Ocean Modeling Discussion

fereshteh

many thanks for your reply. shared-memory is active cluster on my university server. i used #define TS_C4VADVECTION #define TS_C4HADVECTION Also, in older revision i used #define spline that i think reconstruct vertical diffusion and advection,simultaneously. my test does not have very high vertical...

fereshteh

I am running my test in parallel mode (shared-memory) TS-MPDATA option is active in header file, so such error appeared in running step: cannot active option:TS-MPDATA in serial with partitions or shared-memory.. Use distributed-memory (MPI) in parallel run could you please tell me which option coul...

fereshteh

hi
one a simple way is to install netcdf with following command in Ubuntu:
apt-get install *netcdf*
it will set netcdf.mod, netcdf.h and nc-config in you system automatically.
i hope it be useful for u.
cheers
fereshte

fereshteh

It will be solved by adding some directories path into MATLAB, which include old functions for netCDF(such as nc_read) :
addpath ../roms/matlab/netcdf
addpath ../RNT/matlib/mexnc (if you download RNT from roms site)
addpath ../roms/matlab/utility

fereshteh

Do you turn on

Code: Select all

! Logical switches (TRUE/FALSE) to specify which variables to consider on
! tracers point Sources/Sinks (like river runoff): [1:NAT+NPT,Ngrids].
! See glossary below for details.
  LtracerSrc == T T                    ! temperature, salinity, inert

in ocean.in file?

fereshteh

Dear friends
many thanks for your replies.

You are spending a significant fraction of the time in communications

from which part you found this?

fereshteh

You might try turning on the profile output if your mean is to active 'time profile' , I have activated it and then ran same test (coupled and nested for 4 grids)by using 24 cores and then 16 cores of different PC systems (each one Processor is Intel® Core™ i7-4770K CPU @ 3.50GHz × 8 ) . As you can...

fereshteh

Dear it is strange for me that by increasing the number of processors form 16 to 24 ( NnodesWAV = 12 and NnodesOCN = 12), run time improved just 2 hours (it takes 12 and 10 hours long, respectively). is it reasonable :?: I do not know there is some thing wrong in my model setup (Investigated model i...

fereshteh

many thanks.
i will do my smoothing base on rx0 too.

fereshteh

I have changed number of layers in different tests with same horizontal grid. It is strange for me that while rx0 keeps its value, rx1 value decrease by decreasing number of layers (change to 4.8, 1.49 and 0.7 for 32, 10 and 5 layers, respectively). Why?does ROMS do grid's smoothing base on number o...

fereshteh

Dear i have made grid with 32 layers and then initial, climatology, river and other files have been created base on it in 32 layers. I want to know is there any way to change those files form 32 layer to less layers with out needing to make other gird. For example change all files from 32 layers to ...

fereshteh

Thanks for your reply.
therefore it seems that SHORTWAVE option will be active automatically when ever BULK_FLUXES or SOLAR_SOURCE are active. Is not it?
if yes, why it does not appear in stdout file as other options which are active automatically, such as NONLINEAR .
BEST
fereshte

fereshteh

but model has blow up

how can fix it

fereshteh

By checking zeta values in restart file, it has about 2 meter value in right side.i thinks that is because of westerly wind which push water to that side. Do you have any suggestion for me to solve it?
Decreasing river cells runoff or other recommend?
Cheers
fereshte

fereshteh

Dear kate i looked at u and v fields. I just can find some cells with about 10 m/s speed in 2 surface layers in last time step of restart file and fome some cells about 5 m/s. No thing strange were in temp and salt fields. But you say that you limit blow up in 20 m/s :?: . Would you please help me a...

fereshteh

Hi every one i have run roms model for 3 months of 2010 year with out blow up. But when i run it for 1 month of 2007 i gives me blow up after 17 days ( 16614 step) :cry: . It is first time which i faced with blow up. There is not any strange thing in salt and temp distribution in restart file. But f...

