What I want to do is that a user could request 128 slots in just 2 nodes
of 64 cores. Using the parallel environment
$ qsub -q conmat -pe foobar 5 submit.sh
makes the script to be executed in 5 slots, but they could be assigned
to 5 different nodes.
If I try to use the built in complex_value slots:
$ qsub -q conmat -l slosts 5 submit.sh
gives an error so I can't use it:
Unable to run job: "job" denied: use parallel environments instead of
requesting slots explicitly.
Exiting.
So, I have created a new complex_value, slotsfree similar to slots, but
I can use it as a requestable and consumable.
But now, thanks to William, we have observed that slotsfree consmuption
is multiplied by the slots configured in the PE.
Do you understant what my problem is?
Ideally I would like to specify how many slots to use (128 for example)
and in how many different nodes, but without specifying explicitly in
which nodes.
Many thanks for your help!!!
El 15/05/12 16:32, Reuti escribió:
Am 15.05.2012 um 16:23 schrieb Arturo:
<snip>
It doesn't matter to which queue I submit the script.
I would use the built in slot complex, but when I use it gives me this error:
qsub -q conmat -l slots=5 submit.sh
Unable to run job: "job" denied: use parallel environments instead of
requesting slots explicitly.
Exiting.
As the message says: you are not requesting a PE with the proper slot count?
$ qsub -q conmat -pe foobar 5 submit.sh
-- Reuti
Regards
El 15/05/12 16:12, William Hay escribió:
Ok that makes more sense. The queue instance on node045 is called
conmat not test. If test only exists as a single slot on each of
node046 and node047
then when you request -q test you are restricting it to those two
slots which isn't enough for a 4 slot job.
We would really need the full output of qstat -f to be sure though.
William
On 15 May 2012 14:42, Arturo
<[email protected]>
wrote:
More info:
output of qstat -f
---------------------------------------------------------------------------------
[email protected]
BIP 0/0/64 0.00 lx26-amd64
---------------------------------------------------------------------------------
############################################################################
- PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS
############################################################################
74550 0.60500 test arturo qw 05/15/2012 15:26:50 4
qconf -sq test |grep slot
slots 64
qconf -sp openmpi |grep slots
slots 99999
urgency_slots min
Regards
El 15/05/12 15:39, Arturo escribió:
Hi William,
you were right, it was running in various nodos:
74545 0.60500 test arturo r 05/15/2012 15:17:46
[email protected]
MASTER
[email protected]
SLAVE
74545 0.60500 test arturo r 05/15/2012 15:17:46
[email protected]
SLAVE
74545 0.60500 test arturo r 05/15/2012 15:17:46
[email protected]
SLAVE
Well, looking deeply, the problem is that I created a complex value
"slotsfree" consumable and requestable and I assigned it to the node045 with
the value:
slotsfree=8 (for example).
If I submit a job using a parallel environment to this node without
configuring this complex_value, it works perfectly.
And when I submit a job without using a PE to this node, but with this
complex_value configured, it also works,
but when I submit the same job, using a PE and the complex_value, it doen't
work, and in the output it only says this:
cannot run in PE "openmpi" because it only offers 2 slots
Is it more clear now? Why does not work if I PE is configured without slot
imitation, the node has 64 slots, and the slotsfree value is greated than 4?
Thanks for your help.
Regards
Arturo
El 15/05/12 14:33, William Hay escribió:
On 15 May 2012 13:05, Arturo
<[email protected]>
wrote:
Hi,
I have a very strange behaviour when I try to use a parallel environment
with hard_queue_list option.
In my script I have a parallel configuration:
#$ -pe openmpi 4
and if submit the script in the following way it works and runs in node
test@node045
qsub script.sh
But If I submit the script using the hard_queue_list it doesn't run:
qsub -q test script.sh
With this error:
cannot run in PE "openmpi" because it only offers 2 slots
Obviously, the node is always empty. What may be wrong?
It's hard to diagnose what's going on without knowing more about your
configuration.
Are you certain the entire job is running in the queue instance
test@node045 when you submit without a queue list?
One possibility is that queue test@node045 has only two slots. The
master slot of the job plus one slave runs
in test@node045 while the remaining slots run elsewhere.
When the job is running what output do you get from qstat -g t?
William
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