Bug reports, work arounds and fixes
Moderators: arango , robertson
cloudy4568
Posts: 39 Joined: Thu Oct 17, 2019 8:56 pm
Location: Clarkson University
#1
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by cloudy4568 » Mon Dec 16, 2019 5:09 pm
Hi all,
I am running my customized example for the first time. The source code I use is Kate's trunk (
https://github.com/kshedstrom/roms.git ), and the grid file, forcing files, boundary and initial files are prepared. The error is:
Code: Select all
READ_PHYPAR - Variable index not yet loaded, idpthR
Found Error: 05 Line: 162 Source: ROMS/Utility/inp_par.F
Found Error: 05 Line: 111 Source: ROMS/Drivers/nl_ocean.h
Elapsed CPU time (seconds):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Dynamic and Automatic memory (MB) usage for Grid 01: 81x59x11 tiling: 1x1
tile Dynamic Automatic USAGE
0 1.00 0.97 1.97
TOTAL 1.00 0.97 1.97
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
ROMS/TOMS - Output NetCDF summary for Grid 01:
Found Error: 05 Line: 443 Source: ROMS/Utility/close_io.F
ROMS/TOMS - Configuration error ..... exit_flag: 5
ERROR: Illegal model configuration.
I have replaced the varinfo.dat for the newest version, the error still exists and is:
Code: Select all
READ_PHYPAR - Variable index not yet loaded, idUairE
Do you know how to solve this? Thanks in advance.
kate
Posts: 4088 Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA
#2
Unread post
by kate » Mon Dec 16, 2019 6:09 pm
Oh, yeah, sorry. There needs to be a chunk in varinfo.dat with:
Code: Select all
'Uwind_eastward' ! Output
'eastward surface wind component at RHO-points'
'meter second-1' ! [m/s]
'Uwind_eastward, scalar, series'
'ocean_time'
'idUairE'
'r2dvar'
1.0d0
'Vwind_northward' ! Output
'northward surface wind component at RHO-points'
'meter second-1' ! [m/s]
'Vwind_northward, scalar, series'
'ocean_time'
'idVairN'
'r2dvar'
1.0d0
Rather than fight with Hernan's updates to varinfo.dat, I have my own versions in the Apps repository.
cloudy4568
Posts: 39 Joined: Thu Oct 17, 2019 8:56 pm
Location: Clarkson University
#3
Unread post
by cloudy4568 » Mon Dec 16, 2019 6:34 pm
Thank you Kate, this problem has been solved.
cloudy4568
Posts: 39 Joined: Thu Oct 17, 2019 8:56 pm
Location: Clarkson University
#4
Unread post
by cloudy4568 » Mon Dec 16, 2019 7:05 pm
Then there is another error:
Code: Select all
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
romsS 00000000009D6963 Unknown Unknown Unknown
libpthread-2.27.s 00007F83AFE81890 Unknown Unknown Unknown
romsS 00000000007DF325 inp_decode_mod_mp 1662 inp_decode.f90
romsS 000000000079968E read_phypar_ 1914 read_phypar.f90
romsS 00000000006AB0FA inp_par_ 67 inp_par.f90
romsS 00000000004039B1 ocean_control_mod 73 ocean_control.f90
romsS 00000000004034FD MAIN__ 73 master.f90
romsS 0000000000403382 Unknown Unknown Unknown
libc-2.27.so 00007F83AF89BB97 __libc_start_main Unknown Unknown
romsS 000000000040326A Unknown Unknown Unknown
Do you have any idea about this error?
kate
Posts: 4088 Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA
#5
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by kate » Mon Dec 16, 2019 7:25 pm
Probaby, if you tell me what is on this line:
Note that this file is in the build directory.
