[RegCNET] Segmentation error when executing test exercise
LSL
lslrsgis at whu.edu.cn
Tue Aug 24 04:41:27 CEST 2021
Dear RegCNET community,
As a very beginner to RegCM, I have met a problem when executing test
exercise following user’s guide.
After successfully run terrain, sst and icbc, a segmentation error
prompt out when executing ./bin/regcmMPI test_001.in with a sbatch job
in our cluster.
===================
0 /usr/lib64/libucs.so.0(+0x174f0) [0x2af93d9594f0]
1 /usr/lib64/libucs.so.0(+0x176a2) [0x2af93d9596a2]
2 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
3 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
4 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
5 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
6 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
7 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
8 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
9 /lib64/libc.so.6(__libc_start_main+0xf5) [0x2af8bb65e505]
10 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
Any help? Thanks in advance.
LSL
P.S. Detail description of this error can be found in attached slurm file./
/
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This is RegCM trunk
SVN Revision: tag-4.7.1 compiled at: data : Aug 21 2021 time: 17:27:32
: this run start at : 2021-08-24 10:15:08+0800
: it is submitted by : slliu
: it is running on : n0183
: it is using : 8 processors
: in directory : /dat01/slliu/CODE/RegCM-4.7.1/run
CPUS DIM1 = 4
CPUS DIM2 = 2
Reading model namelist file
Using default dynamical parameters.
Using default hydrostatc parameters.
Using default cloud parameter.
Initial date of the global simulation: 1990-06-01 00:00:00 UTC
Initial date of this run : 1990-06-01 00:00:00 UTC
Final date of this run : 1990-06-06 00:00:00 UTC
Total simulation lenght : 120 hours
Timestep in seconds = 100.000000
Split explicit dtau = 25.000000 50.000000
Reading Domain file : input//test_001_DOMAIN000.nc
Setting IPCC scenario to RCP4.5
Create SAV files : T
Create ATM files : T
Create RAD files : T
Create SRF files : T
Create STS files : T
Create SHF files : T
Monthly SAV files are written
Frequency in hours to create ATM : 6.0
Frequency in hours to create RAD : 6.0
Frequency in hours to create SRF : 3.0
Physical Parameterizations
Lateral Boundary conditions : 5
Semi-Lagrangian Advection : 0
Land cumulus conv. scheme : 4
Ocean cumulus conv. scheme : 4
Moisture schem : 1
Ocean Flux scheme : 2
Zeng roughness formula : 1
Zeng roughness method : 1
Coupling with ocean : 0
Coupling with wave : 0
Pressure gradient force : 0
Prescribed LW emissivity : 0
Lake model in BATS : 0
Simulate diurnal sst cycle : 0
Simulate sea ice cover : 0
Simulate desert seasons : 0
Enable chem/aerosol model : 0
Large scale LWP as convect. : 0
Cloud fraction scheme : 0
Marine stratocumulus : 1
Climate O3 dataset : 0
Climate Aerosol dataset : 0
Boundary Pameterizations
Num. of bndy points cross : 12
Num. of bndy points dot : 12
Nudge value high range : 3.000000
Nudge value medium range : 2.000000
Nudge value low range : 1.000000
Nm paramter : -1.000000
Dm paramter : -1.000000
Model Timestep Pameterizations
time step for dynamical model in seconds : 100.000000
time step for surface model in seconds : 600.000000
time step for cumulus model in seconds : 300.000000
time step for radiation model in seconds : 1800.000000
time step for emission model in seconds : 64800.000000
Domain grid parameters:
Map Projection : LAMCON
Dot Grid Full Extent : 64x 34x 18
Model Top Pressure : 5.000000 cb
Model Grid Spacing : 60.000000 km
Grid Center Latitude : 45.390000 deg
Grid Center longitude : 13.480000 deg
True Latitude 1 : 30.000000 deg
True Latitude 2 : 60.000000 deg
PBL limit for Holtstag
Index of highest allowed pbl : 10
Cloud fraction schemes parameters
# of bottom no cloud model levels : 1
Maximum relative humidity : 1.010000
Minimum relative humidity : 0.010000
RH0 temperature threshold : 238.000000
Relative humidity thresholds: Land = 0.800000 Ocean = 0.900000
Maximum total cloud cover for rad : 0.750000
Conv. CF UMF factor deep cumulus : 0.140000
Conv. CF UMF factor shallow cumul : 0.070000
Conv. CF UMF factor K2 : 500.000000
Surface radiation hack : F
Vavrus-Waliser Arctic cloud fix : T
SUBEX large scale precipitation parameters
Auto-conversion rate: Land = 0.000500 Ocean = 0.000500
Gultepe factors: Land = 0.650000 Ocean = 0.300000
Land Raindrop Evaporation Rate : 0.000010
Ocean Raindrop Evaporation Rate : 0.000010
Land Raindrop Accretion Rate : 6.000000
Ocean Raindrop Accretion Rate : 4.000000
Condensation efficiency : 1.000000
Emanuel (1991) Convection Scheme V4.3C used.
