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askap-craco / CELEBI

The CRAFT Effortless Localisation and Enhanced Burst Inspection Pipeline
MIT License
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Space filled up #437

Closed marcinglowacki closed 1 year ago

marcinglowacki commented 1 year ago

Nextflow will not start or continue a process, citing no space left on the device. THis was encountered on the test 'craco' machine', as tempary locations were filled up.

`(base) ubuntu@craco trunk processing> nextflow /home/ubuntu/craco-postproc/craco_postproc/pipelines/main.nf -c configs/220501.config -with-report reports/220501.html -N marcin.glowacki@curtin.edu.au -resume --calibrate /home/ubuntu/nextflow: line 411: cannot create temp file for here-document: No space left on device OpenJDK 64-Bit Server VM warning: Insufficient space for shared memory file: 1934387 Try using the -Djava.io.tmpdir= option to select an alternate temp location.

N E X T F L O W ~ version 21.10.6 Launching /home/ubuntu/craco-postproc/craco_postproc/pipelines/main.nf [magical_rosalind] - revision: a3253cb721 /tmp/nxf-10726065449546234530: No space left on device`

When encountered, investigate space on the device - e.g. df -h and check where temporary files are stored.

marcinglowacki commented 1 year ago

Unlikely to be an error on ozstar without it being caught quickly, but of note if running CELEBI on a separate device. Clear our work directories every once in a while!