Hi all,
I tried to run a easy case and met a segmentation fault. So I turned on the USER_DEBUG, the results show belows:
I tried to figured out the problem but still have no idea yet.
Hope anyone have met this problem. Thanks lol
Segmentation fault
-
zzyfathead
- Posts: 22
- Joined: Wed Sep 18, 2019 1:53 pm
- Location: ANU
Re: Segmentation fault
Model Input Parameters: ROMS/TOMS version 3.7
Friday - January 3, 2020 - 4:44:40 PM
-----------------------------------------------------------------------------
test
Friday - January 3, 2020 - 4:44:40 PM
-----------------------------------------------------------------------------
test
Code: Select all
Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/bin/mpif90
Compiler flags : -frepack-arrays -g -fbounds-check -I/usr/include -ffree-form -ffree-form
Input Script :
SVN Root URL : https:://myroms.org/svn/src
SVN Revision : 65M
Local Root : /home/ubuntu/app/COAWST_V3.2
Header Dir : /home/ubuntu/app/COAWST_V3.2/Projects/test
Header file : test.h
Analytical Dir: /home/ubuntu/app/COAWST_V3.2/Projects/test
Resolution, Grid 01: 0176x0279x025, Parallel Nodes: 1, Tiling: 001x001
Physical Parameters, Grid: 01
=============================
24000 ntimes Number of timesteps for 3-D equations.
0.100 dt Timestep size (s) for 3-D equations.
10 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.
120 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).
10 nHIS Number of timesteps between the writing fields
into history file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
360 nAVG Number of timesteps between the writing of
time-averaged data into averages 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-05 Akv_bak Background vertical mixing coefficient (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).
1.0000E-01 Dcrit Minimum depth for wetting and drying (m).
1 lmd_Jwt Jerlov water type.
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
6.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
10.000 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 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.
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.
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(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idWvel) Write out W-momentum component.
Output/Input Files:
Output Restart File: test_rst.nc
Output History File: test_his.nc
Output Averages File: test_avg.nc
Input Grid File: /home/ubuntu/app/COAWST_V3.2/Projects/test/test_grid.nc
Input Nonlinear Initial File: /home/ubuntu/app/COAWST_V3.2/Projects/test/test_init.nc
Tile partition information for Grid 01: 0176x0279x0025 tiling: 001x001
tile Istr Iend Jstr Jend Npts
Number of tracers: 2
0 1 176 1 279 1227600
Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)
tile Xmin Xmax Ymin Ymax grid
0 0.50 176.50 0.50 279.50 RHO-points
0 1.00 176.00 0.50 279.50 U-points
0 0.50 176.50 1.00 279.00 V-points
Maximum halo size in XI and ETA directions:
HaloSizeI(1) = 374
HaloSizeJ(1) = 578
TileSide(1) = 283
TileSize(1) = 51223
Lateral Boundary Conditions: NLM
============================
Variable Grid West Edge South Edge East Edge North Edge
--------- ---- ---------- ---------- ---------- ----------
zeta 1 Closed Closed Closed Closed
ubar 1 Closed Closed Closed Closed
vbar 1 Closed Closed Closed Closed
u 1 Closed Closed Closed Closed
v 1 Closed Closed Closed Closed
temp 1 Closed Closed Closed Closed
salt 1 Closed Closed Closed Closed
tke 1 Closed Closed Closed Closed
Activated C-preprocessing Options:
TEST test
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
CHARNOK Charnok surface roughness from wind stress.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
GLS_MIXING Generic Length-Scale turbulence closure.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MIX_GEO_TS Mixing of tracers along geopotential surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
N2S2_HORAVG Horizontal smoothing of buoyancy and shear.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
K_GSCHEME Third-order upstream advection of TKE fields.
RADIATION_2D Use tangential phase speed in radiation conditions.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLAR_SOURCE Solar Radiation Source Term.
SOLVE3D Solving 3D Primitive Equations.
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_U3HADVECTION Third-order upstream horizontal advection of 3D momentum.
UV_C4VADVECTION Fourth-order centered vertical advection of momentum.
UV_LOGDRAG Logarithmic bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
WET_DRY Wetting and drying activated.
Process Information:
Node # 0 (pid= 15904) is active.
INITIAL: Configuring and initializing forward nonlinear model ...