cloudy4568
Posts: 39 Joined: Thu Oct 17, 2019 8:56 pm
Location: Clarkson University
#6
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by cloudy4568 » Mon Dec 16, 2019 7:32 pm
It is:
Code: Select all
max_Ffiles=MAXVAL(nSSFfiles)
allocate ( SSF(max_Ffiles,Ngrids) )
allocate ( SSFids(max_Ffiles,Ngrids) )
allocate ( NSSFcount(max_Ffiles,Ngrids) )
SSFids(1:max_Ffiles,1:Ngrids)=-1
NSSFcount(1:max_Ffiles,1:Ngrids)=0
CASE ('SSFNAME')
label='SSF - Sources/Sinks forcing fields'
Npts=load_s2d(Nval, Cval, Cdim, line, label, issffile, & ! LN 1914
& igrid, Ngrids, nSSFfiles, NSSFcount, &
& max_Ffiles, SSF)
CASE ('TIDENAME')
label='TIDE - Tidal forcing fields'
Npts=load_s1d(Nval, Cval, Cdim, line, label, igrid, &
& Nfiles, TIDE)
kate
Posts: 4088 Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA
#7
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by kate » Mon Dec 16, 2019 7:36 pm
You need to set NSSFFILES in your roms.in file, such as:
Code: Select all
NSSFFILES == 2 ! number of boundary files
SSFNAME == /center1/AKWATERS/kshedstrom/Chukchi/Files/JRA_Chukchi_rivers_1993.nc |
/center1/AKWATERS/kshedstrom/Chukchi/Files/JRA_Chukchi_rivers_1994.nc |
/center1/AKWATERS/kshedstrom/Chukchi/Files/JRA_Chukchi_rivers_1995.nc \
/center1/AKWATERS/kshedstrom/Chukchi/Files/river_tracers.nc
If you try to set SSFNAME first, it hasn't allocated the necessary arrays yet. This is a change in my code from the trunk.
cloudy4568
Posts: 39 Joined: Thu Oct 17, 2019 8:56 pm
Location: Clarkson University
#8
Unread post
by cloudy4568 » Tue Dec 17, 2019 6:33 pm
Thank you, Kate. Then there is another error,
Code: Select all
Tile partition information for Grid 01: 81x59x11 tiling: 1x1
tile Istr Iend Jstr Jend Npts
Number of tracers: 2
0 1 81 1 59 52569
Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)
tile Xmin Xmax Ymin Ymax grid
0 0.50 81.50 0.50 59.50 RHO-points
0 0.00 81.00 0.50 59.50 U-points
0 0.50 81.50 0.00 59.00 V-points
READ_IcePar - variable info not yet loaded, idUiceE
Lateral Boundary Conditions: NLM
============================
Variable Grid West Edge South Edge East Edge North Edge
--------- ---- ---------- ---------- ---------- ----------
zeta 1 Closed Closed Chapman Exp Closed
ubar 1 Closed Closed Shchepetkin Closed
vbar 1 Closed Closed Shchepetkin Closed
u 1 Closed Closed Rad + Nud Closed
v 1 Closed Closed Rad + Nud Closed
temp 1 Closed Closed Closed Closed
salt 1 Closed Closed Closed Closed
tke 1 Closed Closed Closed Closed
uice 1 Closed Closed Closed Closed
vice 1 Gradient Gradient Gradient Gradient
aice 1 Closed Closed Closed Closed
hice 1 Closed Closed Closed Closed
tisrf 1 Closed Closed Closed Closed
snow_thick 1 Closed Closed Closed Closed
1ClosedClosedClosedClosed
1ClosedClosedClosedClosed
sig11 1 Closed Closed Closed Closed
sig12 1 Closed Closed Closed Closed
sig22 1 Closed Closed Closed Closed
Found Error: 05 Line: 855 Source: ROMS/Utility/inp_par.F
Found Error: 05 Line: 111 Source: ROMS/Drivers/nl_ocean.h
Elapsed CPU time (seconds):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Dynamic and Automatic memory (MB) usage for Grid 01: 81x59x11 tiling: 1x1
tile Dynamic Automatic USAGE
0 1.00 3.83 4.83
TOTAL 1.00 3.83 4.83
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
ROMS/TOMS - Output NetCDF summary for Grid 01:
Found Error: 05 Line: 443 Source: ROMS/Utility/close_io.F
ROMS/TOMS - Configuration error ..... exit_flag: 5
ERROR: Illegal model configuration.
