[RegCNET] ERROR: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Athanasios Tsikerdekis
atsikerdekis at gmail.com
Tue Jun 30 22:01:51 CEST 2015
Greetings RegCMers,
I am trying to run RegCM with the 12 bin dust option (DU12). But when I
set my domain over the Sahara region I get the following error. When my
domain is set in northern latitudes RegCM seems to run fine. Also when I
lower the number of the total grid points or when I am using the 4 dust
bin option the simulation is completed without any problem. I am
including the *.in file and the output of the model+error.
Since the error is occurs in regcmMPI, there must be a problem with
parallel processing. I am running my experiments on 24 cores. I already
tried the "ulimit -s unlimited" before running mpirun.
Any hint or suggestions is greatly appreciated,
Best wishes,
Thanos
ps: You have to disable the chem BC to test the experiment in the *.in
file I am including.
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> regcmMPI 0000000000A9ACDE Unknown Unknown Unknown
> regcmMPI 0000000000A78FA2 Unknown Unknown Unknown
> regcmMPI 0000000000A3A2BE Unknown Unknown Unknown
> regcmMPI 00000000004427CE Unknown Unknown Unknown
> regcmMPI 000000000059930D Unknown Unknown Unknown
> regcmMPI 000000000040C239 Unknown Unknown Unknown
> regcmMPI 0000000000617F53 Unknown Unknown Unknown
> regcmMPI 000000000040B94C Unknown Unknown Unknown
> libc.so.6 000000373FA1D9F4 Unknown Unknown Unknown
> regcmMPI 000000000040B859 Unknown Unknown Unknown
>
> ========================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = EXIT CODE: 174
> = CLEANING UP REMAINING PROCESSES
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ========================================================
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! QUADIEEMS domain
&dimparam
iy = 102,
jx = 150,
kz = 18,
nsg = 1,
/
&geoparam
iproj = 'ROTMER',
ds = 60.0,
ptop = 5.0,
clat = 27,
clon = 15,
plat = 27,
plon = 15,
truelatl = 5.0,
truelath = 45.0,
i_band = 0,
/
&terrainparam
domname = 'DustRun',
smthbdy = .false.,
lakedpth = .false.,
fudge_lnd = .false.,
fudge_lnd_s = .false.,
fudge_tex = .false.,
fudge_tex_s = .false.,
ltexture = .true.,
dirter = 'input_DU12',
inpter = 'DATASETS',
/
&ioparam
ibyte = 4,
/
&debugparam
debug_level = 1,
dbgfrq = 3,
/
&boundaryparam
nspgx = 12,
nspgd = 12,
/
&globdatparam
ibdyfrq = 6,
ssttyp = 'ERSST',
dattyp = 'EIN15',
gdate1 = 2007093000,
gdate2 = 2007110200,
dirglob = 'input_DU12',
inpglob = 'DATASETS',
/
&globwindow
lat0 = 0.0
lat1 = 0.0
lon0 = 0.0
lon1 = 0.0
/
&restartparam
ifrest = .false.,
mdate0 = 2007100100,
mdate1 = 2007100100,
mdate2 = 2007110100,
/
&timeparam
dtrad = 60.,
dtabem = 18.,
dtsrf = 600.,
dt = 120.,
/
&outparam
ifsave = .true. ,
savfrq = 7200.,
ifatm = .true. ,
atmfrq = 6.,
ifrad = .true. ,
radfrq = 6.,
ifsrf = .true. ,
ifsub = .true. ,
srffrq = 3.,
ifchem = .true.,
ifopt = .true.,
chemfrq = 6.,
dirout='output_DU12'
/
&physicsparam
iboudy = 5,
ibltyp = 1,
icup_lnd = 5,
icup_ocn = 5,
igcc = 1,
ipptls = 1,
iocnflx = 2,
ipgf = 0,
iemiss = 1,
lakemod = 0,
ichem = 1,
scenario = 'A1B',
idcsst = 0,
iseaice = 0,
idesseas = 1,
iconvlwp = 1,
irrtm = 1, ! Use RRTM==1 radiation scheme instead of CCSM
/
&subexparam
qck1land = .250E-03,
qck1oce = .250E-03,
cevaplnd = .100E-02,
cevapoce = .100E-02,
caccrlnd = 3.000,
caccroce = 3.000,
cftotmax = 0.75,
/
&grellparam
/
&emanparam
/
&chemparam
chemsimtype = 'DU12', ! Which chemical tracers to be activated.
