Ocean Modeling Discussion

linzhenhua

https://www.myroms.org/wiki/Frequently_ ... mpile_time

linzhenhua

libguide is a library needed by intel compiler, you need to set up the compile environment for it. A typical command is as follows:

source <Path of your intel compiler>/bin/ifortvars.[sh|csh] [ia32|intel64|ia64]

linzhenhua

Please note that gfortran is a fortran compiler, what you may need is netcdf fortran library.

linzhenhua

You get this problem if you only install the netcdf c library. Please check the following post for more information:

viewtopic.php?f=31&t=2715

linzhenhua

Firstly please igore the linking methods posted previously. The reson you have a "libnetcdff.a" instead of "libnetcdf.a" is because the version you use is netcdf4. One simple method I suggest is to download netcdf 3.6.3, compile and use that version. If you still want to use the available netcdf ...

linzhenhua

The reason for this is the compiler is trying to find the file libnetcdf.a, but the netcdf fortran library in your system is libnetcdff.a.

You could add "-lnetcdff" in your corresponding Compiler/*.mk file.

linzhenhua

mashinde wrote:Hi,

How can I download ROMS3.4 ? can someone give me svn command ?

thanks

This version can be downloaded as a zip archive in the following address:

https://www.myroms.org/projects/src/bro ... s/roms-3.4

linzhenhua

I think you could. But you should know the original version could be easily switched off by changing only one line, which is very convenient.

linzhenhua

I vaguely remembered some flags such as MPDATA (or TS_MPDATA) could alleviate such problems, try search the forum and check if it helps.

Or you may try initializing a smooth transition zone between the low (river) and high salinity (ocean).

linzhenhua

The file location is /home/sergi/.bashrc, after you edit this file, run "source /home/sergi/.bashrc" or open a new terminal window.

linzhenhua

I'm not sure whether the following way can solve your problem. 1. if you still want to use netcdf4. edit the file Compilers/Linux-gfortran.mk change the following line: LIBS := -L$(NETCDF_LIBDIR) -lnetcdf to LIBS := -L$(NETCDF_LIBDIR) -lnetcdf -lnetcdff then delete the Build directory and recompile ...

linzhenhua

The compiler you use to compile ROMS should be the same one you use to compile netcdf.

linzhenhua

You can get the meaning of these variables in the file ROMS/Utility/get_bounds.F, see below: !======================================================================= ! ! ! This routine computes the starting and ending horizontal indices ! ! for each sub-domain partition or tile. ! ! ! ! On Input ...

linzhenhua

New or existing programs that use less than 2GB of memory will probably not require any modifications to their source code or to the way they are compiled. A large-memory program, on the other hand, in addition to the data size issues mentioned above, may need additional compiler flags, depending on ...

linzhenhua

Please try issue the following command and check if it helps

unset OMP_NUM_THREADS

linzhenhua

For your first question. It is easy to clarify, because there is a space in your setting between "/XXX/include" and "/netcdf.mod". As to the second, I think the information provided is not enough to diagnose. Maybe your problem will be solved if you delete the Build direction and try to rebuild the ...

linzhenhua

Thanks for the great work from ROMS dev team. I think non-hydrostatic feature deserves to be on the wist list.

linzhenhua

Try the following commands:

svn checkout --username yinwenbin163 https://www.myroms.org/svn/src/trunk MyDir

You can change "MyDir" to any other name you want to use for the local directory name.

linzhenhua

Hi

From my limited knowledge, if one use domain decomposition, one have to use MPI, not OpenMP. This maybe the reason for the problem encountered above in my opinion.

Please correct me if I'm wrong.

linzhenhua

I think you could type the related code yourself following the video tutorial, it's not a time consuming task in my opinion. ^_^

linzhenhua

If you want to use pyplot, you need first import it.

from matplotlib import pyplot

pyplot.plot()

linzhenhua

Then I have no idea what's wrong. Maybe a fresh reinstall help. The Warning message "netCDF4 not found -- using pupynere." indicate that pyroms could not import netCDF4 module. The error message "ImportError: cannot import name MFDataset" is a consequence of failing to import netCDF4 module.

linzhenhua

Do you install pyroms after you have installed python-netcdf4 successfully?

