Hi everyone. I am new to ROMS. I compiled ROMS (Checked out revision 963)with ./build.bash and the "romsG" executable and "build_romsG" folder was made without any error(on Fedora 25, using gfortran, netcdf 4 and mpich libs). but at the first runnig of upwelling test case by the command: ./oceanG < roms_upwelling.in, i get errors as below:
[ghasedak@nobody upwelling]$ ./romsG < roms_upwelling.in
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Model Input Parameters: ROMS/TOMS version 3.7
Saturday - April 27, 2019 - 7:38:12 PM
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INP_PAR - Unable to open ROMS/TOMS input script file.
In distributed-memory applications, the input
script file is processed in parallel. The Unix
routine GETARG is used to get script file name.
For example, in MPI applications make sure that
command line is something like:
mpirun -np 4 romsM roms.in
and not
mpirun -np 4 romsM < roms.in
Found Error: 02 Line: 111 Source: ROMS/Drivers/nl_ocean.h
Elapsed CPU time (seconds):
memory.f90:58: runtime error: load of null pointer of type 'integer(kind=4)'
ASAN:DEADLYSIGNAL
=================================================================
==13659==ERROR: AddressSanitizer: SEGV on unknown address 0x000000000000 (pc 0x000000408581 bp 0x7fff7bf78ad0 sp 0x7fff7bf78390 T0)
#0 0x408580 in memory_ /home/ghasedak/Projects/upwelling/Build_romsG/memory.f90:58
#1 0x406286 in __ocean_control_mod_MOD_roms_finalize /home/ghasedak/Projects/upwelling/Build_romsG/ocean_control.f90:255
#2 0x404b1b in ocean /home/ghasedak/Projects/upwelling/Build_romsG/master.f90:115
#3 0x404bce in main /home/ghasedak/Projects/upwelling/Build_romsG/master.f90:50
#4 0x7f7d5c2ce430 in __libc_start_main (/lib64/libc.so.6+0x20430)
#5 0x4040e9 in _start (/home/ghasedak/Projects/upwelling/romsG+0x4040e9)
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV /home/ghasedak/Projects/upwelling/Build_romsG/memory.f90:58 in memory_
==13659==ABORTING
______________________________________________________________
! as the error "Found Error: 02 Line: 111 Source: ROMS/Drivers/nl_ocean.h" i think the main error is about "inp_par.f90" but i dont know how change or fix this file. also some other files that mentioned in error lines are attached. Can you kindly help what went wrong
first time running upwelling test case
first time running upwelling test case
- Attachments
-
ocean_control.f90- (9.06 KiB) Downloaded 454 times
-
- master.f90
- (5.43 KiB) Downloaded 438 times
-
- memory.f90
- (8.24 KiB) Downloaded 425 times
-
- upwelling.h
- (1.71 KiB) Downloaded 459 times
-
- roms_upwelling.in
- (131.95 KiB) Downloaded 440 times
-
- inp_par.f90
- (34.15 KiB) Downloaded 474 times
-
- varinfo.dat
- (150.34 KiB) Downloaded 422 times
Re: first time running upwelling test case
ROMS told you the problem:
You need to try "./romsG roms_upwelling.in" or perhaps:
Code: Select all
In distributed-memory applications, the input
script file is processed in parallel. The Unix
routine GETARG is used to get script file name.
For example, in MPI applications make sure that
command line is something like:
mpirun -np 4 romsM roms.in
and not
mpirun -np 4 romsM < roms.inCode: Select all
mpirun -np 4 ./romsG roms_upwelling.inRe: first time running upwelling test case
thanks Kate.
i use "./romsG roms_upwelling.in" and now i get this:
[ghasedak@nobody upwelling]$ ./romsG roms_upwelling.in
--------------------------------------------------------------------------------
Model Input Parameters: ROMS/TOMS version 3.7
Sunday - April 28, 2019 - 1:30:38 PM
--------------------------------------------------------------------------------
Wind-Driven Upwelling/Downwelling over a Periodic Channel
Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/local/bin/mpif90
Compiler flags : -frepack-arrays -g -fbounds-check -fbacktrace -fcheck=all -fsanitize=address -fsanitize=undefined -finit-real=nan -ffpe-trap=invalid,zero,overflow -
MPI Communicator : 1140850688 PET size = 1
Input Script : roms_upwelling.in
SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 963M
Local Root : /home/ghasedak/src
Header Dir : /home/ghasedak/Projects/upwelling
Header file : upwelling.h
Analytical Dir: /home/ghasedak/Projects/upwelling
Resolution, Grid 01: 41x80x16, Parallel Nodes: 1, Tiling: 1x1
Physical Parameters, Grid: 01
=============================
1440 ntimes Number of timesteps for 3-D equations.
300.000 dt Timestep size (s) for 3-D equations.
30 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.
T LcycleRST Switch to recycle time-records in restart file.
288 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).
72 nHIS Number of timesteps between the writing fields
into history file.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
72 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
72 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
5.0000E+00 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-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
3.0000E+00 theta_s S-coordinate surface control parameter.
0.0000E+00 theta_b S-coordinate bottom control parameter.
25.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
0.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+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.
14.000 T0 Background potential temperature (C) constant.
35.000 S0 Background salinity (PSU) constant.
1027.000 R0 Background density (kg/m3) used in linear Equation
of State.
1.7000E-04 Tcoef Thermal expansion coefficient (1/Celsius).
0.0000E+00 Scoef Saline contraction coefficient (1/PSU).
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 Aout(idFsur) Write out averaged free-surface.
T Aout(idUbar) Write out averaged 2D U-momentum component.
T Aout(idVbar) Write out averaged 2D V-momentum component.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idVvel) Write out averaged 3D V-momentum component.