! One in :
! DUST : Activate 4 dust bins scheme
! DU12 : Activate 12 dust bins scheme
! SSLT : Activate 2 bins Sea salt scheme
! CARB : Activate 4 species black/anthropic
! carbon simulations
! SULF : Activate SO2 and SO4 tracers
! SUCA : Activate both SUKF and CARB
! AERO : Activate all DUST, SSLT, CARB and SULF
! CBMZ : Activate gas phase and sulfate
ichsolver = 1, ! Activate the chemical solver
idirect = 1, ! enable or not aerosol feedbacks on radiation and
! dynamics (aerosol direct and semi direct effcts):
! 0 = no coupling. Aerosol are only transported and
! don't interact with radiation scheme.
! 1 = no coupling to dynamic and thermodynamic. However
! the clear sky surface and top of atmosphere
! aerosol radiative forcings are diagnosed.
! 2 = allows aerosol feedbacks on radiative,
! thermodynamic and dynamic fields.
ichdrdepo = 1, ! 1 = enable tracer surface dry deposition. For dust,
! it is calculated by a size settling and dry
! deposition scheme. For other aerosol,a dry
! deposition velocity is simply prescribed further.
! Next release will include an improved aerosol dry
! deposition scheme for non dust aerosols.
ichcumtra = 1, ! 1 = enable tracer convective transport and mixing.
ichsursrc=1, ! Enable the emissions fluxes.
ichremlsc=1, ! 1 = enable tracer rainout
ichdustemd=2, ! Choice for parametrisation of dust emission size distribution
! 1 = use the standard scheme (Alfaro et al., Zakey et al.)
! 2 = use a revised soil granulometry ref +
! Kok et al emission size distribution : Menut et al.,2012; + Kok et al., 2011
rdstemfac = 1, ! Dust emission adjustment factor ( soil erodibility) : linearly reduce or increase the dust flux
ichebdy = 1, ! Enable reading of chemical boundary conditions, otherwise put 0 in boundary conditions.
ichdiag = 0, ! 1 = enable writing of additional tracer tendency diagnostics in the output
/
&clmparam
dirclm = '/set/this/to/where/your/input/clm/data/are',
imask = 1,
clmfrq = 12.,
/
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mkdir: cannot create directory `result': File exists
No snow.nc file to read
TERRAIN Completed!
SST Completed!
ICBC Completed!
CHEM_ICBC completed!
This is RegCM trunk
SVN Revision: tag_4.5-rc1.SVN4771 compiled at: data : Feb 26 2015 time: 23:00:07
: this run start at : 2015-06-30 22:27:03+0300
: it is submitted by :
: it is running on : node007
: it is using : 24 processors
: in directory : /storage05/st6/DustPaper_2007-2012_NEW_DOMAIN
CPUS DIM1 = 4
CPUS DIM2 = 6
Reading model namelist file
Using default Tiedtke parameter.
Using default Holtslag parameter.
Using default RRTM parameter.
DUST 12 bins simulation
Initial date of the global simulation: 2007-10-01 00:00:00 UTC
Initial date of this run : 2007-10-01 00:00:00 UTC
Final date of this run : 2007-11-01 00:00:00 UTC
Total simulation lenght : 744 hours
Timestep in seconds = 120.000000
Split explicit dtau = 30.000000 60.000000
Reading Domain file : input_DU12/DustRun_DOMAIN000.nc
Setting IPCC scenario to A1B
Create SAV files : T
Create ATM files : T
Create RAD files : T
Create SRF files : T
Create STS files : T
Create CHE files : T
Create OPT files : T
Frequency in hours to create SAV : 7200.0
Frequency in hours to create ATM : 6.0
Frequency in hours to create RAD : 6.0
Frequency in hours to create SRF : 3.0
Frequency in hours to create CHE : 6.0
Frequency in hours to create OPT : 6.0
Physical Parameterizations
Lateral Boundary conditions : 5
Semi-Lagrangian Advection : 0
Land cumulus conv. scheme : 5
Ocean cumulus conv. scheme : 5
Moisture schem : 1
Ocean Flux scheme : 2
Zeng roughness formula : 1
Coupling with ROMS ocean : 0
Pressure gradient force : 0
Prescribed LW emissivity : 1
Lake model in BATS : 0
Simulate diurnal sst cycle : 0
Simulate sea ice cover : 0
Simulate desert seasons : 0
Enable chem/aerosol model : 1
Convective LWP scheme : 1
Boundary Pameterizations
Nudge value high range : 3.000000
Nudge value medium range : 2.000000
Nudge value low range : 1.000000
Model Timestep Pameterizations
time step for dynamical model in seconds : 120.000000
time step for surface model in seconds : 600.000000
time step for radiation model in minutes : 60.000000
time step for emission model in hours : 18.000000
Domain grid parameters:
Map Projection : ROTMER
Dot Grid Full Extent : 150x 102x 18
Model Top Pressure : 5.000000 cb
Model Grid Spacing : 60.000000 km
Grid Center Latitude : 27.000000 deg
Grid Center longitude : 15.000000 deg
Pole Latitude : 27.000000 deg
Pole longitude : 15.000000 deg
PBL limit for Holtstag
Index of highest allowed pbl : 10
SUBEX large scale precipitation parameters
# of bottom no cloud model levels : 1
Auto-conversion rate: Land = 0.000250 Ocean = 0.000250
Relative humidity thresholds: Land = 0.800000 Ocean = 0.900000
Gultepe factors: Land = 0.400000 Ocean = 0.400000
Maximum relative humidity : 1.010000
RH0 temperature threshold : 238.000000
Land Raindrop Evaporation Rate : 0.001000
Ocean Raindrop Evaporation Rate : 0.001000
Land Raindrop Accretion Rate : 3.000000
Ocean Raindrop Accretion Rate : 3.000000
Maximum total cloud cover for rad : 0.750000
Condensation threshold : 1.000000
Tiedtke (1986) Convection Scheme ECMWF 38R2 used.
