segmentation fault when running coawst_nonesting

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agpc
Posts: 63
Joined: Mon Jul 27, 2020 7:44 pm
Location: Applied Geophysics Center (AGPC)

segmentation fault when running coawst_nonesting

#1 Unread post by agpc »

Hi all,
I have a problem when running the coawst model with nonesting option. The detail of this issue is presented below:

Code: Select all

[cloud@igplogin COAWST_NONESTING]$ mpirun -np 3 ./coawstM Projects/Sarika/coupling_sarika.in 
 Coupled Input File name = Projects/Sarika/coupling_sarika.in
 Coupled Input File name = Projects/Sarika/coupling_sarika.in

 Model Coupling: 


       Ocean Model MPI nodes: 000 - 000

       Waves Model MPI nodes: 001 - 001

       Atmos Model MPI nodes: 002 - 002

       WAVgrid 01 dt= 180.0 -to- OCNgrid 01 dt=   4.0, CplInt:  1800.0 Steps: 010

       OCNgrid 01 dt=   4.0 -to- WAVgrid 01 dt= 180.0, CplInt:  1800.0 Steps: 450

       ATMgrid 01 dt=  54.0 -to- OCNgrid 01 dt=   4.0, CplInt:  1800.0 Steps: 100

       OCNgrid 01 dt=   4.0 -to- ATMgrid 01 dt=  54.0, CplInt:  1800.0 Steps: ***

       ATMgrid 02 dt=  18.0 -to- OCNgrid 01 dt=   4.0, CplInt:  1800.0 Steps: 100

       OCNgrid 01 dt=   4.0 -to- ATMgrid 02 dt=  18.0, CplInt:  1800.0 Steps: 450

       ATMgrid 01 dt=  54.0 -to- WAVgrid 01 dt= 180.0, CplInt:  1800.0 Steps: 100

       WAVgrid 01 dt= 180.0 -to- ATMgrid 01 dt=  54.0, CplInt:  1800.0 Steps: 030

       ATMgrid 02 dt=  18.0 -to- WAVgrid 01 dt= 180.0, CplInt:  1800.0 Steps: 100

       WAVgrid 01 dt= 180.0 -to- ATMgrid 02 dt=  18.0, CplInt:  1800.0 Steps: 010
--------------------------------------------------------------------------------
 Model Input Parameters:  ROMS/TOMS version 3.8  
                          Thursday - November 26, 2020 -  9:01:58 AM
--------------------------------------------------------------------------------

SWAN grid   1 is preparing computation

 module_io_quilt_old.F        2931 F
Quilting with   1 groups of   0 I/O tasks.
Quilting with   1 groups of   0 I/O tasks.

 Hurricane Sarika

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : ifort
 Compiler command : /work/users/cloud/user/manh/COAWST/LIBRARIES/mpich2/bin/mpif90
 Compiler flags   : -fp-model precise -ip -O3 -traceback -check uninit -assume byterecl -I/work/users/cloud/user/manh/COAWST/LIBRARIES/MCT/include -I/work/users/cloud/user/manh/COAWST/COAWST7//WRF/main -I/work/users/cloud/user/manh/COAWST/COAWST7//WRF/external/esmf_time_f90 -I/work/users/cloud/user/manh/COAWST/COAWST7//WRF/frame -I/work/users/cloud/user/manh/COAWST/COAWST7//WRF/share 
 MPI Communicator : -2080374780  PET size = 1

 Input Script     : 

 SVN Root URL     : https://coawstmodel.sourcerepo.com/coawstmodel/COAWST
 SVN Revision     : 1492

 Local Root       : /work/users/cloud/user/manh/COAWST/COAWST7
 Header Dir       : /work/users/cloud/user/manh/COAWST/COAWST7/Projects/Sandy
 Header file      : sandy.h
 Analytical Dir   : /work/users/cloud/user/manh/COAWST/COAWST7/Projects/Sandy

