Hi George,

 Thanks for your help. The bottom line is that the processes are neatly placed on the nodes/cores,
as far as I can tell from the map :

[...]
        Process OMPI jobid: [33285,1] Process rank: 4
        Process OMPI jobid: [33285,1] Process rank: 5
        Process OMPI jobid: [33285,1] Process rank: 6
        Process OMPI jobid: [33285,1] Process rank: 7

 Data for node: Name: r34i0n1   Num procs: 8
        Process OMPI jobid: [33285,1] Process rank: 8
        Process OMPI jobid: [33285,1] Process rank: 9
        Process OMPI jobid: [33285,1] Process rank: 10
        Process OMPI jobid: [33285,1] Process rank: 11
        Process OMPI jobid: [33285,1] Process rank: 12
        Process OMPI jobid: [33285,1] Process rank: 13
        Process OMPI jobid: [33285,1] Process rank: 14
        Process OMPI jobid: [33285,1] Process rank: 15

 Data for node: Name: r34i0n2   Num procs: 8
        Process OMPI jobid: [33285,1] Process rank: 16
        Process OMPI jobid: [33285,1] Process rank: 17
        Process OMPI jobid: [33285,1] Process rank: 18
        Process OMPI jobid: [33285,1] Process rank: 19
        Process OMPI jobid: [33285,1] Process rank: 20
[...]

 But the perfs are still very low ;-(

 Best,    G.

Le 20 déc. 10 à 22:27, George Bosilca a écrit :

That's a first step. My question was more related to the process overlay on the cores. If the MPI implementation place one process per node, then rank k and rank k+1 will always be on separate node, and the communications will have to go over IB. In the opposite if the MPI implementation places the processes per core, then rank k and k+1 will [mostly] be on the same node and the communications will be over shared memory. Depending on how the processes are placed and how you create the neighborhoods the performance can be drastically impacted.

There is a pretty good description of the problem at: http://www.hpccommunity.org/f55/behind-scenes-mpi-process-placement-640/

Some hints at http://www.open-mpi.org/faq/?category=running#mpirun-scheduling. I suggest you play with the --byslot --bynode options to see how this affect the performance of your application.

For the hardcore cases we provide a rankfile feature. More info at: http://www.open-mpi.org/faq/?category=tuning#using-paffinity

Enjoy,
 george.



On Dec 20, 2010, at 15:45 , Gilbert Grosdidier wrote:

Yes, there is definitely only 1 process per core with both MPI implementations.

Thanks,   G.


Le 20/12/2010 20:39, George Bosilca a écrit :
Are your processes places the same way with the two MPI implementations? Per-node vs. per-core ?

 george.

On Dec 20, 2010, at 11:14 , Gilbert Grosdidier wrote:

Bonjour,

I am now at a loss with my running of OpenMPI (namely 1.4.3)
on a SGI Altix cluster with 2048 or 4096 cores, running over Infiniband.

After fixing several rather obvious failures with Ralph, Jeff and John help,
I am now facing the bottom of this story since :
- there are no more obvious failures with messages
- compared to the running of the application with SGI-MPT, the CPU performances I get
are very low, decreasing when the number of cores increases (cf below)
- these performances are highly reproducible
- I tried a very high number of -mca parameters, to no avail

If I take as a reference the MPT CPU speed performance,
it is of about 900 (in some arbitrary unit), whatever the
number of cores I used (up to 8192).

But, when running with OMPI, I get:
- 700 with 1024 cores (which is already rather low)
- 300 with 2048 cores
- 60   with 4096 cores.

The computing loop, over which the above CPU performance is evaluated, includes
a stack of MPI exchanges [per core : 8 x (MPI_Isend + MPI_Irecv) + MPI_Waitall]

The application is of the 'domain partition' type,
and the performances, together with the memory footprint,
are very identical on all  cores. The memory footprint is twice higher in
the OMPI case (1.5GB/core) than in the MPT case (0.7GB/core).

What could be wrong with all these, please ?

I provided (in attachment) the 'ompi_info -all ' output.
The config.log is in attachment as well.
I compiled OMPI with icc. I checked numa and affinity are OK.

I use the following command to run my OMPI app:
"mpiexec -mca btl_openib_rdma_pipeline_send_length 65536\
-mca btl_openib_rdma_pipeline_frag_size 65536\
-mca btl_openib_min_rdma_pipeline_size 65536\
-mca btl_self_rdma_pipeline_send_length 262144\
-mca btl_self_rdma_pipeline_frag_size 262144\
-mca plm_rsh_num_concurrent 4096 -mca mpi_paffinity_alone 1\
-mca mpi_leave_pinned 1 -mca btl_sm_max_send_size 128\
-mca coll_tuned_pre_allocate_memory_comm_size_limit 128\
-mca btl_openib_cq_size 128 -mca btl_ofud_rd_num 128\
-mca mpool_rdma_rcache_size_limit 131072 -mca mpi_preconnect_mpi 0\
-mca mpool_sm_min_size 131072 -mca mpi_abort_print_stack 1\
-mca btl sm,openib,self -mca btl_openib_want_fork_support 0\
-mca opal_set_max_sys_limits 1 -mca osc_pt2pt_no_locks 1\
-mca osc_rdma_no_locks 1\
$PBS_JOBDIR/phmc_tm_p2.$PBS_JOBID -v -f $Jinput".

