[RegCNET] Model Crashes after regular interval
IMRAN NADEEM
qphoton at gmail.com
Wed May 23 17:26:40 CEST 2007
Hi BI, Moetasim and Gao.
Thanks to all of you for discussion on my problem. I have Physical memory of
15GB ( and 15GB Swap)
which is too much for my domain having 184 x164 grid points. Anyways, I am
working on it and I will
send an email to group if I find some solution.
Regards
Imran
On 5/23/07, XUNQIANG BI <bixq at ictp.it> wrote:
>
>
> Hi, Imran:
>
> It's clear now, Your domain probably reaches the limit of your 4-CPU
> cluster. You know, like it's almost impossible to run a 1000x1000 domain
> by using just 1 CPU (except on super vector computer), a 4-CPU cluster
> has also its own limit. The solution for your problem might be:
>
> 1. Hardware upgrade
> try to see if possible to enlarge the size of memory for the cluster
> try to see if you could have (or add) more CPU for the cluster.
> reinstall the LINUX and give more swap space for system
>
> 2. RegCM configuration
> It seems that you can do multible two-month restart run;
> instead of run 10km, you change to run 12km for the same area;
> try to see if you can reduce the domain size by 4 grids on both side.
>
> Hope the above suggestion helps,
> Xunqiang Bi
>
> On Tue, 22 May 2007, IMRAN NADEEM wrote:
>
> > Hi Bi and Gao,
> >
> > I have checked there is no wall-time set by administrator. Also
> I
> > am using timestep(dt =30) which is exactly three times the horizontal
> > resolution (10km). If it is computational instability, why it occurs so
> > regularly (after every 3 months). It is not possible to make serial run
> for
> > this case immediately because it will take more than a week to reach
> 90th
> > day at which model crashes. From the part of
> > error message "failure occurred while allocating memory for a request
> > object" I guess this problem may be related to memory.
> >
> > Regards
> > Nadeem
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > 5/22/07, XUNQIANG BI <bixq at ictp.it> wrote:
> >>
> >>
> >> Hi, Imran:
> >>
> >> Can you get exact the same results between serial and parallel ?
> >>
> >> If yes, then it's easy to check where the problem is. Run the serail
> >> job for the same case to see if it crashed or not.
> >>
> >> I guess the problem is also a computational instability, the timestep
> >> problem.
> >>
> >> Regards,
> >> Bi
> >>
> >> On Tue, 22 May 2007, IMRAN NADEEM wrote:
> >>
> >> > Hi Gao,
> >> >
> >> > I don't know about wall-time set by administrator but I have not set
> any
> >> > wall-time for any job.
> >> > Yes I can restart the model after crash.
> >> >
> >> > Regards
> >> > Imran
> >> >
> >> > On 5/22/07, gaoxj at cma.gov.cn <gaoxj at cma.gov.cn> wrote:
> >> > >
> >> > > Hi Imran,
> >> > >
> >> > > Quick comments: do you or the administrator set a wall-time for
> your
> >> job
> >> > > in the computer(s)? Can the model be restarted after the crash?
> >> > >
> >> > > Gao
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > ----- Original Message -----
> >> > > *From:* IMRAN NADEEM <qphoton at gmail.com>
> >> > > *To:* regcnet at lists.ictp.it
> >> > > *Sent:* Tuesday, May 22, 2007 4:43 PM
> >> > > *Subject:* [RegCNET] Model Crashes after regular interval
> >> > >
> >> > >
> >> > > Dear RegCNET Users,
> >> > >
> >> > > I am running parallel version of RegCM3 on 4 processors. My model
> >> crashes
> >> > > after every 90 days. The error log, for
> >> > > 3 crashes that occur at 90days , 180days and 270 days, is
> attached.
> >> > > I
> >> did
> >> > > the same simulation on different machine using different
> >> > > compiler but I got the same error. I am running at dx=10km with
> >> > > dt=30.
> >> > >
> >> > > Thanks in advance
> >> > > Imran
> >> > >
> >> > > *******************************First
> >> > > Crash*******************************************
> >> > > BCs are ready from 1998123006 to 1998123012
> >> > > at day = 90.2601, ktau = 259950 : 1st, 2nd time deriv
> of
> >> > > ps
> >> =
> >> > > 0.81562E-05 0.64871E-07, no. of points w/convection = 0
> >> > > at day = 90.2774, ktau = 260000 : 1st, 2nd time deriv
> of
> >> > > ps
> >> =
> >> > > 0.10552E-04 0.65019E-07, no. of points w/convection = 0
> >> > > at day = 90.2948, ktau = 260050 : 1st, 2nd time deriv
> of
> >> > > ps
> >> =
> >> > > 0.12071E-04 0.74096E-07, no. of points w/convection = 0
> >> > > [cli_2]: aborting job:
> >> > > Fatal error in MPI_Sendrecv: Other MPI error, error stack:
> >> > > MPI_Sendrecv(217).........................:
> >> MPI_Sendrecv(sbuf=0x4080c960,
> >> > > scount=184, MPI_DOUBLE_PRECISION, dest=1, stag=2,
> rbuf=0x4080cf20,
> >> > > rcount=184, MPI_DOUBLE_PRECISION, src=3, rtag=2, MPI_COMM_WORLD,
> >> > > status=0x7ee380) failed
> >> > > MPIDI_CH3_Progress_wait(212)..............: an error occurred
> while
> >> > > handling an event returned by MPIDU_Sock_Wait()
> >> > > MPIDI_CH3I_Progress_handle_sock_event(428):
> >> > > MPIDI_EagerContigIsend(512)...............: failure occurred
> while
> >> > > allocating memory for a request object
> >> > > rank 2 in job 9 imp9_52929 caused collective abort of all
> ranks
> >> > > exit status of rank 2: killed by signal 9
> >> > > 36.314u 5.760s 53:58:42.21 0.0% 0+0k 0+0io 0pf+0w
> >> > >
> >> > > ******************************2nd
> >> > > Crash****************************************
> >> > > BCs are ready from 1999033006 to 1999033012
> >> > > at day = 180.2635, ktau = 254200 : 1st, 2nd time deriv
> of
> >> > > ps
> >> =
> >> > > 0.84223E-05 0.10490E-06, no. of points w/convection = 61
> >> > > at day = 180.2809, ktau = 254250 : 1st, 2nd time deriv
> of
> >> > > ps
> >> =
> >> > > 0.11980E-04 0.95740E-07, no. of points w/convection = 84
> >> > > [cli_2]: aborting job:
> >> > > Fatal error in MPI_Sendrecv: Other MPI error, error stack:
> >> > > MPI_Sendrecv(217).........................:
> >> MPI_Sendrecv(sbuf=0x4080c960,
> >> > > scount=184, MPI_DOUBLE_PRECISION, dest=1, stag=2,
> rbuf=0x4080cf20,
> >> > > rcount=184, MPI_DOUBLE_PRECISION, src=3, rtag=2, MPI_COMM_WORLD,
> >> > > status=0x7ee380) failed
> >> > > MPIDI_CH3_Progress_wait(212)..............: an error occurred
> while
> >> > > handling an event returned by MPIDU_Sock_Wait()
> >> > > MPIDI_CH3I_Progress_handle_sock_event(428):
> >> > > MPIDI_EagerContigIsend(512)...............: failure occurred
> while
> >> > > allocating memory for a request object
> >> > > rank 2 in job 10 imp9_52929 caused collective abort of all
> ranks
> >> > > exit status of rank 2: killed by signal 9
> >> > > 33.842u 5.688s 53:02:37.63 0.0% 0+0k 0+0io 431pf+0w
> >> > > ******************************************3rd
> >> > > Crash************************************
> >> > > Writing rad fields at ktau = 513360 1999062806
> >> > > BCs are ready from 1999062806 to 1999062812
> >> > > at day = 270.2635, ktau = 513400 : 1st, 2nd time deriv
> of
> >> > > ps
> >> =
> >> > > 0.10755E-04 0.17164E-06, no. of points w/convection = 1532
> >> > > at day = 270.2809, ktau = 513450 : 1st, 2nd time deriv
> of
> >> > > ps
> >> =
> >> > > 0.12644E-04 0.20978E-06, no. of points w/convection = 2103
> >> > > [cli_2]: aborting job:
> >> > > Fatal error in MPI_Sendrecv: Other MPI error, error stack:
> >> > > MPI_Sendrecv(217).........................:
> >> MPI_Sendrecv(sbuf=0x4080c960,
> >> > > scount=184, MPI_DOUBLE_PRECISION, dest=1, stag=2,
> rbuf=0x4080cf20,
> >> > > rcount=184, MPI_DOUBLE_PRECISION, src=3, rtag=2, MPI_COMM_WORLD,
> >> > > status=0x7ee380) failed
> >> > > MPIDI_CH3_Progress_wait(212)..............: an error occurred
> while
> >> > > handling an event returned by MPIDU_Sock_Wait()
> >> > > MPIDI_CH3I_Progress_handle_sock_event(428):
> >> > > MPIDI_EagerContigIsend(512)...............: failure occurred
> while
> >> > > allocating memory for a request object
> >> > > rank 2 in job 14 imp9_52929 caused collective abort of all
> ranks
> >> > > exit status of rank 2: killed by signal 9
> >> > > 34.102u 5.336s 53:42:44.95 0.0% 0+0k 0+0io 0pf+0w
> >> > > **************************************
> >> > >
> >> > > ------------------------------
> >> > >
> >> > > _______________________________________________
> >> > > RegCNET mailing list
> >> > > RegCNET at lists.ictp.it
> >> > > https://lists.ictp.it/mailman/listinfo/regcnet
> >> > >
> >> > >
> >> >
> >> >
> >> > --
> >> > Imran Nadeem
> >> > PhD Student
> >> > Institute of Meteorology
> >> > Department of Water, Atmosphere and Environment
> >> > Uni. of Natural Resources and Applied Life Sciences (BOKU)
> >> >
> >> > Peter-Jordan Strasse 82
> >> > 1190 Vienna, Austria
> >> >
> >> > Mobile: +43 699 1194 3044
> >> > Tel.: +43 1 47654 5614
> >> > Fax: +43 1 47654 5610
> >> >
> >>
> >> ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >> Dr. Xunqiang Bi email:bixq at ictp.it
> >> Earth System Physics Group
> >> The Abdus Salam ICTP
> >> Strada Costiera, 11
> >> P.O. BOX 586, 34100 Trieste, ITALY
> >> Tel: +39-040-2240302 Fax: +39-040-2240449
> >> ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>
> >
> >
> >
> > --
> > Imran Nadeem
> > PhD Student
> > Institute of Meteorology
> > Department of Water, Atmosphere and Environment
> > Uni. of Natural Resources and Applied Life Sciences (BOKU)
> >
> > Peter-Jordan Strasse 82
> > 1190 Vienna, Austria
> >
> > Mobile: +43 699 1194 3044
> > Tel.: +43 1 47654 5614
> > Fax: +43 1 47654 5610
> >
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. Xunqiang Bi email:bixq at ictp.it
> Earth System Physics Group
> The Abdus Salam ICTP
> Strada Costiera, 11
> P.O. BOX 586, 34100 Trieste, ITALY
> Tel: +39-040-2240302 Fax: +39-040-2240449
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
--
Imran Nadeem
PhD Student
Institute of Meteorology
Department of Water, Atmosphere and Environment
Uni. of Natural Resources and Applied Life Sciences (BOKU)
Peter-Jordan Strasse 82
1190 Vienna, Austria
Mobile: +43 699 1194 3044
Tel.: +43 1 47654 5614
Fax: +43 1 47654 5610
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