Search found 519 matches

by m.hadfield
Sun Nov 17, 2019 9:39 pm
Forum: ROMS Tools and Techniques
Topic: pyroms grid missing libgridgen, unable to solve
Replies: 5
Views: 209

Re: pyroms grid missing libgridgen, unable to solve

For the libgridgen problem, take a look at this issue of GitHub: https://github.com/ESMG/pyroms/issues/26 The original poster on that issue found a solution that involved installing gridgen and its dependencies from the Git repositories. Alternatively, you can install these packages with Conda, but ...
by m.hadfield
Mon Nov 04, 2019 2:13 am
Forum: ROMS Discussion
Topic: PyROMS developments
Replies: 0
Views: 155

PyROMS developments

For anyone who's interested, I am interested in contributing to the development of PyROMS . I have opened a couple of issues: Issue 23 : Improve installation and documentation thereof Issue 24 : Improve documentation and example code As the README says, there are a few rough edges in PyROMS. The rou...
by m.hadfield
Sun Oct 13, 2019 9:05 pm
Forum: ROMS Discussion
Topic: Using ATM_PRESS in combination with M2FLATHER?
Replies: 2
Views: 283

Re: Using ATM_PRESS in combination with M2FLATHER?

Non-linear feedbacks are not included in the code.

The PRESS_COMPENSATE option should be used in the case you describe where the model providing the boundary conditions does not allow for the inverse barometer effect.
by m.hadfield
Mon Mar 11, 2019 2:34 am
Forum: ROMS Discussion
Topic: PyROMS bug
Replies: 5
Views: 1139

Re: PyROMS bug

Thank you. I did not know that lpsolve55 is available via Conda.
by m.hadfield
Tue Feb 19, 2019 3:52 am
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 3242

Re: My ROMS

Hi John I've just created a ticket for PRESS_COMPENSATE on the Trac system: https://www.myroms.org/projects/src/ticket/805 I hadn't noticed your follow-up to my comment, sorry, so didn't take it into account. My work weeks are rather fragmented these days! A result of my semi-retired status, an inju...
by m.hadfield
Thu Feb 07, 2019 3:54 am
Forum: ROMS Bugs
Topic: Bug in inp_decode.F with STATIONS and BIO_FENNEL
Replies: 0
Views: 348

Bug in inp_decode.F with STATIONS and BIO_FENNEL

The UPWELLING test case works OK when either STATIONS or BIO_FENNEL is defined, but fails when both are defined. It gives the message below . I haven't found a solution yet, so I'm just reporting what I've found. It may well make more sense to Hernan. This is the message (Linux-gfortran in serial mo...
by m.hadfield
Sun Jan 27, 2019 10:23 pm
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 3242

Re: My ROMS

Sure. In the next few days.
by m.hadfield
Wed Nov 21, 2018 10:07 pm
Forum: ROMS Tools and Techniques
Topic: Building ROMS grid topography from scattered, sparse data
Replies: 2
Views: 952

Re: Building ROMS grid topography from scattered, sparse dat

Thank you very much for that Sasha.

For a while now I have handed my bathymetry interpolation duties to the GMT surface utility:

http://gmt.soest.hawaii.edu/doc/latest/surface.html

I'll have a good look at what you've done and compare them.
by m.hadfield
Wed Nov 21, 2018 10:01 pm
Forum: ROMS Discussion
Topic: Dye boundary doesn't work when using passive tracer
Replies: 4
Views: 686

Re: Dye boundary doesn't work when using passive tracer

The RadNud boundary condition nudges the boundary value towards the specified value. This will only affect the interior values when the radiative scheme diagnoses inflow. So: Have you set a nudging time scale for dye at the southern boundary? Have you waited long enough to see an effect in the inter...
by m.hadfield
Sun Sep 23, 2018 9:00 pm
Forum: ROMS Bugs
Topic: can't find revision #751 in new source code
Replies: 2
Views: 731

Re: can't find revision #751 in new source code

If you use git svn to clone the trunk, as Kate has talked about from time to time, you will get a copy of the entire history of the repository and can check out any revision you want.
by m.hadfield
Tue Aug 14, 2018 1:30 am
Forum: ROMS Discussion
Topic: PyROMS bug
Replies: 5
Views: 1139