T Aout(idWvel) Write out averaged W-momentum component.
T Aout(idOvel) Write out averaged omega vertical velocity.
T Aout(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt
T Dout(M2rate) Write out 2D momentum acceleration.
T Dout(M2pgrd) Write out 2D momentum pressure gradient.
T Dout(M2fcor) Write out 2D momentum Coriolis force.
T Dout(M2hadv) Write out 2D momentum horizontal advection.
T Dout(M2xadv) Write out 2D momentum horizontal X-advection.
T Dout(M2yadv) Write out 2D momentum horizontal Y-advection.
T Dout(M2hvis) Write out 2D momentum horizontal viscosity.
T Dout(M2xvis) Write out 2D momentum horizontal X-viscosity.
T Dout(M2yvis) Write out 2D momentum horizontal Y-viscosity.
T Dout(M2sstr) Write out 2D momentum surface stress.
T Dout(M2bstr) Write out 2D momentum bottom stress.
T Dout(M3rate) Write out 3D momentum acceleration.
T Dout(M3pgrd) Write out 3D momentum pressure gradient.
T Dout(M3fcor) Write out 3D momentum Coriolis force.
T Dout(M3hadv) Write out 3D momentum horizontal advection.
T Dout(M3xadv) Write out 3D momentum horizontal X-advection.
T Dout(M3yadv) Write out 3D momentum horizontal Y-advection.
T Dout(M3vadv) Write out 3D momentum vertical advection.
T Dout(M3hvis) Write out 3D momentum horizontal viscosity.
T Dout(M3xvis) Write out 3D momentum horizontal X-viscosity.
T Dout(M3yvis) Write out 3D momentum horizontal Y-viscosity.
T Dout(M3vvis) Write out 3D momentum vertical viscosity.
T Dout(iTrate) Write out rate of change of tracer 01: temp
T Dout(iTrate) Write out rate of change of tracer 02: salt
T Dout(iThadv) Write out horizontal advection, tracer 01: temp
T Dout(iThadv) Write out horizontal advection, tracer 02: salt
T Dout(iTxadv) Write out horizontal X-advection, tracer 01: temp
T Dout(iTxadv) Write out horizontal X-advection, tracer 02: salt
T Dout(iTyadv) Write out horizontal Y-advection, tracer 01: temp
T Dout(iTyadv) Write out horizontal Y-advection, tracer 02: salt
T Dout(iTvadv) Write out vertical advection, tracer 01: temp
T Dout(iTvadv) Write out vertical advection, tracer 02: salt
T Dout(iThdif) Write out horizontal diffusion, tracer 01: temp
T Dout(iThdif) Write out horizontal diffusion, tracer 02: salt
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 01: temp
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 02: salt
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 01: temp
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 02: salt
T Dout(iTvdif) Write out vertical diffusion, tracer 01: temp
T Dout(iTvdif) Write out vertical diffusion, tracer 02: salt
Output/Input Files:
Output Restart File: roms_rst.nc
Output History File: roms_his.nc
Output Averages File: roms_avg.nc
Output Diagnostics File: roms_dia.nc
Tile partition information for Grid 01: 41x80x16 tiling: 1x1
tile Istr Iend Jstr Jend Npts
0 1 41 1 80 52480
Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)
tile Xmin Xmax Ymin Ymax grid
0 0.50 41.50 0.50 80.50 RHO-points
0 1.00 41.00 0.50 80.50 U-points
0 0.50 41.50 1.00 80.00 V-points
Maximum halo size in XI and ETA directions:
HaloSizeI(1) = 162
HaloSizeJ(1) = 273
TileSide(1) = 85
TileSize(1) = 4080
Lateral Boundary Conditions: NLM
============================
Variable Grid West Edge South Edge East Edge North Edge
--------- ---- ---------- ---------- ---------- ----------
zeta 1 Periodic Closed Periodic Closed
ubar 1 Periodic Closed Periodic Closed
vbar 1 Periodic Closed Periodic Closed
u 1 Periodic Closed Periodic Closed
v 1 Periodic Closed Periodic Closed
temp 1 Periodic Closed Periodic Closed
salt 1 Periodic Closed Periodic Closed
Activated C-preprocessing Options:
UPWELLING Wind-Driven Upwelling/Downwelling over a Periodic Channel
ANA_BSFLUX Analytical kinematic bottom salinity flux
ANA_BTFLUX Analytical kinematic bottom temperature flux
ANA_GRID Analytical grid set-up
ANA_INITIAL Analytical initial conditions
ANA_SMFLUX Analytical kinematic surface momentum flux
ANA_SSFLUX Analytical kinematic surface salinity flux
ANA_STFLUX Analytical kinematic surface temperature flux
ANA_VMIX Analytical vertical mixing coefficients
ASSUMED_SHAPE Using assumed-shape arrays
AVERAGES Writing out time-averaged nonlinear model fields
!BOUNDARY_ALLGATHER Using mpi_allreduce in mp_boundary routine
!COLLECT_ALL... Using mpi_isend/mpi_recv in mp_collect routine
DIAGNOSTICS_TS Computing and writing tracer diagnostic terms
DIAGNOSTICS_UV Computing and writing momentum diagnostic terms
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002)
DOUBLE_PRECISION Double precision arithmetic numerical kernel.
