[RegCNET] A Segmentation Error when Running RegCM test_002

LSL lslrsgis at whu.edu.cn
Sat Mar 12 04:23:12 CET 2022


Dear RegCM community,


As a beginner, I am writing for an error when running RegCM over domain 
China. After successfully generating ICBC, a segmentation error prompted 
as follows.


10 /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]

===================

[n0021:5045 :0:5045] Caught signal 11 (Segmentation fault: address not 
mapped to object at address (nil))

[n0021:5047 :0:5047] Caught signal 11 (Segmentation fault: address not 
mapped to object at address (nil))


The namelist test_China.in is adopted from default file test_002.in 
./run directory, with only the directory changed while others options 
remain the same.


Detailed description of this error can be found in attached slurm file. 
Any help, thanks.


P.S. By the way, test_001 can be executed successfully.


LSL
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! Chinese domain 
 &dimparam
 iy     = 80,
 jx     = 112,
 kz     = 18,
 nsg    = 1,
 /
 &geoparam
 iproj = 'LAMCON',
 ds = 60.0,
 ptop = 5.0,
 clat = 34,
 clon = 120,
 plat = 34,
 plon = 120,
 truelatl = 25.0,
 truelath = 50.0,
 i_band = 0,
 /
 &terrainparam
 domname = 'test_China',
 lakedpth = .false.,
 fudge_lnd   = .false.,
 fudge_lnd_s = .false.,
 fudge_tex   = .false.,
 fudge_tex_s = .false.,
 dirter = 'input/',
 inpter = '/home/slliu/scratch/RegCM-4.7.1/DATASET',
 /
 &debugparam
 debug_level = 0,
 /
 &boundaryparam
 nspgx  = 12,
 nspgd  = 12,
 /
 &globdatparam
 ibdyfrq = 6,
 ssttyp = 'OI_WK',
 dattyp = 'ERA40',
 gdate1 = 1994010100,
 gdate2 = 1994020100,
 dirglob = 'input/',
 inpglob = '/home/slliu/scratch/RegCM-4.7.1/DATASET',
 /
 &restartparam
 ifrest  = .false. ,
 mdate0  = 1994010100,
 mdate1  = 1994010100,
 mdate2  = 1994010600,
 /
 &timeparam
 dtrad   =    30.,
 dtabem  =    18.,
 dtsrf   =   600.,
 dt      =   120.,
 /
 &outparam
 ifsave  = .true. ,
  savfrq  =    0.,
 ifatm  = .true. ,
 atmfrq  =     6.,
 ifrad   = .true. ,
   radfrq  =     6.,
 ifsrf   = .true. ,
 ifsub   = .true. ,
   srffrq  =     3.,
 ifchem  = .false.,
   chemfrq =     6.,
 dirout = 'output/',
 /
 &physicsparam
 iboudy  =          5,
 ibltyp  =          1,
 icup_lnd =         2,
 icup_ocn =         2,
 ipptls  =          1,
 iocnflx =          2,
 ipgf    =          0,
 iemiss  =          0,
 lakemod =          0,
 ichem   =          0,
 idcsst = 0,
 iseaice = 0,
 idesseas = 0,
 iconvlwp = 0,
 /
 &subexparam
 /
 &grellparam
 /
 &holtslagparam
 /
 &clm_inparm
 fpftcon = 'pft-physiology.c130503.nc',
 fsnowoptics = 'snicar_optics_5bnd_c090915.nc',
 fsnowaging = 'snicar_drdt_bst_fit_60_c070416.nc',
 /
 &clm_soilhydrology_inparm
 /
 &clm_hydrology1_inparm
 /
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#!/bin/sh

#SBATCH --ntasks=8
#SBATCH --partition=hpib
#SBATCH --account=hetao

export FI_PROVIDER=verbs

#srun -n $SLURM_NTASKS ./real.exe
#srun -n $SLURM_NTASKS ./wrf.exe

#srun -n $SLURM_NTASKS ./bin/terrain test_China.in
#srun -n $SLURM_NTASKS ./bin/icbc test_China.in
srun -n $SLURM_NTASKS ./bin/regcmMPI test_China.in
#srun -n $SLURM_NTASKS ./bin/icbc test_001.in
#srun -n $SLURM_NTASKS ./bin/regcmMPI test_001.in
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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  : 2022-03-09 17:45:12+0800
 : it is submitted by : slliu
 : it is running on   : n0021
 : it is using        :            8   processors
 : in directory       : /scratch/slliu/RegCM-4.7.1/run
                       
