ROMS-WW3 error: Inlet_test/WW3 test case

[huyquangtranaus]

Hi John,

I am trying to run a coupled ROMS-WW3 test case in https://github.com/DOI-USGS/COAWST/tree/main/Projects/Inlet_test/WW3 directory using COAWST 3.8 and got an error message below.

Do you have any idea what could go wrong? Thank you.

  Type 6 : Partitioned wave field data
-----------------------------------------
From : 2000/01/01 00:00:00 UTC
To : 2000/01/01 12:00:00 UTC
Interval : 01:00:00

        output dates out of run dates : Restart files second request deactivated
   Wave model ...

malloc(): invalid size (unsorted)

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:
#0 0x15146163e6ef in ???
#1 0x15146168b94c in ???
#2 0x15146163e645 in ???
#3 0x1514616287f2 in ???
#4 0x15146162912f in ???
#5 0x1514616959f6 in ???
#6 0x1514616987db in ???
#7 0x151461699808 in ???
#8 0x8547b7 in __w3initmd_MOD_w3mpio
at /data/gpfs/projects/modelling/COAWST_38/WW3/model/src/w3initmd.F90:5750
#9 0x85e995 in _w3initmd_MOD_w3init
at /data/gpfs/projects/modelling/COAWST_38/WW3/model/src/w3initmd.F90:1518
#10 0x7d708e in ww3_init
at /data/gpfs/projects/modelling/COAWST_38/WW3/model/src/ww3_shel.F90:1944
#11 0x407463 in ???
#12 0x406420 in ???
#13 0x15146162958f in ???
#14 0x15146162963f in ???
#15 0x406474 in ???
#16 0xffffffffffffffff in ???
srun: error: HPC-bm177: task 1: Aborted (core dumped)
slurmstepd: error: mpi/pmix_v4: _errhandler: HPC-bm177 [0]: pmixp_client_v2.c:211: Error handler invoked: status = -61, source = [slurm.pmix.1000316.0:1]
slurmstepd: error: *** STEP 1000316.0 ON HPC-bm177 CANCELLED AT 202

4-11-02T16:04:48 ***
srun: Job step aborted: Waiting up to 122 seconds for job step to finish.
srun: error: HPC-bm177: task 0: Killed

error.out.txt

[jcwarner-usgs]

something to do with
! 2.c Data server mode
what does your ww3_shel.inp look like
$ IOSTYP = 0 : No data server processes, direct access output from
$ each process (requires true parallel file system).
$ 1 : No data server process. All output for each type
$ performed by process that performs computations too.
$ 2 : Last process is reserved for all output, and does no
$ computing.
$ 3 : Multiple dedicated output processes.
$
1

[huyquangtranaus]

