[GE users] mpich <-> sge --> controlling hosts machinefile

Gerolf Ziegenhain mail.gerolf at ziegenhain.com
Wed Jul 4 21:10:20 BST 2007


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Hi Chris,

The result of this experiment is predictable: If I remove the n_slots
threshold, the SGE will also start single slots on nodes which already have
a load of 1. This means it can only start 1 process; however if the
allocation of slots is fixed with "2" nothing will happen: behaviour as
described before.

/BR: Gerolf

2007/7/4, Chris Dagdigian <dag at sonsorol.org>:
>
>
> Hi Gerolf,
>
> I run MPI apps on 2-way compute nodes all the time without problems
> and I've always just let "slots 2" stay in the queue configuration.
> The SGE scheduler always did the right thing. Can you remove your
> n_slots load thresholds and queue consumables and see what happens?
> I'm still curious as to why you had three tasks land on one node.
>
>
>
>
>
> On Jul 4, 2007, at 3:35 PM, Gerolf Ziegenhain wrote:
>
> > Thanks for the very quick reply ;)
> >
> > allocation_rule = $round_robin results in 1job/node. This increases
> > the communication effort. So maybe allocation_rule=2 would be the
> > best choice in my case?
> >
> > This is the configuration of the queue:
> > qconf -sq q_mpich
> > qname                 q_mpich
> > hostlist              lc10 lc11 lc12 lc13 lc14 lc15 lc18 lc19
> > seq_no                21,[@b_hosts=22],[@x_hosts=23]
> > load_thresholds       np_load_avg=1,np_load_short=1,n_slots=2, \
> >
> > [@b_hosts=np_load_avg=1,np_load_short=1,n_slots=2], \
> >
> > [@x_hosts=np_load_avg=1,np_load_short=1,n_slots=2]
> > suspend_thresholds    NONE
> > nsuspend              1
> > suspend_interval      00:05:00
> > priority              0
> > min_cpu_interval      00:05:00
> > processors            UNDEFINED
> > qtype                 BATCH
> > ckpt_list             NONE
> > pe_list               mpich
> > rerun                 TRUE
> > slots                 2
> > tmpdir                /tmp
> > shell                 /bin/bash
> > prolog                NONE
> > epilog                NONE
> > shell_start_mode      unix_behavior
> > starter_method        NONE
> > suspend_method        NONE
> > resume_method         NONE
> > terminate_method      NONE
> > notify                00:00:60
> > owner_list            NONE
> > user_lists            ziegen,[@x_hosts=big]
> > xuser_lists           matlab matlab1 thor
> > subordinate_list      NONE
> > complex_values        synchron=0,virtual_free=3G,n_slots=2, \
> >
> > [@b_hosts=synchron=0,virtual_free=5G,n_slots=2], \
> >                       [@x_hosts=synchron=0,virtual_free=17G,n_slots=2]
> > projects              NONE
> > xprojects             NONE
> > calendar              NONE
> > initial_state         default
> > s_rt                  INFINITY
> > h_rt                  INFINITY
> > s_cpu                 INFINITY
> > h_cpu                 100:00:00
> > s_fsize               INFINITY
> > h_fsize               INFINITY
> > s_data                INFINITY
> > h_data                2G,[@b_hosts=4G],[@x_hosts=16G]
> > s_stack               INFINITY
> > h_stack               INFINITY
> > s_core                INFINITY
> > h_core                INFINITY
> > s_rss                 INFINITY
> > h_rss                 INFINITY
> > s_vmem                INFINITY
> > h_vmem                3G,[@b_hosts=5G],[@x_hosts=17G]
> >
> >
> > /BR:
> >    Gerolf
> >
> >
> > 2007/7/4, Chris Dagdigian <dag at sonsorol.org>:
> > Not sure if this totally answers your question but you can play with
> > the host selection process by adjusting your $allocation_rule in your
> > parallel environment configuration.
> >
> > For instance, you have $fill_up configured which is why your parallel
> > slots are being packed on as few nodes as possible. Changing to
> > $round_robin will spread it out among as many machines as possible.
> >
> > For your main symptom:
> >
> > If your parallel jobs are running more than 2 tasks per node then
> > something may be off with your slot count - perhaps SGE is detecting
> > multi-core CPUs on your 2-way boxes and setting slots=4 on each node.
> > Posting the config of the queue "mpich-qeueue" may help get to the
> > bottom of this as I'm not sure about the n_slots "limit" you are
> > referring to.
> >
> >
> > Regards,
> > Chris
> >
> >
> >
> > On Jul 4, 2007, at 3:14 PM, Gerolf Ziegenhain wrote:
> >
> > > Hi,
> > >
> > > Maybe it is a very stupid question, but: How do I control the
> > > number of jobs per node? Consider the following hardware: 38 nodes
> > > with two processors on each. When I start a job with -pe mpich 8
> > > there should be 4 nodes used with 2 jobs on each. What do I have to
> > > do in order to achieve this?
> > >
> > > My parallel environment is configured like this:
> > > qconf -sp mpich
> > > pe_name           mpich
> > > slots             60
> > > user_lists        NONE
> > > xuser_lists       NONE
> > > start_proc_args   /opt/N1GE/mpi/startmpi.sh -catch_rsh $pe_hostfile
> > > stop_proc_args    /opt/N1GE/mpi/stopmpi.sh
> > > allocation_rule   $fill_up
> > > control_slaves    TRUE
> > > job_is_first_task FALSE
> > > urgency_slots     min
> > >
> > > My mpich-queue has limits:
> > > np_load_av=1
> > > np_load_sh=1
> > > n_slots=2
> > >
> > > However if I start a job, something like this will happen in the
> > > PI1234-file:
> > > lc12.rhrk.uni-kl.de 0 prog
> > > lc19 1 prog
> > > lc19 1 prog
> > > lc19 1 prog
> > > lc14 1 prog
> > > lc14 1 prog
> > > lc13 1 prog
> > > lc13 1 prog
> > >
> > > So there are particularly three jobs on lc19 with only two CPUs, On
> > > of these three jobs would better be running on lc12. How can I fix
> > > this?
> > >
> > >
> > > Thanks in advance:
> > >    Gerolf
> > >
> > >
> > >
> > >
> > > --
> > > Dipl. Phys. Gerolf Ziegenhain
> > > Office: Room 46-332 - Erwin-Schrödinger-Str.46 - TU Kaiserslautern
> > > - Germany
> > > Web: gerolf.ziegenhain.com
> > >
> > >
> >
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> >
> >
> >
> > --
> > Dipl. Phys. Gerolf Ziegenhain
> > Office: Room 46-332 - Erwin-Schrödinger-Str.46 - TU Kaiserslautern
> > - Germany
> > Web: gerolf.ziegenhain.com
> >
>
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>


-- 
Dipl. Phys. Gerolf Ziegenhain
Office: Room 46-332 - Erwin-Schrödinger-Str.46 - TU Kaiserslautern - Germany
Web: gerolf.ziegenhain.com



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