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:
$parallel echo ::: A B C
Error unlinking file ./rTrUcTv2ZS using unlink0 at /home/######/bin/parallel line 5529
Any suggestion on what this means and how to fix it?
Things I have looked into already:
bad install It could be a bad install. To install I used ./configure --prefix=$HOME
. Here is the output of configure.log:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by parallel configure 20140622, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --prefix=/home/######
## --------- ##
## Platform. ##
## --------- ##
hostname = ######
uname -m = x86_64
uname -r = 2.6.32-43-server
uname -s = Linux
uname -v = #97-Ubuntu SMP Wed Sep 5 16:56:41 UTC 2012
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
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
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:
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