Here is my wwm_shel.inp
$ -------------------------------------------------------------------- $
$ WAVEWATCH III shell input file $
$ -------------------------------------------------------------------- $
$ Define input to be used with F/T/C flag for use or nor or coupling and
$ T/F flag for definition as a homogeneous field.
$
$ Include ice and mud parameters only if IC1/2/3/4 used :
F F Ice parameter 1
F F Ice parameter 2
F F Ice parameter 3
F F Ice parameter 4
F F Ice parameter 5
F F Mud parameter 1
F F Mud parameter 2
F F Mud parameter 3
C F Water levels
C F Currents
F F Winds
F F Ice concentrations
F F Atmospheric momentum
F F Air density
F Assimilation data : Mean parameters
F Assimilation data : 1-D spectra
F Assimilation data : 2-D spectra
$
$ Time frame of calculations ----------------------------------------- $
$ - Starting time in yyyymmdd hhmmss format.
$ - Ending time in yyyymmdd hhmmss format.
$
20000101 000000
20000101 120000
$
$ Define output data ------------------------------------------------- $
$
$ Define output server mode. This is used only in the parallel version
$ of the model. To keep the input file consistent, it is always needed.
$ IOSTYP = 1 is generally recommended. IOSTYP > 2 may be more efficient
$ for massively parallel computations. Only IOSTYP = 0 requires a true
$ parallel file system like GPFS.
$
$ IOSTYP = 0 : No data server processes, direct access output from
$ each process (requires true parallel file system).
$ 1 : No data server process. All output for each type
$ performed by process that performs computations too.
$ 2 : Last process is reserved for all output, and does no
$ computing.
$ 3 : Multiple dedicated output processes.
$
1
$
$ Five output types are available (see below). All output types share
$ a similar format for the first input line:
$ - first time in yyyymmdd hhmmss format, output interval (s), and
$ last time in yyyymmdd hhmmss format (all integers).
$ Output is disabled by setting the output interval to 0.
$
$ ------------------------------------------------------------------- $
$
$ Type 1 : Fields of mean wave parameters
$ Standard line and line with logical flags to activate output
$ fields as defined in section 2.4 of the manual. The logical
$ flags are not supplied if no output is requested. The logical
$ flags can be placed on multiple consecutive lines. However,
$ the total number and order of the logical flags is fixed.
$ The raw data file is out_grd.ww3,
$ see w3iogo.ftn for additional doc.
$
20000101 000000 600 20000101 120000
$----------------------------------------------------------------
$ Output request flags identifying fields.
$
$ The table below provides a full definition of field output parameters
$ as well as flags indicating if they are available in different field
$ output output file types (ASCII, grib, NetCDF).
$ Further definitions are found in section 2.4 of the manual.
$
$ Selection of field outputs may be made in two ways:
$ F/T flags: first flag is set to F, requests made per group (1st line)
$ followed by parameter flags (total of 10 groups).
$ Namelists: first line is set to N, next line contains parameter
$ symbol as per table below.
$
$ Example of F/T flag use is given in this sample ww3_shel.inp, below.
$ For namelist usage, see the sample ww3_ounf.inp for an example.
$
$ ----------------------------------------
$ Output field parameter definitions table
$ ----------------------------------------
$
$ All parameters listed below are available in output file of the types
$ ASCII and NetCDF. If selected output file types are grads or grib,
$ some parameters may not be available. The first two columns in the
$ table below identify such cases by flags, cols 1 (GRB) and 2 (GXO)
$ refer to grib (ww3_grib) and grads (gx_outf), respectively.
$
$ Columns 3 and 4 provide group and parameter numbers per group.
$ Columns 5, 6 and 7 provide:
$ 5 - code name (internal)
$ 6 - output tags (names used is ASCII file extensions, NetCDF
$ variable names and namelist-based selection (see ww3_ounf.inp)
$ 7 - Long parameter name/definition
$
$ G G
$ R X Grp Param Code Output Parameter/Group
$ B O Numb Numbr Name Tag Definition
$ --------------------------------------------------
$ 1 Forcing Fields
$ -------------------------------------------------
$ T T 1 1 DW DPT Water depth.
$ T T 1 2 C[X,Y] CUR Current velocity.
$ T T 1 3 UA WND Wind speed.
$ T T 1 4 AS AST Air-sea temperature difference.
$ T T 1 5 WLV WLV Water levels.
$ T T 1 6 ICE ICE Ice concentration.
$ T T 1 7 IBG IBG Iceberg-induced damping.
