Ocean Modeling Discussion

liangliang

Hi bhatt.vihang and rdussin: Thank you for your help ! I have succeed install pyroms . I have refer to http://houstonthereisaproblem.blogspot.hk/2011/12/installation-of-pyroms-into-mac-os-1072.html It's very useful ! I aslo try python2 make_YELLOW_grd_v1.py and can get YELLOW_grd_v1.nc. Thank you ...

liangliang

try : "which f2py" in a terminal. what happens ? You are right . I did not have f2py which instead of f2py2. I change F2PY = f2py2 in /scrip/source/makefile . and type sh install_pyroms.sh > install.log # /pyroms I still get an error . The screen show : [root@chenzhen pyroms]# sh install_pyroms.sh ...

liangliang

I try that , but got an error
make : f2py: Command not found
makefile : 148: recipe for target 'scrip.so' failed

liangliang

rdussin wrote:ok first you can fix the problem of libgridgen.so by simply copying it into the directory where pyroms is installed.

second, rename makefile2 as makefile and run "make f2py". What happens ?

Thank you for your help ! I will have a try !

liangliang

kate wrote:Are you using a cpp option that turns on the radiation stresses? You won't get output from terms you aren't computing.

You are right , kate ! I set WEC_MELLOR and get Sxx and Syy etc result . Thank you !

liangliang

In my ocean.in , I have set Hout(idUvel) == T ! u 3D U-velocity Hout(idVvel) == T ! v 3D V-velocity Hout(idWvel) == T ! w 3D W-velocity Hout(idOvel) == F ! omega omega vertical velocity Hout(idUbar) == T ! ubar 2D U-velocity Hout(idVbar) == T ! vbar 2D V-velocity Hout(idFsur) == T ! zeta free ...

liangliang

is f2py in your PATH ? what is your python version ? and OS ? can you copy/paste the section of the makefile for f2py/scrip.so best, raphael Hi raphael Thank you for your reply ! My OS is Win7 64 , and I installed archlinux on Virtualbox . I can find f2py in /usr/lib/python2.7/site-packages/numpy ...

liangliang

hi chenzhen, we also have found out this problem with new versions of matplotlib. The fix is done and is on its way to github. Regarding the scrip.so, you need to compile scrip with f2py (make f2py). best, raphael Hi raphael I find pyroms updated . I didn't use install_pyroms.sh to install pyroms ...

liangliang

rdussin wrote:hi chenzhen,

we also have found out this problem with new versions of matplotlib. The fix is done and is on its way
to github. Regarding the scrip.so, you need to compile scrip with f2py (make f2py).

best,
raphael

Thank you ! I will have a try ！

liangliang

I also try to install matplotlib 1.2.1, so it has nxutils module . But when I type import pyroms , it shows : scrip.so not found . remapping function will not be available . I have get scrip1.4.tar.gz from http://climate.lanl.gov/Software/SCRIP/#release and compiled it with no error . I can find ...

liangliang

Hi kate: I find pyroms/hgrid.py have an line of code from matplotlib.nxutils import points_inside_poly matplotlib.nxutils has been removed from matplotlib since the last 1.3 versions(http://matplotlib.org/1.3.0/api/api_changes.html). So When I type import pyroms, it shows an error: No module named ...

liangliang

I use python scripts to make boundary files. You need information from a larger domain as well - that's the tricky part. The ROMS convention is that the corner at i,j=0,0 is the Southwest corner. All through the code, the west is at i=0, south is at j=0 and so forth. These are at the outer edge of ...

liangliang

Hi all I have confused with the boundary condition. How did roms find the boundary ?How did it recognize which one is west ,south, north or east ? If the domain is not rectangle ,how did roms find obc and coastline ? I think the answer maybe in BRYNAME file,but how to generate this file? I would ...

liangliang

Hi all : I have met a strange problem. My first case is based on shoreface(you can find some information https://www.myroms.org/wiki/index.php/SHOREFACE_CASE). The domain size is 181*8(Lm*Mm),bathymetric slope is 1/50. I generate a forcing file from swan ,which the value in Y direction are all same ...

liangliang

Clearly, the matlab is trying to execute something called "extract_HC" while what you have is "extract_HC.exe". Perhaps you should change the matlab code to add the ".exe" and see what happens. Your are right ! In otps2frc_v3.m, there is a line of code [s,w]=unix('extract_HC < otps_input'); my ...

