[MITgcm-support] MITgcm-support Digest, Vol 129, Issue 11

李志远 oceanlizy at 163.com
Sun Mar 9 07:02:56 EDT 2014


I think I learned so much, thank your for your advice ,Martin !








At 2014-03-07 21:16:53,mitgcm-support-request at mitgcm.org wrote:
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>Today's Topics:
>
>   1. Re: abnormal with extreme temperature value (Martin Losch)
>   2. Run-time errors on Archer (Dan Jones)
>   3. Re: Run-time errors on Archer (Dan Jones)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 7 Mar 2014 09:32:59 +0100
>From: Martin Losch <Martin.Losch at awi.de>
>To: MITgcm Support <mitgcm-support at mitgcm.org>
>Subject: Re: [MITgcm-support] abnormal with extreme temperature value
>Message-ID: <01254850-F485-4A4B-BFC7-350F5F37FCB3 at awi.de>
>Content-Type: text/plain; charset="utf-8"
>
>Running the (or any) model at high resolution is always a little tricky because of stability. There is the cfl stabilitly for advection and then there are numerical stability criteria for viscosity and diffusion. Please have a look at one of the tutorials, where these numbers a discussed (briefly, e.g. here: <http://mitgcm.org/public/r2_manual/latest/online_documents/node129.html>), or at any numerical modelling textbook, e.g. Steve Griffies? book on Ocean Climate Modeling.
>
>I think that this
>>  viscAh=4.E2,
>>  diffKhT=4.E2,
>>  diffKhS=4.E2,
>is the problem. I suggest to use a different set of parameters:
> viscAhGrid = 0.1,
># you?ll have to play a little with this parameter, but see pkg/mom_common/mom_calc_visc.F for more explanation, or the documentation <http://mitgcm.org/public/r2_manual/latest/online_documents/node85.html> for more options. Using the Leigth scheme is usually a good choice, which will allow you to run with probably the largest time steps possible
> diffKhT = 0.,
> diffKhS = 0., 
># that?s right, no explicit diffusion but then use a stable advection scheme with numerical diffusion to stabilize the run:
> tempAdvScheme = 33,
> saltAdvScheme = 33,
> staggerTimeStep = .TRUE.
># this is the DST3 scheme with flux limiting, see documentation. 
>
>with these parameters, I am guess that you should be able to run with time steps timeStep = 600., or even more. (don?t use deltaTmom/deltaTtracer).
>
>Martin
>
>On Mar 7, 2014, at 8:56 AM, ??? <oceanlizy at 163.com> wrote:
>
>> From: Li zhiyuan <oceanlizy at 163.com
>> >
>> To: MITgcm <
>> mitgcm-support at mitgcm.org
>> >
>> 
>> Subject:"abnormal with extreme temperature value "
>> 
>> Hi,all;
>>      I am running a model of semi-enclosed domain with 134x165x16 grid points . the model is driven by surface wind and heat flux .when I run my mitgcm model for some steps , very large temperature values occur ,then the model blows up .
>>     the STDOUT file is as below :
>> (PID.TID 0005.0001) %MON time_tsnumber                =                   163
>> (PID.TID 0005.0001) %MON time_secondsf                =   7.0416000000000E+06
>> (PID.TID 0005.0001) %MON dynstat_eta_max              =   7.4690610491135E-01
>> (PID.TID 0005.0001) %MON dynstat_eta_min              =  -4.1593172249303E+00
>> (PID.TID 0005.0001) %MON dynstat_eta_mean             =   2.0772424301492E-02
>> (PID.TID 0005.0001) %MON dynstat_eta_sd               =   4.9627339137015E-01
>> (PID.TID 0005.0001) %MON dynstat_eta_del2             =   7.4943932050348E-04
