Hello RegCM Team,
i wanted to run RegCM-4.4-rc28 with CLM-3.5, steps of terrain, sst, icbc and clm2rcm were successful but in the last step mpirun -np 4 ./bin/regcmMPI_clm regcm35.in, the following error message appeared:
This is RegCM trunk
SVN Revision: 4470 - tag 4.4-rc28 compiled at: data : Jul 8 2014 time: 11:52:29
: this run start at : 2014-07-08 13:06:39+0200
: it is submitted by : samy
: it is running on : localhost.localdomain
: it is using : 4 processors
: in directory : /home/samy/rcm28run
CPUS DIM1 = 4
CPUS DIM2 = 1
Reading model namelist stanzas
Initial date of the global simulation: 2008-01-01 00:00:00 UTC
Initial date of this run : 2008-01-01 00:00:00 UTC
Final date of this run : 2008-12-31 00:00:00
UTC
Total simulation lenght : 8760 hours
Timestep in seconds = 150.000000
Split explicit dtau = 37.500000 75.000000
Reading Domain file : ./input/test_001_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
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
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
Coupling with ROMS ocean : 0
Pressure gradient force : 0
Prescribed LW emissivity : 0
Enable chem/aerosol model : 0
Convective LWP scheme : 0
Boundary Pameterizations
Nudge value high range : 1.000000
Nudge value medium range : 2.000000
Nudge value low range : 3.000000
CLM Pameterizations
CLM imask : 1
Frequency in hours to write CLM : 12.000000
Model Timestep Pameterizations
time step for dynamical model in seconds : 150.000000
time step for surface model in seconds : 600.000000
time step for radiation model in minutes : 30.000000
time step for emission model in hours : 18.000000
Domain grid parameters:
Map Projection : ROTMER
Dot Grid Full Extent : 64x 34x 18
Model Top Pressure : 5.000000 cb
Model Grid Spacing : 60.000000 km
Grid Center Latitude : 30.000000 deg
Grid Center longitude : 30.000000 deg
Pole Latitude : 30.000000 deg
Pole longitude : 30.000000 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
Emanuel (1991) Convection Scheme V4.3C used.
Min Convection origin : 0.950000
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 : 0.398148
Convective Cloud Water : 0.000300
The surface energy budget is used to calculate the ground temperature.
The radiation is computed every 12 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. = 0.360000E+05 m^2 s-1
Maximumt hor. diff. coef. = 0.375000E+06 m^2 s-1
READY IC DATA for 2008-01-01 00:00:00 UTC
SEARCH BC data for 2008010106
READY BC from 2008010100 to 2008010106
# Ozone profile at (3,3) #
0.496E-07 0.496E-07 0.496E-07 0.517E-07 0.527E-07 0.527E-07 0.576E-07
0.605E-07 0.670E-07 0.778E-07 0.946E-07 0.121E-06 0.162E-06 0.263E-06
0.263E-06 0.475E-06 0.872E-06 0.149E-05 0.328E-05 0.00
4 pes participating in computation
-----------------------------------
NODE# NAME
( 0) localhost.localdomain
( 1) localhost.localdomain
( 2) localhost.localdomain
( 3) localhost.localdomain
PERF_SETOPTS: Using profile_disable= T
profile_timer= 9 profile_depth_limit= 99999 profile_detail_limit= 0 profile_barrier= F profile_single_file= T
CLM MODEL version 3.5
Attempting to initialize the land model .....
Attempting to initialize run control settings .....
nsrest = 0 dtime = 600
start_ymd = 20080101 start_tod = 0
stop_ymd = 20081231 stop_tod
= 0
calendar = gregorian wrtdia = T
irad = 3
hist_nhtfrq = -12 -12 -12 -12 -12 -12
Successfully initialized run control settings
define run:
run type = initial
case title = clmoutput
input data files:
PFT physiology = /home/samy/RCMDATA/CLM/pft-physiology.c070207
fsurdat, surface dataset not
set
flndtopo not set
fatmgrid not set, using fsurdat
atm grid data =
fatmlndfrc not set, using fatmgrid
land frac data =
fatmtopo not set
NOT using input data for nitrogen deposition
NOT using dynamic input data for nitrogen deposition
vegetation type data = /home/samy/RCMDATA/CLM/test_001_RCMpft.nc
fmax data = /home/samy/RCMDATA/CLM/test_001_RCMfmax.nc
soil texture data = /home/samy/RCMDATA/CLM/test_001_RCMsoitex.10level.nc
soil color data =
/home/samy/RCMDATA/CLM/test_001_RCMsoicol_clm2.nc
lake/water data = /home/samy/RCMDATA/CLM/test_001_RCMlanwat.nc
glacier data = /home/samy/RCMDATA/CLM/test_001_RCMglacier.nc
urban data = /home/samy/RCMDATA/CLM/test_001_RCMurban.nc
LAI data = /home/samy/RCMDATA/CLM/test_001_RCMlai.nc
navyoro data = /home/samy/RCMDATA/CLM/test_001_RCMnavyoro_20min.nc
initial data created by model
Restart parameters:
restart pointer file directory = .
restart pointer file name = lnd.clmoutput.rpointer
initial datasets will not be
produced
model physics parameters:
flag for random perturbation test is not set
solar radiation frequency (iterations) = 3
maxpatch_pft = 4
allocate_all_vegpfts = F
nsegspc = 20
Attempting to read alatlon from fatmgrid
(GETFIL): attempting to find local file test_001_RCMnavyoro_20min.nc
sh: /usr/local/bin/msrcp: No such file or
directory
(shr_file_get) rcode = 0 cmd = /usr/local/bin/msrcp mss:/home/samy/RCMDATA/CLM/test_001_RCMnavyoro_20min.nc test_001_RCMnavyoro_20min.nc
(GETFIL): File test_001_RCMnavyoro_20min.nc read in from:
mss:/home/samy/RCMDATA/CLM/test_001_RCMnavyoro_20min.nc
;
(GETFIL): failed transferring file to local path:
test_001_RCMnavyoro_20min.nc &n
bsp;
ENDRUN:GETFIL: file not transfered to local path
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when
Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 27561 on
node localhost.localdomain exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize"
prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
Any advice Plz