liangliang

Ah, I now see that setting FC to gfortran-4 is inside of an if statement. How about commenting out the if test? Hi kate : Thank you for your help ! It's very useful, I compile it successful . I can see extract_HC.exe in my folder . But when I generate ROMS forcing file with matlab , it show an ...

liangliang

You've told it that FC is gfortran-4. Is that in your $PATH? Thank you for your reply , Kate . Yes ,it's in my path .I have compiled ROMS with gfortran-4 before ,and it work well. I didn't know why it show an error now . I see some people have succeed compiling extract_HC with gfortran-4 in this ...

liangliang

Hi all： when I compile extract_HC ,the following error is shown: f77 -o extract_HC extract_HC.f subs.f -L -I make: f77: Command not found make: *** [extract_HC] Error 127 my compile is gfortran , and I type make extract_HC on Cygwin. makefile is like that : ARCH = $(shell uname -s) ifeq ($(ARCH), ...

liangliang

I want to add radiation stress(calculated by swan ) in ROMS. I know roms can couple with swan ,but I fail to make it on period boundary. So i want to calculate radiation stress by swan ,and add it in ROMS,
Could someone tell me how to make it ? I need some detail. Thank you !

liangliang

i have not been using the Rutgers model for coupling in a while. But if you want to use a more recent version of the coupling, you can try our COAWST modeling system, with a more recent version of swan, and the vortex force method, etc. send me an email at jcwarner@usgs.gov if you would like to try ...

liangliang

It's certainly worth a try. If you get a different answer, that's the proof you need of a parallel bug. Kate : Thank you for your reply ! It's hard to compile serial . There are some errors when I compile it . ocean_coupler.f90:298.32: ocean_coupler.f90:298.32: USE distribute_mod, ONLY : mp_reduce ...

liangliang

Well, that looks to me like a parallel bug. Periodic conditions are very tricky in distributed-memory (MPI). It seems that a parallel exchange is missing somewhere during the coupling. Hi arango, Thank you for your reply ! My case is roms-swan coupling. The case could be calculated by compiling ...

liangliang

I don't know what you've done, but dumping the contents of your ocean_his_2.nc for x_rho all values are 0. So that's clearly not going to work for plotting or much else. ROMS itself only needs the grid metrics pm,pn to run, and those seem OK. Hi wilkin , Thank you for your help ！I just see the m ...

liangliang

just a quick guess - but did you run this tiled 1x2? Hi warner, I find you are right ! I make some test case. The grid is Lm=60 Mm=60, if I set Nthreads(ocean) = 1 Nthreads(waves) = 7 , NtileI == 1 NtileJ == 1 ；the Hsig value in j=1 and j=61 are all 0. PIC-1 60_i1_j1png.png If Nthreads(ocean) = 4 N ...

liangliang

I don't know what you've done, but dumping the contents of your ocean_his_2.nc for x_rho all values are 0. So that's clearly not going to work for plotting or much else. ROMS itself only needs the grid metrics pm,pn to run, and those seem OK. Hi,wilkin Thank you for your help ! You are right ! I ...

liangliang

You don't say how you have read the u,v data you pass to roms_quivergrd, or how you loaded the grd structure. Possibly the u,v data have a leading singleton time dimension or vertical dimension, in which case having 3 or 4 dimensions is inconsistent with angle, which has 2 dimensions. If this is ...

liangliang

I find the problem is the boundary condition. If I give Cloesd condition on the south and north. The significant wave height is OK. But if the boundary is periodic , the significant wave height in the middle domain are all 0 . Could someone give me some advice ?