 Resolution, Grid 01: 300x220x16,  Parallel Nodes: 1,  Tiling: 1x1


 Physical Parameters, Grid: 01
 =============================

      21600  ntimes            Number of timesteps for 3-D equations.
      4.000  dt                Timestep size (s) for 3-D equations.
         28  ndtfast           Number of timesteps for 2-D equations between
                                 each 3D timestep.
          1  ERstr             Starting ensemble/perturbation run number.
          1  ERend             Ending ensemble/perturbation run number.
          0  nrrec             Number of restart records to read from disk.
          F  LcycleRST         Switch to recycle time-records in restart file.
      43200  nRST              Number of timesteps between the writing of data
                                 into restart fields.
          1  ninfo             Number of timesteps between print of information
                                 to standard output.
          T  ldefout           Switch to create a new output NetCDF file(s).
       2700  nHIS              Number of timesteps between the writing fields
                                 into history file.
       2700  ndefHIS           Number of timesteps between creation of new
                                 history files.
          0  nQCK              Number of timesteps between the writing fields
                                 into quicksave file.
          1  ntsAVG            Starting timestep for the accumulation of output
                                 time-averaged data.
      43200  nAVG              Number of timesteps between the writing of
                                 time-averaged data into averages file.
      43200  ndefAVG           Number of timesteps between creation of new
                                 time-averaged file.
 2.0000E-01  nl_tnu2(01)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 01: temp
 2.0000E-01  nl_tnu2(02)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 02: salt
 1.0000E-01  nl_visc2          NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for momentum.
          F  LuvSponge         Turning OFF sponge on horizontal momentum.
          F  LtracerSponge(01) Turning OFF sponge on tracer 01: temp
          F  LtracerSponge(02) Turning OFF sponge on tracer 02: salt
 1.0000E-06  Akt_bak(01)       Background vertical mixing coefficient (m2/s)
                                 for tracer 01: temp
 1.0000E-06  Akt_bak(02)       Background vertical mixing coefficient (m2/s)
                                 for tracer 02: salt
 1.0000E-03  Akt_limit(01)     Vertical diffusion upper threshold (m2/s)
                                 for tracer 01: temp
 1.0000E-03  Akt_limit(02)     Vertical diffusion upper threshold (m2/s)
                                 for tracer 02: salt
 1.0000E-05  Akv_bak           Background vertical mixing coefficient (m2/s)
                                 for momentum.
 1.0000E-03  Akv_limit         Vertical viscosity upper threshold (m2/s)
                                 for momentum.
 5.0000E-06  Akk_bak           Background vertical mixing coefficient (m2/s)
                                 for turbulent energy.
 5.0000E-06  Akp_bak           Background vertical mixing coefficient (m2/s)
                                 for turbulent generic statistical field.
      3.000  gls_p             GLS stability exponent.
      1.500  gls_m             GLS turbulent kinetic energy exponent.
     -1.000  gls_n             GLS turbulent length scale exponent.
 7.6000E-06  gls_Kmin          GLS minimum value of turbulent kinetic energy.
 1.0000E-12  gls_Pmin          GLS minimum value of dissipation.
 5.4770E-01  gls_cmu0          GLS stability coefficient.
 1.4400E+00  gls_c1            GLS shear production coefficient.
 1.9200E+00  gls_c2            GLS dissipation coefficient.
-4.0000E-01  gls_c3m           GLS stable buoyancy production coefficient.
 1.0000E+00  gls_c3p           GLS unstable buoyancy production coefficient.
 1.0000E+00  gls_sigk          GLS constant Schmidt number for TKE.
 1.3000E+00  gls_sigp          GLS constant Schmidt number for PSI.
   1400.000  charnok_alpha     Charnok factor for Zos calculation.
      0.500  zos_hsig_alpha    Factor for Zos calculation using Hsig(Awave).
      0.250  sz_alpha          Factor for Wave dissipation surface tke flux .
    100.000  crgban_cw         Factor for Craig/Banner surface tke flux.
      0.000  wec_alpha         WEC factor for roller/breaking energy distribution.
 3.0000E-04  rdrg              Linear bottom drag coefficient (m/s).
 2.5000E-02  rdrg2             Quadratic bottom drag coefficient.
 2.0000E-02  Zob               Bottom roughness (m).
 2.0000E-02  Zos               Surface roughness (m).
          1  lmd_Jwt           Jerlov water type.
          1  Vtransform        S-coordinate transformation equation.
          1  Vstretching       S-coordinate stretching function.
 1.0000E+01  theta_s           S-coordinate surface control parameter.
 4.0000E-01  theta_b           S-coordinate bottom  control parameter.
     50.000  Tcline            S-coordinate surface/bottom layer width (m) used
                                 in vertical coordinate stretching.
   1025.000  rho0              Mean density (kg/m3) for Boussinesq approximation.
     40.000  dstart            Time-stamp assigned to model initialization (days).
      0.000  tide_start        Reference time origin for tidal forcing (days).
20161216.00  time_ref          Reference time for units attribute (yyyymmdd.dd)
 1.0000E+00  Tnudg(01)         Nudging/relaxation time scale (days)
                                 for tracer 01: temp
 1.0000E+00  Tnudg(02)         Nudging/relaxation time scale (days)
                                 for tracer 02: salt
 9.0000E+01  Tnudg_SSS         Nudging/relaxation time scale (days)
                                 for sea surface salinity.
 0.0000E+00  Znudg             Nudging/relaxation time scale (days)
                                 for free-surface.
 0.0000E+00  M2nudg            Nudging/relaxation time scale (days)
                                 for 2D momentum.
 1.0000E+00  M3nudg            Nudging/relaxation time scale (days)
                                 for 3D momentum.
 0.0000E+00  obcfac            Factor between passive and active
                                 open boundary conditions.
          F  VolCons(1)        NLM western  edge boundary volume conservation.
          F  VolCons(2)        NLM southern edge boundary volume conservation.
          F  VolCons(3)        NLM eastern  edge boundary volume conservation.
          F  VolCons(4)        NLM northern edge boundary volume conservation.
     10.000  T0                Background potential temperature (C) constant.
     30.000  S0                Background salinity (PSU) constant.
      1.000  gamma2            Slipperiness variable: free-slip (1.0) or 
                                                      no-slip (-1.0).
          F  LuvSrc            Turning OFF momentum point Sources/Sinks.
          F  LwSrc             Turning OFF volume influx point Sources/Sinks.
          F  LtracerSrc(01)    Turning OFF point Sources/Sinks on tracer 01: temp
          F  LtracerSrc(02)    Turning OFF point Sources/Sinks on tracer 02: salt
          F  LsshCLM           Turning OFF processing of SSH climatology.
          F  Lm2CLM            Turning OFF processing of 2D momentum climatology.
          F  Lm3CLM            Turning OFF processing of 3D momentum climatology.
          F  LtracerCLM(01)    Turning OFF processing of climatology tracer 01: temp
          F  LtracerCLM(02)    Turning OFF processing of climatology tracer 02: salt
          F  LnudgeM2CLM       Turning OFF nudging of 2D momentum climatology.
          F  LnudgeM3CLM       Turning OFF nudging of 3D momentum climatology.
          F  LnudgeTCLM(01)    Turning OFF nudging of climatology tracer 01: temp
          F  LnudgeTCLM(02)    Turning OFF nudging of climatology tracer 02: salt

