On Sun, Aug 11, 2013 at 12:28 AM, Linda Walsh wrote:
> I was trying to gunzip a bunch of small files ;
> tried
>
> for i in *.gz;do
> sem -j6 $i
> done
You seem to have forgotten gunzip:
for i in *.gz;do
sem -j6 gunzip $i
done
This ought to work just fine.
Personally I hate introducin
Ole Tange wrote:
On Sun, Aug 11, 2013 at 12:28 AM, Linda Walsh wrote:
I was trying to gunzip a bunch of small files ;
tried
for i in *.gz;do
sem -j6 $i
done
You seem to have forgotten gunzip:
for i in *.gz;do
sem -j6 gunzip $i
done
---
oops yup
This ought to work jus
I stopped it with 180 files left after 20 minutes.
I ran:
'ls' -1 *.gz|xargs -n1 -P12 gunzip
It completed in < 2 seconds.
On Sun, Aug 11, 2013 at 11:42 PM, Linda Walsh wrote:
>
> Ole Tange wrote:
>>
>> On Sun, Aug 11, 2013 at 12:28 AM, Linda Walsh wrote:
:
>> Personally I hate introducing an unneeded variable, so I would write it
>> as:
>>
>> parallel gunzip ::: *gz
>
> specialized syntax -- didn't know...
Consid
When run in --semaphore mode GNU Parallel uses hard links to create a
counting semaphore. If your filesystem does not support hard links the
behaviour is undefined - and that is likely what you see.
NTFS supports hard links. However, file accesses are infinitely slower
than
semaphores in
Hi Ole,
The number of lines (reads) in reads.ids is ~9 million. The number of alignment
lines in the SAM/BAM file is ~372,281,262.
Cheers,
Nathan
-Original Message-
From: [email protected] [mailto:[email protected]] On Behalf Of Ole Tange
Sent: Saturday, 10 August 2013 7:05 AM
To:
On Mon, Aug 12, 2013 at 1:05 AM, Linda Walsh wrote:
>> When run in --semaphore mode GNU Parallel uses hard links to create a
>> counting semaphore. If your filesystem does not support hard links the
>> behaviour is undefined - and that is likely what you see.
>
> NTFS supports hard links. Howeve
On Mon, Aug 12, 2013 at 5:50 AM, Nathan S. Watson-Haigh
wrote:
> Hi Ole,
>
> The number of lines (reads) in reads.ids is ~9 million. The number of
> alignment lines in the SAM/BAM file is ~372,281,262.
The only thing I would change is the block size of the first:
$ cat read.ids | parallel --rou
On Sat, Aug 10, 2013 at 11:50 PM, Ole Tange wrote:
> I am considering letting --round-robin become default for --pipe, and
> let --keep-order mean --not-round-robin.
>
> That will mean that the default will not start one job per block, but
> instead on job per CPU. Only when running --keep-order