Re: PyROMS bug

Another PyROMS problem; might as well use the same thread... I have more-or-less successfully (?) built and installed PyROMS with the following commands # The system is CentOS 7 with Miniconda (single-user install). # Python 3.6, numpy, netcdf, etc are installed in a custom environment called "pytho...
by m.hadfield
Mon Aug 13, 2018 5:28 am
Forum: ROMS Discussion
Topic: PyROMS bug
Replies: 5
Views: 1139

Re: PyROMS bug

Sure do! I submitted the one and only pull request I've ever prepared to you a few weeks ago.
by m.hadfield
Mon Aug 13, 2018 4:56 am
Forum: ROMS Discussion
Topic: PyROMS bug
Replies: 5
Views: 1139

PyROMS bug

Python 3.6.6 |Anaconda, Inc.| (default, Jun 28 2018, 17:14:51) [GCC 7.2.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import pyroms_toolbox Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/hadfield/.local/lib/python3.6/site-...
by m.hadfield
Tue Aug 07, 2018 10:25 am
Forum: ROMS Discussion
Topic: River bottom salinity too high
Replies: 9
Views: 1265

Re: River bottom salinity too high

I am running "many rivers scenario" without specifying temperature (only salinity) of the river sources and all is working fine
If you're lucky it will continue to do so. :wink:
by m.hadfield
Sun Aug 05, 2018 10:41 pm
Forum: ROMS Discussion
Topic: River bottom salinity too high
Replies: 9
Views: 1265

Re: River bottom salinity too high

I don't know if this is relevant here, but even with a well-specified river, ROMS tends to generate an estuarine flow (outflow at the surface, inflow at the bottom) at the grid cell the river enters. The advection scheme can then generate hypersaline water at the bottom, which tends to form a plume ...
by m.hadfield
Mon Mar 19, 2018 1:02 am
Forum: ROMS Problems
Topic: Error while using Run Command by Build.bash!
Replies: 1
Views: 591

Re: Error while using Run Command by Build.bash!

Near the end of your build.bash file you should be able to see lines like the following # Go to the users source directory to compile. The options set above will # pick up the application-specific code from the appropriate place. cd ${MY_ROMS_SRC} #---------------------------------------------------...
by m.hadfield
Wed Mar 14, 2018 2:41 am
Forum: ROMS Tools and Techniques
Topic: Error of installing PyCNAL on conda
Replies: 11
Views: 2402

Re: Error of installing PyCNAL on conda

kate wrote:Well, needs evolve. The gang wants to build tools that work with more than one model, supporting ROMS, MOM6, Mitgcm in an object-oriented way.
Too much for a bear of little brain like me, I suspect.

So, will pyroms development cease?
by m.hadfield
Wed Mar 14, 2018 1:00 am
Forum: ROMS Tools and Techniques
Topic: Error of installing PyCNAL on conda
Replies: 11
Views: 2402

Re: Error of installing PyCNAL on conda

I'm getting emails about pyroms suddenly, right when the guys want to scrap it and start over. I want to develop my own library of Python software for ROMS. It seems to me that the key components will be conda, python3, xarray & dask, esmf and matplotlib. The missing component is the vertical coord...
by m.hadfield
Tue Mar 13, 2018 10:05 pm
Forum: ROMS Tools and Techniques
Topic: Error of installing PyCNAL on conda
Replies: 11
Views: 2402

Re: Error of installing PyCNAL on conda

On Ubuntu, I installed netcdf-fortran with apt instead of with conda: sudo apt install libnetcdff-dev Be sure to use nf-config to find the fortran-netcdf because you'll still have the nc-config in conda. When tried to link to the system netCDF I got errors relating to libgfortran.so version incompa...
by m.hadfield
Tue Mar 13, 2018 4:08 am
Forum: ROMS Tools and Techniques
Topic: Error of installing PyCNAL on conda
Replies: 11
Views: 2402

