Merge branch 'master_hpc2024' into 'master'

Master hpc2024 Closes #47 See merge request lpjml/lpjmlkit!98
PIK-LPJmL · Jun 17, 2024 · ee1e2a3 · ee1e2a3
2 parents a4c72de + 8bcb7b3
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diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '3177440'
+ValidationKey: '3381470'
 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: 1.6.0
-date-released: '2024-05-16'
+version: 1.7.0
+date-released: '2024-06-17'
 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: 1.6.0
+Version: 1.7.0
 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: 2024-05-16
+Date: 2024-06-17
diff --git a/R/run_lpjml.R b/R/run_lpjml.R
@@ -19,6 +19,10 @@
 #'   written, including output, restart and configuration files. If `NULL`,
 #'   `model_path` is used. See also [write_config]
 #'
+#' @param run_cmd Character string defining the command used to execute lpjml
+#'   (see details). Defaults to "srun --propagate" (compute ondes of old cluster
+#'   at PIK). Change to "mpirun" for HPC2024 at PIK.
+#'
 #' @param parallel_cores Integer defining the number of available CPU
 #'   cores/nodes for parallelization. Defaults to `1` (no parallelization).
 #'   Please note that parallelization is only supported for SLURM jobs and not
@@ -37,6 +41,8 @@
 #' @return See `x`, extended by columns `"type"`, `"job_id"` and `"status"`.
 #'
 #' @details
+#'
+#' \bold{x}:
 #' A \link[tibble]{tibble} for `x` that has been generated by
 #' [`write_config()`] and can look like the following examples can
 #' supplied:
@@ -62,6 +68,18 @@
 #' Also be aware that the order of the supplied config files is important
 #' (e.g. make sure the spin-up run is run before the transient one).
 #'
+#' \bold{run_cmd}:
+#' The `run_cmd` argument is used to define the command to execute LPJmL. This
+#' is needed because the LPJmL executable can not directly be used on all
+#' machines. Which command has to be used depends on the software installed.
+#' Further information on this can be found in the INSTALL file of LPJmL.
+#' To determine the correct command, check the lpj_submit.sh file in the bin
+#' directory of LPJmL. Using PIK infrastrucure the command is \code{srun} for
+#' the hpc2015 and \code{mpirun} for the hpc2024. To facilitate usage on the
+#' interactive (login) nodes, no command is needed for hpc2015. For the hpc2024
+#' the command remains \code{mpirun} (in these cases \code{run_lpjml} adjusts
+#' \code{run_cmd} accordingly).
+#'
 #' @examples
 #'
 #' \dontrun{
@@ -149,6 +167,7 @@
 run_lpjml <- function(x,
                       model_path = ".",
                       sim_path = NULL,
+                      run_cmd = "srun --propagate",
                       parallel_cores = 1,
                       write_stdout = FALSE,
                       raise_error = TRUE,
@@ -160,6 +179,10 @@ run_lpjml <- function(x,
   if (!dir.exists(model_path)) {
     stop("Folder of model_path \"", model_path, "\" does not exist.")
   }
+  # Check if run_cmd is valid
+  if (!grepl("mpirun|srun", run_cmd) && run_cmd != "") {
+    stop("Please provide a supported run command (\"mpirun\", \"srun\" or \"\")")
+  }
 
   sim_path <- deprecate_arg(new_arg = sim_path,
                             deprec_arg = output_path,
@@ -191,11 +214,11 @@ run_lpjml <- function(x,
 
       if (parallel_cores == 1) {
         do_sequential(
-          sim_names, model_path, sim_path, write_stdout, raise_error
+          sim_names, model_path, sim_path, run_cmd, write_stdout, raise_error
         )
       } else if (parallel_cores > 1 && Sys.getenv("SLURM_JOB_ID") != "") {
         do_parallel(
-          sim_names, model_path, sim_path, parallel_cores, raise_error
+          sim_names, model_path, sim_path, run_cmd, parallel_cores, raise_error
         )
       } else {
         stop(
@@ -209,11 +232,11 @@ run_lpjml <- function(x,
   } else {
     if (parallel_cores == 1) {
       do_sequential(
-        x$sim_name, model_path, sim_path, write_stdout, raise_error
+        x$sim_name, model_path, sim_path, run_cmd, write_stdout, raise_error
       )
     } else if (parallel_cores > 1 && Sys.getenv("SLURM_JOB_ID") != "") {
       do_parallel(
-        x$sim_name, model_path, sim_path, parallel_cores, raise_error
+        x$sim_name, model_path, sim_path, run_cmd, parallel_cores, raise_error
       )
     } else {
       stop(
@@ -233,6 +256,7 @@ run_lpjml <- function(x,
 do_run <- function(sim_name,
                    model_path,
                    sim_path,
+                   run_cmd,
                    write_stdout,
                    raise_error) {
 