Convective Cloud Cover parameters after resolution scaling
Maximum Convective Cloud Cover : 0.398148
Convective Cloud Water : 0.000300
The surface energy budget is used to calculate the ground temperature.
The radiation is computed every 30 time steps.
Relaxation boundary conditions (exponential method)
# k sigma a dsigma twt(1) twt(2) qcon
1 0.0000 0.0250 0.0500 0.0000 0.0000 0.0000
2 0.0500 0.0750 0.0500 0.5000 0.5000 0.5000
3 0.1000 0.1300 0.0600 0.4545 0.5455 0.5455
4 0.1600 0.1950 0.0700 0.4615 0.5385 0.5385
5 0.2300 0.2700 0.0800 0.4667 0.5333 0.5333
6 0.3100 0.3500 0.0800 0.5000 0.5000 0.5000
7 0.3900 0.4300 0.0800 0.5000 0.5000 0.5000
8 0.4700 0.5100 0.0800 0.5000 0.5000 0.5000
9 0.5500 0.5900 0.0800 0.5000 0.5000 0.5000
10 0.6300 0.6700 0.0800 0.5000 0.5000 0.5000
11 0.7100 0.7450 0.0700 0.5333 0.4667 0.4667
12 0.7800 0.8100 0.0600 0.5385 0.4615 0.4615
13 0.8400 0.8650 0.0500 0.5455 0.4545 0.4545
14 0.8900 0.9100 0.0400 0.5556 0.4444 0.4444
15 0.9300 0.9450 0.0300 0.5714 0.4286 0.4286
16 0.9600 0.9700 0.0200 0.6000 0.4000 0.4000
17 0.9800 0.9850 0.0100 0.6667 0.3333 0.3333
18 0.9900 0.9950 0.0100 0.5000 0.5000 0.5000
19 1.0000
Constant hor. diff. coef. = 0.450000E+05 m^2 s-1
Maximumt hor. diff. coef. = 0.468750E+06 m^2 s-1
READY IC DATA for 2007-10-01 00:00:00 UTC
SEARCH BC data for 2007100106
READY BC from 2007100100 to 2007100106
# Ozone profile at (3,3) #
0.496E-07 0.496E-07 0.496E-07 0.496E-07 0.496E-07 0.523E-07 0.527E-07
0.577E-07 0.627E-07 0.715E-07 0.852E-07 0.106E-06 0.149E-06 0.226E-06
0.226E-06 0.414E-06 0.799E-06 0.142E-05 0.318E-05 0.00
tracer cbmz index molw
DUST01 -1 0.000000000000000E+000
DUST02 -1 0.000000000000000E+000
DUST03 -1 0.000000000000000E+000
DUST04 -1 0.000000000000000E+000
DUST05 -1 0.000000000000000E+000
DUST06 -1 0.000000000000000E+000
DUST07 -1 0.000000000000000E+000
DUST08 -1 0.000000000000000E+000
DUST09 -1 0.000000000000000E+000
DUST10 -1 0.000000000000000E+000
DUST11 -1 0.000000000000000E+000
DUST12 -1 0.000000000000000E+000
tracer index coreesponding to bdy species
# ichbdy2trac #
1 2 3 4 5 6 7
8 9 10 11 12 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0
Calling inidust
READY ICCH DATA for 2007-10-01 00:00:00 UTC
SEARCH CHBC data for 2007100106
READY CHBC from 2007100100 to 2007100106
Calculating Vertical Modes
Linearization about standard atmosphere
# sigma #
0.00 0.500E-01 0.100E+00 0.160 0.230 0.310 0.390
0.470 0.550 0.630 0.710 0.780 0.840 0.890
0.890 0.930 0.960 0.980 0.990 1.000
# t mean #
218. 218. 218. 218. 230. 239. 248.