Re: Error of installing PyCNAL on conda

I get a similar error building pyroms (python3 branch): https://github.com/ESMG/pyroms/tree/python3 The system is Python 3.6, Miniconda, CentOS 7. The warning is Warning: distutils distribution has been initialized, it may be too late to add an extension _interp Warning: distutils distribution has b...
by m.hadfield
Fri Feb 23, 2018 6:35 am
Forum: ROMS Discussion
Topic: Got an Error when compiling coawst.bash
Replies: 6
Views: 1293

Re: Got an Error when compiling coawst.bash

I suggest you delete *everything* and start over again, and use a configure command like this

Code: Select all

CPRDEF=INTEL CC=icc FC=ifort MPIFC=mpif90 ./configure
by m.hadfield
Thu Feb 22, 2018 4:45 am
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 3242

Re: My ROMS

wilkin wrote:We'd be interested to know more about your PRESS_COMPENSATE.
See

https://github.com/hadfieldnz/roms-trun ... u2dbc_im.F
https://github.com/hadfieldnz/roms-trun ... v2dbc_im.F

but replace "&" with "&&".
by m.hadfield
Thu Feb 22, 2018 1:27 am
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 3242

Re: My ROMS

Thanks. PRESS_COMPENSATE is something I added to ATM_PRESS. I think it lets you use lateral boundary zeta data from a model without ATM_PRESS (the inverse barometer effect) for a model that does have it. I haven't used ATM_PRESS for a while, but if you're interested in storm surge it's a must-have ....
by m.hadfield
Tue Feb 20, 2018 11:13 pm
Forum: ROMS Problems
Topic: Regarding the option TIDENAME
Replies: 8
Views: 1424

Re: Regarding the option TIDENAME

kate wrote:Though I don't bother with RAMP_TIDES.
An aside: If you have shallow water in your domain and wetting and drying is not enabled, RAMP_TIDES can be useful to avoid transients that drop the water level below the bathymetry, hence crashing the model.
by m.hadfield
Tue Feb 20, 2018 11:08 pm
Forum: ROMS Bugs
Topic: List of analytical header files
Replies: 3
Views: 901

Re: List of analytical header files

arango wrote:So to report all the header files together, I decided to write its usage at the end when there are visible instead of the middle of time-stepping. So when you see weird things like that in ROMS, there is also a reason for it 8) I think that I mentioned this before in the documentation.
:)
by m.hadfield
Mon Feb 19, 2018 10:42 pm
Forum: ROMS Bugs
Topic: List of analytical header files
Replies: 3
Views: 901

List of analytical header files

I'm putting this in ROMS Bugs, but it's really an oddity, not a bug. In output from a ROMS non-linear model, there is a list of directories and files near the start of the output, just before the grid and tiling information. Eg. from one of my runs: Local Root : /home/hadfield/ROMS/roms-trunk-mgh He...
by m.hadfield
Wed Feb 14, 2018 3:37 am
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 3242

My ROMS

Like many ROMS users--I suspect--I have my own lightly hacked version of the ROMS source code and a collection of roms-related scripts. I have just put a selection of these on GitHub.com for the edification and amusement of the ROMS community. There are 3 repositories: roms-trunk-mgh : There are two...
by m.hadfield
Wed Jan 24, 2018 8:55 pm
Forum: ROMS Tools and Techniques
Topic: Pyroms update
Replies: 8
Views: 1755

Re: Pyroms update

What is the advantage on moving the code from python 2.7 to python 3? I'm approaching this as someone who has used Python (version 2) for many years as a scripting language but is looking to adopt it as my main language for data analysis. I have looked at various discussions like this... https://le...
by m.hadfield
Wed Jan 24, 2018 4:44 am
Forum: ROMS Tools and Techniques
Topic: Pyroms update
Replies: 8
Views: 1755

Re: Pyroms update

kate wrote:What are you planning to do exactly?
General stuff: analysis of model output; generating input files. With an emphasis on nested grids.

