no backslash in log file name; tested on SGE 8.1.9

mschubert · Dec 13, 2023 · 5ca9f9b · 5ca9f9b
1 parent 55f66b9
commit 5ca9f9b
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/R/qsys_sge.r b/R/qsys_sge.r
@@ -18,8 +18,7 @@ SGE = R6::R6Class("SGE",
                 opts$log_file = normalizePath(opts$log_file, mustWork=FALSE)
             else if (log_worker)
                 opts$log_file = sprintf("%s-%s.log", private$job_name, private$array_idx)
-            filled = fill_template(private$template, opts,
-                                   required=c("master", "n_jobs"))
+            filled = fill_template(private$template, opts, required=c("master", "n_jobs"))
 
             if (verbose)
                 message("Submitting ", n_jobs, " worker jobs (ID: ", private$job_name, ") ...")
@@ -41,7 +40,7 @@ SGE = R6::R6Class("SGE",
         qsub_stdout = NULL,
         job_name = NULL,
         job_id   = NULL,
-        array_idx = "\\$TASK_ID",
+        array_idx = "$TASK_ID",
         is_cleaned_up = NULL,
 
         finalize = function(quiet = TRUE) { # self$workers_running == 0

diff --git a/vignettes/userguide.Rmd b/vignettes/userguide.Rmd
@@ -354,7 +354,7 @@ In order to log each worker separately, some schedulers support wildcards in
 their log file names. For instance:
 
 * Multicore/Multiprocess: `log_file="/path/to.file.%i"`
-* SGE: `log_file="/path/to.file.\$TASK_ID"`
+* SGE: `log_file="/path/to.file.$TASK_ID"`
 * LSF: `log_file="/path/to.file.%I"`
 * Slurm: `log_file="/path/to.file.%a"`
 * PBS: `log_file="/path/to.file.$PBS_ARRAY_INDEX"`