*******
Vertical S-coordinate System, Grid 01:
level S-coord Cs-curve Z at hmin at hc half way at hmax
25 0.0000000 0.0000000 0.000 0.000 0.000 0.000
24 -0.0400000 -0.0001749 -0.004 -0.201 -0.461 -0.538
23 -0.0800000 -0.0007098 -0.008 -0.404 -1.066 -1.368
22 -0.1200000 -0.0016353 -0.012 -0.608 -1.829 -2.516
21 -0.1600000 -0.0030046 -0.016 -0.815 -2.770 -4.025
20 -0.2000000 -0.0048963 -0.020 -1.024 -3.921 -5.960
19 -0.2400000 -0.0074189 -0.024 -1.237 -5.326 -8.407
18 -0.2800000 -0.0107165 -0.028 -1.454 -7.042 -11.485
17 -0.3200000 -0.0149770 -0.032 -1.675 -9.145 -15.347
16 -0.3600000 -0.0204424 -0.036 -1.902 -11.733 -20.189
15 -0.4000000 -0.0274214 -0.040 -2.137 -14.930 -26.262
14 -0.4400000 -0.0363057 -0.044 -2.382 -18.892 -33.886
13 -0.4800000 -0.0475899 -0.048 -2.638 -23.819 -43.462
12 -0.5200000 -0.0618955 -0.052 -2.909 -29.961 -55.497
11 -0.5600000 -0.0799996 -0.056 -3.200 -37.630 -70.622
10 -0.6000000 -0.1028685 -0.060 -3.514 -47.214 -89.623
9 -0.6400000 -0.1316956 -0.063 -3.858 -59.194 -113.473
8 -0.6800000 -0.1679410 -0.067 -4.240 -74.157 -143.358
7 -0.7200000 -0.2133714 -0.071 -4.667 -92.812 -180.716
6 -0.7600000 -0.2700910 -0.076 -5.150 -116.006 -227.259
5 -0.8000000 -0.3405555 -0.080 -5.703 -144.725 -284.985
4 -0.8400000 -0.4275481 -0.084 -6.338 -180.090 -356.158
3 -0.8800000 -0.5340940 -0.088 -7.070 -223.315 -443.241
2 -0.9200000 -0.6632759 -0.092 -7.916 -275.642 -548.740
1 -0.9600000 -0.8179050 -0.096 -8.890 -338.198 -674.944
0 -1.0000000 -1.0000000 -0.100 -10.000 -411.797 -823.494
Time Splitting Weights for Grid 01: ndtfast = 10 nfast = 15
==================================
Primary Secondary Accumulated to Current Step
1 0.0014850648765542 0.1000000000000000 0.0014850648765542 0.1000000000000000
2 0.0059386031399402 0.0998514935123446 0.0074236680164944 0.1998514935123445
3 0.0133457074936657 0.0992576331983506 0.0207693755101601 0.2991091267106951
4 0.0236484051180389 0.0979230624489840 0.0444177806281990 0.3970321891596791
5 0.0366959666818608 0.0955582219371801 0.0811137473100598 0.4925904110968592
6 0.0521753389587947 0.0918886252689940 0.1332890862688545 0.5844790363658532
7 0.0695217010484137 0.0866710913731145 0.2028107873172682 0.6711501277389678
8 0.0878091442019233 0.0797189212682732 0.2906199315191915 0.7508690490072409
9 0.1056214752525633 0.0709380068480808 0.3962414067717548 0.8218070558553218
10 0.1209031436506851 0.0603758593228245 0.5171445504224399 0.8821829151781463
11 0.1307902921035067 0.0482855449577560 0.6479348425259466 0.9304684601359023
12 0.1314219308195445 0.0352065157474053 0.7793567733454911 0.9656749758833076
13 0.1177312353577226 0.0220643226654509 0.8970880087032138 0.9877392985487585
14 0.0832169680811588 0.0102911991296786 0.9803049767843727 0.9980304976784371
15 0.0196950232156274 0.0019695023215627 1.0000000000000000 0.9999999999999999
ndtfast, nfast = 10 15 nfast/ndtfast = 1.50000
Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):
1.000000000000 1.083803072626 0.541901536313 1.000000000000 1.000000000000
Power filter parameters, Fgamma, gamma = 0.28400 0.00000
Metrics information for Grid 01:
===============================
Minimum X-grid spacing, DXmin = 1.00256452E-01 km
Maximum X-grid spacing, DXmax = 1.00262565E-01 km
Minimum Y-grid spacing, DYmin = 9.95247380E-02 km
Maximum Y-grid spacing, DYmax = 9.95366015E-02 km
Minimum Z-grid spacing, DZmin = 3.96056923E-03 m
Maximum Z-grid spacing, DZmax = 1.48550344E+02 m
Minimum barotropic Courant Number = 3.66827761E-04
Maximum barotropic Courant Number = 1.27240519E-02
Maximum Coriolis Courant Number = 2.26677842E-07
NLM: GET_STATE - Read state initial conditions, t = 0 00:00:00
(Grid 01, File: test_init.nc, Rec=0001, Index=1)
- free-surface
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated v-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- v-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- potential temperature
(Min = 2.00000000E+01 Max = 2.00000000E+01)
- salinity
(Min = 3.50000000E+01 Max = 3.50000000E+01)
At line 101 of file get_data.f90
Fortran runtime error: Index '1' of dimension 2 of array 'frc' above upper bound of 0
Error termination. Backtrace:
[b]#0 0x7ff3e1bdf2da in ???