MIX_S_TS Mixing of tracers along constant S-surfaces
MIX_S_UV Mixing of momentum along constant S-surfaces
MPI MPI distributed-memory configuration
NONLINEAR Nonlinear Model
!NONLIN_EOS Linear Equation of State for seawater
POWER_LAW Power-law shape time-averaging barotropic filter
PROFILE Time profiling activated
REDUCE_ALLGATHER Using mpi_allgather in mp_reduce routine
!RST_SINGLE Double precision fields in restart NetCDF file
SALINITY Using salinity
SOLVE3D Solving 3D Primitive Equations
SPLINES_VDIFF Parabolic Spline Reconstruction for Vertical Diffusion
SPLINES_VVISC Parabolic Spline Reconstruction for Vertical Viscosity
TS_U3HADVECTION Third-order upstream horizontal advection of tracers
TS_C4VADVECTION Fourth-order centered vertical advection of tracers
TS_DIF2 Harmonic mixing of tracers
UV_ADV Advection of momentum
UV_COR Coriolis term
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum
UV_C4VADVECTION Fourth-order centered vertical advection of momentum
UV_LDRAG Linear bottom stress
UV_VIS2 Harmonic mixing of momentum
VAR_RHO_2D Variable density barotropic mode
Process Information:
Node # 0 (pid= 18367) is active.
INITIAL: Configuring and initializing forward nonlinear model ...
*******
ANA_GRID - x-location of PSI-points: x_psi
(Grid = 01, Min = 0.00000000E+00 Max = 4.00000000E+04)
ANA_GRID - y-location of PSI-points: y_psi
(Grid = 01, Min = 0.00000000E+00 Max = 8.00000000E+04)
ANA_GRID - x-location of RHO-points: x_rho
(Grid = 01, Min = 5.00000000E+02 Max = 4.05000000E+04)
ANA_GRID - y-location of RHO-points: y_rho
(Grid = 01, Min = -5.00000000E+02 Max = 8.05000000E+04)
ANA_GRID - x-location of U-points: x_u
(Grid = 01, Min = 0.00000000E+00 Max = 4.00000000E+04)
ANA_GRID - y-location of U-points: y_u
(Grid = 01, Min = -5.00000000E+02 Max = 8.05000000E+04)
ANA_GRID - x-location of V-points: x_v
(Grid = 01, Min = 5.00000000E+02 Max = 4.05000000E+04)
ANA_GRID - y-location of V-points: y_v
(Grid = 01, Min = 0.00000000E+00 Max = 8.00000000E+04)
ANA_GRID - reciprocal XI-grid spacing: pm
(Grid = 01, Min = 1.00000000E-03 Max = 1.00000000E-03)
ANA_GRID - reciprocal ETA-grid spacing: pn
(Grid = 01, Min = 1.00000000E-03 Max = 1.00000000E-03)
ANA_GRID - angle between XI-axis and EAST: angler
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_GRID - Coriolis parameter at RHO-points: f
(Grid = 01, Min = -8.26000000E-05 Max = -8.26000000E-05)
ANA_GRID - bathymetry at RHO-points: h
(Grid = 01, Min = 2.52004887E+01 Max = 1.50000000E+02)
Vertical S-coordinate System, Grid 01:
level S-coord Cs-curve Z at hmin at hc half way at hmax
16 0.0000000 0.0000000 0.000 0.000 0.000 0.000
15 -0.0625000 -0.0019442 -0.809 -0.806 -1.348 -1.589
14 -0.1250000 -0.0078455 -1.668 -1.661 -2.966 -3.687
13 -0.1875000 -0.0179119 -2.580 -2.568 -4.867 -6.321
12 -0.2500000 -0.0324983 -3.549 -3.531 -7.077 -9.535
11 -0.3125000 -0.0521190 -4.581 -4.558 -9.630 -13.397
10 -0.3750000 -0.0774659 -5.686 -5.656 -12.573 -17.996
9 -0.4375000 -0.1094327 -6.875 -6.837 -15.967 -23.445
8 -0.5000000 -0.1491465 -8.162 -8.114 -19.889 -29.890
7 -0.5625000 -0.1980075 -9.564 -9.506 -24.435 -37.512
6 -0.6250000 -0.2577387 -11.104 -11.034 -29.721 -46.531
5 -0.6875000 -0.3304460 -12.808 -12.724 -35.892 -57.218
4 -0.7500000 -0.4186931 -14.709 -14.609 -43.121 -69.903
3 -0.8125000 -0.5255915 -16.846 -16.726 -51.622 -84.987
2 -0.8750000 -0.6549105 -19.266 -19.124 -61.651 -102.953
1 -0.9375000 -0.8112096 -22.028 -21.859 -73.518 -124.388
0 -1.0000000 -1.0000000 -25.200 -25.000 -87.600 -150.000
Time Splitting Weights for Grid 01: ndtfast = 30 nfast = 42
==================================
Primary Secondary Accumulated to Current Step
1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257356 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864348 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001213 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565097 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906204 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716643 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402368 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399432 0.6603333185976138
21 0.0256737146312911 0.0297153720153352 0.1342125541712342 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524359 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729578 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236653 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893981 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886213 0.8237939964192927
27 0.0432936737565710 0.0230872677537126 0.3506756411451924 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772280 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880565 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442384 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256415 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325521 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348098 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479478 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213239 0.9738247715198165
36 0.0503158038019030 0.0080591141492892 0.8085423793232269 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079423 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497611 0.9930692679747334
39 0.0376397765791564 0.0033640675316746 0.9367177506289175 0.9964333355064080
40 0.0305543017255206 0.0021094083123694 0.9672720523544381 0.9985427438187774
41 0.0217382098544504 0.0010909315881854 0.9890102622088885 0.9996336754069628
42 0.0109897377911118 0.0003663245930371 1.0000000000000004 0.9999999999999999
ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000
Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):
1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000
Power filter parameters, Fgamma, gamma = 0.28400 0.18933
Metrics information for Grid 01:
===============================
Minimum X-grid spacing, DXmin = 1.00000000E+00 km
