ubuntuunlinkgnu-parallelvirtual-server

GNU Parallel unlink error


Did a local install of GNU Parallel on a virtual Ubuntu server:

$uname -a
Linux #### 2.6.32-43-server #97-Ubuntu SMP Wed Sep 5 16:56:41 UTC 2012 x86_64 GNU/Linux

when running parallel, i get the following error on STDERR:

$parallel echo ::: A B C
Error unlinking file ./rTrUcTv2ZS using unlink0 at /home/######/bin/parallel line 5529

Any suggestion on what this means and how to fix it?

Things I have looked into already:

Curiously missing is uname -p. lscpu shows:

Architecture:          x86_64
CPU op-mode(s):        64-bit
CPU(s):                48
Thread(s) per core:    1
Core(s) per socket:    12
CPU socket(s):         4
NUMA node(s):          8
Vendor ID:             AuthenticAMD
CPU family:            16
Model:                 9
Stepping:              1
CPU MHz:               800.000
Virtualization:        AMD-V
L1d cache:             64K
L1i cache:             64K 
L2 cache:              512K
L3 cache:              5118K

Solution

  • It turns out the unlink error is a conflict between the NFS filesystem of my home directory and parallel's use of the File::Temp module:

    > "Finally, on NFS file systems the link count of the file handle does not always go to zero immediately after unlinking. Currently, this command is expected to fail on NFS disks."

    PerlDocs File::Temp Module

    To fix the situation, I asked my system administrator for a sticky directory on the volume containing the root folder, which was on a ext4 file system. I then added added this to my environment variables under $TMPDIR with:

    export TMPDIR=/to/the/directory
    

    I also added this line to .bash_profile