Hi Reuti,
I configured OpenMPI to support SGE tight integration and used the defined
below PE for submitting the job:
[16:36][eg@moe:~]$ qconf -sp fill_up
pe_name fill_up
slots 80
user_lists NONE
xuser_lists NONE
start_proc_args /bin/true
stop_proc_args /bin/true
allocation_rule $fill_up
control_slaves TRUE
job_is_first_task FALSE
urgency_slots min
accounting_summary FALSE
Here are the allocation info retrieved from `qstat -g t` for the related job:
---------------------------------------------------------------------------------
smp...@barney.fft BIP 0/1/4 0.70 lx-amd64
hc:num_proc=0
hl:mem_free=31.215G
hl:mem_used=280.996M
hc:mem_available=1.715G
1296 0.54786 semi_direc jj r 04/03/2012 16:43:49 1
---------------------------------------------------------------------------------
smp...@carl.fft BIP 0/1/4 0.69 lx-amd64
hc:num_proc=0
hl:mem_free=30.764G
hl:mem_used=742.805M
hc:mem_available=1.715G
1296 0.54786 semi_direc jj r 04/03/2012 16:43:49 1
---------------------------------------------------------------------------------
smp...@charlie.fft BIP 0/2/8 0.57 lx-amd64
hc:num_proc=0
hl:mem_free=62.234G
hl:mem_used=836.797M
hc:mem_available=4.018G
1296 0.54786 semi_direc jj r 04/03/2012 16:43:49 2
---------------------------------------------------------------------------------
Sge reports whatr pls_gridengine_report does, i.e. what was reserved.
But here is the ouput of the current job (after started by openmpi):
[charlie:05294] ras:gridengine: JOB_ID: 1296
[charlie:05294] ras:gridengine: PE_HOSTFILE:
/opt/sge/default/spool/charlie/active_jobs/1296.1/pe_hostfile
[charlie:05294] ras:gridengine: charlie.fft: PE_HOSTFILE shows slots=2
[charlie:05294] ras:gridengine: barney.fft: PE_HOSTFILE shows slots=1
[charlie:05294] ras:gridengine: carl.fft: PE_HOSTFILE shows slots=1
====================== ALLOCATED NODES ======================
Data for node: Name: charlie Launch id: -1 Arch: ffc91200 State: 2
Num boards: 1 Num sockets/board: 2 Num cores/socket: 4
Daemon: [[54347,0],0] Daemon launched: True
Num slots: 2 Slots in use: 0
Num slots allocated: 2 Max slots: 0
Username on node: NULL
Num procs: 0 Next node_rank: 0
Data for node: Name: barney.fft Launch id: -1 Arch: 0 State: 2
Num boards: 1 Num sockets/board: 2 Num cores/socket: 4
Daemon: Not defined Daemon launched: False
Num slots: 1 Slots in use: 0
Num slots allocated: 1 Max slots: 0
Username on node: NULL
Num procs: 0 Next node_rank: 0
Data for node: Name: carl.fft Launch id: -1 Arch: 0 State: 2
Num boards: 1 Num sockets/board: 2 Num cores/socket: 4
Daemon: Not defined Daemon launched: False
Num slots: 1 Slots in use: 0
Num slots allocated: 1 Max slots: 0
Username on node: NULL
Num procs: 0 Next node_rank: 0
=================================================================
Map generated by mapping policy: 0200
Npernode: 0 Oversubscribe allowed: TRUE CPU Lists: FALSE
Num new daemons: 2 New daemon starting vpid 1
Num nodes: 3
Data for node: Name: charlie Launch id: -1 Arch: ffc91200 State: 2
Num boards: 1 Num sockets/board: 2 Num cores/socket: 4
Daemon: [[54347,0],0] Daemon launched: True
Num slots: 2 Slots in use: 2
Num slots allocated: 2 Max slots: 0
Username on node: NULL
Num procs: 2 Next node_rank: 2
Data for proc: [[54347,1],0]
Pid: 0 Local rank: 0 Node rank: 0
State: 0 App_context: 0 Slot list: NULL
Data for proc: [[54347,1],3]
Pid: 0 Local rank: 1 Node rank: 1
State: 0 App_context: 0 Slot list: NULL
Data for node: Name: barney.fft Launch id: -1 Arch: 0 State: 2
Num boards: 1 Num sockets/board: 2 Num cores/socket: 4
Daemon: [[54347,0],1] Daemon launched: False
Num slots: 1 Slots in use: 1
Num slots allocated: 1 Max slots: 0
Username on node: NULL
Num procs: 1 Next node_rank: 1
Data for proc: [[54347,1],1]
Pid: 0 Local rank: 0 Node rank: 0
State: 0 App_context: 0 Slot list: NULL
Data for node: Name: carl.fft Launch id: -1 Arch: 0 State: 2
Num boards: 1 Num sockets/board: 2 Num cores/socket: 4
Daemon: [[54347,0],2] Daemon launched: False
Num slots: 1 Slots in use: 1
Num slots allocated: 1 Max slots: 0
Username on node: NULL
Num procs: 1 Next node_rank: 1
Data for proc: [[54347,1],2]
Pid: 0 Local rank: 0 Node rank: 0
State: 0 App_context: 0 Slot list: NULL
Regards,
Eloi
-----Original Message-----
From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf
Of Reuti
Sent: mardi 3 avril 2012 16:24
To: Open MPI Users
Subject: Re: [OMPI users] sge tight intregration leads to bad allocation
Hi,
Am 03.04.2012 um 16:12 schrieb Eloi Gaudry:
> Thanks for your feedback.