Maximum X-grid spacing, DXmax = 1.00000000E+00 km
Minimum Y-grid spacing, DYmin = 1.00000000E+00 km
Maximum Y-grid spacing, DYmax = 1.00000000E+00 km
Minimum Z-grid spacing, DZmin = 8.08965824E-01 m
Maximum Z-grid spacing, DZmax = 2.56123321E+01 m
Minimum barotropic Courant Number = 2.22358627E-01
Maximum barotropic Courant Number = 5.42494240E-01
Maximum Coriolis Courant Number = 2.47800000E-02
ANA_INITIAL - vertically integrated u-momentum component: ubar
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - vertically integrated v-momentum component: vbar
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - free-surface: zeta
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - u-momentum component: u
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - v-momentum component: v
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - potential temperature: temp
(Grid = 01, Min = 1.45204834E+01 Max = 2.19365219E+01)
ANA_INITIAL - salinity: salt
(Grid = 01, Min = 3.50000000E+01 Max = 3.50000000E+01)
Basin information for Grid 01:
Maximum grid stiffness ratios: rx0 = 6.931666E-02 (Beckmann and Haidvogel)
rx1 = 8.661243E-01 (Haney)
Initial domain volumes: TotVolume = 3.8843755884E+11 m3
MinCellVol = 8.4521383562E+05 m3
MaxCellVol = 2.5612332106E+07 m3
Max/Min = 3.0302783777E+01
NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 000000000001 - 000000001440)
TIME-STEP YYYY-MM-DD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed
0 0001-01-01 00:00:00.00 0.000000E+00 6.585677E+02 6.585677E+02 3.884376E+11
(00,00,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: roms_his.nc
ASAN:DEADLYSIGNAL
=================================================================
==18367==ERROR: AddressSanitizer: SEGV on unknown address 0x00000000000b (pc 0x7fde4f65ebe1 bp 0x000000000000 sp 0x7ffe80ad5c60 T0)
#0 0x7fde4f65ebe0 in __netcdf_MOD_nf90_create /home/ghasedak/Downloads/netcdf-fortran-4.4.4/fortran/netcdf4_file.f90:111
#1 0x1f23f39 in __mod_netcdf_MOD_netcdf_create /home/ghasedak/Projects/upwelling/Build_romsG/mod_netcdf.f90:6479
#2 0x18f9860 in def_his_ /home/ghasedak/Projects/upwelling/Build_romsG/def_his.f90:69
#3 0x7e4059 in output_ /home/ghasedak/Projects/upwelling/Build_romsG/output.f90:112
#4 0x70a84d in main3d_ /home/ghasedak/Projects/upwelling/Build_romsG/main3d.f90:231
#5 0x406b5c in __ocean_control_mod_MOD_roms_run /home/ghasedak/Projects/upwelling/Build_romsG/ocean_control.f90:181
#6 0x404b16 in ocean /home/ghasedak/Projects/upwelling/Build_romsG/master.f90:108
#7 0x404bce in main /home/ghasedak/Projects/upwelling/Build_romsG/master.f90:50
#8 0x7fde4d05b430 in __libc_start_main (/lib64/libc.so.6+0x20430)
#9 0x4040e9 in _start (/home/ghasedak/Projects/upwelling/romsG+0x4040e9)
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV /home/ghasedak/Downloads/netcdf-fortran-4.4.4/fortran/netcdf4_file.f90:111 in __netcdf_MOD_nf90_create
==18367==ABORTING
________________________________________________________________________
i use "./romsG roms_upwelling.in" and now i get this:
[ghasedak@nobody upwelling]$ ./romsG roms_upwelling.in
--------------------------------------------------------------------------------
Model Input Parameters: ROMS/TOMS version 3.7
Sunday - April 28, 2019 - 1:30:38 PM
--------------------------------------------------------------------------------
Wind-Driven Upwelling/Downwelling over a Periodic Channel
Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/local/bin/mpif90
Compiler flags : -frepack-arrays -g -fbounds-check -fbacktrace -fcheck=all -fsanitize=address -fsanitize=undefined -finit-real=nan -ffpe-trap=invalid,zero,overflow -
MPI Communicator : 1140850688 PET size = 1
Input Script : roms_upwelling.in
SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 963M
Local Root : /home/ghasedak/src
Header Dir : /home/ghasedak/Projects/upwelling
Header file : upwelling.h
Analytical Dir: /home/ghasedak/Projects/upwelling
Resolution, Grid 01: 41x80x16, Parallel Nodes: 1, Tiling: 1x1
Physical Parameters, Grid: 01
=============================
1440 ntimes Number of timesteps for 3-D equations.
300.000 dt Timestep size (s) for 3-D equations.
30 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.
T LcycleRST Switch to recycle time-records in restart file.
288 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).
72 nHIS Number of timesteps between the writing fields
into history file.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
72 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
72 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
5.0000E+00 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-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
3.0000E+00 theta_s S-coordinate surface control parameter.
0.0000E+00 theta_b S-coordinate bottom control parameter.
25.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
0.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+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.
14.000 T0 Background potential temperature (C) constant.
35.000 S0 Background salinity (PSU) constant.
1027.000 R0 Background density (kg/m3) used in linear Equation
of State.
1.7000E-04 Tcoef Thermal expansion coefficient (1/Celsius).
0.0000E+00 Scoef Saline contraction coefficient (1/PSU).
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 Aout(idFsur) Write out averaged free-surface.
T Aout(idUbar) Write out averaged 2D U-momentum component.
T Aout(idVbar) Write out averaged 2D V-momentum component.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idVvel) Write out averaged 3D V-momentum component.
T Aout(idWvel) Write out averaged W-momentum component.
T Aout(idOvel) Write out averaged omega vertical velocity.
T Aout(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt
T Dout(M2rate) Write out 2D momentum acceleration.
T Dout(M2pgrd) Write out 2D momentum pressure gradient.
T Dout(M2fcor) Write out 2D momentum Coriolis force.
