On Wed, Aug 5, 2009 at 8:10 AM, Torgny Faxen <faxen@nsc.liu.se> wrote:

Ralph,
I am running through a locally provided wrapper but it translates to:
/software/mpi/openmpi/1.3b2/i101017/bin/mpirun -np 144 -npernode 8 -mca mpi_show_mca_params env,file /nobac
kup/rossby11/faxen/RCO_scobi/src_161.openmpi/rco2.24pe

a) Upgrade.. This will take some time, it will have to go through the administrator, this is a production cluster
b) -mca .. see output below
c) I used exactly the same optimization flags for all three versions (ScaliMPI, OpenMPI and IntelMPI) and this is Fortran so I am using mpif90 :-)

Regards / Torgny

[n70:30299] ess=env (environment)
[n70:30299] orte_ess_jobid=482607105 (environment)
[n70:30299] orte_ess_vpid=0 (environment)
[n70:30299] mpi_yield_when_idle=0 (environment)
[n70:30299] mpi_show_mca_params=env,file (environment)

Ralph Castain wrote:

Could you send us the mpirun cmd line? I wonder if you are missing some options that could help. Also, you might:

(a) upgrade to 1.3.3 - it looks like you are using some kind of pre-release version

(b) add -mca mpi_show_mca_params env,file - this will cause rank=0 to output what mca params it sees, and where they came from

(c) check that you built a non-debug version, and remembered to compile your application with a -O3 flag - i.e., "mpicc -O3 ...". Remember, OMPI does not automatically add optimization flags to mpicc!

Thanks
Ralph

On Wed, Aug 5, 2009 at 7:15 AM, Torgny Faxen <faxen@nsc.liu.se <mailto:faxen@nsc.liu.se>> wrote:

Pasha,
no collectives are being used.

A simple grep in the code reveals the following MPI functions
being used:
MPI_Init
MPI_wtime
MPI_COMM_RANK
MPI_COMM_SIZE
MPI_BUFFER_ATTACH
MPI_BSEND
MPI_PACK
MPI_UNPACK
MPI_PROBE
MPI_GET_COUNT
MPI_RECV
MPI_IPROBE
MPI_FINALIZE

where MPI_IPROBE is the clear winner in terms of number of calls.

/Torgny

Pavel Shamis (Pasha) wrote:

Do you know if the application use some collective operations ?

Thanks

Pasha

Torgny Faxen wrote:

Hello,
we are seeing a large difference in performance for some
applications depending on what MPI is being used.

Attached are performance numbers and oprofile output
(first 30 lines) from one out of 14 nodes from one
application run using OpenMPI, IntelMPI and Scali MPI
respectively.

Scali MPI is faster the other two MPI:s with a factor of
1.6 and 1.75:

ScaliMPI: walltime for the whole application is 214 seconds
OpenMPI: walltime for the whole application is 376 seconds
Intel MPI: walltime for the whole application is 346 seconds.

The application is running with the main send receive
commands being:
MPI_Bsend
MPI_Iprobe followed by MPI_Recv (in case of there being a
message). Quite often MPI_Iprobe is being called just to
check whether there is a certain message pending.

Any idea on tuning tips, performance analysis, code
modifications to improve the OpenMPI performance? A lot of
time is being spent in "mca_btl_sm_component_progress",
"btl_openib_component_progress" and other internal routines.

The code is running on a cluster with 140 HP ProLiant
DL160 G5 compute servers. Infiniband interconnect. Intel
Xeon E5462 processors. The profiled application is using
144 cores on 18 nodes over Infiniband.

Regards / Torgny
=====================================================================================================================0

OpenMPI 1.3b2
=====================================================================================================================0

Walltime: 376 seconds

CPU: CPU with timer interrupt, speed 0 MHz (estimated)
Profiling through timer interrupt
samples % image name app name symbol name
668288 22.2113 mca_btl_sm.so rco2.24pe mca_btl_sm_component_progress
441828 14.6846 rco2.24pe rco2.24pe step_
335929 11.1650 libmlx4-rdmav2.so rco2.24pe (no symbols)
301446 10.0189 mca_btl_openib.so rco2.24pe btl_openib_component_progress
161033 5.3521 libopen-pal.so.0.0.0 rco2.24pe opal_progress
157024 5.2189 libpthread-2.5.so
<http://libpthread-2.5.so> rco2.24pe pthread_spin_lock

