BUG FIX: The built-in HPC templates indented job scheduler declarations

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.12.2-9934
+Version: 0.12.2-9935
 Depends:
     R (>= 3.2.0),
     parallelly,

inst/templates/lsf.tmpl

@@ -15,17 +15,30 @@
 <% if (length(resources) > 0) {
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-%s=%s", names(opts), opts)
-  cat(sprintf("#BSUB %s\n", opts))
+  writeLines(sprintf("#BSUB %s", opts))
 } %>
 
-echo "Batchtools job name: '<%= job.name %>'"
+echo "Batchtools information:"
+echo "- job name: '<%= job.name %>'"
+echo "- job log file: '<%= log.file %>'"
+echo
 
 echo "Session information:"
-date
-hostname
-which Rscript
-Rscript --version
-Rscript -e ".libPaths()"
+echo "- timestamp: $(date)"
+echo "- hostname: $(hostname)"
+echo "- Rscript path: $(which Rscript)"
+echo "- Rscript version: $(Rscript --version)"
+echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"
+echo
+
+echo "Job submission declarations:"
+<%
+  writeLines(sprintf("echo '#BSUB %s'", opts))
+%>
+
+echo "Job information:"
+bjobs -l "${LSB_JOBID}"
+echo
 
 ## Launch R and evaluate the batchtools R job
 echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."

inst/templates/openlava.tmpl

@@ -15,17 +15,30 @@
 <% if (length(resources) > 0) {
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-%s=%s", names(opts), opts)
-  cat(sprintf("#BSUB %s\n", opts))
+  writeLines(sprintf("#BSUB %s", opts))
 } %>
 
-echo "Batchtools job name: '<%= job.name %>'"
+echo "Batchtools information:"
+echo "- job name: '<%= job.name %>'"
+echo "- job log file: '<%= log.file %>'"
+echo
 
 echo "Session information:"
-date
-hostname
-which Rscript
-Rscript --version
-Rscript -e ".libPaths()"
+echo "- timestamp: $(date)"
+echo "- hostname: $(hostname)"
+echo "- Rscript path: $(which Rscript)"
+echo "- Rscript version: $(Rscript --version)"
+echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"
+echo
+
+echo "Job submission declarations:"
+<%
+  writeLines(sprintf("echo '#BSUB %s'", opts))
+%>
+
+echo "Job information:"
+bjobs -l "${LSB_JOBID}"
+echo
 
 ## Launch R and evaluate the batchtools R job
 echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."

inst/templates/sge.tmpl

@@ -37,17 +37,30 @@
   ## plan(batchtools_sge, resources = list(mem_free = "1G", h_rt="00:20:00"))
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-l %s=%s", names(opts), opts)
-  cat(sprintf("#$ %s\n", opts))
+  writeLines(sprintf("#$ %s", opts))
 } %>
 
-echo "Batchtools job name: '<%= job.name %>'"
+echo "Batchtools information:"
+echo "- job name: '<%= job.name %>'"
+echo "- job log file: '<%= log.file %>'"
+echo
 
 echo "Session information:"
-date
-hostname
-which Rscript
-Rscript --version
-Rscript -e ".libPaths()"
+echo "- timestamp: $(date)"
+echo "- hostname: $(hostname)"
+echo "- Rscript path: $(which Rscript)"
+echo "- Rscript version: $(Rscript --version)"
+echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"
+echo
+
+echo "Job submission declarations:"
+<%
+writeLines(sprintf("echo '#$ %s'", opts))
+%>
+
+echo "Job information:"
+qstat -j "${JOB_ID}"
+echo
 
 ## Launch R and evaluate the batchtools R job
 echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."

inst/templates/slurm.tmpl

@@ -17,17 +17,30 @@ defaults <- list(
 resources <- c(resources, defaults[setdiff(names(defaults), names(resources))])
 opts <- unlist(resources, use.names = TRUE)
 opts <- sprintf("--%s=%s", names(opts), opts)
-cat(sprintf("#SBATCH %s\n", opts))
+writeLines(sprintf("#SBATCH %s", opts))
 %>
 
-echo "Batchtools job name: '<%= job.name %>'"
+echo "Batchtools information:"
+echo "- job name: '<%= job.name %>'"
+echo "- job log file: '<%= log.file %>'"
+echo
 
 echo "Session information:"
-date
-hostname
-which Rscript
-Rscript --version
-Rscript -e ".libPaths()"
+echo "- timestamp: $(date)"
+echo "- hostname: $(hostname)"
+echo "- Rscript path: $(which Rscript)"
+echo "- Rscript version: $(Rscript --version)"
+echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"
+echo
+
+echo "Job submission declarations:"
+<%
+writeLines(sprintf("echo '#SBATCH %s'", opts))
+%>
+
+echo "Slurm job information:"
+scontrol show job "${SLURM_JOB_ID}"
+echo
 
 ## Launch R and evaluate the batchtools R job
 echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."

inst/templates/torque.tmpl

@@ -21,17 +21,30 @@
 <% if (length(resources) > 0) {
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("%s=%s", names(opts), opts)
-  cat(sprintf("#PBS -l %s\n", opts))
+  writeLines(sprintf("#PBS -l %s", opts))
 } %>
 
-echo "Batchtools job name: '<%= job.name %>'"
+echo "Batchtools information:"
+echo "- job name: '<%= job.name %>'"
+echo "- job log file: '<%= log.file %>'"
+echo
 
 echo "Session information:"
-date
-hostname
-which Rscript
-Rscript --version
-Rscript -e ".libPaths()"
+echo "- timestamp: $(date)"
+echo "- hostname: $(hostname)"
+echo "- Rscript path: $(which Rscript)"
+echo "- Rscript version: $(Rscript --version)"
+echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"
+echo
+
+echo "Job submission declarations:"
+<%
+  writeLines(sprintf("echo '#PBS -l %s'", opts))
+%>
+
+echo "Job information:"
+qstat -f "${PBS_JOBID}"
+echo
 
 ## Launch R and evaluate the batchtools R job
 echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."