T Dout(M2hadv) Write out 2D momentum horizontal advection.
T Dout(M2xadv) Write out 2D momentum horizontal X-advection.
T Dout(M2yadv) Write out 2D momentum horizontal Y-advection.
T Dout(M2hvis) Write out 2D momentum horizontal viscosity.
T Dout(M2xvis) Write out 2D momentum horizontal X-viscosity.
T Dout(M2yvis) Write out 2D momentum horizontal Y-viscosity.
T Dout(M2sstr) Write out 2D momentum surface stress.
T Dout(M2bstr) Write out 2D momentum bottom stress.
T Dout(M3rate) Write out 3D momentum acceleration.
T Dout(M3pgrd) Write out 3D momentum pressure gradient.
T Dout(M3fcor) Write out 3D momentum Coriolis force.
T Dout(M3hadv) Write out 3D momentum horizontal advection.
T Dout(M3xadv) Write out 3D momentum horizontal X-advection.
T Dout(M3yadv) Write out 3D momentum horizontal Y-advection.
T Dout(M3vadv) Write out 3D momentum vertical advection.
T Dout(M3hvis) Write out 3D momentum horizontal viscosity.
T Dout(M3xvis) Write out 3D momentum horizontal X-viscosity.
T Dout(M3yvis) Write out 3D momentum horizontal Y-viscosity.
T Dout(M3vvis) Write out 3D momentum vertical viscosity.
T Dout(iTrate) Write out rate of change of tracer 01: temp
T Dout(iTrate) Write out rate of change of tracer 02: salt
T Dout(iThadv) Write out horizontal advection, tracer 01: temp
T Dout(iThadv) Write out horizontal advection, tracer 02: salt
T Dout(iTxadv) Write out horizontal X-advection, tracer 01: temp
T Dout(iTxadv) Write out horizontal X-advection, tracer 02: salt
T Dout(iTyadv) Write out horizontal Y-advection, tracer 01: temp
T Dout(iTyadv) Write out horizontal Y-advection, tracer 02: salt
T Dout(iTvadv) Write out vertical advection, tracer 01: temp
T Dout(iTvadv) Write out vertical advection, tracer 02: salt
T Dout(iThdif) Write out horizontal diffusion, tracer 01: temp
T Dout(iThdif) Write out horizontal diffusion, tracer 02: salt
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 01: temp
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 02: salt
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 01: temp
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 02: salt
T Dout(iTvdif) Write out vertical diffusion, tracer 01: temp
T Dout(iTvdif) Write out vertical diffusion, tracer 02: salt
Output/Input Files:
Output Restart File: roms_rst.nc
Output History File: roms_his.nc
Output Averages File: roms_avg.nc
Output Diagnostics File: roms_dia.nc
Tile partition information for Grid 01: 41x80x16 tiling: 1x1
tile Istr Iend Jstr Jend Npts
0 1 41 1 80 52480
Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)
tile Xmin Xmax Ymin Ymax grid
0 0.50 41.50 0.50 80.50 RHO-points
0 1.00 41.00 0.50 80.50 U-points
0 0.50 41.50 1.00 80.00 V-points
Maximum halo size in XI and ETA directions:
HaloSizeI(1) = 162
HaloSizeJ(1) = 273
TileSide(1) = 85
TileSize(1) = 4080
Lateral Boundary Conditions: NLM
============================
Variable Grid West Edge South Edge East Edge North Edge
--------- ---- ---------- ---------- ---------- ----------
zeta 1 Periodic Closed Periodic Closed
ubar 1 Periodic Closed Periodic Closed
vbar 1 Periodic Closed Periodic Closed
u 1 Periodic Closed Periodic Closed
v 1 Periodic Closed Periodic Closed
temp 1 Periodic Closed Periodic Closed
salt 1 Periodic Closed Periodic Closed
Activated C-preprocessing Options:
UPWELLING Wind-Driven Upwelling/Downwelling over a Periodic Channel
ANA_BSFLUX Analytical kinematic bottom salinity flux
ANA_BTFLUX Analytical kinematic bottom temperature flux
ANA_GRID Analytical grid set-up
ANA_INITIAL Analytical initial conditions
ANA_SMFLUX Analytical kinematic surface momentum flux
ANA_SSFLUX Analytical kinematic surface salinity flux
ANA_STFLUX Analytical kinematic surface temperature flux
ANA_VMIX Analytical vertical mixing coefficients
ASSUMED_SHAPE Using assumed-shape arrays
AVERAGES Writing out time-averaged nonlinear model fields
!BOUNDARY_ALLGATHER Using mpi_allreduce in mp_boundary routine
!COLLECT_ALL... Using mpi_isend/mpi_recv in mp_collect routine
DIAGNOSTICS_TS Computing and writing tracer diagnostic terms
DIAGNOSTICS_UV Computing and writing momentum diagnostic terms
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002)
DOUBLE_PRECISION Double precision arithmetic numerical kernel.
MIX_S_TS Mixing of tracers along constant S-surfaces
MIX_S_UV Mixing of momentum along constant S-surfaces
MPI MPI distributed-memory configuration
NONLINEAR Nonlinear Model
!NONLIN_EOS Linear Equation of State for seawater
POWER_LAW Power-law shape time-averaging barotropic filter
PROFILE Time profiling activated
REDUCE_ALLGATHER Using mpi_allgather in mp_reduce routine
!RST_SINGLE Double precision fields in restart NetCDF file
SALINITY Using salinity
SOLVE3D Solving 3D Primitive Equations
SPLINES_VDIFF Parabolic Spline Reconstruction for Vertical Diffusion
SPLINES_VVISC Parabolic Spline Reconstruction for Vertical Viscosity
TS_U3HADVECTION Third-order upstream horizontal advection of tracers
TS_C4VADVECTION Fourth-order centered vertical advection of tracers
TS_DIF2 Harmonic mixing of tracers
UV_ADV Advection of momentum
UV_COR Coriolis term
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum
UV_C4VADVECTION Fourth-order centered vertical advection of momentum
UV_LDRAG Linear bottom stress
UV_VIS2 Harmonic mixing of momentum
VAR_RHO_2D Variable density barotropic mode
Process Information:
Node # 0 (pid= 18367) is active.
