Merge branch 'hotfix_run_lpjml_parallel' into 'master'

FIxed issue with parallelization of runs

See merge request lpjml/lpjmlkit!111

Author: stephnwirth

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '34827570'
+ValidationKey: '34863336'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

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: 1.7.10
-date-released: '2025-10-06'
+version: 1.7.11
+date-released: '2025-10-15'
 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

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: lpjmlkit
 Type: Package
 Title: Toolkit for Basic LPJmL Handling
-Version: 1.7.10
+Version: 1.7.11
 Authors@R: c(
     person("Jannes", "Breier", , "jannesbr@pik-potsdam.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9055-6904")),
     person("Sebastian","Ostberg", , "ostberg@pik-potsdam.de", role = "aut", comment = c(ORCID = "0000-0002-2368-7015")),
@@ -56,4 +56,4 @@ Suggests:
     R6
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Date: 2025-10-06
+Date: 2025-10-15

R/run_lpjml.R

@@ -400,14 +400,15 @@ do_parallel <- function(sim_names,
     # Write single call
     tryCatch({
 
-      if (is_slurm_available() && Sys.getenv("SLURM_JOB_ID") != "") {
+      if (is_slurm_available() && Sys.getenv("SLURM_JOB_ID") != "" && !grepl("mpirun", run_cmd)) {
         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, run_cmd, write_stdout = TRUE, raise_error
+        sim_name, model_path, sim_path, run_cmd, write_stdout = TRUE,
+        raise_error, debug = FALSE
       )
 
       # Stop when error occures

README.md

@@ -1,6 +1,6 @@
 # <a href=''><img src='inst/img/logo.png' align='right' alt='logo' height=139 /></a> Toolkit for Basic LPJmL Handling
 
-R package **lpjmlkit**, version **1.7.10**
+R package **lpjmlkit**, version **1.7.11**
 
 [![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, Hötten D, Müller C (2025). "lpjmlkit: Toolkit for Basic LPJmL Handling." doi:10.5281/zenodo.7773134 <https://doi.org/10.5281/zenodo.7773134>, Version: 1.7.10, <https://github.com/PIK-LPJmL/lpjmlkit>.
+Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Hötten D, Müller C (2025). "lpjmlkit: Toolkit for Basic LPJmL Handling." doi:10.5281/zenodo.7773134 <https://doi.org/10.5281/zenodo.7773134>, Version: 1.7.11, <https://github.com/PIK-LPJmL/lpjmlkit>.
 
 A BibTeX entry for LaTeX users is
 
@@ -85,9 +85,9 @@ 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 David Hötten and Christoph Müller},
   doi = {10.5281/zenodo.7773134},
-  date = {2025-10-06},
+  date = {2025-10-15},
   year = {2025},
   url = {https://github.com/PIK-LPJmL/lpjmlkit},
-  note = {Version: 1.7.10},
+  note = {Version: 1.7.11},
 }
 ```