Does PyCNAL have a Python 3 version?
by m.hadfield
Tue Jan 23, 2018 4:02 am
Forum: ROMS Tools and Techniques
Topic: Pyroms update
Replies: 8
Views: 1755

Re: Pyroms update

I have created a python3 branch of the pyroms repository on github. This is much like the previous PyCNAL repository, but the guys want to start fresh with all new PyCNAL code. So, if I want to develop my own ROMS Python 3 code (using existing packages like xarray) but also want to build on (and so...
by m.hadfield
Sun Dec 17, 2017 8:38 pm
Forum: ROMS Sediment
Topic: SVN server problem: Can't find anything on this.
Replies: 6
Views: 1695

Re: SVN server problem: Can't find anything on this.

OK, so an all-Git ROMS would be better for people like us. And for everyone after the transition period.
by m.hadfield
Sat Dec 16, 2017 3:04 am
Forum: ROMS Sediment
Topic: SVN server problem: Can't find anything on this.
Replies: 6
Views: 1695

Re: SVN server problem: Can't find anything on this.

kate wrote:Honestly, I've had mixed to bad luck with "git svn" on Linux. I gave up and do that through the Mac.
I've been using Git and Git-SVN on Cygwin, but have now switched to Linux, with good results so far. I'll keep an eye out for problems. I should have though Git was very platform-agnostic.
by m.hadfield
Sat Dec 16, 2017 1:09 am
Forum: ROMS Sediment
Topic: SVN server problem: Can't find anything on this.
Replies: 6
Views: 1695

Re: SVN server problem: Can't find anything on this.

kate wrote:Hernan hates my suggestion of switching to git. :twisted:
The good new is that (as you know, Kate) all the users can ignore Hernan's choice of repository format and use git svn to clone their own copy.
by m.hadfield
Fri Dec 15, 2017 12:05 am
Forum: ROMS Problems
Topic: Compiling ROMs in Ubuntu
Replies: 7
Views: 1543

Re: Compiling ROMs in Ubuntu

Hi Jamie

Good to hear.

One quibble: if USE_NETCDF4 is "on" then you shouldn't need NETCDF_INCDIR; if it's off then setting NF_CONFIG should have no effect.

Mark
by m.hadfield
Thu Dec 14, 2017 8:59 am
Forum: ROMS Problems
Topic: Compiling ROMs in Ubuntu
Replies: 7
Views: 1543

Re: Compiling ROMs in Ubuntu

has-f03 is "yes" so it should work with ROMS.
by m.hadfield
Thu Dec 14, 2017 5:52 am
Forum: ROMS Problems
Topic: Compiling ROMs in Ubuntu
Replies: 7
Views: 1543

Re: Compiling ROMs in Ubuntu

According to this https://www.unidata.ucar.edu/software/netcdf/netcdf-4/newdocs/netcdf-install/Binaries.html "The easiest way to get netCDF is through a package management program, such as rpm, yum, adept, and others. NetCDF is available from many different repositories, including the default Red Ha...
by m.hadfield
Wed Dec 06, 2017 1:34 am
Forum: ROMS Installation
Topic: Make files for Cray cluster
Replies: 3
Views: 1003

Re: Make files for Cray cluster

Here, for completeness, is Linux-ftn-gnu.mk. Build time with the Gnu programming environment is much less than for the others; I conjecture this might be due to a lack of inter-procedural optimizations at link time. I expect run-time performance to be poor, but the Gnu option might be useful when de...
by m.hadfield
Tue Dec 05, 2017 9:46 pm
Forum: ROMS Installation
Topic: Make files for Cray cluster
Replies: 3
Views: 1003

Re: Make files for Cray cluster

Oops, forgot compiler options needed for OpenMP on the Intel variant. Corrected file attached.
by m.hadfield
Tue Dec 05, 2017 9:30 pm
Forum: ROMS Installation
Topic: Make files for Cray cluster
Replies: 3
Views: 1003

Make files for Cray cluster

Here in New Zealand we have access to a new Cray XC50 (whoopee!) and I have been working out how to build ROMS on it. As discussed in this thread https://www.myroms.org/forum/viewtopic.php?f=31&t=4086&p=15704&hilit=Linux+ftn#p15704 it has 3 programming environments, PrgEnv-cray, PrgEnv-intel, PrgEnv...
by m.hadfield
Thu Nov 23, 2017 9:10 pm
Forum: ROMS Discussion
Topic: Unable to inquire about contents of netCDF in svn881
Replies: 1
Views: 776

