forrtl: severe (174): SIGSEGV, segmentation fault occurred

Message

chenzhixing · Fri Mar 04, 2022 7:53 am

Hi everyone,
I want to simulate an river plume by inputing only the grid, initial field, river and boundary files, and the boundary file contains a tidal signal,
but I got the error when I ran the ROMS, the log file are described in the below, and the in and h files are added as attachments:
(just output quicksave file)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% log%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
nohup: 忽略输入

Model Input Parameters: ROMS/TOMS version 3.7
Wednesday - March 2, 2022 - 5:15:21 PM
-----------------------------------------------------------------------------

Test_tide

Operating system : Linux
CPU/hardware : x86_64
Compiler system : ifort
Compiler command : /opt/software/mpich2-intel/bin/mpif90
Compiler flags : -heap-arrays -fp-model precise -ip -O3 -free -free -free

Input Script :

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 853M

Local Root : /disk3/chenzhixing/ROMS/trunk_853
Header Dir : /disk3/chenzhixing/ROMS/cases/laizhou
Header file : test_tide.h
Analytical Dir: /disk3/chenzhixing/ROMS/cases/laizhou

Resolution, Grid 01: 1054x1094x020, Parallel Nodes: 24, Tiling: 004x006

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

264840 ntimes Number of timesteps for 3-D equations.
30.000 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.
86400 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).
0 nHIS Number of timesteps between the writing fields
into history file.
120 nQCK Number of timesteps between the writing fields
into quicksave file.
1440 ndefQCK Number of timesteps between creation of new
brief snpashots files.
0 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
0 nAVG Number of timesteps between the writing of
time-averaged data into averages 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
0.0000E+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
5.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
5.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
5.0000E-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.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
2.5000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
4.0000E+00 theta_s S-coordinate surface control parameter.
8.0000E-01 theta_b S-coordinate bottom control parameter.
5.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1028.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
20210601.00 time_ref Reference time for units attribute (yyyymmdd.dd)
1.2000E+02 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
1.2000E+02 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
1.2000E+02 Znudg Nudging/relaxation time scale (days)
for free-surface.
1.2000E+02 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
1.2000E+02 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
6.0000E+01 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 Qout(idFsur) Write out free-surface.
T Qout(idUvel) Write out 3D U-momentum component.
T Qout(idVvel) Write out 3D V-momentum component.
T Qout(idWvel) Write out W-momentum component.
T Qout(idTvar) Write out tracer 02: salt

Output/Input Files:

Output Restart File: /disk3/chenzhixing/ROMS/cases/laizhou/laizhou_rst.nc
Output Averages File: /disk3/chenzhixing/ROMS/cases/laizhou/laizhou_avg.nc
Input Grid File: /disk3/chenzhixing/ROMS/cases/laizhou/laizhou-grid.nc
Input Nonlinear Initial File: /disk3/chenzhixing/ROMS/cases/laizhou/laizhou-ini.nc
Input Boundary File: /disk3/chenzhixing/ROMS/cases/laizhou/laizhou-bry.nc

Tile partition information for Grid 01: 1054x1094x0020 tiling: 004x006

tile Istr Iend Jstr Jend Npts

0 1 263 1 181 952060
1 264 527 1 181 955680
2 528 791 1 181 955680
3 792 1054 1 181 952060
4 1 263 182 364 962580
5 264 527 182 364 966240
6 528 791 182 364 966240
7 792 1054 182 364 962580
8 1 263 365 547 962580
9 264 527 365 547 966240
10 528 791 365 547 966240
11 792 1054 365 547 962580
12 1 263 548 730 962580
13 264 527 548 730 966240
14 528 791 548 730 966240
15 792 1054 548 730 962580
16 1 263 731 913 962580
17 264 527 731 913 966240
18 528 791 731 913 966240
19 792 1054 731 913 962580
20 1 263 914 1094 952060
21 264 527 914 1094 955680
22 528 791 914 1094 955680
23 792 1054 914 1094 952060

Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 263.50 0.50 181.50 RHO-points
1 263.50 527.50 0.50 181.50 RHO-points
2 527.50 791.50 0.50 181.50 RHO-points
3 791.50 1054.50 0.50 181.50 RHO-points
4 0.50 263.50 181.50 364.50 RHO-points
5 263.50 527.50 181.50 364.50 RHO-points
6 527.50 791.50 181.50 364.50 RHO-points
7 791.50 1054.50 181.50 364.50 RHO-points
8 0.50 263.50 364.50 547.50 RHO-points
9 263.50 527.50 364.50 547.50 RHO-points
10 527.50 791.50 364.50 547.50 RHO-points
11 791.50 1054.50 364.50 547.50 RHO-points
12 0.50 263.50 547.50 730.50 RHO-points
13 263.50 527.50 547.50 730.50 RHO-points
14 527.50 791.50 547.50 730.50 RHO-points
15 791.50 1054.50 547.50 730.50 RHO-points
16 0.50 263.50 730.50 913.50 RHO-points
17 263.50 527.50 730.50 913.50 RHO-points
18 527.50 791.50 730.50 913.50 RHO-points
19 791.50 1054.50 730.50 913.50 RHO-points
20 0.50 263.50 913.50 1094.50 RHO-points
21 263.50 527.50 913.50 1094.50 RHO-points
22 527.50 791.50 913.50 1094.50 RHO-points
23 791.50 1054.50 913.50 1094.50 RHO-points

0 1.00 263.50 0.50 181.50 U-points
1 263.50 527.50 0.50 181.50 U-points
2 527.50 791.50 0.50 181.50 U-points
3 791.50 1054.00 0.50 181.50 U-points
4 1.00 263.50 181.50 364.50 U-points
5 263.50 527.50 181.50 364.50 U-points
6 527.50 791.50 181.50 364.50 U-points
7 791.50 1054.00 181.50 364.50 U-points
8 1.00 263.50 364.50 547.50 U-points
9 263.50 527.50 364.50 547.50 U-points
10 527.50 791.50 364.50 547.50 U-points
11 791.50 1054.00 364.50 547.50 U-points
12 1.00 263.50 547.50 730.50 U-points
13 263.50 527.50 547.50 730.50 U-points
14 527.50 791.50 547.50 730.50 U-points
15 791.50 1054.00 547.50 730.50 U-points
16 1.00 263.50 730.50 913.50 U-points
17 263.50 527.50 730.50 913.50 U-points
18 527.50 791.50 730.50 913.50 U-points
19 791.50 1054.00 730.50 913.50 U-points
20 1.00 263.50 913.50 1094.50 U-points
21 263.50 527.50 913.50 1094.50 U-points
22 527.50 791.50 913.50 1094.50 U-points
23 791.50 1054.00 913.50 1094.50 U-points

0 0.50 263.50 1.00 181.50 V-points
1 263.50 527.50 1.00 181.50 V-points
2 527.50 791.50 1.00 181.50 V-points
3 791.50 1054.50 1.00 181.50 V-points
4 0.50 263.50 181.50 364.50 V-points
5 263.50 527.50 181.50 364.50 V-points
6 527.50 791.50 181.50 364.50 V-points
7 791.50 1054.50 181.50 364.50 V-points
8 0.50 263.50 364.50 547.50 V-points
9 263.50 527.50 364.50 547.50 V-points
10 527.50 791.50 364.50 547.50 V-points
11 791.50 1054.50 364.50 547.50 V-points
12 0.50 263.50 547.50 730.50 V-points
13 263.50 527.50 547.50 730.50 V-points
14 527.50 791.50 547.50 730.50 V-points
15 791.50 1054.50 547.50 730.50 V-points
16 0.50 263.50 730.50 913.50 V-points
17 263.50 527.50 730.50 913.50 V-points
18 527.50 791.50 730.50 913.50 V-points
19 791.50 1054.50 730.50 913.50 V-points
20 0.50 263.50 913.50 1094.00 V-points
21 263.50 527.50 913.50 1094.00 V-points
22 527.50 791.50 913.50 1094.00 V-points
23 791.50 1054.50 913.50 1094.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 834
HaloSizeJ(1) = 591
TileSide(1) = 272
TileSize(1) = 51952