INITIAL: Configuring and initializing forward nonlinear model ...
*******
ANA_GRID - x-location of PSI-points: x_psi
(Grid = 01, Min = 0.00000000E+00 Max = 4.00000000E+04)
ANA_GRID - y-location of PSI-points: y_psi
(Grid = 01, Min = 0.00000000E+00 Max = 8.00000000E+04)
ANA_GRID - x-location of RHO-points: x_rho
(Grid = 01, Min = 5.00000000E+02 Max = 4.05000000E+04)
ANA_GRID - y-location of RHO-points: y_rho
(Grid = 01, Min = -5.00000000E+02 Max = 8.05000000E+04)
ANA_GRID - x-location of U-points: x_u
(Grid = 01, Min = 0.00000000E+00 Max = 4.00000000E+04)
ANA_GRID - y-location of U-points: y_u
(Grid = 01, Min = -5.00000000E+02 Max = 8.05000000E+04)
ANA_GRID - x-location of V-points: x_v
(Grid = 01, Min = 5.00000000E+02 Max = 4.05000000E+04)
ANA_GRID - y-location of V-points: y_v
(Grid = 01, Min = 0.00000000E+00 Max = 8.00000000E+04)
ANA_GRID - reciprocal XI-grid spacing: pm
(Grid = 01, Min = 1.00000000E-03 Max = 1.00000000E-03)
ANA_GRID - reciprocal ETA-grid spacing: pn
(Grid = 01, Min = 1.00000000E-03 Max = 1.00000000E-03)
ANA_GRID - angle between XI-axis and EAST: angler
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_GRID - Coriolis parameter at RHO-points: f
(Grid = 01, Min = -8.26000000E-05 Max = -8.26000000E-05)
ANA_GRID - bathymetry at RHO-points: h
(Grid = 01, Min = 2.52004887E+01 Max = 1.50000000E+02)
Vertical S-coordinate System, Grid 01:
level S-coord Cs-curve Z at hmin at hc half way at hmax
16 0.0000000 0.0000000 0.000 0.000 0.000 0.000
15 -0.0625000 -0.0019442 -0.809 -0.806 -1.348 -1.589
14 -0.1250000 -0.0078455 -1.668 -1.661 -2.966 -3.687
13 -0.1875000 -0.0179119 -2.580 -2.568 -4.867 -6.321
12 -0.2500000 -0.0324983 -3.549 -3.531 -7.077 -9.535
11 -0.3125000 -0.0521190 -4.581 -4.558 -9.630 -13.397
10 -0.3750000 -0.0774659 -5.686 -5.656 -12.573 -17.996
9 -0.4375000 -0.1094327 -6.875 -6.837 -15.967 -23.445
8 -0.5000000 -0.1491465 -8.162 -8.114 -19.889 -29.890
7 -0.5625000 -0.1980075 -9.564 -9.506 -24.435 -37.512
6 -0.6250000 -0.2577387 -11.104 -11.034 -29.721 -46.531
5 -0.6875000 -0.3304460 -12.808 -12.724 -35.892 -57.218
4 -0.7500000 -0.4186931 -14.709 -14.609 -43.121 -69.903
3 -0.8125000 -0.5255915 -16.846 -16.726 -51.622 -84.987
2 -0.8750000 -0.6549105 -19.266 -19.124 -61.651 -102.953
1 -0.9375000 -0.8112096 -22.028 -21.859 -73.518 -124.388
0 -1.0000000 -1.0000000 -25.200 -25.000 -87.600 -150.000
Time Splitting Weights for Grid 01: ndtfast = 30 nfast = 42
==================================
Primary Secondary Accumulated to Current Step
1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257356 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864348 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001213 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565097 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906204 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716643 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402368 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399432 0.6603333185976138
21 0.0256737146312911 0.0297153720153352 0.1342125541712342 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524359 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729578 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236653 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893981 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886213 0.8237939964192927
27 0.0432936737565710 0.0230872677537126 0.3506756411451924 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772280 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880565 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442384 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256415 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325521 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348098 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479478 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213239 0.9738247715198165
36 0.0503158038019030 0.0080591141492892 0.8085423793232269 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079423 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497611 0.9930692679747334
39 0.0376397765791564 0.0033640675316746 0.9367177506289175 0.9964333355064080
40 0.0305543017255206 0.0021094083123694 0.9672720523544381 0.9985427438187774
41 0.0217382098544504 0.0010909315881854 0.9890102622088885 0.9996336754069628
42 0.0109897377911118 0.0003663245930371 1.0000000000000004 0.9999999999999999
ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000
Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):
1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000
Power filter parameters, Fgamma, gamma = 0.28400 0.18933
Metrics information for Grid 01:
===============================
Minimum X-grid spacing, DXmin = 1.00000000E+00 km
Maximum X-grid spacing, DXmax = 1.00000000E+00 km
Minimum Y-grid spacing, DYmin = 1.00000000E+00 km
Maximum Y-grid spacing, DYmax = 1.00000000E+00 km
Minimum Z-grid spacing, DZmin = 8.08965824E-01 m
Maximum Z-grid spacing, DZmax = 2.56123321E+01 m
Minimum barotropic Courant Number = 2.22358627E-01
Maximum barotropic Courant Number = 5.42494240E-01
Maximum Coriolis Courant Number = 2.47800000E-02
ANA_INITIAL - vertically integrated u-momentum component: ubar
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - vertically integrated v-momentum component: vbar
