Skip to content

Fix output error status in slurm email using apptainer #2497

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
simonkrogmann merged 1 commit into from
Oct 18, 2026
+5 −5
Merged

Fix output error status in slurm email using apptainer #2497

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -141,7 +141,7 @@ test-full: ## Run all tests, including coupling tests and a default
test-full-slurm: ##test-full, but on slurm
$(info Full tests take more than an hour to run, please be patient)
make ensure-reqs
@sbatch --qos=priority --wrap="$(RSCRIPT_SLURM_HOOK) make test-full" --job-name=test-full --mail-type=END,FAIL --output=test-full.log --comment="test-full.log"
@sbatch --qos=priority --wrap="set -e; $(RSCRIPT_SLURM_HOOK) make test-full" --job-name=test-full --mail-type=END,FAIL --output=test-full.log --comment="test-full.log"

test-validation: ## Run validation tests, requires a full set of runs in the output folder
$(info Run validation tests, requires a full set of runs in the output folder)
Expand Down
2 changes: 1 addition & 1 deletion output.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -338,7 +338,7 @@ runSingle <- function(output, outputdirs, slurmConfig, interactiveSession, test)
hookedRscript <- trimws(paste(Sys.getenv("RSCRIPT_SLURM_HOOK", unset = ""), "Rscript"))
Rscripts <- paste0(hookedRscript, " scripts/output/single/", name, " --outputdir=", outputdir, collapse = "; ")
slurmcmd <- paste0("sbatch ", slurmConfig, " --job-name=", logfile, " --output=", logfile,
" --mail-type=END,FAIL --comment=output.R --wrap='", Rscripts, "'")
" --mail-type=END,FAIL --comment=output.R --wrap='set -e; ", Rscripts, "'")
message("Sending to slurm: ", paste(name, collapse = ", "), ". Find log in ", logfile)
system(slurmcmd)
}
Expand Down
2 changes: 1 addition & 1 deletion scripts/output/comparison/compareScenarios2.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ startComp <- function(
" --mail-type=END,FAIL --time=200",
if (!grepl("--mem", slurmConfig)) " --mem=8000",
# Prefix RSCRIPT_SLURM_HOOK for piam-apptainer integration (empty if unset)
" --wrap=\"", trimws(paste(Sys.getenv("RSCRIPT_SLURM_HOOK", unset = ""), "Rscript")), " ", script,
" --wrap=\"set -e; ", trimws(paste(Sys.getenv("RSCRIPT_SLURM_HOOK", unset = ""), "Rscript")), " ", script,
" --outputdirs=", shQuote(paste(outputdirs, collapse = ",")),
" --profileName=", shQuote(profileName),
" --outFileName=", shQuote(outFileName),
Expand Down
4 changes: 2 additions & 2 deletions scripts/output/comparison/validateScenarios.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ startVal <- function(outputDirs, validationConfig, validationReportName, nameCor
" --error=", jobName, ".out",
" --mail-type=END --time=200 --mem-per-cpu=8000",
# Prefix RSCRIPT_SLURM_HOOK for piam-apptainer integration (empty if unset)
" --wrap=\"", trimws(paste(Sys.getenv("RSCRIPT_SLURM_HOOK", unset = ""), "Rscript")), " ", script,
" --wrap=\"set -e; ", trimws(paste(Sys.getenv("RSCRIPT_SLURM_HOOK", unset = ""), "Rscript")), " ", script,
" --outputdirs=", shQuote(paste(outputDirs, collapse = ",")),
" --validationConfig=", shQuote(validationConfig),
" --validationReportName=", shQuote(validationReportName),
Expand Down Expand Up @@ -112,4 +112,4 @@ nameCore <- glue::glue("{prefix}{valName}{repInfix}-{timeStamp}")
outputDirs = outputdirs,
validationConfig = validationConfig,
validationReportName = validationReportName,
nameCore = nameCore)
nameCore = nameCore)
Loading