Lateral Boundary Conditions: NLM
============================

Variable Grid West Edge South Edge East Edge North Edge
--------- ---- ---------- ---------- ---------- ----------

zeta 1 Chapman Imp Chapman Imp Chapman Imp Chapman Imp

ubar 1 Flather Flather Flather Flather

vbar 1 Flather Flather Flather Flather

u 1 Rad + Nud Rad + Nud Rad + Nud Rad + Nud

v 1 Rad + Nud Rad + Nud Rad + Nud Rad + Nud

temp 1 Rad + Nud Rad + Nud Rad + Nud Rad + Nud

salt 1 Rad + Nud Rad + Nud Rad + Nud Rad + Nud

tke 1 Gradient Gradient Gradient Gradient

Activated C-preprocessing Options:

TEST_TIDE Test_tide
ANA_FSOBC Analytical free-surface boundary conditions.
ANA_M2OBC Analytical 2D momentum boundary conditions.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
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.
MY25_MIXING Mellor/Yamada Level-2.5 mixing closure.
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 Single precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
TS_MPDATA Recursive flux corrected MPDATA 3D 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_QDRAG Quadratic bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.

Process Information:

Node # 0 (pid= 20873) is active.
Node # 8 (pid= 20881) is active.
Node # 12 (pid= 20885) is active.
Node # 16 (pid= 20889) is active.
Node # 4 (pid= 20877) is active.
Node # 18 (pid= 20891) is active.
Node # 20 (pid= 20893) is active.
Node # 10 (pid= 20883) is active.
Node # 6 (pid= 20879) is active.
Node # 14 (pid= 20887) is active.
Node # 19 (pid= 20892) is active.
Node # 11 (pid= 20884) is active.
Node # 7 (pid= 20880) is active.
Node # 15 (pid= 20888) is active.
Node # 1 (pid= 20874) is active.
Node # 17 (pid= 20890) is active.
Node # 2 (pid= 20875) is active.
Node # 3 (pid= 20876) is active.
Node # 22 (pid= 20895) is active.
Node # 23 (pid= 20896) is active.
Node # 9 (pid= 20882) is active.
Node # 5 (pid= 20878) is active.
Node # 13 (pid= 20886) is active.
Node # 21 (pid= 20894) 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

20 0.0000000 0.0000000 0.000 0.000 0.000 0.000
19 -0.0500000 -0.0086212 -0.250 -0.250 -0.333 -0.417
18 -0.1000000 -0.0205861 -0.500 -0.500 -0.699 -0.898
17 -0.1500000 -0.0373105 -0.750 -0.750 -1.111 -1.472
16 -0.2000000 -0.0606038 -1.000 -1.000 -1.586 -2.173
15 -0.2500000 -0.0926076 -1.250 -1.250 -2.146 -3.042
14 -0.3000000 -0.1355364 -1.500 -1.500 -2.811 -4.122
13 -0.3500000 -0.1911203 -1.750 -1.750 -3.599 -5.448
12 -0.4000000 -0.2597592 -2.000 -2.000 -4.513 -7.026
11 -0.4500000 -0.3396662 -2.250 -2.250 -5.536 -8.822
10 -0.5000000 -0.4265802 -2.500 -2.500 -6.627 -10.754
9 -0.5500000 -0.5145610 -2.750 -2.750 -7.728 -12.706
8 -0.6000000 -0.5977111 -3.000 -3.000 -8.783 -14.565
7 -0.6500000 -0.6718995 -3.250 -3.250 -9.750 -16.251
6 -0.7000000 -0.7355623 -3.500 -3.500 -10.616 -17.732
5 -0.7500000 -0.7894233 -3.750 -3.750 -11.387 -19.025
4 -0.8000000 -0.8356515 -4.000 -4.000 -12.084 -20.169
3 -0.8500000 -0.8770322 -4.250 -4.250 -12.735 -21.220
2 -0.9000000 -0.9164330 -4.500 -4.500 -13.366 -22.232
1 -0.9500000 -0.9565735 -4.750 -4.750 -14.004 -23.259
0 -1.0000000 -1.0000000 -5.000 -5.000 -14.674 -24.349

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 = 1.22152151E-01 km
Maximum X-grid spacing, DXmax = 1.24165565E-01 km
Minimum Y-grid spacing, DYmin = 1.22154924E-01 km
Maximum Y-grid spacing, DYmax = 1.24164651E-01 km
Minimum Z-grid spacing, DZmin = 2.50000000E-01 m
Maximum Z-grid spacing, DZmax = 1.95233487E+00 m