: Hsig.png (9.52 KiB) Viewed 6438 times

liangliang

just a quick guess - but did you run this tiled 1x2? Thank you for your reply ,Warner ! My case is changed from inlet_case. My computer is Inter core i7 So i set that coupling inputfile : Nthreads(ocean) = 4 Nthreads(waves) = 4 ocean inputfile : NtileI == 2 ! I-direction partition NtileJ == 2 ! J ...

liangliang

Well, I don’t use any post-processing routine from ROMS but if you want to get a velocity plot with matlab is quite simple with the quiver function. You could do something like this: quiver(lon_rho,lat_rho,u_eastward( : , : , ‘level’, ‘time’), v_northward( : , : , ‘level’, ‘time’)) Where u_eastward ...

liangliang

Try putting a dot before the multiplication in {sqrt(-1)*v} So it should look like {sqrt(-1).*v} I think the reason dimensions do not agree is because you are doing a matrix multiplication of a single value and a matrix instead of an element-wise (or point-wise) multiplication of the matrix with ...

liangliang

My case is about roms-swan coupling . The domain is 1200m*1200m, slope=1/8. The max depth =12m , min depth =0.1m. I plot it with hslope.m, which can be found in attachments. The boundary in ocean is : ad_LBC(isFsur) == Cha Per Clo Per ! free-surface ad_LBC(isUbar) == Fla Per Clo Per ! 2D U-momentum ...

liangliang

i have got the ocean_his.nc. i want to get the vector of current.And I use wilkin's roms_quivergrd.m to plot velocity vectors . But matlab shows an error . Error using + Matrix dimensions must agree. Error in roms_quivergrd (line 96) uveitheta = (u+sqrt(-1)*v).*exp(sqrt(-1)*angle); Easygrid can ...

liangliang

My grid is wrong . I change it ,and reduce time step . It is OK !

liangliang

You want a periodic channel in which you are specifying the transport? Sure, you can make a rectangular domain and put a line of sinks on one end and a line of sources on the other. See the thread about instability of tracers when mixing sources and sinks, though. Thank you! My domain is ...

liangliang

I try to couple ROMS with swan .But when i run it ,it is blowing up !
I find that :
Maximum grid stiffness ratios: rx0 = 6.666667E-01 (Beckmann and Haidvogel)
rx1 = 1.262620E+01 (Haney)
Does that mean i should smooth my grid ?

liangliang

I once thought about creating periodic grids from a tool that is inherently non-periodic. I believe you can do it using an iterative technique, at least for those tools using the Ives and Zacharias algorithm. I'm assuming you want to make a periodic channel (east-west) with bumps along one wall. If ...

liangliang

I want to make some cases with delft3D ,and compare it with ROMS . There are two problems
a、 I can't find periodic boundary in delft3D ,how could i implement it ?
b、 Where I can find periodic boundary source code in ROMS ?

Thank you !

liangliang

moritz.wandres wrote:Hi,
I seem to have encountered a similar problem. Did you find a solution yet?

Jwarner is right .I didn't set 'inlet_test_bathy.bot' and 'inlet_test_grid_coord.grd ' in swan_inlet_test.in.
You can try it ,it will be OK .

liangliang

I find it show Ocean Model MPI nodes: 000 - 003 Waves Model MPI nodes: 004 - 007 at the beginning . But it show Node # 0 (pid= 0) is active. Node # 1 (pid= 0) is active. Node # 2 (pid= 0) is active. Node # 3 (pid= 0) is active. in the end . Is that mean Ocean Model is active ,but there are some ...

liangliang

I have succeed compiling inlet_test case ,but when I run it . It seems wrong. There were no error messages. When i run it , it shows " Node # 0 (pid= 0) is active. Node # 1 (pid= 0) is active. Node # 2 (pid= 0) is active. Node # 3 (pid= 0) is active." I wait for about 10 minutess ,it still show that ...

liangliang

I want to couple ROMS with swan , so I do this svn checkout https://www.myroms.org/svn/src/test/inlet_test MyTest . I find there is no #define SWAN_COUPLING in inlet_test.h ,but I can find #define SWAN_COUPLING in My folder /trunk/ROMS/Include/inlet_test.h . What is the difference between them ? If ...

liangliang

I can't say for SWAN, but the ROMS story is a little confusing. As it is now, USE_NETCDF4 means that the build system can count on the existence of nc-config (or perhaps it is sometimes nf-config). It can ask nc-config how to link things together, whether hdf is needed or not, whether -lnetcdff is ...

liangliang

It is because some of us are so stuck in our ways as to be using a Unix shell in the csh family. Job redirection is different between the sh family (including bash) and the other family. In this statement: oceanM coupling_inlet_test.in > & log & the first "&" sends the error output to the file log ...

