Using array fills my home with many files like "~/nf-PROC_NAME_(6294).o6823940.88"

[lindenb]

Bug report

version 24.04.2

as in https://nextflow.slack.com/archives/C02T98A23U7/p1719476348728329

I started using the array keyword, but i see an accumulation of files in my home

~/nf-PROC_NAME_(6294).o6823940.66
~/nf-PROC_NAME_(6294).o6823940.67
~/nf-PROC_NAME_(6294).o6823940.68
~/nf-PROC_NAME_(6294).o6823940.69
~/nf-PROC_NAME_(6294).o6823940.7
~/nf-PROC_NAME_(6294).o6823940.70
~/nf-PROC_NAME_(6294).o6823940.71
~/nf-PROC_NAME_(6294).o6823940.72
~/nf-PROC_NAME_(6294).o6823940.73
~/nf-PROC_NAME_(6294).o6823940.74
~/nf-PROC_NAME_(6294).o6823940.75
~/nf-PROC_NAME_(6294).o6823940.76
~/nf-PROC_NAME_(6294).o6823940.77
~/nf-PROC_NAME_(6294).o6823940.78
~/nf-PROC_NAME_(6294).o6823940.79
~/nf-PROC_NAME_(6294).o6823940.8
~/nf-PROC_NAME_(6294).o6823940.80
~/nf-PROC_NAME_(6294).o6823940.81
~/nf-PROC_NAME_(6294).o6823940.82
~/nf-PROC_NAME_(6294).o6823940.83
~/nf-PROC_NAME_(6294).o6823940.84
~/nf-PROC_NAME_(6294).o6823940.85
~/nf-PROC_NAME_(6294).o6823940.86
~/nf-PROC_NAME_(6294).o6823940.87
~/nf-PROC_NAME_(6294).o6823940.88
~/nf-PROC_NAME_(6294).o6823940.89
~/nf-PROC_NAME_(6294).o6823940.9
~/nf-PROC_NAME_(6294).o6823940.90
~/nf-PROC_NAME_(6294).o6823940.91
~/nf-PROC_NAME_(6294).o6823940.92
~/nf-PROC_NAME_(6294).o6823940.93
~/nf-PROC_NAME_(6294).o6823940.94
~/nf-PROC_NAME_(6294).o6823940.95
~/nf-PROC_NAME_(6294).o6823940.96
~/nf-PROC_NAME_(6294).o6823940.97
~/nf-PROC_NAME_(6294).o6823940.98
(...)

it's filling my home.

export NXF_TEMP=path/to/dir

doesn't fix

sorry, I'm in a hurry, I doesn't have the time to provide more data. For now I can handle this by deleting the files.

[bentsherman]

Which executor are you using? I think the problem might be that the job array isn't specifying an -o option so it's being written to a default file. We should redirect it to /dev/null

[lindenb]

@bentsherman it's sge

[lindenb]

ok here is a minimal example:

workflow {
	RUN(Channel.of(1..10))
}

process RUN {
executor="sge"
clusterOptions = "-S /bin/bash -q max-24h.q -l h='!(js4jb5j*)' "
cache = "lenient"
penv = "make"

array 10
input:
	val(x)
script:
"""
echo $x
"""
}

nextflow run jeter.nf 
N E X T F L O W  ~  version 24.04.2
Launching `jeter.nf` [silly_wright] DSL2 - revision: ba8c8285a0
[6e/3e2328] Submitted process > RUN (2)
[58/2aa4b7] Submitted process > RUN (1)
[dd/dfc49e] Submitted process > RUN (3)
[55/4565f5] Submitted process > RUN (4)
[36/d47d43] Submitted process > RUN (5)
[45/f29b4e] Submitted process > RUN (6)
[d4/bb1225] Submitted process > RUN (7)
[ec/f3570e] Submitted process > RUN (8)
[74/3590f7] Submitted process > RUN (9)
[96/f75c6b] Submitted process > RUN (10)

$ file ~/nf-RUN_\(1\).*
/home/lindenbaum-p/nf-RUN_(1).e6824647.1:  ASCII text
/home/lindenbaum-p/nf-RUN_(1).e6824647.10: ASCII text
/home/lindenbaum-p/nf-RUN_(1).e6824647.2:  ASCII text
/home/lindenbaum-p/nf-RUN_(1).e6824647.3:  ASCII text
/home/lindenbaum-p/nf-RUN_(1).e6824647.4:  ASCII text
/home/lindenbaum-p/nf-RUN_(1).e6824647.5:  ASCII text
/home/lindenbaum-p/nf-RUN_(1).e6824647.6:  ASCII text
/home/lindenbaum-p/nf-RUN_(1).e6824647.7:  ASCII text
/home/lindenbaum-p/nf-RUN_(1).e6824647.8:  ASCII text
/home/lindenbaum-p/nf-RUN_(1).e6824647.9:  ASCII text
/home/lindenbaum-p/nf-RUN_(1).o6824647.1:  empty
/home/lindenbaum-p/nf-RUN_(1).o6824647.10: empty
/home/lindenbaum-p/nf-RUN_(1).o6824647.2:  empty
/home/lindenbaum-p/nf-RUN_(1).o6824647.3:  empty
/home/lindenbaum-p/nf-RUN_(1).o6824647.4:  empty
/home/lindenbaum-p/nf-RUN_(1).o6824647.5:  empty
/home/lindenbaum-p/nf-RUN_(1).o6824647.6:  empty
/home/lindenbaum-p/nf-RUN_(1).o6824647.7:  empty
/home/lindenbaum-p/nf-RUN_(1).o6824647.8:  empty
/home/lindenbaum-p/nf-RUN_(1).o6824647.9:  empty

$ cat "/home/lindenbaum-p/nf-RUN_(1).e6824647.10"
10

[bentsherman]

For now if you add -o /dev/null to clusterOptions it should disable those files