#1 0x7ff3e1bdfec5 in ???
#2 0x7ff3e1be0297 in ???
#3 0x555ef59c8e30 in get_data_
at /home/ubuntu/app/COAWST_V3.2/Build/get_data.f90:101
#4 0x555ef59c5c3e in initial_
at /home/ubuntu/app/COAWST_V3.2/Build/initial.f90:296
#5 0x555ef57bfbbd in __ocean_control_mod_MOD_roms_initialize
at /home/ubuntu/app/COAWST_V3.2/Build/ocean_control.f90:131
#6 0x555ef57bec15 in ocean
at /home/ubuntu/app/COAWST_V3.2/Build/master.f90:95
#7 0x555ef57bede1 in main
at /home/ubuntu/app/COAWST_V3.2/Build/master.f90:50[/b]
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[1340,1],0]
Exit code: 2
--------------------------------------------------------------------------
Re: Segmentation fault
What is on this line?
Oops, didn't see this:at /home/ubuntu/app/COAWST_V3.2/Build/get_data.f90:101
Did you tell it NFFILES before the list of forcing files?Fortran runtime error: Index '1' of dimension 2 of array 'frc' above upper bound of 0
-
zzyfathead
- Posts: 22
- Joined: Wed Sep 18, 2019 1:53 pm
- Location: ANU
Re: Segmentation fault
Hi Kate,
Thanks for your reply.
I don't want to input any forcing file, so I use '!' to comment out the code, as shown in the figure below. And the problem happend.
Then I delete '!' and change this code to 'NFFILES=0' , but ROMS told me NFFILES must be greater than 1.
I wonder that if it's necessay to input forcing files.
Thanks!
- Attachments
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-
zzyfathead
- Posts: 22
- Joined: Wed Sep 18, 2019 1:53 pm
- Location: ANU
Re: Segmentation fault
zzyfathead wrote: ↑Sat Jan 04, 2020 6:57 amHi Kate,
Thanks for your reply.
I don't want to input any forcing file, so I use '!' to comment out the code, as shown in the figure below. And the problem happened.
Then I delete '!' and change this code to 'NFFILES=0' , but ROMS told me NFFILES must be greater than 1.
I wonder that if it's necessay to input forcing files (Because I don't want to do that).
Thanks!
Re: Segmentation fault
Well, you could try submitting a bug report for this case of no forcing files, but most of us just set NFFILES to 1 and move on.
-
zzyfathead
- Posts: 22
- Joined: Wed Sep 18, 2019 1:53 pm
- Location: ANU
Re: Segmentation fault
Kate
Thanks for your reply, you really help me out! So people usually input at least one forcing file, my case is not common.
By the way, where can I submit a bug report?
Last edited by zzyfathead on Sat Jan 04, 2020 10:33 am, edited 2 times in total.
Re: Segmentation fault
If you log into: https://www.myroms.org/projects/src you can submit a bug report.
-
arango
- Site Admin
- Posts: 1367
- Joined: Wed Feb 26, 2003 4:41 pm
- Location: DMCS, Rutgers University
- Contact:
Re: Segmentation fault
This is not a bug. It always has to be equal or greater than one by design. If no input forcing files are needed, ROMS will ignore those values on standard input. I don't understand what it is the Fuzz about it. There are a lot of parameters in ROMS standard input that will be only relevant for a specific configuration. If not, they will be IGNORED!
NFFILES is needed to allocate an internal ROMS structure and initialize several parameters even if it is not used.
NFFILES is needed to allocate an internal ROMS structure and initialize several parameters even if it is not used.
-
zzyfathead
- Posts: 22
- Joined: Wed Sep 18, 2019 1:53 pm
- Location: ANU
Re: Segmentation fault
Thanks, I set NFFILES = 1 and input forcing file(though values = 0), it works now.arango wrote: ↑Sat Jan 04, 2020 7:35 pm This is not a bug. It always has to be equal or greater than one by design. If no input forcing files are needed, ROMS will ignore those values on standard input. I don't understand what it is the Fuzz about it. There are a lot of parameters in ROMS standard input that will be only relevant for a specific configuration. If not, they will be IGNORED!
NFFILES is needed to allocate an internal ROMS structure and initialize several parameters even if it is not used.
