Ocean Modeling Discussion

machaielder

Hello Kate
perhaps I need to improve my understand in relation to forcing;
I am forcing it with SST, SSS, surface v momentum stress, u momentum stress; (FRCNAME ==)
I expected that to have time varying outputs.

another issue
I would like to locate the River and define sediments while I work out ...

machaielder

Hello Kate, thanks
I made the following sets the model runs..but gives me a constant value of salt and temp...and didn't bring sediment.
what should be the cause of no changes in salt and temp. if it is caused by using analytical forcing how should I do to change it.

#define SALINITY
#define ...

machaielder

Hello Kate
Thank you
Are you meaning this part of globaldefs.h ? if yes, do I need do define all this inputs in my Sofala.h?

#ifdef SOLVE3D
# ifdef BULK_FLUXES
# ifdef ANA_SMFLUX
# undef ANA_SMFLUX
# endif
# ifdef ANA_STFLUX
# undef ANA_STFLUX
# endif
# endif
# if !defined ANA_BTFLUX ...

machaielder

Hello Kate
Thanks for replying.
I think the missing part of error is:

NETCDF_OPEN - unable to open existing NetCDF file:
frc.nc
call from: check_multifile.F, check_file

Elapsed CPU time (seconds):

Thread # 0 CPU: 0.836
Total: 0.836

Nonlinear model elapsed time profile:

Allocation and ...

machaielder

Dear all
I am sorry for catting, I think this is an ideal discussion to clear out my doubts.
My aim with the model is simulate suspended sediments from River interring the shelf and I am still getting familiar with the model.
I firs run the upwelling example to test my roms and it runs ok.
Now I ...

machaielder

Dear Kate
thank you for replying.my ROMS version 3.7.
I send in attachment my ocean.in

Kindest Regards

machaielder

Dear all
a have the following error message. What could be the cause. what could I do to solve.
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7FBDF417B777
#1 0x7FBDF417BD7E
#2 0x7FBDF3ACDD3F
#3 0x7FBDF3BE7159
#4 0x4C9809 in check ...

machaielder

Hello Every one. I am having the the following error error message (see the log file in attachment) ; my compiler is gfortran;
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Any help please

machaielder

Hello Nark and Kate

I am having the problem discussed here; I could find out that it is not related to disk space because it happens only when I define BBL;

the error is :

137 0.15856 6.605088329E-03 1.7256302E+00 1.7322353E+00 3.2980447E+12 0
138 0.15972 6.698147648E-03 1.7255837E+00 1.7322819E ...

machaielder

yes I read ..that is what I am trying to figure out.[option]..I am searching it. Thank you kate

machaielder

I installed ncview..and it gives the following error when I launch

root@dell-Inspiron-N5110:/home/dell# ncview
Ncview 2.1.5 David W. Pierce 18 Mar 2015
http://meteora.ucsd.edu:80/~pierce/ncview_home_page.html
Copyright (C) 1993 through 2015, David W. Pierce
Ncview comes with ABSOLUTELY NO WARRANTY ...

machaielder

Thanks kate..I will have a look on them. Regard

machaielder

Hello Kate..it is solved..I made changes in upwelling.h

Total: 17.190 94.6877

All percentages are with respect to total time = 18.154

ROMS/TOMS - Output NetCDF summary for Grid 01:
number of time records written in HISTORY file = 00000005
number of time records written in RESTART file ...

machaielder

when I #include "mb_bbl.h" in checkdefs.F I fet the following error

GRID(ng) % ZoBot, &
1
Error: 'zobot' at (1) is not a member of the 't_grid' structure
make: *** [/home/dell/Roms/projects/upwelling/Build/checkdefs.o] Error 1
root@dell-Inspiron-N5110:/home/dell/Roms/projects/upwelling#

machaielder

solved using https://www.myroms.org/forum/viewtopic.php?f=31&t=1

now I get the following error
root@dell-Inspiron-N5110:/home/dell/Roms/projects/upwelling# ./oceanS <ocean_upwelling.in