99526 3.3079 no-vmlinux no-vmlinux (no symbols)
93887 3.1204 mca_btl_sm.so rco2.24pe opal_using_threads
69979 2.3258 mca_pml_ob1.so rco2.24pe mca_pml_ob1_iprobe
58895 1.9574 mca_bml_r2.so rco2.24pe mca_bml_r2_progress
55095 1.8311 mca_pml_ob1.so rco2.24pe mca_pml_ob1_recv_request_match_wild
49286 1.6381 rco2.24pe rco2.24pe tracer_
41946 1.3941 libintlc.so.5 rco2.24pe __intel_new_memcpy
40730 1.3537 rco2.24pe rco2.24pe scobi_
36586 1.2160 rco2.24pe rco2.24pe state_
20986 0.6975 rco2.24pe rco2.24pe diag_
19321 0.6422 libmpi.so.0.0.0 rco2.24pe PMPI_Unpack
18552 0.6166 libmpi.so.0.0.0 rco2.24pe PMPI_Iprobe
17323 0.5757 rco2.24pe rco2.24pe clinic_
16194 0.5382 rco2.24pe rco2.24pe k_epsi_
15330 0.5095 libmpi.so.0.0.0 rco2.24pe PMPI_Comm_f2c
13778 0.4579 libmpi_f77.so.0.0.0 rco2.24pe mpi_iprobe_f
13241 0.4401 rco2.24pe rco2.24pe s_recv_
12386 0.4117 rco2.24pe rco2.24pe growth_
11699 0.3888 rco2.24pe rco2.24pe testnrecv_
11268 0.3745 libmpi.so.0.0.0 rco2.24pe mca_pml_base_recv_request_construct
10971 0.3646 libmpi.so.0.0.0 rco2.24pe ompi_convertor_unpack
10034 0.3335 mca_pml_ob1.so rco2.24pe mca_pml_ob1_recv_request_match_specific
10003 0.3325 libimf.so rco2.24pe exp.L
9375 0.3116 rco2.24pe rco2.24pe subbasin_
8912 0.2962 libmpi_f77.so.0.0.0 rco2.24pe mpi_unpack_f

=====================================================================================================================0

Intel MPI, version 3.2.0.011/ <http://3.2.0.011/>

=====================================================================================================================0

Walltime: 346 seconds

CPU: CPU with timer interrupt, speed 0 MHz (estimated)
Profiling through timer interrupt
samples % image name app name symbol name
486712 17.7537 rco2 rco2 step_
431941 15.7558 no-vmlinux no-vmlinux (no symbols)
212425 7.7486 libmpi.so.3.2 rco2 MPIDI_CH3U_Recvq_FU
188975 6.8932 libmpi.so.3.2 rco2 MPIDI_CH3I_RDSSM_Progress
172855 6.3052 libmpi.so.3.2 rco2 MPIDI_CH3I_read_progress
121472 4.4309 libmpi.so.3.2 rco2 MPIDI_CH3I_SHM_read_progress
64492 2.3525 libc-2.5.so <http://libc-2.5.so> rco2 sched_yield

52372 1.9104 rco2 rco2 tracer_
48621 1.7735 libmpi.so.3.2 rco2 .plt
45475 1.6588 libmpiif.so.3.2 rco2 pmpi_iprobe__
44082 1.6080 libmpi.so.3.2 rco2 MPID_Iprobe
42788 1.5608 libmpi.so.3.2 rco2 MPIDI_CH3_Stop_recv
42754 1.5595 libpthread-2.5.so
<http://libpthread-2.5.so> rco2 pthread_mutex_lock

42190 1.5390 libmpi.so.3.2 rco2 PMPI_Iprobe
41577 1.5166 rco2 rco2 scobi_
40356 1.4721 libmpi.so.3.2 rco2 MPIDI_CH3_Start_recv
38582 1.4073 libdaplcma.so.1.0.2 rco2 (no symbols)
37545 1.3695 rco2 rco2 state_
35597 1.2985 libc-2.5.so <http://libc-2.5.so> rco2 free
34019 1.2409 libc-2.5.so <http://libc-2.5.so> rco2 malloc

31841 1.1615 rco2 rco2 s_recv_
30955 1.1291 libmpi.so.3.2 rco2 __I_MPI___intel_new_memcpy
27876 1.0168 libc-2.5.so <http://libc-2.5.so> rco2 _int_malloc

26963 0.9835 rco2 rco2 testnrecv_
23005 0.8391 libpthread-2.5.so
<http://libpthread-2.5.so> rco2 __pthread_mutex_unlock_usercnt

