problem in svn and nf_config

[javadi]

Dear users

I have problems in compiling as follow:

svn: E155007: '/home/jav/Documents/roms' is not a working copy

/import/home/kshedstrom/bin/nf-config: Command not found

please help me with your interesting comments

[kate]

I don't know that the svn error matters.

/import/home/kshedstrom/bin/nf-config

This is a hard-coded path on a computer here to my home-built netcdf-fortran. You'll have to change it.

[javadi]

Dear kate
thank you for your response. where can download compatible NetCDF and version? I use gfortran to compile.

[kate]

The version of netcdf-fortran doesn't matter, but it has to be compiled with the same version of gfortran as you are using. Just search for "netcdf-fortran download" and you find it. Then you need to follow the instructions for compiling it. Or if you have control of the computer, something like "sudo apt install netcdf-fortran" might work. It just depends.

[javadi]

Dear Kate

No. My problem is not related to the version of my netcdf and gfortran. Based on your suggestion, I have checked with the trunk and the model compile without any problem both in single and parallel. Thus, it shows that my packages install correctly. I guess that my problem is installing your branch in my system. I use git svn clone https://github.com/kshedstrom/roms.git to install my system. Hence, this leads to an issue about svn. I decided to add ice in my model so I try to use your branch.

[kate]

Just change that path to my nf-config to your path to your nf-config.

[javadi]

Dear kate

Yes. Thanks for your help. I compile the upwelling test case using your branch both single and parallel. However, I have faced a new error in running time. Here is the detail of that. In the trunk, there is not any problem
Model Input Parameters: ROMS/TOMS version 3.9
Sunday - January 24, 2021 - 1:47:03 AM
--------------------------------------------------------------------------------

READ_PHYPAR - Variable index not yet loaded, idStr
Found Error: 05 Line: 164 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: 41x80x16 tiling: 2x2

tile Dynamic Automatic USAGE MPI-Buffers

0 0.98 0.96 1.94 0.00
1 0.98 0.97 1.96 0.00
2 0.98 0.96 1.94 0.00
3 0.98 0.96 1.94 0.00

TOTAL 3.94 3.85 7.79 0.00

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

ROMS/TOMS - Output NetCDF summary for Grid 01:
Found Error: 05 Line: 423 Source: ROMS/Utility/close_io.F

ROMS/TOMS - Configuration error ..... exit_flag: 5


ERROR: Illegal model configuration.

[kate]

This is due to a change in the varinfo.dat file. Search through mine for that string idStr and you'll find it.

[javadi]

Dear Kate

Thank you so much for your help

I understand how to add it in my varinfo.dat. I solve the previous error when looking your comments in this forum. Now I have faced the new error about id3dPVI
READ_PHYPAR - Variable index not yet loaded, id3dPVI

I do not find anything about this.

[kate]

Code: Select all

chinook02.rcs.alaska.edu 203% grep id3dPVI var*
varinfo.dat:  'id3dPVI'
varinfo.dat.cobalt:  'id3dPVI'
varinfo_jra.dat:  'id3dPVI'

I ran this in the Apps directory.

[javadi]

Dear kate

I add some variables in vainfo.dat thanks to your help. I solve these errors but I have faced a new one. It is not related to my system as I have checked with the trunk.



0 0001-01-01 00:00:00.00 0.000000E+00 6.585677E+02 6.585677E+02 3.884376E+11
(00,00,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: roms_his.nc
Found Error: ** Line: 8222 Source: ROMS/Modules/mod_netcdf.F, netcdf_create

NETCDF_CREATE - unable to create output NetCDF file:
roms_his.nc
call from: ROMS/Utility/def_his.F
NetCDF: Malformed URL
Found Error: 03 Line: 105 Source: ROMS/Utility/def_his.F

DEF_HIS - unable to create history NetCDF file: roms_his.nc
Found Error: 03 Line: 151 Source: ROMS/Nonlinear/output.F
Found Error: 03 Line: 600 Source: ROMS/Nonlinear/main3d.F
Found Error: 03 Line: 303 Source: ROMS/Drivers/nl_ocean.h