255. 262. 268. 273. 277. 280. 283.
283. 285. 286. 287. 287.
# ps mean #
100.0
Vertical mode problem for kz = 18
Number of errors (should be 0) = 0
Split : 1 => aam : 4.0000, fac : 26.6667
Split : 2 => aam : 2.0000, fac : 48.0000
Opening new output file output_DU12//DustRun_ATM.2007100100.nc
Opening new output file output_DU12//DustRun_SRF.2007100100.nc
Opening new output file output_DU12//DustRun_STS.2007100100.nc
Opening new output file output_DU12//DustRun_RAD.2007100100.nc
Opening new output file output_DU12//DustRun_DUST01.2007100100.nc
Opening new output file output_DU12//DustRun_DUST02.2007100100.nc
Opening new output file output_DU12//DustRun_DUST03.2007100100.nc
Opening new output file output_DU12//DustRun_DUST04.2007100100.nc
Opening new output file output_DU12//DustRun_DUST05.2007100100.nc
Opening new output file output_DU12//DustRun_DUST06.2007100100.nc
Opening new output file output_DU12//DustRun_DUST07.2007100100.nc
Opening new output file output_DU12//DustRun_DUST08.2007100100.nc
Opening new output file output_DU12//DustRun_DUST09.2007100100.nc
Opening new output file output_DU12//DustRun_DUST10.2007100100.nc
Opening new output file output_DU12//DustRun_DUST11.2007100100.nc
Opening new output file output_DU12//DustRun_DUST12.2007100100.nc
Opening new output file output_DU12//DustRun_OPT.2007100100.nc
JDay 273.00 solar declination angle = -2.42297491 degrees
solar TSI irradiance = 1367.0000 W/m^2
$$$ 2007-10-01 03:00:00 UTC, ktau = 90
$$$ 1st, 2nd time deriv of ps = 0.27566E-04 0.21781E-06
$$$ no. of points w/convection = 846
SRF variables written at 2007-10-01 03:00:00 UTC
$$$ 2007-10-01 06:00:00 UTC, ktau = 180
$$$ 1st, 2nd time deriv of ps = 0.22532E-04 0.19863E-06
$$$ no. of points w/convection = 952
SEARCH BC data for 2007100112
READY BC from 2007100106 to 2007100112
SEARCH CHBC data for 2007100112
READY CHBC from 2007100106 to 2007100112
ATM variables written at 2007-10-01 06:00:00 UTC
SRF variables written at 2007-10-01 06:00:00 UTC
OPT variables written at 2007-10-01 06:00:00 UTC
CHE variables written at 2007-10-01 06:00:00 UTC
RAD variables written at 2007-10-01 06:00:00 UTC
$$$ 2007-10-01 09:00:00 UTC, ktau = 270
$$$ 1st, 2nd time deriv of ps = 0.23594E-04 0.25640E-06
$$$ no. of points w/convection = 842
SRF variables written at 2007-10-01 09:00:00 UTC
$$$ 2007-10-01 12:00:00 UTC, ktau = 360
$$$ 1st, 2nd time deriv of ps = 0.25462E-04 0.31513E-06
$$$ no. of points w/convection = 954
SEARCH BC data for 2007100118
READY BC from 2007100112 to 2007100118
SEARCH CHBC data for 2007100118
READY CHBC from 2007100112 to 2007100118
ATM variables written at 2007-10-01 12:00:00 UTC
SRF variables written at 2007-10-01 12:00:00 UTC
OPT variables written at 2007-10-01 12:00:00 UTC
CHE variables written at 2007-10-01 12:00:00 UTC
RAD variables written at 2007-10-01 12:00:00 UTC
$$$ 2007-10-01 15:00:00 UTC, ktau = 450
$$$ 1st, 2nd time deriv of ps = 0.19236E-04 0.20775E-06
$$$ no. of points w/convection = 810
SRF variables written at 2007-10-01 15:00:00 UTC
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
regcmMPI 0000000000A9ACDE Unknown Unknown Unknown
regcmMPI 0000000000A78FA2 Unknown Unknown Unknown
regcmMPI 0000000000A3A2BE Unknown Unknown Unknown
regcmMPI 00000000004427CE Unknown Unknown Unknown
regcmMPI 000000000059930D Unknown Unknown Unknown
regcmMPI 000000000040C239 Unknown Unknown Unknown
regcmMPI 0000000000617F53 Unknown Unknown Unknown
regcmMPI 000000000040B94C Unknown Unknown Unknown
libc.so.6 000000373FA1D9F4 Unknown Unknown Unknown
regcmMPI 000000000040B859 Unknown Unknown Unknown
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 174
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
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