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ROMS-WW3 error: Inlet_test/WW3 test case #330

Open huyquangtranaus opened 3 weeks ago

huyquangtranaus commented 3 weeks ago

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 ww3init

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 commented 3 weeks ago

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 commented 3 weeks ago

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 $

    1. 'point1'
    1. 'point2'
    1. '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 commented 3 weeks ago

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

Thank you