          T  Hout(idFsur)      Write out free-surface.
          T  Hout(idUbar)      Write out 2D U-momentum component.
          T  Hout(idVbar)      Write out 2D V-momentum component.
          T  Hout(idUvel)      Write out 3D U-momentum component.
          T  Hout(idVvel)      Write out 3D V-momentum component.
          T  Hout(idWvel)      Write out W-momentum component.
          T  Hout(idOvel)      Write out omega vertical velocity.
          T  Hout(idTvar)      Write out tracer 01: temp
          T  Hout(idTvar)      Write out tracer 02: salt
          T  Hout(idUsms)      Write out surface U-momentum stress.
          T  Hout(idVsms)      Write out surface V-momentum stress.
          T  Hout(idUbms)      Write out bottom U-momentum stress.
          T  Hout(idVbms)      Write out bottom V-momentum stress.
          T  Hout(idU2Sd)      Write out 2D u-momentum stokes velocity.
          T  Hout(idV2Sd)      Write out 2D v-momentum stokes velocity.
          T  Hout(idU3Sd)      Write out 3D u-momentum stokes velocity.
          T  Hout(idV3Sd)      Write out 3D v-momentum stokes velocity.
          T  Hout(idW3Sd)      Write out 3D omega-momentum stokes velocity.
          T  Hout(idW3St)      Write out 3D w-momentum stokes velocity.
          T  Hout(idWztw)      Write out WEC quasi-static sea level adjustment.
          T  Hout(idWqsp)      Write out WEC quasi-static pressure.
          T  Hout(idWbeh)      Write out WEC Bernoulli head.
          T  Hout(idWamp)      Write out wave height.
          T  Hout(idWlen)      Write out wavelength.
          T  Hout(idWlep)      Write out peak wavelength.
          T  Hout(idWdir)      Write out mean wave direction.
          T  Hout(idWptp)      Write out wave surface period.
          T  Hout(idWpbt)      Write out wave bottom period.
          T  Hout(idWorb)      Write out wave bottom orbital velocity.
          T  Hout(idUwav)      Wave-avg surface u-velocity.
          T  Hout(idVwav)      Wave-avg surface v-velocity.
          T  Hout(idVvis)      Write out vertical viscosity: AKv.
          T  Hout(idMtke)      Write out turbulent kinetic energy.
          T  Hout(idMtls)      Write out turbulent generic length-scale.

