Hi,
it looks like all jobs are executed on the first server regardless of
server file. I am using:
cat proteins.fasta | parallel --no-notice -vv -j ${SLOTS} --tmpdir tmp
--wait --slf servers --block 200k --recstart '>' --pipe blastp -evalue
1e-05 -outfmt 6 -db proteins -query - -out result_{#}
(SLOTS=192)
with serverfile given by:
> more servers
24/cresco3x045.portici.enea.it
16/cresco3x047.portici.enea.it
16/cresco3x049.portici.enea.it
24/cresco3x060.portici.enea.it
24/cresco3x065.portici.enea.it
24/cresco3x073.portici.enea.it
16/cresco3x078.portici.enea.it
24/cresco3x079.portici.enea.it
24/cresco3x080.portici.enea.it
for i in `cat servers |sed -e s:^[0-9]*/::g` ; do echo
"------------------------------------------------- "$i ; ssh $i ps -ef
|egrep blastp |wc -l ; done
-------------------------------------------------
cresco3x045.portici.enea.it
0
-------------------------------------------------
cresco3x047.portici.enea.it
0
-------------------------------------------------
cresco3x049.portici.enea.it
0
-------------------------------------------------
cresco3x060.portici.enea.it
0
-------------------------------------------------
cresco3x065.portici.enea.it
614
-------------------------------------------------
cresco3x073.portici.enea.it
0
-------------------------------------------------
cresco3x078.portici.enea.it
0
-------------------------------------------------
cresco3x079.portici.enea.it
0
-------------------------------------------------
cresco3x080.portici.enea.it
0
According to manual (https://www.gnu.org/software/parallel/man.html) I
expected a maximum of 24 blastp instances on cresco3x045.portici.enea.it, a
maximum of 16 blastp instances on cresco3x047.portici.enea.it, etc. It also
looks like option "--wait" is neglected and GNU parallel is trying to run
all 192 instances at the same time on a single server.
Could anyone tell me, please, what's going wrong?
Thanks in advance,
Giuseppe
On Thu, Apr 23, 2015 at 1:56 PM, Giuseppe Aprea <giuseppe.ap...@gmail.com>
wrote:
> Hi!
>
> Mea culpa, I am sorry. You are right, I should have tried the
> ncpu/sshlogin syntax before writing my message.
>
> g
>
>
>
>
>
> On Thu, Apr 23, 2015 at 1:32 AM, Ole Tange <o...@tange.dk> wrote:
>
>> On Wed, Apr 22, 2015 at 9:57 AM, Giuseppe Aprea
>> <giuseppe.ap...@gmail.com> wrote:
>>
>> > Anyway now my main concern is how do I specify the maximum job number
>> per
>> > host when I am using multiple worker nodes?
>>
>> Have you read the section on --sshlogin and --slf in the man page?
>>
>>
>> /Ole
>>
>
>
>
