TORQUE trouble
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Description
I am having trouble running batchtools jobs on a local installation of TORQUE on Ubuntu 16.04. I think TORQUE is working because the following test.pbs produces the expected output.
#PBS -N test
#PBS -l nodes=1:ppn=1
#PBS -l walltime=0:01:00
cd $PBS_O_WORKDIR
touch done.txt
echo "done"
However, all my jobs hang in the E state. For example, the following R script waits indefinitely.
library("batchtools")
cf <- makeClusterFunctionsTORQUE("torque.tmpl")
reg <- makeRegistry(NA)
reg$cluster.functions <- cf
batchMap(fun = identity, x = 1:4)
submitJobs()
waitForJobs() # waits here indefinitely
reduceResultsList() # not reached
In my case, the console message of wait_for_jobs()
Waiting (S:4 R:4 D:0 E:0) [-------------------] 0% eta: ?s
does not match qstat, which shows jobs hanging in the E state.
Job id Name User Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
98.localhost ...8d7bd98804b04 wlandau 00:00:00 E batch
99.localhost ...fcce12fedcace wlandau 00:00:00 E batch
100.localhost ...dc63017b37ac6 wlandau 00:00:00 E batch
101.localhost ...b060e52879b8e wlandau 00:00:00 E batch
I am using the @HenrikBengtsson's torque.tmpl from future.batchtools.
Related: see my Stack Overflow post here and HenrikBengtsson/future.batchtools#12.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the reported R script, especially makeClusterFunctionsTORQUE, submitJobs, and waitForJobs, and inspect the referenced torque.tmpl from future.batchtools. Reproduce the four-job example alongside qstat, then trace how batchtools reads job states. Done means the jobs no longer remain in E and waitForJobs reports their actual completion.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- distributed-systems, hpc
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100