Search found 64 matches

by linzhenhua
Wed Jul 30, 2014 1:20 am
Forum: ROMS Installation
Topic: ld: cannot find -lguide
Replies: 1
Views: 1791

Re: ld: cannot find -lguide

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]
by linzhenhua
Tue Mar 18, 2014 4:50 am
Forum: ROMS Tools and Techniques
Topic: plotting package installation
Replies: 8
Views: 2481

Re: plotting package installation

Please note that gfortran is a fortran compiler, what you may need is netcdf fortran library.
by linzhenhua
Tue Mar 18, 2014 3:32 am
Forum: ROMS Tools and Techniques
Topic: plotting package installation
Replies: 8
Views: 2481

Re: plotting package installation

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
by linzhenhua
Sat Feb 08, 2014 3:15 am
Forum: ROMS Installation
Topic: help with ROMS compiling
Replies: 4
Views: 4577

Re: help with ROMS compiling

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 lib...
by linzhenhua
Fri Feb 07, 2014 3:06 am
Forum: ROMS Installation
Topic: help with ROMS compiling
Replies: 4
Views: 4577

Re: help with ROMS compiling

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.
by linzhenhua
Thu Oct 17, 2013 2:35 pm
Forum: ROMS Problems
Topic: how can i download old versions of ROMS
Replies: 1
Views: 1348

Re: how can i download old versions of ROMS

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
by linzhenhua
Tue Jan 10, 2012 2:30 pm
Forum: ROMS Discussion
Topic: question on define
Replies: 1
Views: 881

Re: question on define

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.
by linzhenhua
Tue Dec 13, 2011 1:21 am
Forum: ROMS Discussion
Topic: river salinity overshoot
Replies: 11
Views: 4433

Re: river salinity overshoot

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).
by linzhenhua
Fri Nov 11, 2011 1:07 am
Forum: ROMS Installation
Topic: Problem with test case Upwelling - build.bash (solved)
Replies: 7
Views: 4436

Re: Problem with test case Upwelling - build.bash

The file location is /home/sergi/.bashrc, after you edit this file, run "source /home/sergi/.bashrc" or open a new terminal window.
by linzhenhua
Thu Nov 10, 2011 1:09 am
Forum: ROMS Installation
Topic: Problem with test case Upwelling - build.bash (solved)
Replies: 7
Views: 4436

Re: Problem with test case Upwelling - build.bash

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 ...
by linzhenhua
Wed Nov 09, 2011 1:11 am
Forum: ROMS Installation
Topic: Problem with test case Upwelling - build.bash (solved)
Replies: 7
Views: 4436

Re: Problem with test case Upwelling - build.bash

The compiler you use to compile ROMS should be the same one you use to compile netcdf.
by linzhenhua
Thu Nov 03, 2011 3:34 am
Forum: ROMS Discussion
Topic: Some questions encountered reading the code
Replies: 2
Views: 870

Re: Some questions encountered reading the code

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: ! ...
by linzhenhua
Wed Oct 26, 2011 2:01 am
Forum: ROMS Discussion
Topic: The Segmentation fault of ROMS 3.6
Replies: 15
Views: 3504

Re: The Segmentation fault of ROMS 3.6

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...
by linzhenhua
Fri Oct 14, 2011 8:46 am
Forum: ROMS Discussion
Topic: How to set the parallel threads?
Replies: 1
Views: 829

Re: How to set the parallel threads?

Please try issue the following command and check if it helps

unset OMP_NUM_THREADS
by linzhenhua
Fri Oct 14, 2011 1:45 am
Forum: ROMS Problems
Topic: compiling problem upwelling by the newest ROMS
Replies: 6
Views: 4624

Re: compiling problem upwelling by the newest ROMS

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 ...
by linzhenhua
Sat Sep 10, 2011 1:47 am
Forum: ROMS Wish List
Topic: ROMS Wish List
Replies: 6
Views: 4026

Re: ROMS Wish List

Thanks for the great work from ROMS dev team. I think non-hydrostatic feature deserves to be on the wist list.
by linzhenhua
Sat May 14, 2011 12:43 am
Forum: ROMS Installation
Topic: Help! a problem in download
Replies: 2
Views: 1081

Re: Help! a problem in download

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.
by linzhenhua
Fri Apr 01, 2011 12:45 am
Forum: ROMS Problems
Topic: Problems with averages_detide and OpenMp
Replies: 2
Views: 963

Re: Problems with averages_detide and OpenMp

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.
by linzhenhua
Wed Mar 30, 2011 9:37 am
Forum: ROMS Discussion
Topic: Who can log into the Linux training server dods.o3d.org ?
Replies: 3
Views: 1195

Re: Who can log into the Linux training server dods.o3d.org

I think you could type the related code yourself following the video tutorial, it's not a time consuming task in my opinion. ^_^
by linzhenhua
Wed Mar 30, 2011 3:43 am
Forum: ROMS Tools and Techniques
Topic: pyroms problem running/installing
Replies: 8
Views: 3313