 CPUS DIM1 =            2
 CPUS DIM2 =            4
 
 Reading model namelist file
 Using default dynamical parameters.
 Using default hydrostatc parameters.
 Using default cloud parameter.
 Initial date of the global simulation:  1994-01-01 00:00:00 UTC        
 Initial date of this run             :  1994-01-01 00:00:00 UTC        
 Final date of this run               :  1994-01-06 00:00:00 UTC        
 Total simulation lenght              :          120  hours
 Timestep in seconds =  120.000000
 Split explicit dtau =   30.000000  60.000000
 Reading Domain file : input//test_China_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   :  2
  Ocean cumulus conv. scheme  :  2
  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 :   120.000000
  time step for surface   model in seconds :   600.000000
  time step for cumulus   model in seconds :   240.000000
  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  :  112x  80x 18
  Model Top Pressure    :    5.000000 cb
  Model Grid Spacing    :   60.000000 km
  Grid Center Latitude  :   34.000000 deg
  Grid Center longitude :  120.000000 deg
  True Latitude 1       :   25.000000 deg
  True Latitude 2       :   50.000000 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
 Grell Convection Scheme used.
  Conversion rate :    0.002000
  Max Shear       :    0.900000
  Min Shear       :    0.300000
  Max PPT eff     :    0.800000
  Min PPT eff     :    0.200000
  Max PPT eff(o)  :    0.800000
  Min PPT eff(o)  :    0.200000
  Max PPT eff(x)  :    0.800000
  Min PPT eff(x)  :    0.200000
  Max PBC         :   50.000000
  Min Cloud Depth :  150.000000
  Max Cloud Base  :    0.400000
  Max Heating     :  500.000000
  Min Heating     : -250.000000
  Fritsch-Chappell (1980) Closure Assumption
  ABE removal timescale :   30.000000
 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  1994-01-01 00:00:00 UTC        
 SEARCH BC data for 1994010106 , step =        0
 READY  BC from     1994010100  to 1994010106 
 At  1994-01-01 00:00:00 UTC        
 JDay      0.00000 solar declination angle = -23.10177678 degrees
                   solar TSI irradiance    =    1361.1322 W/m^2
 Constant hor. diff. coef. =  0.450000E+05 m^2 s-1
 Maximum  hor. diff. coef. =  0.468750E+06 m^2 s-1
 Computed background diff. coeff. =  0.620731E+01 - 0.450000E+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 :    26.6667
 Split :    2 => aam :     2.0000, fac :    48.0000
 Opening new output file output//test_China_ATM.1994010100.nc
 Opening new output file output//test_China_SHF.1994010100.nc
 Opening new output file output//test_China_SRF.1994010100.nc
 Opening new output file output//test_China_STS.1994010100.nc
 Opening new output file output//test_China_RAD.1994010100.nc
 ATM variables written at  1994-01-01 00:00:00 UTC        
[n0021:5048 :0:5048] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[n0021:5055 :0:5055] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
[n0021:5054 :0:5054] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[n0021:5044 :0:5044] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
[n0021:5053 :0:5053] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
    0  /usr/lib64/libucs.so.0(+0x174f0) [0x2b98273204f0]
    1  /usr/lib64/libucs.so.0(+0x176a2) [0x2b98273206a2]
    2  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
    3  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
    4  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
    5  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
    6  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
    7  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
    8  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
    9  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b97a5025505]
   10  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
    0  /usr/lib64/libucs.so.0(+0x174f0) [0x2b2598ff54f0]
    1  /usr/lib64/libucs.so.0(+0x176a2) [0x2b2598ff56a2]
    2  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
    3  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
    4  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
    5  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
    6  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
    7  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
    8  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
    9  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b2516af3505]
   10  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
==== backtrace ====
    0  /usr/lib64/libucs.so.0(+0x174f0) [0x2b5492c514f0]
    1  /usr/lib64/libucs.so.0(+0x176a2) [0x2b5492c516a2]
    2  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
    3  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
    4  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
    5  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
    6  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
    7  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
    8  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
    9  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b5410956505]
   10  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
[n0021:5045 :0:5045] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[n0021:5047 :0:5047] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
==== backtrace ====
    0  /usr/lib64/libucs.so.0(+0x174f0) [0x2acb2c9ef4f0]
[n0021:5056 :0:5056] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
    1  /usr/lib64/libucs.so.0(+0x176a2) [0x2acb2c9ef6a2]
    0  /usr/lib64/libucs.so.0(+0x174f0) [0x2b20220104f0]
    1  /usr/lib64/libucs.so.0(+0x176a2) [0x2b20220106a2]
    2  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
    3  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
    4  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
    5  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
    6  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
    7  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
    8  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
    9  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b1f9fd15505]
   10  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
    2  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
    0  /usr/lib64/libucs.so.0(+0x174f0) [0x2b150c9ff4f0]
    1  /usr/lib64/libucs.so.0(+0x176a2) [0x2b150c9ff6a2]
    2  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
    3  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
    4  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
    5  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
    6  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
    7  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
    8  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
    9  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b148a704505]
   10  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
    3  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
    4  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
    5  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
    6  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
    7  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
    8  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
    9  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2acaaa6f4505]
   10  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
    0  /usr/lib64/libucs.so.0(+0x174f0) [0x2b7e3ac504f0]
    1  /usr/lib64/libucs.so.0(+0x176a2) [0x2b7e3ac506a2]
    2  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
    3  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
    4  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
    5  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
    6  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
    7  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
    8  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
    9  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b7db8955505]
   10  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
==== backtrace ====
    0  /usr/lib64/libucs.so.0(+0x174f0) [0x2b3425aed4f0]
    1  /usr/lib64/libucs.so.0(+0x176a2) [0x2b3425aed6a2]
    2  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x810d1b]
    3  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5015e6]
    4  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x604acb]
    5  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x5e5208]
    6  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x4120be]
    7  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x682e25]
    8  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x412022]
    9  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b33a37f2505]
   10  /scratch/slliu/RegCM-4.7.1/run/./bin/regcmMPI() [0x411f29]
===================
srun: error: n0021: tasks 0-7: Segmentation fault
-------------- next part --------------
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