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - free-surface: zeta
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - u-momentum component: u
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - v-momentum component: v
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - potential temperature: temp
(Grid = 01, Min = 1.45204834E+01 Max = 2.19365219E+01)
ANA_INITIAL - salinity: salt
(Grid = 01, Min = 3.50000000E+01 Max = 3.50000000E+01)
Basin information for Grid 01:
Maximum grid stiffness ratios: rx0 = 6.931666E-02 (Beckmann and Haidvogel)
rx1 = 8.661243E-01 (Haney)
Initial domain volumes: TotVolume = 3.8843755884E+11 m3
MinCellVol = 8.4521383562E+05 m3
MaxCellVol = 2.5612332106E+07 m3
Max/Min = 3.0302783777E+01
NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 000000000001 - 000000001440)
TIME-STEP YYYY-MM-DD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed
0 0001-01-01 00:00:00.00 0.000000E+00 6.585677E+02 6.585677E+02 3.884376E+11
(00,00,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: roms_his.nc
ASAN:DEADLYSIGNAL
=================================================================
==18367==ERROR: AddressSanitizer: SEGV on unknown address 0x00000000000b (pc 0x7fde4f65ebe1 bp 0x000000000000 sp 0x7ffe80ad5c60 T0)
#0 0x7fde4f65ebe0 in __netcdf_MOD_nf90_create /home/ghasedak/Downloads/netcdf-fortran-4.4.4/fortran/netcdf4_file.f90:111
#1 0x1f23f39 in __mod_netcdf_MOD_netcdf_create /home/ghasedak/Projects/upwelling/Build_romsG/mod_netcdf.f90:6479
#2 0x18f9860 in def_his_ /home/ghasedak/Projects/upwelling/Build_romsG/def_his.f90:69
#3 0x7e4059 in output_ /home/ghasedak/Projects/upwelling/Build_romsG/output.f90:112
#4 0x70a84d in main3d_ /home/ghasedak/Projects/upwelling/Build_romsG/main3d.f90:231
#5 0x406b5c in __ocean_control_mod_MOD_roms_run /home/ghasedak/Projects/upwelling/Build_romsG/ocean_control.f90:181
#6 0x404b16 in ocean /home/ghasedak/Projects/upwelling/Build_romsG/master.f90:108
#7 0x404bce in main /home/ghasedak/Projects/upwelling/Build_romsG/master.f90:50
#8 0x7fde4d05b430 in __libc_start_main (/lib64/libc.so.6+0x20430)
#9 0x4040e9 in _start (/home/ghasedak/Projects/upwelling/romsG+0x4040e9)
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV /home/ghasedak/Downloads/netcdf-fortran-4.4.4/fortran/netcdf4_file.f90:111 in __netcdf_MOD_nf90_create
==18367==ABORTING
________________________________________________________________________
Re: first time running upwelling test case
It failed in the call to DEF_HIS. Are you trying to write to somewhere where you don't have permissions? Do you have a local computer support staff to ask for help?
Does this line have "CALL netcdf_create"?
Has your netcdf library been tested in any way so that you know it works?
Code: Select all
#2 0x18f9860 in def_his_ /home/ghasedak/Projects/upwelling/Build_romsG/def_his.f90:69Has your netcdf library been tested in any way so that you know it works?
-
neelbasak08
- Posts: 99
- Joined: Wed Dec 09, 2020 3:58 pm
- Location: Thapar Institute of Engineering and Technology, Patiala, PN, India
Re: first time running upwelling test case
Hello!
I am facing some similar sort of issues while trying to run my model in a parallel mode. I am attaching the complete output of the Linux terminal. The following is a part of the output in the terminal :
Any leads as to how to solve these issues?
Kind regards
-Neel
I am facing some similar sort of issues while trying to run my model in a parallel mode. I am attaching the complete output of the Linux terminal. The following is a part of the output in the terminal :
I was able to sort out the tiling issue as it was very clearly mentioned in the error what is to be done but I was unable to sort out the other errors in the latter part of log file.SINGAPORE ISLAND MODEL
Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/bin/gfortran
Compiler flags : -frepack-arrays -g -O0 -fbounds-check -fbacktrace -fcheck=all -fsanitize=address -fsanitize=undefined -finit-real=nan -ffpe-trap=invalid,zero,overflow -fopenmp -static-libgcc -
SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 1061
Local Root : /home/lkannappan/roms
Header Dir : /home/lkannappan/roms/project/singapore
Header file : singapore.h
Analytical Dir : /home/lkannappan/roms/project/singapore
Resolution, Grid 01: 298x148x15, Parallel Threads: 16, Tiling: 8x1
ROMS/TOMS: Wrong choice of grid 01 partition or number of parallel threads.
NtileI*NtileJ must be a positive multiple of the number of threads.
Change number of threads (environment variable) or
change domain partition in input script.
Found Error: 06 Line: 191 Source: ROMS/Utility/inp_par.F
Found Error: 06 Line: 115 Source: ROMS/Drivers/nl_ocean.h, ROMS_initialize
Elapsed wall CPU time for each process (seconds):
At line 127 of file memory.f90
Fortran runtime error: Index '15' of dimension 1 of array 'dsize' outside of expected range (7:0)
Error termination. Backtrace:
inp_par.f90:93: runtime error: load of null pointer of type 'struct t_adv'
ASAN:DEADLYSIGNAL
=================================================================
==21230==ERROR: AddressSanitizer: SEGV on unknown address 0x000000000010 (pc 0x7fc8104a6e91 bp 0x7fffcde09ae0 sp 0x7fffcde05d40 T0)
==21230==The signal is caused by a READ memory access.