@@ -248,8 +272,8 @@ do_run <- function(sim_name,
 
   # When running inside a slurm job it ensures to propagate ressources
   inner_command <-  paste0(ifelse(Sys.getenv("SLURM_JOB_ID") == "",
-                                  "",
-                                  "srun --propagate "),
+                                  ifelse(grepl("mpirun", run_cmd), run_cmd, ""),
+                                  run_cmd),
                            model_path,
                            "/bin/lpjml ", # nolint:absolute_path_linter.
                            sim_path,
@@ -289,9 +313,9 @@ do_run <- function(sim_name,
                 echo = !testthat::is_testing(),
                 cleanup_tree = TRUE,
                 spinner = ifelse(write_stdout &&
-                                 Sys.getenv("SLURM_JOB_ID") == "",
-                                            TRUE,
-                                            FALSE),
+                                   Sys.getenv("SLURM_JOB_ID") == "",
+                                 TRUE,
+                                 FALSE),
                 error_on_status = raise_error,
                 wd = sim_path)
 }
@@ -302,6 +326,7 @@ do_run <- function(sim_name,
 do_sequential <- function(sim_names,
                           model_path,
                           sim_path,
+                          run_cmd,
                           write_stdout,
                           raise_error) {
 
@@ -311,14 +336,19 @@ do_sequential <- function(sim_names,
   tryCatch({
 
     # Check if slurm is available
-    if (is_slurm_available() && Sys.getenv("SLURM_JOB_ID") == "") {
+    if (is_slurm_available() && Sys.getenv("SLURM_JOB_ID") == "" && !grepl("mpirun", run_cmd)) {
       mpi_var <- Sys.getenv("I_MPI_DAPL_UD_PROVIDER")
       Sys.unsetenv("I_MPI_DAPL_UD_PROVIDER")# nolint:undesirable_function_linter.
     } else {
       mpi_var <- NULL
+      # If not specified by the user set number of processes to 1 to run lpjml
+      #  in interactive mode
+      if (run_cmd == "mpirun") {
+        run_cmd <- paste0(run_cmd, " -np 1 ")
+      }
     }
     for (sim_name in sim_names) {
-      do_run(sim_name, model_path, sim_path, write_stdout, raise_error)
+      do_run(sim_name, model_path, sim_path, run_cmd, write_stdout, raise_error)
     }
   }, finally = {
     # Check if slurm is available
@@ -333,6 +363,7 @@ do_sequential <- function(sim_names,
 do_parallel <- function(sim_names,
                         model_path,
                         sim_path,
+                        run_cmd,
                         parallel_cores,
                         raise_error) {
 
@@ -346,16 +377,23 @@ do_parallel <- function(sim_names,
 
   # Parallel foreach sim_name.
   job_details <- foreach::foreach(sim_name = sim_names, # nolint:object_usage_linter.
-                                  .errorhandling = "stop"
+    .errorhandling = "stop"
   ) %dopar% {
 
     # Write single call
     tryCatch({
+
+      if (is_slurm_available() && Sys.getenv("SLURM_JOB_ID") != "") {
+        mpi_lib <- Sys.getenv("I_MPI_PMI_LIBRARY")
+        Sys.setenv(I_MPI_PMI_LIBRARY = "/p/system/slurm/lib/libpmi.so") # nolint
+      } else {
+        mpi_lib <- NULL
+      }
       do_run(
-        sim_name, model_path, sim_path, write_stdout = TRUE, raise_error
+        sim_name, model_path, sim_path, run_cmd, write_stdout = TRUE, raise_error
       )
 
-    # Stop when error occures
+      # Stop when error occures
     }, error = function(e) {
 