Elapsed CPU time (seconds):

Node # 2 CPU: 0.095
Node # 0 CPU: 0.095
Node # 3 CPU: 0.088
Node # 1 CPU: 0.100
Total: 0.378

Nonlinear ocean model elapsed time profile, Grid: 01

Allocation and array initialization .............. 0.182 (48.0680 %)
Ocean state initialization ....................... 0.143 (37.8447 %)
Reading of input data ............................ 0.000 ( 0.0098 %)
Processing of input data ......................... 0.007 ( 1.9689 %)
Processing of output time averaged data .......... 0.000 ( 0.0611 %)
Computation of vertical boundary conditions ...... 0.002 ( 0.4882 %)
Computation of global information integrals ...... 0.003 ( 0.9216 %)
2D/3D coupling, vertical metrics ................. 0.035 ( 9.2953 %)
Omega vertical velocity .......................... 0.014 ( 3.7545 %)
Equation of state for seawater ................... 0.008 ( 2.0846 %)
Total: 0.395 104.4967

Nonlinear model message Passage profile, Grid: 01

Message Passage: 2D halo exchanges ............... 0.050 (13.1181 %)
Message Passage: 3D halo exchanges ............... 0.050 (13.1684 %)
Message Passage: 4D halo exchanges ............... 0.003 ( 0.7941 %)
Message Passage: data broadcast .................. 0.003 ( 0.6880 %)
Message Passage: data reduction .................. 0.039 (10.3654 %)
Message Passage: synchronization barrier ......... 0.003 ( 0.7203 %)
Total: 0.147 38.8542

Unique code regions profiled ..................... 0.395 104.4967 %
Residual, non-profiled code ...................... -0.017 -4.4967 %


All percentages are with respect to total time = 0.378


>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Dynamic and Automatic memory (MB) usage for Grid 01: 41x80x16 tiling: 2x2

tile Dynamic Automatic USAGE MPI-Buffers

0 23.29 1.20 24.49 0.53
1 21.58 1.15 22.73 0.53
2 23.81 1.20 25.01 0.53
3 22.06 1.15 23.21 0.53

TOTAL 90.74 4.70 95.44 2.11

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

ROMS/Functionals/ana_btflux.h
/home/javadbabagoli/Documents/Test/ana_grid.h
/home/javadbabagoli/Documents/Test/ana_initial.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h
ROMS/Functionals/ana_vmix.h
Found Error: 03 Line: 423 Source: ROMS/Utility/close_io.F

ROMS/TOMS - Output error ............ exit_flag: 3


ERROR: Abnormal termination: NetCDF OUTPUT.
REASON: NetCDF: Malformed URL

[kate]

Wow, I've never seen that one before. I would check for hidden characters in the ocean.in file where you provide the file names. Or is that file somehow in DOS mode?

[javadi]

Dear kate

I do not change anything in the code only varinfo.dat. I add some variables at the end of the file when your greb .... does not work in my system. Here is my varinfo.dat. I try to run upwelling test case. It may be the source of the problem?

[kate]

Code: Select all

NETCDF_CREATE - unable to create output NetCDF file:
roms_his.nc
call from: ROMS/Utility/def_his.F
NetCDF: Malformed URL
Found Error: 03 Line: 105 Source: ROMS/Utility/def_his.F

I don't think your problem is in varinfo.dat.

[Patilc103]

I'm getting similar error while running a nested application case. The error is

TIDES_DATE - Variable index not yet loaded, idTref
Update your metadata file: /scratch/cdschai/ROMS_Working/nested_Bob_Exp/varinfo.dat
Found Error: 05 Line: 136 Source: ROMS/Utility/tides_date.F
Found Error: 05 Line: 211 Source: ROMS/Utility/inp_par.F
Found Error: 05 Line: 126 Source: ROMS/Drivers/nl_roms.h, ROMS_initialize

Please help me resolve this.

[wilkin]

There's you answer:

Update your metadata file: /scratch/cdschai/ROMS_Working/nested_Bob_Exp/varinfo.dat

Your varinfo.dat -- really you should be updated to using varinfo.yaml -- is not consistent with your code.