          T  Aout(idSdif)      Write out averaged vertical diffusion: AKt(isalt).

 Output/Input Files:

               Output Restart File:  ocean_rst1.nc
          Prefix for History Files:  ocean_hist1
         Prefix for Averages Files:  ocean_avg1
          Physical parameters File:  
                   Input Grid File:  Projects/Sarika/ROMS_COAWST_grd1.nc
      Input Nonlinear Initial File:  Projects/Sarika/Sarika_ini.nc
                Tidal Forcing File:  Projects/Sarika/tide_forc_Sarika.nc
 Ntasks in X            1 , ntasks in Y            1
 Ntasks in X            1 , ntasks in Y            1
WRF V4.1.5 MODEL
WRF V4.1.5 MODEL
 *************************************
 Parent domain
 ids,ide,jds,jde            1         301           1         221
 ims,ime,jms,jme           -4         306          -4         226
 *************************************
 Parent domain
 ids,ide,jds,jde            1         301           1         221
 ims,ime,jms,jme           -4         306          -4         226
 ips,ipe,jps,jpe            1         301           1         221
 *************************************
 ips,ipe,jps,jpe            1         301           1         221
 *************************************
DYNAMICS OPTION: Eulerian Mass Coordinate
DYNAMICS OPTION: Eulerian Mass Coordinate
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
coawstM            0000000003C193AA  Unknown               Unknown  Unknown
libpthread-2.17.s  00007F1C3961B5D0  Unknown               Unknown  Unknown
coawstM            000000000090FC93  read_phypar_             3082  read_phypar.f90
coawstM            0000000000796709  inp_par_                   87  inp_par.f90
coawstM            00000000004455D9  ocean_control_mod          90  ocean_control.f90
coawstM            000000000041EE5D  MAIN__                    373  master.f90
coawstM            0000000000418FE2  Unknown               Unknown  Unknown
libc-2.17.so       00007F1C38D5B495  __libc_start_main     Unknown  Unknown
coawstM            0000000000418EE9  Unknown               Unknown  Unknown
I also attach all of my namelist files.
Please help me to address it.
Many thanks!
Best Regards,
Attachments
Bound_spec_command.txt
(433 Bytes) Downloaded 155 times
namelist.input.txt
(4.67 KiB) Downloaded 155 times
swan_sarika.in
(4.11 KiB) Downloaded 159 times
sarika.h
(2.22 KiB) Downloaded 167 times
ocean_sarika.in
(149.63 KiB) Downloaded 175 times
coupling_sarika.in
(8.44 KiB) Downloaded 152 times

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