fereshteh

Dear kate i have tried your new approach.3-days-long model (16 to 18 jan)from beginning and 5-day-long model (18 to 22 jan) started from the restart file of 3-day-long model. In first one: Dt=90 Ntimes=2880 %3 days NRREC=0 LcycleRST=F NRST=960 %1 day LDEFOUT == T Dstart=15.2188 Time_ref=20090101.0 ...

fereshteh

Dear kate i use #define perfect_restart but again results are different :evil: this is my header file: #define ROMS_MODEL #define SALINITY #define SOLVE3D #define MASKING #define SPLINES #define OUT_DOUBLE /* advection, dissipation, pressure grad, etc. */ #define DJ_GRADPS #define UV_ADV #define UV_...

fereshteh

Dear Arango i have checked the approach that you said for several times. I run two models: first one cold-start (from 16 to 22t January) which in it: Dt=90 Ntimes=7680 %8 days NRREC=0 LcycleRST=F NRST=1920 %2 days Dstart=15.2188 Time_ref=20090101.0 ININAME=initial.nc and when ever new record was wri...

fereshteh

Dear i want to know that it is possible to create separately restart files after every N time steps? And then use nth restart file (for example second restrat file) as a initial file of hot start modelling? By LcycleRST == F NRST ==1920 i just can create one restart file which in it there were writt...

fereshteh

hi
i know that d_ecmwf2roms.m updated recently. But in new version for 'Qair', its variable's name (v2d) have not changed to d2m. because in ECMWF-interim data this variables named as a d2m. and also v2t and v2d should be changed to t2m and d2m, respectively.
cheers
fereshte

fereshteh

hi I know that Vstretching parameter has effect on rx1 value. therefore one criterions to choose appropriate Vstretching is locating rx1 in good Range. but please inform me that if there are another criterions for determining best value for Vstretching? is there any recommended values for this param...

fereshteh

Dear jivica

it is function of minimum grid size and max depth
dt=0.85./sqrt(9.81*grid.h.*(grid.pm.^2+grid.pn.^2))

do you mean
grid.h= hmax
grid.pm=dx or 1/dx
grid.pn=dy or 1/dy
in both states dx and dy minimum?
thanks

fereshteh

Dear how can i become sure that computed Courant Number is a nice value for my model. in my model dt=80s and model grid sizes are as: Minimum X-grid spacing, DXmin = 3.33514538E+00 km Maximum X-grid spacing, DXmax = 3.98831267E+00 km Minimum Y-grid spacing, DYmin = 3.33800882E+00 km Maximum Y-grid s...

fereshteh

Dear ymamoutos
many thanks for your answer
i have got what is my problem

sincerely yours
fereshte

fereshteh

many thanks
so i will try to find the other sources of problems.
all the best
fereshte

fereshteh

sorry i can find them
but about evaporation i belive that it should be added to that m file,is not it?
thanks

fereshteh

Dear all user for using d_ecmwf2roms.m file all needed files exist in ECMWF_ERA Interim except shflux, swflux, sustr, svstr, and photosynthetically active radiation at surface . i have 2 question: 1- for computing swflux, evaporation is necessary while it have not defined in that m file? Why? 2- sus...

fereshteh

dear all rip_current test of COAWST compiling gives this error: [fkomijani@localhost Rip_current]$ ./coawst.bash make: *** No rule to make target `clean'. Stop. make: *** No rule to make target `wrfclean'. Stop. make: *** No rule to make target `wrf'. Stop. make: *** No targets specified and no make...

fereshteh

dear Warner
would you please tell me that COAWST's ROMS updating has been done with Rutgers version, Simultaneously?
it means with svn update command, both of them will update or not?
thanks
fereshte

fereshteh

hi
if you want to create Rectangular grid ,i suggest you use roms-agrif version. it is so easy to use program.
http://www.romsagrif.org/
be Successful
fereshte

fereshteh

dear Warner At first thanks for your suggestion . i use it and set Ntilei=1, Ntilej=1 ,Nthreads (ocean)=1 and Nthreads (waves)=1 but in every run which 1 cpu set for swan model (in this example:also 1 procc for ocean model) it reply mpirun -np 2 ./oceanG coupling_inlet-test.in>mpi.log application ca...