liangliang

I have succeed compiling it . My machine had mpich2 and openmpi before . And I uninstalled openmpi . Then I compiled it again . Then I typed mpirun -np 4 ./oceanM coupling_inlet_test.in It works well . It seems there is a conflict between mpich2 and openmpi . But I still have a question about it ...

liangliang

Dear everyone: I try to run the inlet test case ,I know that it is a case of coupling between roms and swan. I have succeed compiling it . My platform is unbuntu 12.10 ,mpif90 gfortran mpich2 mct When I want to run it ,I get an error ! Please help me ! Thank you ! next is the information on the ...

liangliang

everyone: I know 'hc' is citical depth ,and 'Tcline' is surface/bottom layer width,hc=min(hmin,Tcline) But in my model ,the water is very shallow ,so there are many negative values in the 'h'. I want to ask some qustions: If the min 'h' is negative, is the 'depthmin' set to negative value? And can ...

liangliang

hi: I want add the free-surface boundary conditions on the open boundary.I konw that it is contained in the bry.nc.But in the bry.nc,there are many other variables ,for example,'ubar,vbar,u,v,temp,salt'. If i want add the free-surface boundary condition,which cpp option should be activated? whether ...

liangliang

Thanks for your reply!

liangliang

everyone:

when i couple the roms and swan by "two way",whether should i add swan_wind field on swan and roms_wind field on roms ?Is it repetitious?

liangliang

jcwarner:
I have succeeded in running the case of TEST_HEAD.
the problem is from MCT.When i install mct ,i use the mpi-serial and the real4double8.that is wrong.
Thanks for your help! Best wish to you!
besides,some variables in the "test_head_ini.nc" are wrong.

liangliang

jcwarner: Thank you for your suggestion! Before,i use the absolute path,which is wrong.now,i have changed the path relative to the oceanM.It is available. But there are some other problems. I think the program have read the input files,but i don't know what lead the program aborted. The information ...

liangliang

I have run many of the test cases before release of roms 3.0. I did not run them all, but I did run about 14 of them. TEST_HEAD was one of them, and it worked fine for me. This is an application that requires model coupling, so the user needs to make sure that they activated SWAN_COUPLING ?= on in ...

liangliang

jcwarner: Thank you very much! You are right,my input file's location is wrong. but after i corrected the location,the model still didn't run.The difference is that it created some files Now ,my computer is a two-kernel PC,and i have installed MCT and MPI,which have been tested. next is the ...

liangliang

Everyone: Hello! I have succeeded in compiling the case of TEST_HEAD without ARPACK and created the "oceanM". And then ,when I ran the model,i writed the command line "mpirun -np 2 oceanM coupling_test_head.in", but the result is only one line "coupled input file = coupling_test_head.in",then it's ...

liangliang

I have the same trouble.
If i comment out the line ,whether will it have a bad effect on the model running.

liangliang

Dear everyone: Happy new year! Now i try to run the TEST_HEAD case,i know that it is a case of coupling between roms and swan.I have installed the MCT and MPI,and then i want to install the ARPACK lib,but i have a trouble in compling it.I want to ask whether the version of MPI is specified,or the ...

liangliang

nganju :
THanks for your reply !
If the option SED_MORPH is actived,is there some new variables in the output files.For example,which variable can express the bed level change,the'change'?

liangliang

Hello all:
In my study region,there are some coastal structures .For example ,breakwaters,jetties ,and so on.
Usually,the size of structures is too small for grid size to generate in grid.Whether can i add coastal structures into model in other method?
Thanks!

liangliang

Everyone:
hello!
I have a question about the morphological changes in sea floor when i simulate an estuary's evolvement .In the output files,which variable reflects the change of bed?
Thanks!

liangliang

Pick a time origin and be consistent. I'm in a group which discussed this no end, but we finally decided on a time origin of January 1, 1900, before any of our runs begin. This is what goes in TIME_REF. Then DSTART is in days, relative to the TIME_REF. I currently have DSTART=25202, early in 1969 ...

liangliang

Hello: everyone! I am a newer to roms.I want to simulata an estuary,so i need to create a forcing file of river.There is a variable of river_time.In the case of latte_C,i found that the river_time is from -370 to 260.I want to know how to set the river_time.Why can the river_time be negative? And ...

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