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HenrikBengtssonHenrikBengtsson
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Built-in templates will query job stats conditioned on the command tool is available [#26]
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‎DESCRIPTION‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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Package: future.batchtools
2-
Version: 0.12.2-9978
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Version: 0.12.2-9979
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Depends:
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R (>= 3.2.0),
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parallelly,

‎inst/templates/lsf.tmpl‎

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Original file line numberDiff line numberDiff line change
@@ -70,9 +70,11 @@ echo "Job submission declarations:"
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writeLines(sprintf("echo '%s'", job_declarations))
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%>
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echo "Job information:"
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bjobs -l "${LSB_JOBID}"
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echo
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if command -v bjobs > /dev/null; then
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echo "Job information:"
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bjobs -l "${LSB_JOBID}"
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echo
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fi
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## Launch R and evaluate the batchtools R job
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echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."
@@ -82,7 +84,10 @@ echo " - exit code: ${res}"
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echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
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## End-of-job summary
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bjobs -l "${LSB_JOBID}"
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if command -v bjobs > /dev/null; then
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echo "Job summary:"
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bjobs -l "${LSB_JOBID}"
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fi
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<% if (length(shutdown) > 0) {
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## Inject optional shell code

‎inst/templates/openlava.tmpl‎

Lines changed: 9 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -70,9 +70,11 @@ echo "Job submission declarations:"
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writeLines(sprintf("echo '%s'", job_declarations))
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%>
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73-
echo "Job information:"
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bjobs -l "${LSB_JOBID}"
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echo
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if command -v bjobs > /dev/null; then
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echo "Job information:"
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bjobs -l "${LSB_JOBID}"
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echo
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fi
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## Launch R and evaluate the batchtools R job
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echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."
@@ -82,7 +84,10 @@ echo " - exit code: ${res}"
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echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
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## End-of-job summary
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bjobs -l "${LSB_JOBID}"
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if command -v bjobs > /dev/null; then
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echo "Job summary:"
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bjobs -l "${LSB_JOBID}"
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fi
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<% if (length(shutdown) > 0) {
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## Inject optional shell code

‎inst/templates/sge.tmpl‎

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Original file line numberDiff line numberDiff line change
@@ -79,9 +79,11 @@ echo "Job submission declarations:"
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writeLines(sprintf("echo '%s'", job_declarations))
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%>
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echo "Job information:"
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qstat -j "${JOB_ID}"
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echo
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if command -v qstat > /dev/null; then
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echo "Job information:"
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qstat -j "${JOB_ID}"
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echo
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fi
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## Launch R and evaluate the batchtools R job
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echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."
@@ -91,7 +93,10 @@ echo " - exit code: ${res}"
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echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
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## End-of-job summary
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qstat -j "${JOB_ID}"
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if command -v qstat > /dev/null; then
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echo "Job summary:"
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qstat -j "${JOB_ID}"
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fi
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<% if (length(shutdown) > 0) {
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## Inject optional shell code

‎inst/templates/slurm.tmpl‎

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Original file line numberDiff line numberDiff line change
@@ -69,9 +69,11 @@ echo "Job submission declarations:"
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writeLines(sprintf("echo '%s'", job_declarations))
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%>
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echo "Slurm job information:"
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scontrol show job "${SLURM_JOB_ID}"
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echo
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if command -v scontrol > /dev/null; then
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echo "Slurm job information:"
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scontrol show job "${SLURM_JOB_ID}"
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echo
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fi
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## Launch R and evaluate the batchtools R job
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echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."
@@ -81,7 +83,10 @@ echo " - exit code: ${res}"
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echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
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## End-of-job summary
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sstat --format="JobID,AveCPU,MaxRSS,MaxPages,MaxDiskRead,MaxDiskWrite" --allsteps --jobs="${SLURM_JOB_ID}"
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if command -v sstat > /dev/null; then
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echo "Job summary:"
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sstat --format="JobID,AveCPU,MaxRSS,MaxPages,MaxDiskRead,MaxDiskWrite" --allsteps --jobs="${SLURM_JOB_ID}"
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fi
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<% if (length(shutdown) > 0) {
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## Inject optional shell code

‎inst/templates/torque.tmpl‎

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Original file line numberDiff line numberDiff line change
@@ -56,9 +56,9 @@ echo
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} %>
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echo "Load environment modules:"
59-
<%
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writeLines(sprintf("module load %s", modules))
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%>
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<% if (length(modules) > 0) {
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writeLines(c(sprintf("module load %s", modules), "module list"))
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} %>
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echo "Session information:"
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echo "- timestamp: $(date)"
@@ -73,9 +73,11 @@ echo "Job submission declarations:"
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writeLines(c(sprintf("module load %s", modules), "module list"))
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} %>
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76-
echo "Job information:"
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qstat -f "${PBS_JOBID}"
78-
echo
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if command -v qstat > /dev/null; then
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echo "Job information:"
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qstat -f "${PBS_JOBID}"
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echo
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fi
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## Launch R and evaluate the batchtools R job
8183
echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."
@@ -85,7 +87,10 @@ echo " - exit code: ${res}"
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echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
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## End-of-job summary
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qstat -f "${PBS_JOBID}"
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if command -v qstat > /dev/null; then
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echo "Job summary:"
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qstat -f "${PBS_JOBID}"
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fi
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<% if (length(shutdown) > 0) {
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## Inject optional shell code

‎man/batchtools_lsf.Rd‎

Lines changed: 9 additions & 4 deletions
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‎man/batchtools_openlava.Rd‎

Lines changed: 9 additions & 4 deletions
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‎man/batchtools_sge.Rd‎

Lines changed: 9 additions & 4 deletions
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‎man/batchtools_slurm.Rd‎

Lines changed: 9 additions & 4 deletions
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