linzhenhua

I think you should first check that you have installed python-netcdf4 package successfully.

linzhenhua

I remember I have encountered similar problems when installing netcdf4-python, which could not recognize the environment variables.
I solve this problem by editing the netcdf4-python setup.py file.

linzhenhua

Try to search "MPDATA" in the forum and check if the related discussions help.

linzhenhua

It seems that you have not installed numpy. You can check if you have the directory: /usr/lib/Your_Python_version/site-packages/numpy/distutils/fcompiler Your_Python_version is the python version in your system, python2.6 in my system. If you indeed have installed numpy package, then I doubt whether ...

linzhenhua

You should change #define NEW_CPP to #ifdef NEW_CPP in my opinion, or this code segment will always be included whether you define this flag or not. But this is not related to the problem you confront with.

linzhenhua

The volume for a specific region is not conserved because there is a free surface.

linzhenhua

I recently confused about mass conservation problem in ROMS. I use the model output U,V,W on each grid, and calculated Pu/Px + Pv/Py + Pw/Pz problems on designed model grid. I could not get a completely zero on each grid. Can we get an idealized mass conservation from this way in calculation? I ...

linzhenhua

If I remember correctly, Rob has stopped the development of pyroms for some time, try octant.

http://code.google.com/p/octant/

linzhenhua

I think the time you spend on compiling netcdf yourself is less than that you need to negotiate with system admin to do it for you. It's really fast and do not require system privilege.

linzhenhua

I do not know whether you just install a binary version of netcdf or not.

If this is the case, please compile netcdf from source using the same compiler.

linzhenhua

Hi Just have a close look at your set up. Please notice the definition of NDTFAST: ! NDTFAST Number of barotropic time-steps between each baroclinic time ! step. So it should be an integer. In your configuration file you set it to 0.5, this is not right. I change it to 5, and it works. Also notice ...

linzhenhua

I do not know whether the files you uploaded are exactly the files you are using for the numerical simulation.

In your ocean_upwelling_2.in file, you set your project name UPWELLING, so it will try to use upwelling.h, not upwelling_2.h. I'm not sure whether this is the reason for the problem.

linzhenhua

Below is part of the discussion from Martin Schmidt to MOM4 mailing list,I guess it may help: the modern intel architecture allows for several models how floating point operations are defined. The default is a "sloppy" mode where speed gain is preferred against reproducibilty. Accurate results are ...

linzhenhua

Try first change current directory to /root/.matlab/R2008b/ and then run the command.

linzhenhua

I have had the same problem for idealized simulations.

In ROMS, even you do not need surface heat or momentum flux, you have to explicitly define it and set it's value to zero.

linzhenhua

The cpi example works because it does not need the HDF library.

linzhenhua

Hi, I do not know the reason of the different results you get.But I have a question,how can you anticipate tracer to be constant with open boundary used? And personally I do not think the MPDATA result is inferior to Default result,at least it could reflect the tidal signal,and on average the two ...

linzhenhua

I just read that now ROMS include more options for the vertical coordinate,congratulations. But this also remind me of one old question I ever have,I present it below,hopefully some experts could shed some light on this. To my knowledge,now sigma coordinate is used extensively in the ocean models ...

linzhenhua

there are manuals for Fortran and C to read and write NETCDF on the Unidata website.

http://www.unidata.ucar.edu/software/netcdf/docs/

linzhenhua

Some personal opinion. If you run 3D simulation,you should change ROMS file,using the file from Kate,and should also use this pressure calculation method. If you have a low pressure at the center while high around,it's possible to get a sea surface elevation in my opinion,through the convergence ...

linzhenhua

I have a related quation about this topic. Since this issue may be related to the time step.I know the famous CFL critera, delta_t<delta_x/velocity for simple case. I want to know,when using ROMS,for 3D simulations,generally how you calculate the time step? Or a similiar question,when the model blow ...

linzhenhua

In such cases,I think it may be better for ROMS to issue an error and stop the running if wet_dry is defined,until it's could be used.

linzhenhua

I guess this thread may be useful for your question.

viewtopic.php?f=19&t=1087

linzhenhua

Hi,Kate Thanks for your information.I try to comprehend the meaning. The RHS of 2D equation consists of 2 parts,one slow terms,one, say ,fast terms.The difference of the two parts are computed with difference time steps.The slow terms are computed every baroclinic time step,while the fast terms are ...