Re: pyroms problem running/installing

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

from matplotlib import pyplot

pyplot.plot()
by linzhenhua
Tue Mar 29, 2011 1:42 am
Forum: ROMS Tools and Techniques
Topic: pyroms problem running/installing
Replies: 8
Views: 3313

Re: pyroms problem running/installing

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.
by linzhenhua
Mon Mar 28, 2011 1:44 am
Forum: ROMS Tools and Techniques
Topic: pyroms problem running/installing
Replies: 8
Views: 3313

Re: pyroms problem running/installing

Do you install pyroms after you have installed python-netcdf4 successfully?
by linzhenhua
Mon Mar 28, 2011 12:51 am
Forum: ROMS Tools and Techniques
Topic: pyroms problem running/installing
Replies: 8
Views: 3313

Re: pyroms problem running/installing

I think you should first check that you have installed python-netcdf4 package successfully.
by linzhenhua
Wed Mar 23, 2011 12:51 am
Forum: ROMS Tools and Techniques
Topic: netcdf4-python
Replies: 7
Views: 4513

Re: netcdf4-python

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.
by linzhenhua
Thu Feb 17, 2011 12:13 am
Forum: ROMS Bugs
Topic: Minus sediment concentration in river sediment case
Replies: 52
Views: 16020

Re: Minus sediment concentration in river sediment case

Try to search "MPDATA" in the forum and check if the related discussions help.
by linzhenhua
Wed Jan 19, 2011 1:04 pm
Forum: ROMS Tools and Techniques
Topic: Pyroms installing problem
Replies: 4
Views: 2626

Re: Pyroms installing problem

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...
by linzhenhua
Wed Jun 09, 2010 12:10 am
Forum: ROMS Discussion
Topic: Adding a new ana_XXX.h to ROMS
Replies: 3
Views: 1121

Re: Adding a new ana_XXX.h to ROMS

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.
by linzhenhua
Tue Jun 08, 2010 7:26 am
Forum: ROMS Problems
Topic: Can we get the mass balance from the model output U,V,W?
Replies: 3
Views: 1356

Re: Can we get the mass balance from the model output U,V,W?

The volume for a specific region is not conserved because there is a free surface.
by linzhenhua
Tue Jun 08, 2010 12:13 am
Forum: ROMS Problems
Topic: Can we get the mass balance from the model output U,V,W?
Replies: 3
Views: 1356

Re: Can we get the mass balance from the model output U,V,W?

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 thi...
by linzhenhua
Wed May 26, 2010 12:45 am
Forum: ROMS Tools and Techniques
Topic: Question about python-roms tools
Replies: 1
Views: 1539

Re: Question about python-roms tools

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

http://code.google.com/p/octant/
by linzhenhua
Fri May 21, 2010 11:05 pm
Forum: ROMS Installation
Topic: After installation of NetCDF3
Replies: 13
Views: 4375

Re: After installation of NetCDF3

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.
by linzhenhua
Thu May 20, 2010 12:15 am
Forum: ROMS Installation
Topic: After installation of NetCDF3
Replies: 13
Views: 4375

Re: After installation of NetCDF3

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.
by linzhenhua
Thu Apr 29, 2010 12:52 pm
Forum: ROMS Discussion
Topic: zeta output all zeros
Replies: 3
Views: 835

Re: zeta output all zeros

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 t...
by linzhenhua
Wed Apr 28, 2010 2:27 am
Forum: ROMS Discussion
Topic: zeta output all zeros
Replies: 3
Views: 835

Re: zeta output all zeros

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.
by linzhenhua
Sat Oct 10, 2009 1:17 am
Forum: ROMS Discussion
Topic: Weird experience with ROMS3.72
Replies: 5
Views: 1271

Re: Weird experience with ROMS3.72

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 o...
by linzhenhua
Sun Jul 26, 2009 6:26 am
Forum: ROMS Installation
Topic: problem with install seagrid
Replies: 1
Views: 975

Re: problem with install seagrid

Try first change current directory to /root/.matlab/R2008b/ and then run the command.
by linzhenhua
Wed Jul 22, 2009 7:27 am
Forum: ROMS Discussion
Topic: is STFLUX and BTFLUX necessary?
Replies: 2
Views: 1150

Re: is STFLUX and BTFLUX necessary?

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.
by linzhenhua
Sat Jun 20, 2009 7:08 am
Forum: ROMS Problems
Topic: NEED HELP!!
Replies: 8
Views: 2463

Re: NEED HELP!!

The cpi example works because it does not need the HDF library.
by linzhenhua
Sun Mar 08, 2009 12:17 pm
Forum: ROMS Problems
Topic: passive tracer not conserved with TS_MPDATA in shallow water
Replies: 5
Views: 1973

Re: passive tracer not conserved with TS_MPDATA in shallow water

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 re...
by linzhenhua
Sat Mar 07, 2009 5:28 pm
Forum: ROMS Discussion
Topic: A question with coordinate transformation
Replies: 0
Views: 824

A question with coordinate transformation

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,su...
by linzhenhua
Tue Nov 18, 2008 8:32 am
Forum: ROMS Discussion
Topic: netcdf file reading with FORTRAN
Replies: 3
Views: 1871

Re: netcdf file reading with FORTRAN

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

http://www.unidata.ucar.edu/software/netcdf/docs/
by linzhenhua
Wed Nov 12, 2008 8:24 am
Forum: ROMS Problems
Topic: smflux using analytical expression
Replies: 15
Views: 4095

Re: smflux using analytical expression

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 pro...
by linzhenhua
Sun Nov 09, 2008 4:46 pm
Forum: ROMS Discussion
Topic: timestep musings
Replies: 8
Views: 2986

Re: timestep musings

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...
by linzhenhua
Wed Nov 05, 2008 7:19 pm
Forum: ROMS Problems
Topic: blows up in shallow water! wet_dry problem?
Replies: 7
Views: 2251

Re: blows up in shallow water! wet_dry problem?