Minimum barotropic Courant Number = 7.97921689E-02
Maximum barotropic Courant Number = 1.78930152E-01
Maximum Coriolis Courant Number = 2.70245031E-03

NLM: GET_STATE - Read state initial conditions, 2021-06-01 00:00:00.00
(Grid 01, t = 0.0000, File: laizhou-ini.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 = 0.00000000E+00 Max = 1.98465481E+01)
- salinity
(Min = 0.00000000E+00 Max = 3.01934223E+01)
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
oceanM 0000000000710094 Unknown Unknown Unknown
oceanM 00000000006FC429 Unknown Unknown Unknown
oceanM 000000000064421A Unknown Unknown Unknown
oceanM 00000000004A01E2 Unknown Unknown Unknown
oceanM 00000000004054CF Unknown Unknown Unknown
oceanM 0000000000404E3D Unknown Unknown Unknown
oceanM 0000000000404D0C Unknown Unknown Unknown
libc.so.6 0000003244A1ED5D Unknown Unknown Unknown
oceanM 0000000000404C09 Unknown Unknown Unknown

robertson · #2 Unread post by **robertson** » Fri Mar 04, 2022 5:33 pm

Recompile your code in debug mode (un-comment the USE_DEBUG line in your build_roms.sh or build_roms.csh), then run your model again with the resulting romsG (instead of romsM or romsS) executable. That will hopefully give you an idea where in the code the segfault is coming from to narrow down the possible causes.

chenzhixing · Sat Mar 05, 2022 6:51 am

Thanks for your reply, this suggestion is really useful. After modification according to your suggestion, the problem is as follows,

******************** log *********************
forrtl: severe (408): fort: (2): Subscript #2 of the array FRC has value 1 which is greater than the upper bound of -1

Image PC Routine Line Source
oceanG 00000000021A266E Unknown Unknown Unknown
oceanG 00000000021A1106 Unknown Unknown Unknown
oceanG 00000000021553F2 Unknown Unknown Unknown
oceanG 000000000211509B Unknown Unknown Unknown
oceanG 00000000021155B1 Unknown Unknown Unknown
oceanG 00000000014F36CD get_data_ 101 get_data.f90
oceanG 000000000071DDAE initial_ 274 initial.f90
oceanG 0000000000406260 ocean_control_mod 130 ocean_control.f90
oceanG 0000000000404F00 MAIN__ 95 master.f90
oceanG 0000000000404D2C Unknown Unknown Unknown
libc.so.6 0000003244A1ED5D Unknown Unknown Unknown
oceanG 0000000000404C29 Unknown Unknown Unknown

How can we fix this problem?

wilkin · #4 Unread post by **wilkin** » Sat Mar 05, 2022 1:07 pm

The error occurs in get_data, so there is something wrong with one of your netcdf forcing files.

oceanG 00000000014F36CD get_data_ 101 get_data.f90

Look in get_data.f90 at what ROMS is reading at when the error occurs, and fix that file.

jcwarner · #5 Unread post by **jcwarner** » Sat Mar 05, 2022 6:48 pm

"forrtl: severe (408): fort: (2): Subscript #2 of the array FRC has value 1 which is greater than the upper bound of -1"

i looked in your ocean.in and you have:

!NFFILES = 1 ! number of unique forcing files
!FRCNAME == /disk3/chenzhixing/ROMS/cases/laizhou/laizhou-frc.nc ! forcing file 1, grid 1

depending on your compiler and version of the code, it may need to read these values even if they are not used.
so uncomment them and try again:

NFFILES = 1 ! number of unique forcing files
FRCNAME == /disk3/chenzhixing/ROMS/cases/laizhou/laizhou-frc.nc ! forcing file 1, grid 1

chenzhixing · Sun Mar 06, 2022 2:57 am

Thanks for your reply. I annotated these two lines because there is no frc file when using ROMS

chenzhixing · Sun Mar 06, 2022 2:59 am

wilkin wrote: ↑Sat Mar 05, 2022 1:07 pm The error occurs in get_data, so there is something wrong with one of your netcdf forcing files.

oceanG 00000000014F36CD get_data_ 101 get_data.f90
Look in get_data.f90 at what ROMS is reading at when the error occurs, and fix that file.