>> (PID.TID 0005.0001) %MON dynstat_uvel_max             =   3.5280025421360E+00
>> (PID.TID 0005.0001) %MON dynstat_uvel_min             =  -1.4035655480410E+00
>> (PID.TID 0005.0001) %MON dynstat_uvel_mean            =  -1.8326591842827E-02
>> (PID.TID 0005.0001) %MON dynstat_uvel_sd              =   4.5870513051871E-02
>> (PID.TID 0005.0001) %MON dynstat_uvel_del2            =   9.8327354406657E-05
>> (PID.TID 0005.0001) %MON dynstat_vvel_max             =   2.4380767316715E+00
>> (PID.TID 0005.0001) %MON dynstat_vvel_min             =  -2.3087621147168E+00
>> (PID.TID 0005.0001) %MON dynstat_vvel_mean            =   3.4329723926579E-02
>> (PID.TID 0005.0001) %MON dynstat_vvel_sd              =   9.0964738317473E-02
>> (PID.TID 0005.0001) %MON dynstat_vvel_del2            =   1.9834779107181E-04
>> (PID.TID 0005.0001) %MON dynstat_wvel_max             =   2.6286782112003E-02
>> (PID.TID 0005.0001) %MON dynstat_wvel_min             =  -9.6061814986124E-02
>> (PID.TID 0005.0001) %MON dynstat_wvel_mean            =   3.6700902646170E-05
>> (PID.TID 0005.0001) %MON dynstat_wvel_sd              =   3.4462742242225E-03
>> (PID.TID 0005.0001) %MON dynstat_wvel_del2            =   7.4810854960120E-06
>> (PID.TID 0005.0001) %MON dynstat_theta_max            =   5.7517891007917E+01
>> (PID.TID 0005.0001) %MON dynstat_theta_min            =  -1.0228097331456E+03
>> (PID.TID 0005.0001) %MON dynstat_theta_mean           =   7.8087020365565E+00
>> (PID.TID 0005.0001) %MON dynstat_theta_sd             =   6.2079576234231E+00
>> (PID.TID 0005.0001) %MON dynstat_theta_del2           =   1.3811582622522E-02
>> (PID.TID 0005.0001) %MON dynstat_salt_max             =   3.5000000000152E+01
>> (PID.TID 0005.0001) %MON dynstat_salt_min             =   3.4999999953140E+01
>> (PID.TID 0005.0001) %MON dynstat_salt_mean            =   3.4999999999999E+01
>>  
>> my data file :
>> # | Model parameters |
>> # ====================
>> #
>> # Continuous equation parameters
>>  &PARM01
>>  tRef = 16*20.,
>>  sRef = 16*35.,
>>  viscAz=1.E-4,
>>  viscAh=4.E2,
>>  diffKhT=4.E2,
>>  diffKzT=3.E-5,
>>  diffKhS=4.E2,
>>  diffKzS=3.E-5,
>>  rhoConst=1035.,
>>  rhoConstFresh=1000.,
>>  eosType = 'LINEAR',
>>  ivdc_kappa=10.,
>>  implicitDiffusion=.TRUE.,
>>  allowFreezing=.FALSE.,
>>  exactConserv=.TRUE.,
>>  hFacMin=.3,
>>  readBinaryPrec=32,
>>  &
>> 
>> # Elliptic solver parameters
>>  &PARM02
>>  cg2dMaxIters=500,
>>  cg2dTargetResidual=1.E-13,
>>  &
>> 
>> # Time stepping parameters
>>  &PARM03
>>  nIter0 =      0,
>>  nTimeSteps = 200,
>>  deltaTmom = 30.,
>>  deltaTtracer = 1200.,
>>  deltaTClock  = 43200.,
>>  abEps = 0.1,
>>  dumpFreq=   864000.,
>>  monitorFreq=1.,
>>  &
>> 
>> # Gridding parameters
>>  &PARM04
>>  usingSphericalPolarGrid=.TRUE.,
>>  delz= 10,20,25,30,50,100,100,
>>         200,300,400,500,500,500,
>>         500,500,500,
>>  ygOrigin=24.500,
>>  xgOrigin=117.525,
>>  delX=134*0.1,
>>  delY=165*0.1,
>>  &
>> 
>> # Input datasets
>>  &PARM05
>>  bathyFile=      'topo.bin',
>>  hydrogThetaFile='t16.bin',
>> # hydrogSaltFile= 'Lev_clim_salt.bin',
>> # zonalWindFile=  'Taux.bin',
>> # meridWindFile=  'Tauy.bin',
>> #thetaClimFile=  'SST.bin',
>> # saltClimFile=   'SSS.bin',
>>  &
>> 
>> I guess it  blow up because  mixing coefficients or advection scheme in my model  is incorrect , how I can avoid such problems ?
>> 
>> any quick reply is great appreciated !
>> lizhi
>> 
>> 
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>
>
>------------------------------
>
>Message: 2
>Date: Fri, 7 Mar 2014 13:12:23 +0000
>From: Dan Jones <dcjones.work at gmail.com>
>To: mitgcm-support at mitgcm.org
>Subject: [MITgcm-support] Run-time errors on Archer
>Message-ID:
>	<CAPj3iHTi__dunCGo+gxc45WMraarMMnPOWsWVtdG6fM0fShUMg at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Greetings:
>
>I am having trouble getting MITgcm to run on Archer.  I am using the Intel
>compiler (14.0.1.106) with the following defines/flags in the build options
>file:
>
>DEFINES='-DALLOW_USE_MPI -DALWAYS_USE_MPI -D_BYTESWAPIO -DWORDLENGTH=4
>-DHAVE_FLUSH'
>LIBS='-L${CRAY_MPICH2_DIR}/lib -L${HDF5_DIR}/lib -L$NETCDF_DIR/lib -lnetcdf
>-lnetcdff  -lhdf5 -lhdf5_hl'
>INCLUDES='-I${CRAY_MPICH2_DIR}/include -I${HDF5_DIR}/include
>-I${NETCDF_DIR}/include -I${HDF5_INCLUDE_OPTS}'
>FFLAGS='-h byteswapio -assume byterecl -convert big_endian -heap-arrays -O2
>-g -traceback'
>
>The code compiles with no errors, but it does not run.  The code crashes
>with the error:
>
>ABNORMAL END: S/R INI_THETA
>
>with no other information.  The initial theta file is fine and has been
>used successfully in other MITgcm model setups.  When I turn on the
>debugger (i.e. set debugMode=.TRUE. in input/eedata and set the
>debugLevel=4 in input/data), I get a *different* error that appears to
>occur in an *earlier* part of the code.  The code crashes as it tries to
>read in the bathymetry file:
>
>forrtl: error (63): output conversion error, unit -5, file Internal
>Formatted Write
>
>
>Image              PC                Routine            Line
>Source
>mitgcmuv    00000000023CCCBC  print_maprs_         4981  print.f
>mitgcmuv    000000000297FD81   plot_field_xyrs_       1841  plot_field.f
>mitgcmuv    000000000276CDC2  ini_depths_           3271  ini_depths.f
>mitgcmuv    0000000002932628   initialise_fixed_      1908
>initialise_fixed.f
>mitgcmuv    0000000002B03175   the_model_main       3052  the_model_main.f
>mitgcmuv    00000000023A38F1   MAIN__           4407  main.f
>
>Again, the bathymetry file is fine and has been used successfully before.
>The problem indicated above in ini_depths.f happens in this function:
>
>        CALL PRINT_LIST_I( OB_Jnorth, 1, OBNS_Nx, INDEX_I,
>    &                    .FALSE., .TRUE., standardMessageUnit )
>
>I can suppress the output conversion error by re-compiling with a -check
>nooutput_conversion flag, but the code quickly produces a segmentation
>fault at about the same place (ini_depths.f and the functions that call it):
>
>forrtl: severe (194): SIGSEGV, segmentation fault occurred
>
>mitgcmuv           00000000006FFAE7  print_maprs_             4982  print.f
>mitgcmuv           00000000007950D3  plot_field_xyrs_         1841
>plot_field.f
>mitgcmuv           0000000000760811  ini_depths_              3271
>ini_depths.f
>mitgcmuv           000000000078699A  initialise_fixed_        1908
>initialise_fixed.f
>mitgcmuv           00000000007AFA93  the_model_main_          3052
>the_model_main.f
>mitgcmuv           00000000006F5C41  MAIN__                   4407  main.f
>
>The fact that turning on the debugger produces an error *earlier* in the
>code is the most interesting/distressing bit here.  Is this an I/O issue?
>Has anyone else run into something like this?  I have contacted the Archer
>support team, but I thought it would be worth asking around here as well.
>
>Many thanks,
>Dan
>
>-- 
>*************************************************
>
>Dr Dan Jones
>Open Oceans Group
>British Antarctic Survey
>Cambridge, UK
>
>Phone: +44 (0)1223 221505
>Fax: +44 (0)1223 362616
>
>*************************************************
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>------------------------------
>
>Message: 3
>Date: Fri, 7 Mar 2014 13:16:45 +0000
>From: Dan Jones <dcjones.work at gmail.com>
>To: mitgcm-support at mitgcm.org
>Subject: Re: [MITgcm-support] Run-time errors on Archer
>Message-ID:
>	<CAPj3iHQJqocGZYF_dM6KS2BcWM-d06MKBf3j6xnPrJYH1tRV9Q at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Correction:
>
>The snippet of source code listed above actually comes from yet *another*
>error produced if the obcs package is included in packages.conf:
>
> forrtl: error (63): output conversion error, unit -5, file Internal
>Formatted Write
>Image              PC                Routine            Line
>Source
>mitgcmuv           000000000302A3EA  Unknown               Unknown  Unknown
>mitgcmuv           00000000023B5F85  print_list_i_            3331  print.f
>mitgcmuv           0000000001A302E7  obcs_readparms_          2425
>obcs_readparms.f
>mitgcmuv           000000000297EBF0  packages_readparm        1907
>packages_readparms.f
>mitgcmuv           0000000002932168  initialise_fixed_        1874
>initialise_fixed.f
>mitgcmuv           0000000002B03175  the_model_main_          3052
>the_model_main.f
>mitgcmuv           00000000023A38F1  MAIN__                   4407  main.f
>mitgcmuv           0000000000400F06  Unknown               Unknown  Unknown
>mitgcmuv           00000000030A8124  Unknown               Unknown  Unknown
>mitgcmuv           0000000000400DD1  Unknown               Unknown  Unknown
>
>      IF ( debugLevel.GE.debLevA ) THEN
>        CALL PRINT_LIST_I( OB_Jnorth, 1, OBNS_Nx, INDEX_I,
>    &                    .FALSE., .TRUE., standardMessageUnit )
>
>It does *not* come from ini_depths, but from obcs_readparms.  Sorry about
>that.