OpenIB info:

1) OFED-1.4.1, installed by SGI SGI

2) Linux xxxxxx 2.6.16.60-0.42.10-smp #1 SMP Tue Apr 27 05:11:27 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux
OS : SGI ProPack 6SP5 for Linux, Build 605r1.sles10-0909302200

3) Running most probably an SGI subnet manager

4)>  ibv_devinfo (on a worker node)
hca_id:    mlx4_0
   fw_ver:                2.7.000
   node_guid:            0030:48ff:ffcc:4c44
   sys_image_guid:            0030:48ff:ffcc:4c47
   vendor_id:            0x02c9
   vendor_part_id:            26418
   hw_ver:                0xA0
   board_id:            SM_2071000001000
   phys_port_cnt:            2
       port:    1
           state:            PORT_ACTIVE (4)
           max_mtu:        2048 (4)
           active_mtu:        2048 (4)
           sm_lid:            1
           port_lid:        6009
           port_lmc:        0x00

       port:    2
           state:            PORT_ACTIVE (4)
           max_mtu:        2048 (4)
           active_mtu:        2048 (4)
           sm_lid:            1
           port_lid:        6010
           port_lmc:        0x00

5)>  ifconfig -a (on a worker node)
eth0      Link encap:Ethernet  HWaddr 00:30:48:CE:73:30
         inet adr:192.168.159.10  Bcast:192.168.159.255  Masque:255.255.255.0
         adr inet6: fe80::230:48ff:fece:7330/64 Scope:Lien
         UP BROADCAST NOTRAILERS RUNNING MULTICAST  MTU:1500  Metric:1
         RX packets:32337499 errors:0 dropped:0 overruns:0 frame:0
         TX packets:34733462 errors:0 dropped:0 overruns:0 carrier:0
         collisions:0 lg file transmission:1000
         RX bytes:11486224753 (10954.1 Mb)  TX bytes:16450996864 (15688.8 Mb)
         Mémoire:fbc60000-fbc80000

eth1      Link encap:Ethernet  HWaddr 00:30:48:CE:73:31
         BROADCAST MULTICAST  MTU:1500  Metric:1
         RX packets:0 errors:0 dropped:0 overruns:0 frame:0
         TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
         collisions:0 lg file transmission:1000
         RX bytes:0 (0.0 b)  TX bytes:0 (0.0 b)
         Mémoire:fbce0000-fbd00000

ib0       Link encap:UNSPEC  HWaddr 80-00-00-48-FE-C0-00-00-00-00-00-00-00-00-00-00
         inet adr:10.148.9.198  Bcast:10.148.255.255  Masque:255.255.0.0
         adr inet6: fe80::230:48ff:ffcc:4c45/64 Scope:Lien
         UP BROADCAST RUNNING MULTICAST  MTU:65520  Metric:1
         RX packets:115055101 errors:0 dropped:0 overruns:0 frame:0
         TX packets:5390843 errors:0 dropped:182 overruns:0 carrier:0
         collisions:0 lg file transmission:256
         RX bytes:49592870352 (47295.4 Mb)  TX bytes:43566897620 (41548.6 Mb)

ib1       Link encap:UNSPEC  HWaddr 80-00-00-49-FE-C0-00-00-00-00-00-00-00-00-00-00
         inet adr:10.149.9.198  Bcast:10.149.255.255  Masque:255.255.0.0
         adr inet6: fe80::230:48ff:ffcc:4c46/64 Scope:Lien
         UP BROADCAST RUNNING MULTICAST  MTU:65520  Metric:1
         RX packets:673448 errors:0 dropped:0 overruns:0 frame:0
         TX packets:187 errors:0 dropped:5 overruns:0 carrier:0
         collisions:0 lg file transmission:256
         RX bytes:37713088 (35.9 Mb)  TX bytes:11228 (10.9 Kb)

lo        Link encap:Boucle locale
         inet adr:127.0.0.1  Masque:255.0.0.0
         adr inet6: ::1/128 Scope:Hôte
         UP LOOPBACK RUNNING  MTU:16436  Metric:1
         RX packets:33504149 errors:0 dropped:0 overruns:0 frame:0
         TX packets:33504149 errors:0 dropped:0 overruns:0 carrier:0
         collisions:0 lg file transmission:0
         RX bytes:5100850397 (4864.5 Mb)  TX bytes:5100850397 (4864.5 Mb)

sit0      Link encap:IPv6-dans-IPv4
         NOARP  MTU:1480  Metric:1
         RX packets:0 errors:0 dropped:0 overruns:0 frame:0
         TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
         collisions:0 lg file transmission:0
         RX bytes:0 (0.0 b)  TX bytes:0 (0.0 b)

6)>  limit (on a worker node)
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    300000 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  16384
memorylocked unlimited
maxproc      303104

If some info is still missing despite all my efforts, please ask.

Thanks in advance for any hints,   Best,      G.


<config.log.gz><ompi_info-all.001.gz>_______________________________________________