Tools (#2) - [domcfg] NEMO v4 DOMAINcfg tool (#94) - Message List
[domcfg] NEMO v4 DOMAINcfg tool
unsolved
Hi there
Been trying to use the domain cfg tool, but without success. I am new to nemo v4. The MPI also fails. I attached the ocean.output and part of the name list below. If anyone has Ideas, please let me know. Thank you in advance.
Here is the output from my ocean.output file. please excuse the length of text:
CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC
NEMO team
Ocean General Circulation Model
version 3.7 (2015)
mynode : mpi initialisation
~~~~~~
Namelist nammpp
mpi send type cn_mpi_send = I
size exported buffer nn_buffer = 0 bytes
jpni, jpnj and jpnij will be calculated automatically
avoid use of mpi_allgather at the north fold ln_nnogather = F
Immediate non-blocking send (isend)
AAAAAAAA
nemo_ctl: Control prints & Benchmark
~~~~~~~
Namelist namctl
run control (for debugging) ln_ctl = F
level of print nn_print = 0
Start i indice for SUM control nn_ictls = 0
End i indice for SUM control nn_ictle = 0
Start j indice for SUM control nn_jctls = 0
End j indice for SUM control nn_jctle = 0
number of proc. following i nn_isplt = 1
number of proc. following j nn_jsplt = 1
benchmark parameter (0/1) nn_bench = 0
timing activated (0/1) nn_timing = 0
namcfg : configuration initialization through namelist read
~~~~~~~
Namelist namcfg
vertical scale factors =T: e3.=dk[depth] ln_e3_dep = T
=F: old definition
configuration name cp_cfg = orca
configuration zoom name cp_cfz = no zoom
configuration resolution jp_cfg = 4
1st lateral dimension ( >= jpiglo ) jpidta = 20
2nd " " ( >= jpjglo ) jpjdta = 20
3nd " " jpkdta = 10
1st dimension of global domain in i jpiglo = 20
2nd - - in j jpjglo = 20
left bottom i index of the zoom (in data domain) jpizoom = 1
left bottom j index of the zoom (in data domain) jpizoom = 1
lateral cond. type (between 0 and 6) jperio = 0
use file attribute if exists as i/p j-start ln_use_jattr = F
mpp_init : Message Passing MPI
~~~~~~~~
mpp_init: defines mpp subdomains
~~~~~~ ----------------------
iresti= 1 irestj= 2
jpni= 1 jpnj= 2
sum ilcit(i,1)= 20.000000000000000 jpiglo= 20
sum ilcit(1,j)= 20.000000000000000 jpjglo= 20
****************
* *
2 * 20 x 11 *
* 1 *
* *
****************
* *
1 * 20 x 11 *
* 0 *
* *
****************
1
nproc = 0
nowe = -1 noea = 1
nono = 1 noso = -1
nbondi = 2
nbondj = -1
npolj = 0
nperio = 0
nlci = 20
nlcj = 11
nimpp = 1
njmpp = 1
nreci = 2 npse = 0
nrecj = 2 npsw = -2
jpreci = 1 npne = 2
jprecj = 1 npnw = 0
mpp_init_ioipsl : iloc = 20 11
~~~~~~~~~~~~~~~ iabsf = 1 1
ihals = 0 0
ihale = 0 1
phy_cst : initialization of ocean parameters and constants
~~~~~~~
Domain info
dimension of model
Local domain Global domain Data domain
jpi : 20 jpiglo : 20 jpidta : 20
jpj : 11 jpjglo : 20 jpjdta : 20
jpk : 10 jpk : 10 jpkdta : 10
jpij : 220
mpp local domain info (mpp)
jpni : 1 jpreci : 1
jpnj : 2 jprecj : 1
jpnij : 2
lateral domain boundary condition type : jperio = 0
Constants
mathematical constant rpi = 3.1415926535897931
day rday = 86400.000000000000 s
sideral year rsiyea = 31558149.010110732 s
sideral day rsiday = 86164.099655911836 s
omega omega = 7.2921150830460618E-005 s^-1
nb of months per year raamo = 12.000000000000000 months
nb of hours per day rjjhh = 24.000000000000000 hours
nb of minutes per hour rhhmm = 60.000000000000000 mn