Re: Unable to inquire about contents of netCDF in svn881

> Did anybody have similar issue? Yes, a week or two ago. ROMS seemed to object to one forcing file in a sequence, the third or fourth as I recall, but the file was similar to all the others as far as I could see. I resolved to look into this at some stage, but haven't got around to it. I have delet...
by m.hadfield
Thu Oct 26, 2017 6:56 am
Forum: ROMS Discussion
Topic: ROMS tidal forcing with water elevation ONLY
Replies: 8
Views: 3936

Re: ROMS tidal forcing with water elevation ONLY

To answer Mark Hadfield's remark that coastal modelers have been content to use zeta-only boundary conditions for many years I might cynically suggest that modelers have been happy to accept a lot of things that aren't necessarily particularly good or in any way optimal. No argument from me! :wink:
by m.hadfield
Mon Jul 10, 2017 3:01 am
Forum: ROMS Tools and Techniques
Topic: IDL-ROMS on GitHub
Replies: 3
Views: 1823

Re: IDL-ROMS on GitHub

I'm afraid there is no manual. But I will add some extra documentation (installation, examples) to both the IDL-Motley and IDL-ROMS packages in the next few days and update the repository.

IDL-ROMS requires IDL-Motley. Have you managed to install IDL-Motley?
by m.hadfield
Thu Jul 06, 2017 3:04 am
Forum: ROMS Tools and Techniques
Topic: IDL-ROMS on GitHub
Replies: 3
Views: 1823

IDL-ROMS on GitHub

I know there are very few ROMS modellers using IDL out there, but those who are might be interested in my IDL-ROMS package, which is now hosted on GitHub along with my IDL-Motley package, which it requires: https://github.com/hadfieldnz/idl-roms https://github.com/hadfieldnz/idl-motley IDL-ROMS does...
by m.hadfield
Sun Jun 25, 2017 9:44 pm
Forum: ROMS Problems
Topic: Problems with a leap-year (1996)
Replies: 5
Views: 2132

Re: Problems with a leap-year (1996)

+1 to what Kate said. Keeping your local modifications in a Subversion working copy is skating on thin ice. The modifications have no back-up and no history. Personally I use Mercurial with the hgsubversion extension, but Git is more widely supported and Kate has written instructions for using it wi...
by m.hadfield
Wed Jun 21, 2017 4:57 am
Forum: ROMS Problems
Topic: Problems with a leap-year (1996)
Replies: 5
Views: 2132

Re: Problems with a leap-year (1996)

See this thread

viewtopic.php?f=19&t=4521&p=17727&hilit=y2k#p17727

and update your ROMS
by m.hadfield
Mon May 01, 2017 11:00 pm
Forum: ROMS Bugs
Topic: A new Y2K bug!
Replies: 2
Views: 1495

A new Y2K bug!

I think I've found a Y2K leap year bug in the new string-based date-time output. I have a simulation that runs from mid-1999 to mid-2000. Below are some excerpts from the log file's time-step output. Shortly after 2000-02-28 12:30, the date string switches from 2000-02-28 (which is correct) to 1999-...
by m.hadfield
Thu Apr 13, 2017 2:38 am
Forum: ROMS Installation
Topic: netcdf installation-gfortran
Replies: 11
Views: 6916

Re: netcdf installation-gfortran

With Cygwin these days you should install the pre-built Cygwin netCDF libraries rather than building from source.

There are a few Cygwin netCDF packages. I think the one you really need is netcdf-devel, but the others may come in useful too.
by m.hadfield
Thu Mar 16, 2017 10:06 pm
Forum: ROMS Discussion
Topic: ROMS not bit-reproducible: northern boundary?
Replies: 32
Views: 7360

Re: ROMS not bit-reproducible: northern boundary?