==21230==Hint: address points to the zero page.
inp_par.f90:93: runtime error: load of null pointer of type 'struct t_adv'
ASAN:DEADLYSIGNAL
=================================================================
==21231==ERROR: AddressSanitizer: SEGV on unknown address 0x000000000010 (pc 0x7ffa284a6e91 bp 0x7fffc626eed0 sp 0x7fffc626b130 T0)
==21231==The signal is caused by a READ memory access.
==21231==Hint: address points to the zero page.
Any leads as to how to solve these issues?
Kind regards
-Neel
- Attachments
-
- roms error.txt
- (13.74 KiB) Downloaded 365 times
Re: first time running upwelling test case
In order have any idea what is going on we would need to see the error after you fixed your tiling error.
-
neelbasak08
- Posts: 99
- Joined: Wed Dec 09, 2020 3:58 pm
- Location: Thapar Institute of Engineering and Technology, Patiala, PN, India
Re: first time running upwelling test case
Thanks Mr. Robertson,
The tiling error was removed as stated by me earlier but the error in the latter sections of the previous log still persists:
The tiling error was removed as stated by me earlier but the error in the latter sections of the previous log still persists:
Here is my updated error loginp_par.f90:93: runtime error: load of null pointer of type 'struct t_adv'
ASAN:DEADLYSIGNAL
=================================================================
==21348==ERROR: AddressSanitizer: SEGV on unknown address 0x000000000010 (pc 0x7f92c78a6e91 bp 0x7fffc2f867b0 sp 0x7fffc2f82a10 T0)
==21348==The signal is caused by a READ memory access.
==21348==Hint: address points to the zero page.
#0 0x7f92c78a6e90 in __inp_par_mod_MOD_inp_par /home/lkannappan/roms/project/singapore/Build_romsG/inp_par.f90:93
#1 0x7f92c6910a21 in __ocean_control_mod_MOD_roms_initialize /home/lkannappan/roms/project/singapore/Build_romsG/ocean_control.f90:83
#2 0x7f92c690d38a in ocean /home/lkannappan/roms/project/singapore/Build_romsG/master.f90:73
#3 0x7f92c690da00 in main /home/lkannappan/roms/project/singapore/Build_romsG/master.f90:50
#4 0x7f92c1901bf6 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21bf6)
#5 0x7f92c690d1d9 in _start (/home/lkannappan/roms/project/singapore/romsG+0x1f0d1d9)
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV /home/lkannappan/roms/project/singapore/Build_romsG/inp_par.f90:93 in __inp_par_mod_MOD_inp_par
==21348==ABORTING
inp_par.f90:93: runtime error: load of null pointer of type 'struct t_adv'
ASAN:DEADLYSIGNAL
=================================================================
==21349==ERROR: AddressSanitizer: SEGV on unknown address 0x000000000010 (pc 0x7f008eca6e91 bp 0x7ffff734c500 sp 0x7ffff7348760 T0)
==21349==The signal is caused by a READ memory access.
==21349==Hint: address points to the zero page.
#0 0x7f008eca6e90 in __inp_par_mod_MOD_inp_par /home/lkannappan/roms/project/singapore/Build_romsG/inp_par.f90:93
#1 0x7f008dd10a21 in __ocean_control_mod_MOD_roms_initialize /home/lkannappan/roms/project/singapore/Build_romsG/ocean_control.f90:83
#2 0x7f008dd0d38a in ocean /home/lkannappan/roms/project/singapore/Build_romsG/master.f90:73
#3 0x7f008dd0da00 in main /home/lkannappan/roms/project/singapore/Build_romsG/master.f90:50
#4 0x7f0088d01bf6 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21bf6)
#5 0x7f008dd0d1d9 in _start (/home/lkannappan/roms/project/singapore/romsG+0x1f0d1d9)
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV /home/lkannappan/roms/project/singapore/Build_romsG/inp_par.f90:93 in __inp_par_mod_MOD_inp_par
==21349==ABORTING
inp_par.f90:93: runtime error: load of null pointer of type 'struct t_adv'
ASAN:DEADLYSIGNAL
=================================================================
==21350==ERROR: AddressSanitizer: SEGV on unknown address 0x000000000010 (pc 0x7f7d71ea6e91 bp 0x7fffcc7a0cb0 sp 0x7fffcc79cf10 T0)
==21350==The signal is caused by a READ memory access.
==21350==Hint: address points to the zero page.
#0 0x7f7d71ea6e90 in __inp_par_mod_MOD_inp_par /home/lkannappan/roms/project/singapore/Build_romsG/inp_par.f90:93
#1 0x7f7d70f10a21 in __ocean_control_mod_MOD_roms_initialize /home/lkannappan/roms/project/singapore/Build_romsG/ocean_control.f90:83
#2 0x7f7d70f0d38a in ocean /home/lkannappan/roms/project/singapore/Build_romsG/master.f90:73
#3 0x7f7d70f0da00 in main /home/lkannappan/roms/project/singapore/Build_romsG/master.f90:50
#4 0x7f7d6bf01bf6 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21bf6)
#5 0x7f7d70f0d1d9 in _start (/home/lkannappan/roms/project/singapore/romsG+0x1f0d1d9)
- Attachments
-
- roms error.txt
- updated log from terminal
- (28.92 KiB) Downloaded 346 times
Re: first time running upwelling test case
Is it possible that you are trying to run an OpenMP (shared memory) ROMS executable using an 'mpirun' command? You have -fopenmp in your list of flags but the multiple occurrences of:
suggest MPI is being used with a non-MPI compiled executable.--------------------------------------------------------------------------------
Model Input Parameters: ROMS/TOMS version 3.9
Monday - May 3, 2021 - 10:50:38 PM
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