linzhenhua

Kate,Thanks for your reply. Now for the 3d case,Could you clarify the following words: The pressure change from the atmosphere will become part of the slowly-varying terms on ubar/vbar. These terms are updated once per baroclinic timestep, which should be often enough. Because now I'm still confused ...

linzhenhua

Hi,Kate Thanks for your clarification and upload the file. But still I have one more question.Since you only refer to pregrd32 file,I guess you think this is the only file that should be changed to include the atmospheric pressure.The prsgrd code is called by the 3d calculation. From the physical ...

linzhenhua

Hi Just have a glance at the forcing package.I think the Best template for you is Makefile.Gnu ,you need to change the compiler,path etc. And it seems that it depends on ncar graphics,so you should first install it. And the code was written 8 years ago,I'm not sure whether ROMS group still support ...

linzhenhua

Since you could find file "Makefile.cray",it seems that you use an old roms version. Use Makefile.gfortran if you have this file,or change Makefile.ifort or Makefile.pgi for the gfortran compiler. Generally,The developers advise you to update to the newest version.The new version has a new makefile ...

linzhenhua

Hello,one question about the ATM_PRESS and Pair.

I could see ATM_PRESS in the set_data and get_data code,but could not find it in other files in the Nonlinear directory. At least I think it should influence the ocean pressure gradient calculation,right?

e.g. P(z)=Pair+rho*g*(zeta+z)

linzhenhua

Hi,Thanks for your information and sorry for the late test report. First to clarify the "and/or" issue. I know that EAST_FSCLAMPED and EAST_CHAPMAN could not used at the same time. I just want to say that if I use WEST_FSCLAMPED and EAST_CHAPMAN at the same time,I could not maintain the surface ...

linzhenhua

Hi,m.hadfield.Thanks for your reply.I'd like to expand your reply with my comprehension. First,I'm not quite sure about the word "and/or".If I remember correctly,when I tried xxxx_FSCLAMPED with xxxx_FSCHAPMAN in one setup for two BCs,I could not maintain the surface slope to drive the flow. So I ...

linzhenhua

Hi,I have a question about the open boundary conditions of barotropic channel flow,take an east-west channel as example.What I want to simulate is an east-west barotropic surface elevation difference driven flow,and hope the model could reach a steady state.The Coriolis effect is not considered. For ...

linzhenhua

Problem seems to be solved after I define all the analytical surface and bottom forcing.

So I guess I have to define all analytical forcing macros,or I have to provide netcdf input,even though I do not need them.

linzhenhua

Hello,I want to start a simple setup,without any external meteorological forcing,the model compiles ok,but when I run the model.The model stop with the error message: READ_PHYPAR - could not find input file: ocean_frc.nc Because I do not want to use any netcdf forcing files,I then change NFFILES=0 ...

linzhenhua

Hello,with limited python knowledge,I think there is something wrong with your netcdf4-python install.

Can you use the netcdf4-python packages? Try "import netCDF4" to see whether it works or not.

linzhenhua

One possible reason might be that you do not compile netcdf with the same compiler as you compile roms.

linzhenhua

mod_kinds.f90 /bin/sh: pgf90: not found make: *** [Build/mod_kinds.o] Error 127 i am running it on linux using gfortran as compiler Laia Hello,because the model try to use pgf90 as the fortran compiler which you do not have,instead of the gfortran compiler you want. So,change the FORT variable from ...

linzhenhua

Hello I have never used smartsvn but hope to provide some information to you. It has been reported that one will have trouble if he first check out roms source code to a windows platform and then upload to a linux OS. So even though you can get the source code successfully,you will have trouble ...

linzhenhua

It seems that the fortran compiler should be specified by the environmental variable F90 instead of FC90.

linzhenhua

the one which with we registered on ROMS website should be used.

As I use subversion-1.4.4-7,I could not answer the first.

linzhenhua

Hello,Zhou I have access to the same SGI as you. I just try ROMS on it. At first I'm lazy to compile the netcdf library myself and download the binary version from unidata, I meet with similiar fortcom problems as you, but with a different fortran 90 file. Then I compile the netcdf library from ...

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