Sincerely thank you, I will carefully read the get_data.f90. Does this 101 stand for line 101 in get_data.f90 ?

wilkin · #8 Unread post by **wilkin** » Sun Mar 06, 2022 1:34 pm

... I annotated these two lines because there is no frc file when using ROMS

You don't have any ANA_* functionals defined for forcing (wind stress, heat flux etc.), so ROMS is trying to read those from a forcing netcdf file. Even if you want zero forcing, you need to set how that is implemented. The default ANA_SMFLUX for example will set stresses to zero. But you have to define it.

chenzhixing · Mon Mar 07, 2022 4:27 am

Thank you very much. I'll give it a try.

Joeailvyou · Thu Aug 03, 2023 8:46 am

robertson wrote: ↑Fri Mar 04, 2022 5:33 pm Recompile your code in debug mode (un-comment the USE_DEBUG line in your build_roms.sh or build_roms.csh), then run your model again with the resulting romsG (instead of romsM or romsS) executable. That will hopefully give you an idea where in the code the segfault is coming from to narrow down the possible causes.

When I build and run roms standalone , everything gose well. But If I mpirun oceanG after build ROMS coupled with CICE (i.e. the METROMS https://github.com/metno/metroms), it turned forrtl: severe (174): SIGSEGV, segmentation fault occurred.
Could you please help me out ? I have tried many ways but still not solved it. I have upload my output log file and in file:
https://github.com/joeailvyou/METROMS-output-log
Even in debug mode (but coupled to CICE), the error is not detail enouth:

Code: Select all

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
oceanG             00000000012153C1  Unknown               Unknown  Unknown
oceanG             0000000001213B17  Unknown               Unknown  Unknown
libmpi.so.12       00002AF06FB10762  Unknown               Unknown  Unknown
libmpi.so.12       00002AF06FB105B6  Unknown               Unknown  Unknown
libmpi.so.12       00002AF06FAFEE1C  Unknown               Unknown  Unknown
libmpi.so.12       00002AF06FAE07C8  Unknown               Unknown  Unknown
libpthread.so.0    00002AF07015B5E0  Unknown               Unknown  Unknown
oceanG             0000000000FD44A8  Unknown               Unknown  Unknown
oceanG             0000000000FD156C  Unknown               Unknown  Unknown
oceanG             0000000000FBC6FC  Unknown               Unknown  Unknown
oceanG             0000000000F13600  Unknown               Unknown  Unknown
oceanG             0000000000408403  MAIN__                    106  master.f90
oceanG             0000000000406DCE  Unknown               Unknown  Unknown
libc.so.6          00002AF07058DC05  Unknown               Unknown  Unknown
oceanG             0000000000406CD9  Unknown               Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
oceanG             00000000012153C1  Unknown               Unknown  Unknown
oceanG             0000000001213B17  Unknown               Unknown  Unknown
libmpi.so.12       00002B8F2D10F762  Unknown               Unknown  Unknown
libmpi.so.12       00002B8F2D10F5B6  Unknown               Unknown  Unknown
libmpi.so.12       00002B8F2D0FDE1C  Unknown               Unknown  Unknown
libmpi.so.12       00002B8F2D0DF7C8  Unknown               Unknown  Unknown
libpthread.so.0    00002B8F2D75A5E0  Unknown               Unknown  Unknown
oceanG             0000000000FD44A8  Unknown               Unknown  Unknown
oceanG             0000000000FD156C  Unknown               Unknown  Unknown
oceanG             0000000000FBC6FC  Unknown               Unknown  Unknown
oceanG             0000000000F13600  Unknown               Unknown  Unknown
oceanG             0000000000408403  MAIN__                    106  master.f90
oceanG             0000000000406DCE  Unknown               Unknown  Unknown
libc.so.6          00002B8F2DB8CC05  Unknown               Unknown  Unknown
oceanG             0000000000406CD9  Unknown               Unknown  Unknown
real 0.49
user 5.06
sys 5.64

Ocean Modeling Discussion

forrtl: severe (174): SIGSEGV, segmentation fault occurred

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred