                   paste0(" -dependency ", dependency),
                                   ""),
+                           further_slurm_options,
                            " -o ", stdout,
                            " -e ", stderr,
                            " ",

diff --git a/R/write_config.R b/R/write_config.R
@@ -120,7 +120,8 @@
 #' (`wtime`) for the transient run than the spin-up run to get a higher priority
 #' in the SLURM queue. This can be achieved by supplying this option as a
 #' parameter to `param`. \cr
-#' 4 options are available, namely `sclass`, `ntask`, `wtime`, `blocking`. \cr
+#' 6 options are available, namely `sclass`, `ntasks`, `wtime`, `blocking`,
+#' `constraint` and `slurm_options`. Use as arguments for [submit_lpjml()`].\cr
 #' If specified in `param`, they overwrite the corresponding function arguments
 #' in [`submit_lpjml()`].
 #'
@@ -313,7 +314,9 @@ write_config <- function(x,
                                order = NA,
                                dependency = NA)
 
-  slurm_args <- c("sclass", "ntask", "wtime", "blocking")
+  slurm_args <- c(
+    "sclass", "ntasks", "wtime", "blocking", "constraint", "slurm_options"
+  )
 
   config_tmp[slurm_args] <- NA
 

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Toolkit for Basic LPJmL Handling <a href=''><img src='inst/img/logo.png' align='right' height='139' /></a>
 
-R package **lpjmlkit**, version **1.1.7**
+R package **lpjmlkit**, version **1.1.8**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/lpjmlkit)](https://cran.r-project.org/package=lpjmlkit) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7773134.svg)](https://doi.org/10.5281/zenodo.7773134) [![R build status](https://github.com/PIK-LPJmL/lpjmlkit/workflows/check/badge.svg)](https://github.com/PIK-LPJmL/lpjmlkit/actions) [![codecov](https://codecov.io/gh/PIK-LPJmL/lpjmlkit/branch/master/graph/badge.svg)](https://app.codecov.io/gh/PIK-LPJmL/lpjmlkit) [![r-universe](https://pik-piam.r-universe.dev/badges/lpjmlkit)](https://pik-piam.r-universe.dev/builds)
 
@@ -76,7 +76,7 @@ In case of questions / problems please contact Jannes Breier <jannesbr@pik-potsd
 
 To cite package **lpjmlkit** in publications use:
 
-Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Müller C (2023). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi: 10.5281/zenodo.7773134 (URL: https://doi.org/10.5281/zenodo.7773134), R package version 1.1.7, <URL: https://github.com/PIK-LPJmL/lpjmlkit>.
+Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Müller C (2023). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi: 10.5281/zenodo.7773134 (URL: https://doi.org/10.5281/zenodo.7773134), R package version 1.1.8, <URL: https://github.com/PIK-LPJmL/lpjmlkit>.
 
 A BibTeX entry for LaTeX users is
 
@@ -85,7 +85,7 @@ A BibTeX entry for LaTeX users is
   title = {lpjmlkit: Toolkit for Basic LPJmL Handling},
   author = {Jannes Breier and Sebastian Ostberg and Stephen Björn Wirth and Sara Minoli and Fabian Stenzel and Christoph Müller},
   year = {2023},
-  note = {R package version 1.1.7},
+  note = {R package version 1.1.8},
   doi = {10.5281/zenodo.7773134},
   url = {https://github.com/PIK-LPJmL/lpjmlkit},
 }

diff --git a/man/submit_lpjml.Rd b/man/submit_lpjml.Rd
diff --git a/man/write_config.Rd b/man/write_config.Rd
diff --git a/vignettes/lpjml-runner.Rmd b/vignettes/lpjml-runner.Rmd
@@ -262,7 +262,7 @@ params <- tibble(
   dependency = c(NA, "spinup", "spinup"),
   # slurm option wtime: analogous to sbatch -wtime defines slurm option
   #   individually per config, overwrites submit_lpjml argument
-  #   (same for sclass, ntasks, blocking)
+  #   (same for sclass, ntasks, blocking or constraint)
   wtime = c("15:00:00", "3:00:00", "3:00:00")
 )