fereshteh

dear all in inlet test, after solving some errors which appear in Print_xx files and Errofile_xx files, now mentioned test is running but again some empty Print_xx files and Errofile_xx files created in project directory while linux shell shows model is still running. i check created .log file. End ...

fereshteh

Base on arango reply The plotting package is able to recognize such masked values All ROMS plotting package files have been checked to fine where and how _Fillvalue is added in masked region. Finally I find in csec.F (which located inroms/plot/src/Drivers) following lines: Set area mask, if any. Lms...

fereshteh

Dear For inlet test I have updates its files as suggested in forum. I could compile it but for running, some errors appear. forum has been checked for solving them but its suggestions (for example set 1 cpu for swan) cannot help me therefore I send .log file contains created after run command: $ Mpi...

fereshteh

Dear Arango At first thanks for your reply. What I found from your reply is that since parameter's variation range is not in color bar range, this form appears. But please look at attached file. Its min and max are zero and 6.5 E+38, respectively. While color bar range is from 0.00 E+38 till 6.55 E+...

fereshteh

Dear I can solve above problem :P . But recent problem of mine is that I can't see results time changes in section plots. For example salinity has same values all the time. Therefore I need your experience to find what cause this problem :wink: . It is necessary to say that this test is same as upwe...

fereshteh

Dear all I have modified upwelling test for my own bathymetry. It compiled and run without errors. But its cross-section plots seem incorrect becouse the maximum depth of my domain is about 1020 m. I know that it gives my grid because the processing after typing csecG<csec.in shows correct Lm, Mm an...

fereshteh

Dear arango
i will use your guidance
thanks

fereshteh

dear arango
in above you say that you usually choose 10 m as minimum depth. so it seems that Roms model has not capability for nearshore modeling? Is not it.
What is your idea?
Thanks
fereshte

fereshteh

dear kate
be sure that i will aware you about what happen, after applying that option
thanks for your patient to answer me
fereshte

fereshteh

dear arango
would like to offer my heartfelt appreciation for your attention and complite reply.
best regard
fereshte

fereshteh

dear kate
thanks so much for your reply. it help me
i found that minimum clipping depth is idem hmin to specific bathymetry lower limit.
in my domain (Caspian sea) there is not tide.
sincerely yours
fereshte

fereshteh

dear kate
thanke so mush
yes, because my domain has land as well as sea, i will use WET_DRY option.
so with this option can clip bathymetry value.is not it?
thanks again
cheers
fereshte

fereshteh

Dear arango
thanks so much for your reply and attention
would you please tell me that computed the land/sea masking by SeaGrid is just Land/Sea masking at RHO-points (2D array) or it Compute Land/Sea U-, V- and PSI-mask too?
Thanks in advance
cheers

fereshteh

Dear user my requested hydrography data (for Caspian sea) have been provided from GEBCO (1 minute resolution).its minimum depth is 1 m and also some points have zero value (attached picture show these points). with regard that for generating grid, there should not be zero value, eliminating them tha...

fereshteh

Dear user last question of mine showed that my mind was mixed with different concepts(sorry :oops: ) I have tried to manage my questions as below: 1- infact smoothing and land/sea masking process should be done after creating grid (by Seagrid). isnot it? 2- are dx and dy for computing r-factor grid'...

fereshteh

dear all i want to use seagrid.this program has not smoothing step. but reading most post in roms forum shows smoothing importance to get rx0 in appropriate limit. what make me confused is serialization of grid generation by seagrid. (1) should smoothing be first done on bathymetry (h(x,y)) and then...

fereshteh

Dear i have questions about smoothing. I have got that smoothing applied on bathymetry file which is 2d array (h(x,y)) not on grid file(if my Thought is wrong please tell me). but in your answer you said I then follow with a regular Shapiro filter everywhere to knock off the 2 dx stuff. 1- What is t...

fereshteh

hi all user i am trying to create my real bathymetry by seagrid. my domain contains land and sea. minimum depth in my coarse sea is 1 m. i want to know that minimum clipping depth is just a considered depth that user should change bathymetry values less than it to that, that is because i can't find ...