22290 0.8131 libmpi.so.3.2 rco2 MPID_Segment_manipulate
22086 0.8056 libmpi.so.3.2 rco2 MPIDI_CH3I_read_progress_expected
19146 0.6984 rco2 rco2 diag_
18250 0.6657 rco2 rco2 clinic_
=====================================================================================================================0

Scali MPI, version 3.13.10-59413
=====================================================================================================================0

Walltime:

CPU: CPU with timer interrupt, speed 0 MHz (estimated)
Profiling through timer interrupt
samples % image name app name symbol name
484267 30.0664 rco2.24pe rco2.24pe step_
111949 6.9505 libmlx4-rdmav2.so rco2.24pe (no symbols)
73930 4.5900 libmpi.so rco2.24pe scafun_rq_handle_body
57846 3.5914 libmpi.so rco2.24pe invert_decode_header
55836 3.4667 libpthread-2.5.so
<http://libpthread-2.5.so> rco2.24pe pthread_spin_lock

53703 3.3342 rco2.24pe rco2.24pe tracer_
40934 2.5414 rco2.24pe rco2.24pe scobi_
40244 2.4986 libmpi.so rco2.24pe scafun_request_probe_handler
37399 2.3220 rco2.24pe rco2.24pe state_
30455 1.8908 libmpi.so rco2.24pe invert_matchandprobe
29707 1.8444 no-vmlinux no-vmlinux (no symbols)
29147 1.8096 libmpi.so rco2.24pe FMPI_scafun_Iprobe
27969 1.7365 libmpi.so rco2.24pe decode_8_u_64
27475 1.7058 libmpi.so rco2.24pe scafun_rq_anysrc_fair_one
25966 1.6121 libmpi.so rco2.24pe scafun_uxq_probe
24380 1.5137 libc-2.5.so <http://libc-2.5.so> rco2.24pe memcpy

22615 1.4041 libmpi.so rco2.24pe .plt
21172 1.3145 rco2.24pe rco2.24pe diag_
20716 1.2862 libc-2.5.so <http://libc-2.5.so> rco2.24pe memset

18565 1.1526 libmpi.so rco2.24pe openib_wrapper_poll_cq
18192 1.1295 rco2.24pe rco2.24pe clinic_
17135 1.0638 libmpi.so rco2.24pe PMPI_Iprobe
16685 1.0359 rco2.24pe rco2.24pe k_epsi_
16236 1.0080 libmpi.so rco2.24pe PMPI_Unpack
15563 0.9662 libmpi.so rco2.24pe scafun_r_rq_append
14829 0.9207 libmpi.so rco2.24pe scafun_rq_test_finished
13349 0.8288 rco2.24pe rco2.24pe s_recv_
12490 0.7755 libmpi.so rco2.24pe flop_matchandprobe
12427 0.7715 libibverbs.so.1.0.0 rco2.24pe (no symbols)
12272 0.7619 libmpi.so rco2.24pe scafun_rq_handle
12146 0.7541 rco2.24pe rco2.24pe growth_
10175 0.6317 libmpi.so rco2.24pe wrp2p_test_finished
9888 0.6139 libimf.so rco2.24pe exp.L
9179 0.5699 rco2.24pe rco2.24pe subbasin_
9082 0.5639 rco2.24pe rco2.24pe testnrecv_
8901 0.5526 libmpi.so rco2.24pe openib_wrapper_purge_requests
7425 0.4610 rco2.24pe rco2.24pe scobimain_
7378 0.4581 rco2.24pe rco2.24pe scobi_interface_
6530 0.4054 rco2.24pe rco2.24pe setvbc_
6471 0.4018 libfmpi.so rco2.24pe pmpi_iprobe
6341 0.3937 rco2.24pe rco2.24pe snap_

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-- ---------------------------------------------------------
Torgny Faxén National Supercomputer Center
Linköping University S-581 83 Linköping
Sweden
Email:faxen@nsc.liu.se <mailto:Email%3Afaxen@nsc.liu.se>

Telephone: +46 13 285798 (office) +46 13 282535 (fax)
http://www.nsc.liu.se
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--
---------------------------------------------------------
Torgny Faxén
National Supercomputer Center
Linköping University
S-581 83 Linköping
Sweden

Email:faxen@nsc.liu.se
Telephone: +46 13 285798 (office) +46 13 282535 (fax)
http://www.nsc.liu.se
---------------------------------------------------------

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