Min Convection origin : 0.950000, (16)
Autoconversion Threshold (ocean) : 0.001100
Autoconversion Threshold (land) : 0.001100
Autoconversion Threshold to zero : -55.000000
Entrainment Coefficient : 1.500000
Fractional area of uns. downdraft : 0.050000
Fractional area of uns. downdraft : 0.050000
Fall speed of rain : 50.000000
Fall speed of snow : 5.500000
Rain evaporation coefficient : 1.000000
Snow evaporation coefficient : 0.800000
Convective momentum transport coef: 0.700000
Downdraft velocity scale : 10.000000
Max negative perturbation blw LFC : 0.900000
Quasi-equilibrium approach rate 1 : 0.200000
Quasi-equilibrium approach rate 2 : 0.100000
Precipitation efficienct (land) : 0.999000
Precipitation efficienct (ocean) : 0.999000
Convective Cloud Cover parameters after resolution scaling
Maximum Convective Cloud Cover : 0.348765
Convective Cloud Water : 0.000300
The surface energy budget is used to calculate the ground temperature.
The radiation is computed every 30. minutes.
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
READY IC DATA for 1990-06-01 00:00:00 UTC
SEARCH BC data for 1990060106 , step = 0
READY BC from 1990060100 to 1990060106
At 1990-06-01 00:00:00 UTC
JDay 151.00000 solar declination angle = 21.85865568 degrees
solar TSI irradiance = 1361.7785 W/m^2
Constant hor. diff. coef. = 0.540000E+05 m^2 s-1
Maximum hor. diff. coef. = 0.562500E+06 m^2 s-1
Computed background diff. coeff. = 0.881127E+02 - 0.540000E+05 m^2 s-1
Calculating Vertical Modes
Linearization about standard atmosphere
# sigma #
0.00 0.500E-01 0.100 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 1.00
# t mean #
218. 218. 218. 218. 230. 239. 248.
255. 262. 268. 273. 277. 280. 283.
283. 285. 286. 287. 287.
# ps mean #
100.
Vertical mode problem for kz = 18
Number of errors (should be 0) = 0
Split : 1 => aam : 4.0000, fac : 22.2222
Split : 2 => aam : 2.0000, fac : 40.0000
Opening new output file output//test_001_ATM.1990060100.nc
Opening new output file output//test_001_SHF.1990060100.nc
Opening new output file output//test_001_SRF.1990060100.nc
Opening new output file output//test_001_STS.1990060100.nc
Opening new output file output//test_001_RAD.1990060100.nc
ATM variables written at 1990-06-01 00:00:00 UTC
[n0183:28294:0:28294] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
[n0183:28295:0:28295] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[n0183:28296:0:28296] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
[n0183:28298:0:28298] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
[n0183:28297:0:28297] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
[n0183:28299:0:28299] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
[n0183:28301:0:28301] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
0 /usr/lib64/libucs.so.0(+0x174f0) [0x2abaf11c34f0]
1 /usr/lib64/libucs.so.0(+0x176a2) [0x2abaf11c36a2]
2 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
3 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
4 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
5 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
6 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
7 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
8 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
9 /lib64/libc.so.6(__libc_start_main+0xf5) [0x2aba6ecc1505]
10 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
0 /usr/lib64/libucs.so.0(+0x174f0) [0x2b242010a4f0]
1 /usr/lib64/libucs.so.0(+0x176a2) [0x2b242010a6a2]
2 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
3 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
4 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
5 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
6 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
7 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
8 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
9 /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b239de0f505]
10 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
0 /usr/lib64/libucs.so.0(+0x174f0) [0x2b57c42844f0]
1 /usr/lib64/libucs.so.0(+0x176a2) [0x2b57c42846a2]
2 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
3 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
4 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
5 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
6 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
7 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
8 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
9 /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b5741f89505]
10 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
0 /usr/lib64/libucs.so.0(+0x174f0) [0x2b59de0814f0]
0 /usr/lib64/libucs.so.0(+0x174f0) [0x2b55ab7e24f0]
1 /usr/lib64/libucs.so.0(+0x176a2) [0x2b55ab7e26a2]
2 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
3 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
4 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
5 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
6 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
7 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
8 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
9 /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b55294e7505]
10 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
0 /usr/lib64/libucs.so.0(+0x174f0) [0x2b631f3f54f0]
1 /usr/lib64/libucs.so.0(+0x176a2) [0x2b631f3f56a2]
2 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
3 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
4 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
5 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
6 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
7 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
8 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
9 /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b629d0fa505]
10 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
1 /usr/lib64/libucs.so.0(+0x176a2) [0x2b59de0816a2]
2 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
3 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
4 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
5 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
6 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
7 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
8 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
9 /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b595bd86505]
10 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
[n0183:28300:0:28300] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
==== backtrace ====
0 /usr/lib64/libucs.so.0(+0x174f0) [0x2b1d575844f0]
1 /usr/lib64/libucs.so.0(+0x176a2) [0x2b1d575846a2]
2 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
3 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
4 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
5 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
6 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
7 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
8 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
9 /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b1cd5289505]
10 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
0 /usr/lib64/libucs.so.0(+0x174f0) [0x2af93d9594f0]
1 /usr/lib64/libucs.so.0(+0x176a2) [0x2af93d9596a2]
2 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
3 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
4 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
5 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
6 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
7 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
8 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
9 /lib64/libc.so.6(__libc_start_main+0xf5) [0x2af8bb65e505]
10 /dat01/slliu/CODE/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
srun: error: n0183: tasks 0-7: Segmentation fault
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