Possibly related issue: Since I updated to 3.7 I have also occasionally had segfaults that don't reproduce themselves. That is, it will segfault, I resubmit the job without even recompiling, and then it doesn't segfault. I understand segfaults that show up inconsistently are often related to variab...
by m.hadfield
Mon Feb 20, 2017 8:57 pm
Forum: ROMS Installation
Topic: Problem with compiling build.bash and netcdf on cygwin
Replies: 17
Views: 3593

Re: Problem with compiling build.bash and netcdf on cygwin

The oceanS executable gets the location of the varinfo.dat file from the following line in ocean_upwelling.in ! Input variable information file name. This file needs to be processed ! first so all information arrays can be initialized properly. VARNAME = ROMS/External/varinfo.dat Your output log sug...
by m.hadfield
Mon Feb 20, 2017 4:35 am
Forum: ROMS Installation
Topic: Problem with compiling build.bash and netcdf on cygwin
Replies: 17
Views: 3593

Re: Problem with compiling build.bash and netcdf on cygwin

Oops, that advice in the tutorial is about a decade out of date!
by m.hadfield
Mon Dec 12, 2016 3:16 am
Forum: ROMS Installation
Topic: ROMS build problem due to faulty nf-config on CentOS Linux
Replies: 0
Views: 1275

ROMS build problem due to faulty nf-config on CentOS Linux

I have a problem which I think is ultimately due to a broken netCDF binary package on CentOS Linux, but before taking it up with the package maintainers I want to raise it on the ROMS forum. I've also raised it on the netCDF group... http://www.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/201...
by m.hadfield
Mon Nov 07, 2016 9:07 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

I second John's suggestion. Don't build netCDF on Cygwin yourself; use the Cygwin packages.

Also, don't try adding extra command-line switches like -lnetcdff; make sure build.bash sets USE_NETCDF4 and let nc-config sort it out.
by m.hadfield
Tue Nov 01, 2016 2:36 am
Forum: ROMS Tools and Techniques
Topic: Cylc for operational systems
Replies: 0
Views: 4821

Cylc for operational systems

This is not specific to ROMS, but please bear with me. There are quite a few groups running ROMS routinely, in configurations that might variously be called operational, quasi-operational and not-really-operational. At the ROMS Asia-Pacific Workshop in Hobart I talked to a few people about a tool th...
by m.hadfield
Wed Oct 26, 2016 2:56 am
Forum: ROMS Installation
Topic: Problem for the upwelling case when turning OpenMP on
Replies: 4
Views: 5666

Re: Problem for the upwelling case when turning OpenMP on

The quick-save output facility introduced in ticket 704 had a bug that was fixed in ticket 708:

https://www.myroms.org/projects/src/ticket/704
https://www.myroms.org/projects/src/ticket/708
by m.hadfield
Tue Aug 09, 2016 10:03 pm
Forum: ROMS Bugs
Topic: ROMS attempts to close un-named files
Replies: 3
Views: 3613

Re: ROMS attempts to close un-named files

That was quick!

Thanks for the info.
by m.hadfield
Tue Aug 09, 2016 3:42 am
Forum: ROMS Bugs
Topic: ROMS attempts to close un-named files
Replies: 3
Views: 3613

ROMS attempts to close un-named files

This is arguably not a bug, rather than an opportunity for user error. When I updated to the latest version of the code, with the new, quick-save file functionality and ran an existing case I got NETCDF_CLOSE - error during closing of file, ncid = 0 file: call from: close_out, close_io.F To cut a lo...
by m.hadfield
Sun Jul 24, 2016 11:20 pm
Forum: ROMS Discussion
Topic: Can ROMS read in albedo field from external files?
Replies: 7
Views: 2471

Re: Can ROMS read in albedo field from external files?