nb of seconds per minute rmmss = 60.000000000000000 s
earth radius ra = 6371229.0000000000 m
gravity grav = 9.8066499999999994 m/s^2
triple point of temperature rtt = 273.16000000000003 K
freezing point of water rt0 = 273.14999999999998 K
melting point of snow rt0_snow = 273.14999999999998 K
melting point of ice rt0_ice = 273.05000000000001 K
reference density and heat capacity now defined in eosbn2.f90
thermal conductivity of the snow = 0.22000000000000000 J/s/m/K
thermal conductivity of the ice = 2.0343960000000001 J/s/m/K
fresh ice specific heat = 2093.0000000000000 J/kg/K
latent heat of fusion of fresh ice / snow = 333700.00000000000 J/kg
density times specific heat for snow = 690690.00000000000 J/m^3/K
density times specific heat for ice = 1883700.0000000000 J/m^3/K
volumetric latent heat fusion of sea ice = 300330000.00000000 J/m
latent heat of sublimation of snow = 2800000.0000000000 J/kg
volumetric latent heat fusion of snow = 110121000.00000000 J/m^3
density of sea ice = 900.00000000000000 kg/m^3
density of snow = 330.00000000000000 kg/m^3
emissivity of snow or ice = 0.96999999999999997
salinity of ice = 6.0000000000000000 psu
salinity of sea = 34.700000000000003 psu
latent heat of evaporation (water) = 2500000.0000000000 J/m^3
correction factor for solar radiation = 0.90000000000000002
von Karman constant = 0.40000000000000002
Stefan-Boltzmann constant = 5.6699999999999998E-008 J/s/m^2/K^4
conversion: degre ==> radian rad = 1.7453292519943295E-002
smallest real computer value rsmall = 1.1102230246251565E-016
eos_init : equation of state
~~~~~~~~
Namelist nameos : Chosen the Equation Of Seawater (EOS)
TEOS-10 : rho=F(Conservative Temperature, Absolute Salinity, depth) ln_TEOS10 = T
EOS-80 : rho=F(Potential Temperature, Practical Salinity, depth) ln_EOS80 = F
S-EOS : rho=F(Conservative Temperature, Absolute Salinity, depth) ln_SEOS = F
use of TEOS-10 equation of state (cons. temp. and abs. salinity)
model uses Conservative Temperature
Important: model must be initialized with CT and SA fields
volumic mass of reference rau0 = 1026.0000000000000 kg/m^3
1. / rau0 r1_rau0 = 9.7465886939571145E-004 m^3/kg
ocean specific heat rcp = 3991.8679571196299 J/Kelvin
rau0 * rcp rau0_rcp = 4095656.5240047402
1. / ( rau0 * rcp ) r1_rau0_rcp = 2.4416109948160356E-007
dom_cfg : set the ocean configuration
~~~~~~~
ocean model configuration used : cp_cfg = orca jp_cfg = 4
global domain lateral boundaries
jperio= 0, closed
dom_glo : domain: data / local
~~~~~~~
data input domain : jpidta = 20 jpjdta = 20 jpkdta = 10
global or zoom domain: jpiglo = 20 jpjglo = 20 jpk = 10
local domain : jpi = 20 jpj = 11 jpk = 10
south-west indices jpizoom = 1 jpjzoom = 1
zoom flags :
lzoom = F (T = zoom, F = global )
lzoom_e = F (T = forced closed east boundary)
lzoom_w = F (T = forced closed west boundary)
lzoom_s = F (T = forced closed South boundary)
lzoom_n = F (T = forced closed North boundary)
dom_init : domain initialization
~~~~~~~~
dom_nam : domain initialization through namelist read
~~~~~~~
Namelist namrun
job number nn_no = 0
experiment name for output cn_exp = domaincfg
file prefix restart input cn_ocerst_in= restart
restart input directory cn_ocerst_indir= .
file prefix restart output cn_ocerst_out= restart
restart output directory cn_ocerst_outdir= .