Model Input Parameters: ROMS/TOMS version 3.7
Saturday - April 18, 2015 - 8:05:48 AM ...

machaielder

solved using https://www.myroms.org/forum/viewtopic.php?f=31&t=1
now I get the following error
root@dell-Inspiron-N5110:/home/dell/Roms/projects/upwelling# ./oceanS <ocean_upwelling.in

Model Input Parameters: ROMS/TOMS version 3.7
Saturday - April 18, 2015 - 8:05:48 AM ...

machaielder

root@dell-Inspiron-N5110:/home/dell/Roms/projects/upwelling# ./oceanS <ocean_upwelling.in

Model Input Parameters: ROMS/TOMS version 3.7
Saturday - April 18, 2015 - 7:46:19 AM
-----------------------------------------------------------------------------

MOD_NCPARAM - Unable to open variable ...

machaielder

I Kate it seams to work..here is a new problem
root@dell-Inspiron-N5110:/home/dell/Roms/projects/upwelling# ./oceanS <ocean_upwelling.in

Model Input Parameters: ROMS/TOMS version 3.7
Saturday - April 18, 2015 - 7:46:19 AM ...

machaielder

I tried the option you gave but the error persists...thanks Kate

machaielder

hello Kate I am using ubuntu. whe do I type that command

machaielder

hello Soeyanto ..did you manage to solve the problem...I am having the same problem now

machaielder

the libhdf5_hl.so.7 is located in /usr/local/include/lib..what do I do

machaielder

/oceanS <ocean_upwelling.in
./oceanS: error while loading shared libraries: libhdf5_hl.so.7: cannot open shared object file: No such file or directory
Hello Kate; thank you
It does not robleun and I am now try to understand the cause; I found a similar problem in he forum. see the link

https://www ...

machaielder

USR/LOCAL/INCLUDE
dell@dell-Inspiron-N5110:/usr/local/lib/netcdf-fortran/include$ ls
netcdf.inc netcdf.mod typesizes.mod
USR/LOCAL/LIB
ell@dell-Inspiron-N5110:/usr/local/lib$ ls
bin libnetcdf.settings libz.so pkgconfig zlib
etc libnetcdf.so libz.so.1 python2.7
hdf5 libnetcdf.so.7 libz.so.1.2.8 ...

machaielder

yes use netcdf =on..I am trying with both makefile and build.bash but nothing helps.
see the settings in build.bash
if [ -n "${USE_NETCDF4:+1}" ]; then
if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then
if [ "${which_MPI}" = "mpich2" ]; then
export NC_CONFIG=/usr/local/lib/netcdf ...

machaielder

hello Kate
Where do I use these commands.
bash-3.2$ nc-config --flibs
-L/usr/local/lib -lnetcdff -lnetcdf -lnetcdf thanks

I wonder if you could give me the new manner of compiling the netcdf-foertran..I used long command in hdf5, netcdf and netcdf-fortran.

many

machaielder

I did what you suggested and nothing changed; then Tried to follow a discussion in which you participated.. it is suggested to define FC, F77 and enable-fortran,-f90 -f77 in hdf5, netcdf end netcdf-fortran

when I do that I get the following error while compiling netcdf-fortran? Might it be the ...

machaielder

see the installation of netcdf-fortran
zlib

./configure --prefix=/usr/local/lib/zlib
make
make test
make install

hdf5
ir na pasta descompactada hdf5
./configure --with-zlib=/usr/local/lib/zlib/ --prefix=/usr/local/lib/hdf5
make check
make install

netcdf-c
ir na pasta descompactada netcdf-c ...

machaielder

ster -ICompilers -D'HEADER_DIR="/home/dell/Roms/trunk/ROMS/Include"' ROMS/Nonlinear/Sediment/sed_surface.F > Build/sed_surface.f90
ROMS/Bin/cpp_clean Build/sed_surface.f90
cd Build; /usr/bin/gfortran -c -frepack-arrays -O3 -ffast-math sed_surface.f90
cd Build; /usr/bin/gfortran -c -frepack-arrays ...

machaielder

I installed netcdf-fortran and now I am getting the following error. anyone to help...