$ T T 1 8 D50 D50 Median sediment grain size.
$ T T 1 9 IC1 IC1 Ice thickness.
$ T T 1 10 IC5 IC5 Ice flow diameter.
$ -------------------------------------------------
$ 2 Standard mean wave Parameters
$ -------------------------------------------------
$ T T 2 1 HS HS Wave height.
$ T T 2 2 WLM LM Mean wave length.
$ T T 2 3 T02 T02 Mean wave period (Tm02).
$ T T 2 4 T0M1 T0M1 Mean wave period (Tm0,-1).
$ T T 2 5 T01 T01 Mean wave period (Tm01).
$ T T 2 6 FP0 FP Peak frequency.
$ T T 2 7 THM DIR Mean wave direction.
$ T T 2 8 THS SPR Mean directional spread.
$ T T 2 9 THP0 DP Peak direction.
$ T T 2 10 HIG HIG Infragravity height
$ T T 2 11 STMAXE MXE Max surface elev (STE)
$ T T 2 12 STMAXD MXES St Dev of max surface elev (STE)
$ T T 2 13 HMAXE MXH Max wave height (STE)
$ T T 2 14 HCMAXE MXHC Max wave height from crest (STE)
$ T T 2 15 HMAXD SDMH St Dev of MXC (STE)
$ T T 2 16 HCMAXD SDMHC St Dev of MXHC (STE)
$ F T 2 17 WBT WBT Dominant wave breaking probability bT
$ -------------------------------------------------
$ 3 Spectral Parameters (first 5)
$ -------------------------------------------------
$ T T 3 1 EF EF Wave frequency spectrum
$ T T 3 2 TH1M TH1M Mean wave direction from a1,b2
$ T T 3 3 STH1M STH1M Directional spreading from a1,b2
$ T T 3 4 TH2M TH2M Mean wave direction from a2,b2
$ T T 3 5 STH2M STH2M Directional spreading from a2,b2
$ T T 3 6 WN WN Wavenumber array
$ -------------------------------------------------
$ 4 Spectral Partition Parameters
$ -------------------------------------------------
$ T T 4 1 PHS PHS Partitioned wave heights.
$ T T 4 2 PTP PTP Partitioned peak period.
$ T T 4 3 PLP PLP Partitioned peak wave length.
$ T T 4 4 PDIR PDIR Partitioned mean direction.
$ T T 4 5 PSI PSPR Partitioned mean directional spread.
$ T T 4 6 PWS PWS Partitioned wind sea fraction.
$ T T 4 7 PTHP0 PDP Peak wave direction of partition.
$ T T 4 8 PQP PQP Goda peakdedness parameter of partition.
$ T T 4 9 PPE PPE JONSWAP peak enhancement factor of partition.
$ T T 4 10 PGW PGW Gaussian frequency width of partition.
$ T T 4 11 PSW PSW Spectral width of partition.
$ T T 4 12 PTM1 PTM10 Mean wave period (m-1,0) of partition.
$ T T 4 13 PT1 PT01 Mean wave period (m0,1) of partition.
$ T T 4 14 PT2 PT02 Mean wave period (m0,2) of partition.
$ T T 4 15 PEP PEP Peak spectral density of partition.
$ T T 4 16 PWST TWS Total wind sea fraction.
$ T T 4 17 PNR PNR Number of partitions.
$ -------------------------------------------------
$ 5 Atmosphere-waves layer
$ -------------------------------------------------
$ T T 5 1 UST UST Friction velocity.
$ F T 5 2 CHARN CHA Charnock parameter
$ F T 5 3 CGE CGE Energy flux
$ F T 5 4 PHIAW FAW Air-sea energy flux
$ F T 5 5 TAUWI[X,Y] TAW Net wave-supported stress
$ F T 5 6 TAUWN[X,Y] TWA Negative part of the wave-supported stress
$ F F 5 7 WHITECAP WCC Whitecap coverage
$ F F 5 8 WHITECAP WCF Whitecap thickness
$ F F 5 9 WHITECAP WCH Mean breaking height
$ F F 5 10 WHITECAP WCM Whitecap moment
$ F F 5 11 FWS FWS Wind sea mean period
$ -------------------------------------------------
$ 6 Wave-ocean layer
$ -------------------------------------------------
$ F F 6 1 S[XX,YY,XY] SXY Radiation stresses.
$ F F 6 2 TAUO[X,Y] TWO Wave to ocean momentum flux
$ F F 6 3 BHD BHD Bernoulli head (J term)
$ F F 6 4 PHIOC FOC Wave to ocean energy flux
$ F F 6 5 TUS[X,Y] TUS Stokes transport
$ F F 6 6 USS[X,Y] USS Surface Stokes drift
$ F F 6 7 [PR,TP]MS P2S Second-order sum pressure
$ F F 6 8 US3D USF Spectrum of surface Stokes drift
$ F F 6 9 P2SMS P2L Micro seism source term
$ F F 6 10 TAUICE TWI Wave to sea ice stress
$ F F 6 11 PHICE FIC Wave to sea ice energy flux
$ F F 6 12 USSP USP Partitioned surface Stokes drift
$ -------------------------------------------------
$ 7 Wave-bottom layer
$ -------------------------------------------------
$ F F 7 1 ABA ABR Near bottom rms amplitides.
$ F F 7 2 UBA UBR Near bottom rms velocities.
$ F F 7 3 BEDFORMS BED Bedforms
$ F F 7 4 PHIBBL FBB Energy flux due to bottom friction
$ F F 7 5 TAUBBL TBB Momentum flux due to bottom friction
$ -------------------------------------------------
$ 8 Spectrum parameters
$ -------------------------------------------------
$ F F 8 1 MSS[X,Y] MSS Mean square slopes
$ F F 8 2 MSC[X,Y] MSC Spectral level at high frequency tail
$ F F 8 3 WL02[X,Y] WL02 East/X North/Y mean wavelength compon
$ F F 8 4 ALPXT AXT Correl sea surface gradients (x,t)
$ F F 8 5 ALPYT AYT Correl sea surface gradients (y,t)
$ F F 8 6 ALPXY AXY Correl sea surface gradients (x,y)
$ -------------------------------------------------