restart logical ln_rstart = F
start with forward time step nn_euler = 1
control of time step nn_rstctl = 1
number of the first time step nn_it000 = 1
number of the last time step nn_itend = 75
initial calendar date aammjj nn_date0 = 10101
initial time of day in hhmm nn_time0 = 0
leap year calendar (0/1) nn_leapy = 0
initial state output nn_istate = 0
frequency of restart file nn_stock = 75
frequency of output file nn_write = 1
mask land points ln_mskland = F
additional CF standard metadata ln_cfmeta = F
overwrite an existing file ln_clobber = T
NetCDF chunksize (bytes) nn_chunksz = 0
IS coupling at the restart step ln_iscpl = F
===>>> : W A R N I N G
===============
ln_rstart =.FALSE., nn_euler is forced to 0
The IOIPSL calendar is "noleap", i.e. no leap year
Namelist namdom : space & time domain
flag read/compute bathymetry nn_bathy = 0
Depth (if =0 bathy=jpkm1) rn_bathy = 4500.0000000000000
min depth of the ocean (>0) or rn_hmin = -3.0000000000000000
min number of ocean level (<0)
treshold to open the isf cavity rn_isfhmin = 1.0000000000000000 (m)
minimum thickness of partial rn_e3zps_min = 20.000000000000000 (m)
step level rn_e3zps_rat = 0.10000000000000001
create mesh/mask file(s) nn_msh = 1
= 0 no file created
= 1 mesh_mask
= 2 mesh and mask
= 3 mesh_hgr, msh_zgr and mask
ocean time step rn_rdt = 360.00000000000000
asselin time filter parameter rn_atfp = 0.10000000000000001
suppression of closed seas (=0) nn_closea = 0
online coarsening of dynamical fields ln_crs = F
type of horizontal mesh jphgr_msh = 1
longitude of first raw and column T-point ppglam0 = 0.0000000000000000
latitude of first raw and column T-point ppgphi0 = -60.000000000000000
zonal grid-spacing (degrees) ppe1_deg = 0.25000000000000000
meridional grid-spacing (degrees) ppe2_deg = 0.25000000000000000
zonal grid-spacing (degrees) ppe1_m = 10.000000000000000
meridional grid-spacing (degrees) ppe2_m = 10.000000000000000
ORCA r4, r2 and r05 coefficients ppsur = -1033.1942952833849
ppa0 = 100.83253696641530
ppa1 = 100.36159186018899
ppkth = 17.285203724197910
ppacr = 5.0000000000000000
Minimum vertical spacing ppdzmin = 1.0000000000000000
Maximum depth pphmax = 7000.0000000000000
Use double tanf function for vertical coordinates ldbletanh = F
Double tanh function parameters ppa2 = 999999.00000000000
ppkth2 = 999999.00000000000
ppacr2 = 999999.00000000000
dom_clo : closed seas
~~~~~~~
dom_hgr : define the horizontal mesh from ithe following par_oce parameters
~~~~~~~ type of horizontal mesh jphgr_msh = 1
position of the first row and ppglam0 = 0.0000000000000000
column grid-point (degrees) ppgphi0 = -60.000000000000000
zonal grid-spacing (degrees) ppe1_deg = 0.25000000000000000
meridional grid-spacing (degrees) ppe2_deg = 0.25000000000000000
zonal grid-spacing (meters) ppe1_m = 10.000000000000000
meridional grid-spacing (meters) ppe2_m = 10.000000000000000
geographical mesh on the sphere with regular grid-spacing
given by ppe1_deg and ppe2_deg
dom_zgr : vertical coordinate
~~~~~~~
Namelist namzgr : set vertical coordinate
z-coordinate - full steps ln_zco = T
z-coordinate - partial steps ln_zps = F
s- or hybrid z-s-coordinate ln_sco = F
ice shelf cavities ln_isfcav = F
linear free surface ln_linssh = F
zgr_z : Reference vertical z-coordinates
~~~~~~~
Value of coefficients for vertical mesh:
zsur = -1033.1942952833849
za0 = 100.83253696641530
za1 = 100.36159186018899
namelist:
!----------------------------------------------------------------------- &namcfg ! parameters of the configuration !----------------------------------------------------------------------- ! ln_e3_dep = .true. ! =T : e3=dk[depth] in discret sens. ! ! ===>>> will become the only possibility in v4.0 ! ! =F : e3 analytical derivative of depth function ! ! only there for backward compatibility test with v3.6 ! ! cp_cfg = "orca" ! name of the configuration jp_cfg = 4 ! resolution of the configuration jpidta = 20 ! 1st lateral dimension ( >= jpi ) jpjdta = 20 ! 2nd " " ( >= jpj ) jpkdta = 10 ! number of levels ( >= jpk ) jpiglo = 20 ! 1st dimension of global domain --> i =jpidta jpjglo = 20 ! 2nd - - --> j =jpjdta jpizoom = 1 ! left bottom (i,j) indices of the zoom jpjzoom = 1 ! in data domain indices jperio = 0 ! lateral cond. type (between 0 and 6) / !----------------------------------------------------------------------- &namzgr ! vertical coordinate !----------------------------------------------------------------------- ln_zps = .false. ! z-coordinate - partial steps ln_linssh = .false. ! linear free surface ln_sco = .false. ln_zco = .true. / !----------------------------------------------------------------------- &namzgr_sco ! s-coordinate or hybrid z-s-coordinate !----------------------------------------------------------------------- ln_s_sh94 = .false. ! Song & Haidvogel 1994 hybrid S-sigma (T)| ln_s_sf12 = .true. ! Siddorn & Furner 2012 hybrid S-z-sigma (T)| if both are false the !NEMO tanh stretching is applied ln_sigcrit = .true. ! use sigma coordinates below critical depth (T) or Z coordinates !!(F) for Siddorn & Furner stretch ! ! stretching coefficients for all functions rn_hc = 50.0 ! critical depth for transition to stretched coordinates / !----------------------------------------------------------------------- &namdom ! space and time domain (bathymetry, mesh, timestep) !----------------------------------------------------------------------- nn_bathy = 0 ! compute (=0) or read (=1) the bathymetry file rn_bathy = 4500. ! value of the bathymetry. if (=0) bottom flat at jpkm1 rn_rdt = 360. ! time step for the dynamics (and tracer if nn_acc=0) jphgr_msh = 1 ! type of horizontal mesh ppglam0 = 0.0 ! longitude of first raw and column T-point (jphgr_msh = 1) ppgphi0 = -60.0 ! latitude of first raw and column T-point (jphgr_msh = 1) ppe1_deg = 0.25 ! zonal grid-spacing (degrees) ppe2_deg = 0.25 ! meridional grid-spacing (degrees) ppe1_m = 10.0 ! zonal grid-spacing (degrees) ppe2_m = 10.0 ! meridional grid-spacing (degrees) ppsur = -1033.194295283385 ! ORCA r4, r2 and r05 coefficients ppa0 = 100.8325369664153 ! (default coefficients) ppa1 = 100.3615918601890 ! ppkth = 17.28520372419791 ! ppacr = 5.0 ! ppdzmin = 1.0 ! Minimum vertical spacing pphmax = 7000.0 ! Maximum depth ldbletanh = .FALSE. ! Use/do not use double tanf function for vertical ppa2 = 999999.0 ! Double tanh function parameters ppkth2 = 999999.0 ! ppacr2 = 999999.0 ! /
mpi run output:
$ mpirun -v ./make_domain_cfg.exe Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x7f924caadcd1 in ??? #1 0x7f924caacea5 in ??? #2 0x7f924c77820f in ??? #3 0x7f924c7f114c in ??? #4 0x560a28a76a40 in ??? #5 0x560a28995d4c in ??? #6 0x560a289cbec1 in ??? #7 0x560a28948af9 in ??? #8 0x560a28920d5e in ??? #9 0x560a2892322d in ??? #10 0x560a2891fb2e in ??? #11 0x7f924c7590b2 in ??? #12 0x560a2891fb6d in ??? #13 0xffffffffffffffff in ??? -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. --------------------------------------------------------------------------
kirodh
2020-09-11 11:10 CEST
(4 years ago)