I have turned LuvSrc, LwSrc and LtracerSrc all F(no river.nc input). Others are almost the same with your NWGOA example.
kate
Posts: 4088 Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA
#9
Unread post
by kate » Tue Dec 17, 2019 6:52 pm
Code: Select all
READ_IcePar - variable info not yet loaded, idUiceE
Code: Select all
'uice_eastward' ! Output
'ice eastward momentum component at RHO-points'
'meter second-1' ! [m/s]
'uice_eastward, scalar, series'
'ocean_time'
'idUiceE'
'r2dvar'
1.0d0
'vice_northward' ! Output
'ice northward momentum component at RHO-points'
'meter second-1' ! [m/s]
'vice_northward, scalar, series'
'ocean_time'
'idViceN'
'r2dvar'
1.0d0
cloudy4568
Posts: 39 Joined: Thu Oct 17, 2019 8:56 pm
Location: Clarkson University
#10
Unread post
by cloudy4568 » Wed Dec 18, 2019 3:59 pm
Thank you, Kate! I have replaced varinfo.dat with the one in your Apps repository. But another error happened:
Code: Select all
INITIAL: Configuring and initializing forward nonlinear model ...
*******
GET_GRID - unable to open grid NetCDF file: wtype_grid
GET_GRID - unable to open grid NetCDF file: /home/cyue/cyue/bohai/data/bohai24.nc
Found Error: 02 Line: 301 Source: ROMS/Nonlinear/initial.F
Found Error: 02 Line: 188 Source: ROMS/Drivers/nl_ocean.h
Elapsed CPU time (seconds):
Thread # 0 CPU: 0.027
Total: 0.027
Nonlinear ocean model elapsed time profile, Grid: 01
Allocation and array initialization .............. 0.027 (99.0968 %)
Total: 0.027 99.0968
Unique code regions profiled ..................... 0.027 99.0968 %
Residual, non-profiled code ...................... 0.000 0.9032 %
All percentages are with respect to total time = 0.027
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Dynamic and Automatic memory (MB) usage for Grid 01: 81x59x11 tiling: 1x1
tile Dynamic Automatic USAGE
0 33.37 3.83 37.20
TOTAL 33.37 3.83 37.20
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
ROMS/TOMS - Output NetCDF summary for Grid 01:
Found Error: 02 Line: 443 Source: ROMS/Utility/close_io.F
ROMS/TOMS - Input error ............. exit_flag: 2
ERROR: Abnormal termination: NetCDF INPUT.
REASON: No error
I have checked my grid NC file, it's good and I can open it with ncview. What is wtype_grid? Should I 'undef wtype_grid' in the .h file?
robertson
Site Admin
Posts: 219 Joined: Wed Feb 26, 2003 3:12 pm
Location: IMCS, Rutgers University
#11
Unread post
by robertson » Wed Dec 18, 2019 4:16 pm
Are you sure that the grid file is at /home/cyue/cyue/bohai/data? It looks like your username (cyue) is doubled in there.
cloudy4568
Posts: 39 Joined: Thu Oct 17, 2019 8:56 pm
Location: Clarkson University
#12
Unread post
by cloudy4568 » Wed Dec 18, 2019 4:26 pm
Thank you, but I think the path is right. And I have modified the grid NC file already, last time the error is that it can't find 'xl' in the grid NC file, then I added it to the NC file.
Attachments
image.png (25.69 KiB) Viewed 7789 times
kate
Posts: 4088 Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA
#13
Unread post
by kate » Wed Dec 18, 2019 6:43 pm
Code: Select all
GET_GRID - unable to open grid NetCDF file: wtype_grid
I am adding this field to the grid file and it is saying you are missing the field. You can turn off having a spatially variable water type or you can provide the field. I set it as a function of depth using the attached script.
Attachments
add_Jwtype_map.py
(866 Bytes) Downloaded 235 times