Slurm testing on Travis, update SLURM templates

.gitignore

@@ -1,3 +1,5 @@
+.Rhistory
+*~
 .DS_Store
 /inst/doc
 /src/*.so

.travis.yml

@@ -1,5 +1,4 @@
-dist: trusty
-sudo: false
+sudo: true
 language: r
 cache: packages
 
@@ -13,6 +12,7 @@ addons:
     packages:
       - libopenmpi-dev
       - openmpi-bin
+      - slurm-llnl 
 
 r:
   - oldrel
@@ -23,5 +23,16 @@ r_packages:
   - covr
   - Rmpi
 
+script:
+  - sudo cp inst/conf/slurm.conf /etc/slurm-llnl
+  - sudo service munge start
+  - sudo /etc/init.d/slurmctld restart
+  - sudo /etc/init.d/slurmd restart
+  - sinfo
+  - R CMD build .
+  - R CMD check *tar.gz
+
 after_success:
   - if [[ "${TRAVIS_R_VERSION_STRING}" == "release" ]]; then Rscript -e 'covr::coveralls()'; fi
+
+

inst/conf/slurm.R

@@ -0,0 +1,5 @@
+## this is used in tests/testthat/test_slurm.R
+cluster.functions = makeClusterFunctionsSlurm(system.file(
+  file.path("templates", "slurm-simple.tmpl"),
+  package="batchtools",
+  mustWork=TRUE))

inst/conf/slurm.conf

@@ -0,0 +1,55 @@
+# this file is used in tests/testthat/test_slurm.R
+
+# slurm.conf file generated by configurator easy.html.
+# Put this file on all nodes of your cluster.
+# See the slurm.conf man page for more information.
+#
+ControlMachine=localhost
+#ControlAddr=
+# 
+#MailProg=/bin/mail 
+MpiDefault=none
+#MpiParams=ports=#-# 
+ProctrackType=proctrack/pgid
+ReturnToService=1
+SlurmctldPidFile=/var/run/slurm-llnl/slurmctld.pid
+#SlurmctldPort=6817 
+SlurmdPidFile=/var/run/slurm-llnl/slurmd.pid
+#SlurmdPort=6818 
+SlurmdSpoolDir=/var/lib/slurm-llnl/slurmd
+SlurmUser=slurm
+#SlurmdUser=root 
+StateSaveLocation=/var/lib/slurm-llnl/slurmctld
+SwitchType=switch/none
+TaskPlugin=task/none
+# 
+# 
+# TIMERS 
+#KillWait=30 
+#MinJobAge=300 
+#SlurmctldTimeout=120 
+#SlurmdTimeout=300 
+# 
+# 
+# SCHEDULING 
+FastSchedule=1
+SchedulerType=sched/backfill
+SchedulerParameters=kill_invalid_depend
+#SchedulerPort=7321 
+SelectType=select/linear
+# 
+# 
+# LOGGING AND ACCOUNTING 
+AccountingStorageType=accounting_storage/none
+ClusterName=cluster
+#JobAcctGatherFrequency=30 
+JobAcctGatherType=jobacct_gather/none
+#SlurmctldDebug=3 
+SlurmctldLogFile=/var/log/slurm-llnl/slurmctld.log
+#SlurmdDebug=3 
+SlurmdLogFile=/var/log/slurm-llnl/slurmd.log
+# 
+# 
+# COMPUTE NODES 
+NodeName=localhost CPUs=1 State=UNKNOWN 
+PartitionName=debug Nodes=localhost Default=YES MaxTime=INFINITE State=UP

inst/templates/slurm-dortmund.tmpl

@@ -14,7 +14,7 @@ if (backend == "mpi") {
 }
 
 # relative paths are not handled well by Slurm
-log.file = fs::path_expand(log.file)
+log.file = shQuote(fs::path_expand(log.file))
 -%>
 
 #SBATCH --job-name=<%= job.name %>

inst/templates/slurm-lido3.tmpl

@@ -16,6 +16,9 @@
 
 <%
 
+# relative paths are not handled well by Slurm
+log.file = shQuote(fs::path_expand(log.file))
+
 # queue
 walltime = asInt(resources$walltime, lower = 60L, upper = 31L * 24L * 60L * 60L)
 memory = asInt(resources$memory, lower = 100L, upper = 1024L * 1024L)

inst/templates/slurm-simple.tmpl

@@ -19,7 +19,7 @@
 
 <%
 # relative paths are not handled well by Slurm
-log.file = fs::path_expand(log.file)
+log.file = shQuote(fs::path_expand(log.file))
 -%>
 
 

tests/testthat/test_slurm.R

@@ -0,0 +1,32 @@
+if(interactive())library(testthat)
+if(interactive())library(batchtools)
+context("slurm")
+
+conf.file <- system.file(
+  "conf", "slurm.R", package="batchtools", mustWork=TRUE)
+res.list <- list(
+  walltime = 3600, #in seconds.
+  ncpus=1,
+  ntasks=1)
+sinResult <- function(reg.name){
+  reg.path <- file.path(tempdir(), reg.name)
+  unlink(reg.path, recursive=TRUE)
+  reg <- makeRegistry(reg.path, conf.file=conf.file)
+  batchMap(sin, c(0, pi/2), reg=reg)
+  submitJobs(resources=res.list, reg=reg)
+  waitForJobs(reg=reg)
+  st <- getJobStatus(reg=reg)
+  sapply(st$job.id, loadResult)
+}
+expected <- c(0, 1)
+
+test_that("registry with NO spaces/parens works on slurm", {
+  computed <- sinResult("reg")
+  expect_equal(computed, expected)
+})
+
+test_that("registry WITH spaces/parens works on slurm", {
+  computed <- sinResult("reg (!)")
+  expect_equal(computed, expected)
+})
+