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Subject: Re: [OMPI users] Performance difference on OpenMPI, IntelMPI and ScaliMPI
From: Torgny Faxen (faxen_at_[hidden])
Date: 2009-08-05 10:10:17


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_at_[hidden]
> <mailto:faxen_at_[hidden]>> 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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> users_at_[hidden] <mailto:users_at_[hidden]>
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
>
> --
> ---------------------------------------------------------
> Torgny Faxén
> National Supercomputer Center
> Linköping University
> S-581 83 Linköping
> Sweden
>
> Email:faxen_at_[hidden] <mailto:Email%3Afaxen_at_[hidden]>
> Telephone: +46 13 285798 (office) +46 13 282535 (fax)
> http://www.nsc.liu.se
> ---------------------------------------------------------
>
>
> _______________________________________________
> users mailing list
> users_at_[hidden] <mailto:users_at_[hidden]>
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> ------------------------------------------------------------------------
>
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-- 
---------------------------------------------------------
   Torgny Faxén		
   National Supercomputer Center
   Linköping University	
   S-581 83 Linköping
   Sweden	
   Email:faxen_at_[hidden]
   Telephone: +46 13 285798 (office) +46 13 282535  (fax)
   http://www.nsc.liu.se
---------------------------------------------------------