Forcing files require a time variable, but that can be given the attribute "calendar" with the value "none", in which case only a single value is required and will be applied to all times. I assume Kate's albedo files work the same way, and if they don't it wouldn't be hard to fix the code so they do.
by m.hadfield
Tue May 31, 2016 11:06 pm
Forum: ROMS Installation
Topic: problems in runing Roms with tidal forcing
Replies: 16
Views: 7452

Re: problems in runing Roms with tidal forcing

Not only do you know that the crash occurs in check_multifile, you know that it involves a variable called check_multifile_$LCHECK (which I think is a local or module level variable called lcheck in the scope of check_multifile) being used at line 74 without a value being set. Time to employ the mag...
by m.hadfield
Mon May 30, 2016 9:51 pm
Forum: ROMS Discussion
Topic: integration of vertical speed for floats; types of floats?
Replies: 5
Views: 3170

Re: integration of vertical speed for floats; types of float

FLOAT_VWALK enables a vertical random walk for the floats. VWALK_FORWARD has an effect only if FLOAT_VWALK is activated. With VWALK_FORWARD, the float vertical movement is implemented using a forward-only time-stepping scheme, otherwise it uses the same predictor-corrector method as the rest of the ...
by m.hadfield
Wed Dec 16, 2015 4:49 am
Forum: ROMS Problems
Topic: Error in running ROMS (test case)
Replies: 4
Views: 2205

Re: Error in running ROMS (test case)

You should try (and you should be able to) install all the software components you need as Cygwin packages. This includes svn, gfortran, openmpi, netcdf and the miscellanous development tools: make, perl, etc. There are various things that suggest you haven't done this... If you used Cygwin svn to c...
by m.hadfield
Fri Oct 30, 2015 4:00 am
Forum: ROMS Installation
Topic: ROMS with gfortran 5.2?
Replies: 21
Views: 6832

Re: ROMS with gfortran 5.2?

In an earlier post you said The program stops at the same point as for this user, although it does give me a line number I believe Does it still give you a line number? If so, what is it? Is there any other output to stderr that you haven't shown us? Once you have a source code line number you can u...
by m.hadfield
Sun Oct 18, 2015 8:13 pm
Forum: ROMS Problems
Topic: Blow up with LMD_MIXING and GLS_MIXING but BVF_MIXING works
Replies: 8
Views: 3313

Re: Blow up with LMD_MIXING and GLS_MIXING but BVF_MIXING wo

kate wrote:I see you have zero depth at the coast. Try deepening that just a bit.
A note for novices: without wetting and drying enabled, ROMS will blow up if zeta drops below -h at any grid point.
by m.hadfield
Thu Jul 16, 2015 5:09 am
Forum: ROMS Discussion
Topic: IMPOSED SEA LEVEL AND TIDE. Inversed barometer effect
Replies: 3
Views: 1595

Re: IMPOSED SEA LEVEL AND TIDE. Inversed barometer effect

You can add non-tidal boundary values to your tidal boundary conditions with the options ADD_FSOBC and ADD_M2OBC. See ROMS/Include/cppdefs.h. The relevant comments in that file say, "use to add tidal elevation/current to processed OBC data". Actually, I think it would more accurate to say "use to ad...
by m.hadfield
Tue Apr 07, 2015 10:33 pm
Forum: ROMS Sediment
Topic: Problem during simulating sediment from point source
Replies: 8
Views: 4302

Re: Problem during simulating sediment from point source

I have never successfully set up a point source detached from the land mask using the standard ROMS facilities. (If someone can tell me how, I would love to hear it.) For point sources of this type I add code to step3d_t.F. This represents the source of sediment mass, but not the accompanying water ...
by m.hadfield
Tue Apr 07, 2015 12:18 am
Forum: ROMS Sediment
Topic: Problem during simulating sediment from point source
Replies: 8
Views: 4302

Re: Problem during simulating sediment from point source

How are you implementing your point source and how do you know it stops after 24 hours?
by m.hadfield
Thu Mar 26, 2015 1:30 am
Forum: ROMS Installation
Topic: Problems compiling Upwelling Case
Replies: 6
Views: 4153

Re: Problems compiling Upwelling Case

It doesn't really matter whether you modify the master file system table (/etc/fstab) or the user table (/etc/fstab.d/hadfield in my case). However putting things in the user table is cleaner, in my opinion. As you say, the user table does not exist by default: if you want one, you need to create it...
by m.hadfield
Wed Mar 25, 2015 9:09 pm
Forum: ROMS Installation
Topic: Problems compiling Upwelling Case
Replies: 6
Views: 4153