fereshteh

dear all i use fedora 16 (gcc4.6.2). by applying ./build.bash, after copied netcdf.mod and typesizes.mod in Build folder, this error arise: :? cpp: error trying to exec 'cc1': execvp: No such file or directory also it said some thing about permission denied (in detaile /bin/sh: ./ROMS/Bin/sfmakeddep...

fereshteh

Dear Warner my aim is coupling roms and swan models for nearshore application. i need your experience to choice appropriate test that can help me for providing inputs and modeling method. Since i am roms newbie would you please guide me toward find best method for starting my research. Also i see so...

fereshteh

no, i dont think so that i will need ice branch. now, what is your recomendation.
whould you please tell me what is COAWST.
cheers
fereshte

fereshteh

hi dear
i need your experience to chose appropriate test for my application. my aim is coupling roms and swan and use nesting approach for rip current modeling.
thanks in advance
best regard
fereshte

fereshteh

Dear
i found my mistake. But I do not think I would solve it without your guides. Thank you so much for your help.
cheers
fereshte

fereshteh

thanks so mush

fereshteh

dear Arango thanks i really try to do ROMS compiling step by step base on your constructions. And i was able to compile it for test case. My recent question was just about “ Installing the ROMS/TOMS Plotting Package ” section. As you told in this part i should check the user-defined options section ...

fereshteh

Hi dear Kate i found that linux-gfortran.mk should not been changed (thank for this :idea: ). with regard build.bash setting (that use USE_NETCDF4=on , FORT=gfortran and USE_DEBUG=on) i defined and active some options in makefile for example: [color=#800000]MY_HEADER_DIR ?=/home/fkomijani/projects/u...

fereshteh

i chose gfortran as roms compiler 1-should i change ifdef USE_NETCDF4 NC_CONFIG ?= nc-config NETCDF_INCDIR ?= $(shell $(NC_CONFIG) --prefix)/include LIBS := $(shell $(NC_CONFIG) --flibs) in linux-gfortran.mk file that located in Compilers forder to my own path? 2- what else i should change in linux-...

fereshteh

hi i set export NETCDF_INCDIR=/home/fkomijani/NETCD4.2.1.1/include in build file (in gfortran section) and with this path, upwelling example execution does not have error that it shows it can find netcfd.mod path correctly.i change FORT=? pgi to gfortranin makefile, and by executing "make"...

fereshteh

Would you please tell me that if i change user define options in build.bash file it must change in make file automatically ,or i must change it by hand? For example i disable USE_LARGE=on in build.bash (by # sign) but when i check makefile i see that there is USE_LARGE ?= on and it seems that in mak...

fereshteh

Hi i can run upwelling test succesfully and get some netcdf files as out put. Also i install NCL6.1.2 binary eithout OpeNDAP support . And i download PLOT directory too. i choice gfortran as roms comliler Also i set netcdf libraries in build.bash file as bellow: export NC_CONFIG=/home/fkomijani/NETC...

fereshteh

hi dear i want to download latte test.i have downloaded roms source by https://www.myroms.org/svn/src/trunk command, therefore i used same svn checkout for downloading latte test : svn checkout http://coast-enviro.er.usgs.gov/models/Latte/ , it reply that svn: Repository moved permanently to 'http:/...

fereshteh

hi dear
i am really appreciate for your reply
finally,my problem soleved by downloading and installing netcdf4.2-fortran lib, and ocean.G is built.

thanks again
sinserely yours

fereshte

fereshteh

hi dear i am really really appreciate for your reply finally my problem soleved by downloading and installing netcdf4.2-fortran lib, and ocean.G is built. :D :D But please tell me how and where you add --enable-hl flag? is this falg necessary for parallel I/O? thanks again sincerely yours fereshte

fereshteh

hi dear my system is linux fedore16. i have installed netcdf4.2.1.1 with zlib and HDF5 in following way: 1- Cd /home/fkomijani/zlib 1.2.7 ./configure --prefix=/home/fkomijani/NETCD4.2.1.1 make check install 2- cd /home/fkomijani/HDF5 1.8.9 ./configure --with-zlib=/home/fkomijani/NETCD4.2.1.1 -- pref...

