Dave Trudgian dtrudg

Containers, HPC, Scientific Computing at @sylabs

dtrudg / main.nf

Created September 30, 2016 13:57

SLURM requeue test

	// Path to an input file, or a pattern for multiple inputs
	// Note - $baseDir is the location of this workflow file main.nf
	params.story = "$baseDir/../test_data/mobydick.txt"

	stories = Channel.fromPath( params.story )

	process uppercase {

	cpus 1

dtrudg / .nextflow.log

Created June 30, 2016 03:21

	-bash-4.1$ cat .nextflow.log
	Jun-29 22:15:56.636 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [proxy.swmed.edu, 3128]
	Jun-29 22:15:56.688 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [proxy.swmed.edu, 3128]
	Jun-29 22:15:56.688 [main] DEBUG nextflow.cli.Launcher - $> /cm/shared/apps/nextflow/0.20.1/bin/nextflow test.nextflow
	Jun-29 22:15:56.688 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.20.1
	Jun-29 22:15:56.689 [main] INFO nextflow.cli.CmdRun - Launching test.nextflow
	Jun-29 22:15:57.155 [main] DEBUG nextflow.Session - Session uuid: c95fb10b-1a83-4278-a005-753ebb1cd5a7
	Jun-29 22:15:57.156 [main] DEBUG nextflow.Session - Executor pool size: 8
	Jun-29 22:15:57.180 [main] DEBUG nextflow.cli.CmdRun -
	Version: 0.20.1 build 3853

dtrudg / gist:82dc9934e5b866fbd5ce227f69f594a6

Created June 30, 2016 03:20

	-bash-4.1$ jstack -l 13606
	Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128
	2016-06-29 22:19:09
	Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.51-b03 mixed mode):

	"Attach Listener" daemon prio=10 tid=0x00007fa478001000 nid=0x35cc waiting on condition [0x0000000000000000]
	java.lang.Thread.State: RUNNABLE

	Locked ownable synchronizers:
	- None

dtrudg / stuck_testcase.nf

Last active June 30, 2016 03:16