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.
by linzhenhua
Fri Oct 31, 2008 10:49 am
Forum: ROMS Problems
Topic: blows up in shallow water! wet_dry problem?
Replies: 7
Views: 2251

Re: blows up in shallow water! wet_dry problem?

I guess this thread may be useful for your question.

viewtopic.php?f=19&t=1087
by linzhenhua
Sat Oct 11, 2008 6:12 pm
Forum: ROMS Problems
Topic: smflux using analytical expression
Replies: 15
Views: 4095

Re: smflux using analytical expression

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 ...
by linzhenhua
Tue Oct 07, 2008 7:47 am
Forum: ROMS Problems
Topic: smflux using analytical expression
Replies: 15
Views: 4095

Re: smflux using analytical expression

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...
by linzhenhua
Mon Oct 06, 2008 9:33 am
Forum: ROMS Problems
Topic: smflux using analytical expression
Replies: 15
Views: 4095

Re: smflux using analytical expression

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 vi...
by linzhenhua
Mon Oct 06, 2008 7:24 am
Forum: ROMS Tools and Techniques
Topic: Questions about processing package
Replies: 8
Views: 2967

Re: Questions about processing package

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 it.
by linzhenhua
Sun Oct 05, 2008 7:16 am
Forum: ROMS Tools and Techniques
Topic: Questions about processing package
Replies: 8
Views: 2967

Re: Questions about processing package

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 ...
by linzhenhua
Thu Oct 02, 2008 7:55 am
Forum: ROMS Problems
Topic: smflux using analytical expression
Replies: 15
Views: 4095

Re: smflux using analytical expression

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)
by linzhenhua
Wed Oct 01, 2008 5:16 pm
Forum: ROMS Discussion
Topic: OBC for barotropic channel flow
Replies: 7
Views: 2150

Re: OBC for barotropic channel flow

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 slop...
by linzhenhua
Tue Sep 23, 2008 1:46 pm
Forum: ROMS Discussion
Topic: OBC for barotropic channel flow
Replies: 7
Views: 2150

Re: OBC for barotropic channel flow

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 re...
by linzhenhua
Mon Sep 22, 2008 3:57 pm
Forum: ROMS Discussion
Topic: OBC for barotropic channel flow
Replies: 7
Views: 2150

OBC for barotropic channel flow

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...
by linzhenhua
Sun Sep 21, 2008 8:43 am
Forum: ROMS Discussion
Topic: Problem with FRCNAME
Replies: 1
Views: 1073

Re: Problem with FRCNAME

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.
by linzhenhua
Sun Sep 21, 2008 1:56 am
Forum: ROMS Discussion
Topic: Problem with FRCNAME
Replies: 1
Views: 1073

Problem with FRCNAME

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,t...
by linzhenhua
Fri Jul 11, 2008 9:15 am
Forum: ROMS Tools and Techniques
Topic: pyroms -- a suite of tools for working with ROMS in Python
Replies: 5
Views: 4784

Re: pyroms -- a suite of tools for working with ROMS in Python

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.
by linzhenhua
Mon Jun 09, 2008 5:17 am
Forum: ROMS Information
Topic: compile in fedora 8 with intel fortran
Replies: 2
Views: 2119

One possible reason might be that you do not compile netcdf with the same compiler as you compile roms.
by linzhenhua
Mon Jun 09, 2008 5:13 am
Forum: ROMS Installation
Topic: error pgf90:not found - compiling roms in linux
Replies: 3
Views: 3819

Re: error pgf90:not found - compiling roms in linux

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...
by linzhenhua
Thu Feb 21, 2008 8:34 am
Forum: ROMS Installation
Topic: doubt about installing roms-3.0
Replies: 6
Views: 2093

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 later.
by linzhenhua
Wed Jan 30, 2008 7:51 am
Forum: ROMS Installation
Topic: netCDF 3.6.2, Ubuntu 7.10, 32bit, Intel Fortran
Replies: 12
Views: 5457

It seems that the fortran compiler should be specified by the environmental variable F90 instead of FC90.
by linzhenhua
Tue Dec 11, 2007 9:09 am
Forum: ROMS Installation
Topic: SVN Checkout error
Replies: 2
Views: 1585

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.
by linzhenhua
Tue Jul 31, 2007 2:25 pm
Forum: ROMS Problems
Topic: Compiling error in SGI workstation
Replies: 7
Views: 3291

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 sour...