$ 9 Numerical diagnostics
$ -------------------------------------------------
$ T T 9 1 DTDYN DTD Average time step in integration.
$ T T 9 2 FCUT FC Cut-off frequency.
$ T T 9 3 CFLXYMAX CFX Max. CFL number for spatial advection.
$ T T 9 4 CFLTHMAX CFD Max. CFL number for theta-advection.
$ F F 9 5 CFLKMAX CFK Max. CFL number for k-advection.
$ -------------------------------------------------
$ 10 User defined
$ -------------------------------------------------
$ F F 10 1 U1 User defined #1. (requires coding ...)
$ F F 10 2 U2 User defined #1. (requires coding ...)
$ -------------------------------------------------
$
$ Section 4 consist of a set of fields, index 0 = wind sea, index
$ 1:NOSWLL are first NOSWLL swell fields.
$
$ Actual active parameter selection section
$
$ (1) Forcing Fields
T
$ DPT CUR WND AST WLV ICE IBG D50 IC1 IC5
T T F T T F F F F F
$ (2) Standard mean wave Parameters
T
$ HS LM T02 T0M1 T01 FP DIR SPR DP
T T T T T T T T T
$ (3) Frequency-dependent parameters
T
$ EF TH1M STH1M TH2M STH2M WN
F F F F F F
$ (4) Spectral Partition Parameters
T
$ PHS PTP PLP PDIR PSPR PWS TWS PNR
T T T T T T T T
$ (5) Atmosphere-waves layer
T
$ UST CHA CGE FAW TAW TWA WCC WCF WCH WCM
T T T T T T T T T T
$ (6) Wave-Ocean layer
T
$ SXY TWO BHD FOC TUS USS P2S USF P2L TWI FIC
T T T T T T T F F F F
$ (7) Wave-bottom layer
T
$ ABR UBR BED FBB TBB
T T T T T
$ (8) Spectrum parameters
T
$ MSS MSC WL02 AXT AYT AXY
T T T T T T
$ (9) Numerical diagnostics
T
$ DTD FC CFX CFD CFK
T T T T T
$ (10) User defined (NOEXTR flags needed)
F
$ U1 U2
$ T T
$
$----------------------------------------------------------------
$
$ Type 2 : Point output
$ Standard line and a number of lines identifying the
$ longitude, latitude and name (C*10) of output points.
$ The list is closed by defining a point with the name
$ 'STOPSTRING'. No point info read if no point output is
$ requested (i.e., no 'STOPSTRING' needed).
$ Example for spherical grid.
$ The raw data file is out_pnt.ww3,
$ see w3iogo.ftn for additional doc.
$
$ NOTE : Spaces may be included in the name, but this is not
$ advised, because it will break the GrADS utility to
$ plots spectra and source terms, and will make it more
$ difficult to use point names in data files.
$
20000101 000000 3600 20000101 120000
$
1300. 2200. 'point1'
1450. 2200. 'point2'
1450. 1500. 'point3'
$
0.0 0.0 'STOPSTRING'
$
$ Type 3 : Output along track.
$ Flag for formatted input file.
$ The data files are track_i.ww3 and
$ track_o.ww3, see w3iotr.ftn for ad. doc.
$
20000101 000000 3600 20000101 120000
F
$
$ Type 4 : Restart files (no additional data required).
$ The data file is restartN.ww3, see
$ w3iors.ftn for additional doc.
$
20000101 000000 3600 20000101 120000
$
$ Type 5 : Boundary data (no additional data required).
$ The data file is nestN.ww3, see
$ w3iobcmd.ftn for additional doc.
$
20000101 000000 3600 20000101 120000
$
$ Type 6 : Separated wave field data (dummy for now).
$ First, last step IX and IY, flag for formatted file
$
20000101 000000 3600 20000101 120000
0 999 1 0 999 1 F
$
$ Type 7 : Coupling. (must be fully commented if not used with switch COU)
$ Namelist type selection is used here.
$ Diagnostic fields to exchange. (see namcouple for more information)
$
$ 19680606 000000 3600 20010102 000000
$ N
$
$ - Sent fields by ww3:
$ - Ocean model : T0M1 OCHA OHS DIR BHD TWO UBR FOC TAW TUS USS LM DRY
$ - Atmospheric model : ACHA AHS TP (or FP) FWS
$ - Ice model : IC5 TWI
$
$ CHA
$
$ - Received fields by ww3:
$ - Ocean model : SSH CUR
$ - Atmospheric model : WND
$ - Ice model : ICE IC1 IC5
$
$ WND
$
$ Homogeneous field data --------------------------------------------- $
$ Homogeneous fields can be defined by a list of lines containing an ID
$ string 'LEV' 'CUR' 'WND', date and time information (yyyymmdd
$ hhmmss), value (S.I. units), direction (current and wind, oceanogr.
$ convention degrees)) and air-sea temperature difference (degrees C).
$ 'STP' is mandatory stop string.
$ Also defined here are the speed with which the grid is moved
$ continuously, ID string 'MOV', parameters as for 'CUR'.
$
$ 'LEV' 19680606 010000 1.00
$ 'CUR' 19680606 073125 2.0 25.
$ 'WND' 19680606 000000 20. 145. 2.0
$ 'MOV' 19680606 013000 4.0 25.
'STP'
$
$ -------------------------------------------------------------------- $
$ End of input file $
$ -------------------------------------------------------------------- $

[huyquangtranaus]

Hi John @jcwarner-usgs , is there any more insight? Have you recently tested the Inlet_test/WW3 test case yet?

Thank you