Following up on some previous posts, I’m trying to test run Tractoflow on an interactive node and am running into a memory allocation issue. I am on a node with 128G mem/16 cores but when I launch Tractoflow, I get this error (full output at the bottom of post):
Local avail `memory` attribute cannot zero. Expression: (availMemory > 0). Values: availMemory = 0
-- Check script 'tractoflow/main.nf' at line: 352 or see '.nextflow.log' file for more details
I’m checking with my HPC admins to see if there’s some permissions error in accessing memory, for whatever reason. Not sure if this could be caused by the fact that I’m using a locally installed Nextflow? In the meantime, if you have any ideas about this, please let me know! Thanks.
Here is the full output and also the lines referred to in main.nf.
Full output:
nsharif@c29:/nafs/narr/nooralsh>/nafs/narr/nooralsh/nextflow run /nafs/narr/nooralsh/tractoflow/main.nf --input /nafs/narr/nooralsh/input/ --fodf_shells "5 1500 3000" -with-singularity /nafs/narr/nooralsh/tractoflow_2.2.1.sif -w /nafs/narr/nooralsh/tf_results/ -resume
NOTE: Nextflow is not tested with Java 1.8.0_282 -- It's recommended the use of version 11 up to 18
N E X T F L O W ~ version 22.04.5
Launching `/nafs/narr/nooralsh/tractoflow/main.nf` [festering_fermi] DSL1 - revision: 3fb5c2dda4
TractoFlow pipeline
===================
Start time: 2022-09-28T10:01:16.835-07:00
Max DTI shell extracted: 1200
DTI shells extracted: 5 1500 3000
Input: /nafs/narr/nooralsh/input/
Local avail `memory` attribute cannot zero. Expression: (availMemory > 0). Values: availMemory = 0
-- Check script 'tractoflow/main.nf' at line: 352 or see '.nextflow.log' file for more details
main.nf lines:
352 process README {
353 cpus 1
354 publishDir = params.Readme_Publish_Dir
355 tag = "README"
356
357 output:
358 file "readme.txt"
359
360 script:
361 String list_options = new String();
362 for (String item : params) {
363 list_options += item + "\n"
364 }
365 """
366 echo "TractoFlow pipeline\n" >> readme.txt
367 echo "Start time: $workflow.start\n" >> readme.txt
368 echo "[Command-line]\n$workflow.commandLine\n" >> readme.txt
369 echo "[Git Info]\n" >> readme.txt
370 echo "$workflow.repository - $workflow.revision [$workflow.commitId]\n" >> readme.txt
371 echo "[Options]\n" >> readme.txt
372 echo "$list_options" >> readme.txt
373 """
374 }