> No, this is the other way around, the "reserved" slots on all nodes are ok
> but the "used" slots are different.
>
> Basically, I'm using SGE to schedule and book resources for a distributed
> job. When the job is finally launched, it uses a different allocation than
> the one that was reported by pls_gridengine_info.
>
> pls_grid_engine_info report states that 3 nodes were booked: barney (1 slot),
> carl (1 slot) and charlie (2 slots). This booking was done by sge depending
> on the memory requirements of the job (among others).
>
> When orterun starts the jobs (i.e. when Sge finally start the scheduled job),
> it uses 3 nodes but the first one (barney: 2 slots instead of 1) is
> oversubscribed and the last one (carl: 1 slot instead of 2) is underused.
you configured Open MPI to support SGE tight integration and used a PE for
submitting the job? Can you please post the defintion of the PE.
What was the allocation you saw in SGE's `qstat -g t ` for the job?
-- Reuti
> If you need further information, please let me know.
>
> Eloi
>
> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On
> Behalf Of Ralph Castain
> Sent: mardi 3 avril 2012 15:58
> To: Open MPI Users
> Subject: Re: [OMPI users] sge tight intregration leads to bad allocation
>
> I'm afraid there isn't enough info here to help. Are you saying you only
> allocated one slot/node, so the two slots on charlie is in error?
>
> Sent from my iPad
>
> On Apr 3, 2012, at 6:23 AM, "Eloi Gaudry" <eloi.gau...@fft.be> wrote:
>
> Hi,
>
> I've observed a strange behavior during rank allocation on a distributed run
> schedule and submitted using Sge (Son of Grid Egine 8.0.0d) and OpenMPI-1.4.4.
> Briefly, there is a one-slot difference between allocated rank/slot for Sge
> and OpenMPI. The issue here is that one node becomes oversubscribed at
> runtime.
>
> Here is the output of the allocation done for gridengine:
>
> ====================== ALLOCATED NODES ======================
>
> Data for node: Name: barney Launch id: -1 Arch: ffc91200
> State: 2
> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2
> Daemon: [[22904,0],0] Daemon launched: True
> Num slots: 1 Slots in use: 0
> Num slots allocated: 1 Max slots: 0
> Username on node: NULL
> Num procs: 0 Next node_rank: 0
> Data for node: Name: carl.fft Launch id: -1 Arch: 0
> State: 2
> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2
> Daemon: Not defined Daemon launched: False
> Num slots: 1 Slots in use: 0
> Num slots allocated: 1 Max slots: 0
> Username on node: NULL
> Num procs: 0 Next node_rank: 0
> Data for node: Name: charlie.fft Launch id: -1
> Arch: 0 State: 2
> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2
> Daemon: Not defined Daemon launched: False
> Num slots: 2 Slots in use: 0
> Num slots allocated: 2 Max slots: 0
> Username on node: NULL
> Num procs: 0 Next node_rank: 0
>
>
> And here is the allocation finally used:
> =================================================================
>
> Map generated by mapping policy: 0200
> Npernode: 0 Oversubscribe allowed: TRUE CPU Lists: FALSE
> Num new daemons: 2 New daemon starting vpid 1
> Num nodes: 3
>
> Data for node: Name: barney Launch id: -1 Arch: ffc91200
> State: 2
> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2
> Daemon: [[22904,0],0] Daemon launched: True
> Num slots: 1 Slots in use: 2
> Num slots allocated: 1 Max slots: 0
> Username on node: NULL
> Num procs: 2 Next node_rank: 2
> Data for proc: [[22904,1],0]
> Pid: 0 Local rank: 0 Node rank: 0
> State: 0 App_context: 0
> Slot list: NULL
> Data for proc: [[22904,1],3]
> Pid: 0 Local rank: 1 Node rank: 1
> State: 0 App_context: 0
> Slot list: NULL
>
> Data for node: Name: carl.fft Launch id: -1 Arch: 0
> State: 2
> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2
> Daemon: [[22904,0],1] Daemon launched: False
> Num slots: 1 Slots in use: 1
> Num slots allocated: 1 Max slots: 0
> Username on node: NULL
> Num procs: 1 Next node_rank: 1
> Data for proc: [[22904,1],1]
> Pid: 0 Local rank: 0 Node rank: 0
> State: 0 App_context: 0
> Slot list: NULL
>
> Data for node: Name: charlie.fft Launch id: -1
> Arch: 0 State: 2
> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2
> Daemon: [[22904,0],2] Daemon launched: False
> Num slots: 2 Slots in use: 1
> Num slots allocated: 2 Max slots: 0
> Username on node: NULL
> Num procs: 1 Next node_rank: 1
> Data for proc: [[22904,1],2]
> Pid: 0 Local rank: 0 Node rank: 0
> State: 0 App_context: 0
> Slot list: NULL
>
> Has anyone already encounter the same behavior ?
> Is there a simple fix than not using the tight integration mode between Sge
> and OpenMPI ?
>
> Eloi
>
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