/home/dell/Roms/projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_dim':
mod_netcdf.f90:(.text+0x11843): undefined reference to `__netcdf_MOD_nf90_inquire'
mod_netcdf.f90 ...

machaielder

hello Kate
the the limk you sent me is empty..it is not possible to download

I ma still trying to solve the problem;

Regards

machaielder

Hello Kate
I thanks te problem Was my-cpp-flags.now I disabled -diverages. ..and I seams tô bê ok. I still havent found outro te solution to have netcdf.mod

machaielder

Thank you Kate
Now make command is working
Now i have the following error..which i can imagine its souce..I have to install to build fortran libraries for netcdf intead of copy netcdf from a folder;

Now I am trying to understand how to do it.............

Regards

USE netcdf
1
Fatal Error: File ...

machaielder

Hello Kate
Thank you one more time; I prefered re do the instalation of netcdf..please check the steps until the final result..and the next steps
Regards

cd zlib-1.2.8/
./configure --prefix=/usr/local/
sudo make check instal

cd hdf5-1.8.11/
sudo ./configure --with-zlib=/usr/local --prefix=/urs ...

machaielder

Hello
Thank you...the problem is not solved yet but i can see that i'm getting there.
now the outcomes are different ..there are changes fter editing makefile as you sugested..
now..i suspect that the ''make'' function has some problems in my linux ...i have stalled netcdf a week ago and today i ...

machaielder

Hello Kate
Can you please have a look at the buid.bash i attached in my last post...

t seams tha buid.bash does call the makefile on its own; see the results after typing make makefaile.case and make -f make file in src.

Can you help me to understand the error? in fact there is netcdf.mod in usr ...

machaielder

Hello Kate
perhaps this can help you to understand my problem.
I made the followinf changes in build.bash

export MY_ROOT_DIR=/home/dell/src
export MY_PROJECT_DIR=/home/dell/Projects/upwelling

export MY_ROMS_SRC=/home/dell/src
#export MY_ROMS_SRC=${MY_ROOT_DIR}/trunk
make

export COMPILERS=${MY ...

machaielder

thank you for the help
I put make but nothing changed..any hint?

make: *** No targets specified and no makefile found. Stop.
make: *** No rule to make target `clean'. Stop.
make: *** No targets specified and no makefile found. Stop.
dell@dell-Inspiron-N5110:~/Projects/upwelling$

machaielder

Many thanks for the reply
i am following the tutorial from https://www.myroms.org/wiki/index.php/ROMS_UNSW2008
and i am getting the followin error.

Can you please help me to understand the error....
Thank you in advance

dell@dell-Inspiron-N5110:~/Projects/upwelling$ ./build.bash
make: *** No rule ...

machaielder

Dear users

I have just downloaded the roms packages and install matlab R2012a to run it;
Sorry, i am new on this.

Can anyone explain me carefully the steps i have to follow to have roms running in may linux.

Thank you in advance
Helder

machaielder

dear
not bring any solution to the problem but more of a problem .

I am new to the forum and I have just download the main Roms packages , but not yet started running the model simply because I'm having problems in matlab6 installation.

the error that appears is as follows:
dell@dell-Inspiron ...

machaielder

hello

Soory, i am new here; i am trying to install matlab6 for roms in my ubunto. when i launch it i get the following error:

dell@dell-Inspiron-N5110:~$ matlab
dell@dell-Inspiron-N5110:~$ matlab6
/home/dell/Documents/fialho/Matlab6/bin/glnx86/matlab: error while loading shared libraries: /lib ...

machaielder

Hi I am new on this. my objetive is simulate the sediment plume of Zambezi River in Mozambique using Roms. i have already download the packages of Roms but i am facing problems in installing matlab6 on my ubunto. i would like to know the versons of matlab which i can install for roms and how to get ...

Search found 43 matches