       # Check if error is returned
@@ -379,6 +417,10 @@ do_parallel <- function(sim_names,
           " parallelization"
         )
       }
+    }, finally = {
+      if (!is.null(mpi_lib)) {
+        Sys.setenv(I_MPI_PMI_LIBRARY = mpi_lib) # nolint:undesirable_function_linter.
+      }
     })
   }
 

diff --git a/R/submit_lpjml.R b/R/submit_lpjml.R
@@ -20,7 +20,7 @@
 #'   `model_path` is used. See also [write_config]
 #'
 #' @param group Character string defining the user group for which the job is
-#'   submitted. Defaults to `"lpjml"`.
+#'   submitted.
 #'
 #' @param sclass Character string defining the job classification. Available
 #'   options at PIK: `c("short", "medium", "long", "priority", "standby", "io")`
@@ -185,7 +185,7 @@
 submit_lpjml <- function(x, # nolint:cyclocomp_linter.
                          model_path,
                          sim_path = NULL,
-                         group = "lpjml",
+                         group = "",
                          sclass = "short",
                          ntasks = 256,
                          wtime = "",
@@ -254,7 +254,7 @@ submit_lpjml <- function(x, # nolint:cyclocomp_linter.
         # to this function by mapply call
         slurm_param <- (
           x[slurm_args[slurm_args %in% colnames(x)]][
-              sim_idx, ]
+                                                     sim_idx, ]
         )
 
         mapply( # nolint:undesirable_function_linter.
@@ -306,7 +306,7 @@ submit_lpjml <- function(x, # nolint:cyclocomp_linter.
       # this function by mapply call
       slurm_param <- (
         x[slurm_args[slurm_args %in% colnames(x)]][
-            sim_idx, ]
+                                                   sim_idx, ]
       )
 
       mapply( # nolint:undesirable_function_linter.
@@ -375,28 +375,28 @@ submit_run <- function(sim_name,
   timestamp <- format(Sys.time(), "%Y%m%d_%H%M")
 
   stdout <- paste0(sim_path,
-                  "/output/",
-                  sim_name,
-                  "/",
-                  "outfile_",
-                  timestamp,
-                  ".out")
+                   "/output/",
+                   sim_name,
+                   "/",
+                   "outfile_",
+                   timestamp,
+                   ".out")
 
   stderr <- paste0(sim_path,
-                  "/output/",
-                  sim_name,
-                  "/",
-                  "errfile_",
-                  timestamp,
-                  ".err")
+                   "/output/",
+                   sim_name,
+                   "/",
+                   "errfile_",
+                   timestamp,
+                   ".err")
 
   output_config <- paste0(sim_path,
-                  "/output/",
-                  sim_name,
-                  "/",
-                  "config_",
-                  timestamp,
-                  ".json")
+                          "/output/",
+                          sim_name,
+                          "/",
+                          "config_",
+                          timestamp,
+                          ".json")
 
   if (is.list(slurm_options) && length(slurm_options) > 0) {
     further_slurm_options <- paste0(
@@ -409,7 +409,9 @@ submit_run <- function(sim_name,
   inner_command <-  paste0(model_path, "/bin/lpjsubmit", # nolint:absolute_path_linter.
                            " -nocheck",
                            " -class ", sclass,
-                           " -group ", group,
+                           ifelse(group != "",
+                                  paste0(" -group ", group),
+                                  ""),
                            ifelse(wtime != "",
                                   paste0(" -wtime ", wtime),
                                   ""),

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 **1.6.0**
+R package **lpjmlkit**, version **1.7.0**
 
 [![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 (2024). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi: 10.5281/zenodo.7773134 (URL: https://doi.org/10.5281/zenodo.7773134), R package version 1.6.0, <URL: https://github.com/PIK-LPJmL/lpjmlkit>.
+Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Müller C (2024). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi: 10.5281/zenodo.7773134 (URL: https://doi.org/10.5281/zenodo.7773134), R package version 1.7.0, <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 = {2024},
-  note = {R package version 1.6.0},
+  note = {R package version 1.7.0},
   doi = {10.5281/zenodo.7773134},
   url = {https://github.com/PIK-LPJmL/lpjmlkit},
 }

diff --git a/man/run_lpjml.Rd b/man/run_lpjml.Rd