fereshteh

Hi dear after having problem with netcdf4.0 which does not have nc-config i decide to use netcdf4.21.1. I have install it in this way: 1- Cd /home/fkomijani/zlib 1.2.7 ./configure --prefix=/home/fkomijani/NETCD4.2.1.1 make check install 2- cd /home/fkomijani/HDF5 1.8.9 ./configure --with-zlib=/home/...

fereshteh

hi every one since I am new with compiler concept, there are a lot basic questions in my mind. generally I found that some program such as netcdf, swan, roms need compiler (such as icc,ifort, gfortran and ... ) and also I read in forum that linux has dev files that compile with gfortran and gcc not ...

fereshteh

hi
Dear kate
Generally, your answer help me always and I am appreciate for this. I decided to use Mark Hadfield's version of nc_config and search it in forum, but I have not found it.
please tell me where it is

thanks
fereshte

fereshteh

Hi dear i am providing some needs that it is necessary for running ROMS. I am reding wikiroms site and understand that i need hdf5 as well as netcdf. but when i installed netcdf4.0 i didn't see hdf5. My first request is that, how i can add it to my netcdf and I become so appreciate to receive link f...

fereshteh

Dear Raphael first of all, thanks for your information , it help me to understand some details. I utilize netcdf 4.0 and linux fedora 16, and i like to say that linux have not been installed with yum command but rather with cd. Also I check /home/fkomijani/NETCDF/bin, It just has 2 files:ncdump and ...

fereshteh

Dear kate i have opted USE_NETCDF4=on and with regard that i execute in serial version, i have determined its required address as below: export NC_CONFIG=/usr/bin/nc-config export NETCDF_INCDIR=/home/fkomijani/NETCDF/include because when i located nc-confige in home directory, Its reply was in /usr/...

fereshteh

hi i choose IFORT as compiler i my test and netcdf4 libries. I have problem with build.bash which appear following errors: /opt/intel/Compiler/11.1/080/bin/ia32/ifort -heap-arrays -fp-model precise -g -check uninit -ftrapuv -traceback /home/fkomijani/projects/upwelling/Build/roms_import.o /home/fko...

fereshteh

Dear Kate first of all i am extremely appreciate for you complete reply. With regard that i want to nest me coarse domain with coastal domain (nearshore region) i have bathymetry value less that 1 m. Base on your reply, i found that when e have depth value less that 1 m,we must notice to bathymetry ...

fereshteh

hi dear Kate thanks for your attention but sine i haven't used ROMS model, i don't know application of WET-DRY (unfortunately). therefore i did not completely catch you. You mean that I must replace zero value in the sea area with value less that minimum depth or not? :roll: Also i become grateful t...

fereshteh

Hello every one i could make coastline and boundary file for my closed domain by seagrid. And now i am preparing its bathymetry file. With regard to Grid generation page of ROMS site, that say for a 'typical' application by roms, the bathymetry can not have values of 0 or any negative values; Most u...

fereshteh

hi i am working with seagrid. i make my coastline and bathymetry, my coastline is for caspian sea which is closed. my problem is that when i compute depth, in seagrid window show taht inter my closed coast line is mask and out of it is water that reality it is vice versa. can seagrid make mesh for c...

fereshteh

Hi dear I am using seagrid2roms.m. For this i have installed snctools and mexnc and ROMS matlabtoolkit(from roms site) that latter included mexcdf5 and netdfc directories. there is 2 errors in running this function: >> seagrid2roms('test','m','a','spline',1) ## SeaGrid Source File : test ## ROMS Des...

fereshteh

hi dear for Making continuous coastline, i downlad join_cst.m and fixcoast.m too. but for using this command as: newcoast=joincst(caspian,.001), matlab give this error: Too many input arguments. and when i type newcoast=join_cst(caspian,.001) give error: File: join_cst.m Line: 34 Column: 6 that is a...

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