>
>Dan
>
>
>On Fri, Mar 7, 2014 at 1:12 PM, Dan Jones <dcjones.work at gmail.com> wrote:
>
>> Greetings:
>>
>> I am having trouble getting MITgcm to run on Archer.  I am using the Intel
>> compiler (14.0.1.106) with the following defines/flags in the build options
>> file:
>>
>> DEFINES='-DALLOW_USE_MPI -DALWAYS_USE_MPI -D_BYTESWAPIO -DWORDLENGTH=4
>> -DHAVE_FLUSH'
>> LIBS='-L${CRAY_MPICH2_DIR}/lib -L${HDF5_DIR}/lib -L$NETCDF_DIR/lib
>> -lnetcdf -lnetcdff  -lhdf5 -lhdf5_hl'
>> INCLUDES='-I${CRAY_MPICH2_DIR}/include -I${HDF5_DIR}/include
>> -I${NETCDF_DIR}/include -I${HDF5_INCLUDE_OPTS}'
>> FFLAGS='-h byteswapio -assume byterecl -convert big_endian -heap-arrays
>> -O2 -g -traceback'
>>
>> The code compiles with no errors, but it does not run.  The code crashes
>> with the error:
>>
>> ABNORMAL END: S/R INI_THETA
>>
>> with no other information.  The initial theta file is fine and has been
>> used successfully in other MITgcm model setups.  When I turn on the
>> debugger (i.e. set debugMode=.TRUE. in input/eedata and set the
>> debugLevel=4 in input/data), I get a *different* error that appears to
>> occur in an *earlier* part of the code.  The code crashes as it tries to
>> read in the bathymetry file:
>>
>> forrtl: error (63): output conversion error, unit -5, file Internal Formatted Write
>>
>>
>> Image              PC                Routine            Line
>> Source
>> mitgcmuv    00000000023CCCBC  print_maprs_         4981  print.f
>> mitgcmuv    000000000297FD81   plot_field_xyrs_       1841  plot_field.f
>> mitgcmuv    000000000276CDC2  ini_depths_           3271  ini_depths.f
>> mitgcmuv    0000000002932628   initialise_fixed_      1908
>> initialise_fixed.f
>> mitgcmuv    0000000002B03175   the_model_main       3052  the_model_main.f
>> mitgcmuv    00000000023A38F1   MAIN__           4407  main.f
>>
>> Again, the bathymetry file is fine and has been used successfully before.
>> The problem indicated above in ini_depths.f happens in this function:
>>
>>         CALL PRINT_LIST_I( OB_Jnorth, 1, OBNS_Nx, INDEX_I,
>>     &                    .FALSE., .TRUE., standardMessageUnit )
>>
>> I can suppress the output conversion error by re-compiling with a -check
>> nooutput_conversion flag, but the code quickly produces a segmentation
>> fault at about the same place (ini_depths.f and the functions that call it):
>>
>> forrtl: severe (194): SIGSEGV, segmentation fault occurred
>>
>> mitgcmuv           00000000006FFAE7  print_maprs_             4982  print.f
>> mitgcmuv           00000000007950D3  plot_field_xyrs_         1841  plot_field.f
>>
>> mitgcmuv           0000000000760811  ini_depths_              3271  ini_depths.f
>> mitgcmuv           000000000078699A  initialise_fixed_        1908  initialise_fixed.f
>> mitgcmuv           00000000007AFA93  the_model_main_          3052  the_model_main.f
>>
>> mitgcmuv           00000000006F5C41  MAIN__                   4407  main.f
>>
>> The fact that turning on the debugger produces an error *earlier* in the
>> code is the most interesting/distressing bit here.  Is this an I/O issue?
>> Has anyone else run into something like this?  I have contacted the Archer
>> support team, but I thought it would be worth asking around here as well.
>>
>> Many thanks,
>> Dan
>>
>> --
>> *************************************************
>>
>> Dr Dan Jones
>> Open Oceans Group
>> British Antarctic Survey
>> Cambridge, UK
>>
>> Phone: +44 (0)1223 221505
>> Fax: +44 (0)1223 362616
>>
>> *************************************************
>>
>
>
>
>-- 
>*************************************************
>
>Dr Dan Jones
>Open Oceans Group
>British Antarctic Survey
>Cambridge, UK
>
>Phone: +44 (0)1223 221505
>Fax: +44 (0)1223 362616
>
>*************************************************
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>End of MITgcm-support Digest, Vol 129, Issue 11
>***********************************************
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