Re: Problems compiling Upwelling Case

You appear to have a directory name with spaces (/cygdrive/c/Program Files/AMD APP/bin/x86) on your path. Bad idea. The cure is to add an entry like this to your mount table: C:/Program Files on /prog type ntfs (binary,user) That way, Cygwin will convert the above path to /prog/AMD APP/bin/x86 at st...
by m.hadfield
Wed Mar 25, 2015 8:31 pm
Forum: ROMS Installation
Topic: Problems compiling Upwelling Case
Replies: 6
Views: 4153

Re: Problems compiling Upwelling Case

What detraceyb says. You did download using Cygwin tools, didn't you? Also, you don't say what netCDF packages you installed, but these days you should use the ones available through Cygwin setup. If you're using Cygwin, you can save yourself a lot of grief by using Cygwin all the way. That, plus on...
by m.hadfield
Fri Mar 20, 2015 4:34 am
Forum: ROMS Discussion
Topic: i have a question
Replies: 11
Views: 2395

Re: i have a question

Or if the data are supposed to repeat year on year, you could add a cycle_length attribute to the zeta_west variable.
by m.hadfield
Wed Mar 18, 2015 10:09 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

I think the names you mention are commands (or maybe packages) that were needed during the transition from GCC 3.x to GCC 4.x, to select version 4 instead of version 3. GCC 4.x is the default now. If you install Cygwin and ensure the following packages are selected (they are currently at version 4.9...
by m.hadfield
Wed Mar 11, 2015 4:37 am
Forum: ROMS Tools and Techniques
Topic: the depth of rho points for ROMS
Replies: 2
Views: 57811

Re: the depth of rho points for ROMS

What Hernan said, but do remember that
  • ROMS levels are numbered from the bottom to the top; and
  • The ROMS s coordinate is -1 at z=-h and 0 at z-zeta.
I periodically confuse myself by forgetting that s is negative!
by m.hadfield
Tue Feb 17, 2015 9:14 pm
Forum: User Applications
Topic: Segmentation fault at the start
Replies: 7
Views: 4005

Re: Segmentation fault at the start

I suggest you get into read_fltpar with a debugger or (my choice) add some WRITE statements. It would be helpful if your compiler told you the line number at which the error occurred. Most compilers can be persuaded to do this. For Gfortran (on most platforms) you just need to set the USE_DEBUG make...
by m.hadfield
Thu Dec 04, 2014 9:37 pm
Forum: Job Opportunities
Topic: ROMS numerical modeller, NIWA New Zealand
Replies: 0
Views: 2332

ROMS numerical modeller, NIWA New Zealand

Based in Wellington, New Zealand Permanent, full-time NIWA is a dynamic research organisation whose purpose is to enhance the economic value and sustainable management of New Zealand's aquatic resources and environments, to provide understanding of climate and the atmosphere and increase resilience...
by m.hadfield
Tue Nov 18, 2014 9:33 pm
Forum: ROMS Bugs
Topic: Lnudging logic
Replies: 1
Views: 1836

Lnudging logic

The code to set the Lnudging switch for each grid in inp_par.F (lines 853-863) is #ifdef SOLVE3D IF (LnudgeM3CLM(ng).or. & & LnudgeM3CLM(ng).or. & & ANY(LnudgeTCLM(:,ng))) THEN Lnudging(ng)=.TRUE. END IF #else IF (LnudgeM2CLM(ng)) THEN Lnudging(ng)=.TRUE. END IF #endif At line 854, shouldn't that be...
by m.hadfield
Thu Oct 30, 2014 3:56 am
Forum: ROMS Bugs
Topic: Problem with compact tracer Rad + Nud boundaries
Replies: 2
Views: 2093

Re: Problem with compact tracer Rad + Nud boundaries

Hang on, the fix can be simpler than that, just copy the value of the boundary structure's acquire field along with the others: #ifdef SOLVE3D ! ! If processing tracers and last standard input entry (Icont=0), set ! unspecified tracer values to the last tracer entry. ! IF ((iTrcStr.gt.0).and.(iTrcEn...
by m.hadfield
Thu Oct 30, 2014 3:35 am
Forum: ROMS Bugs
Topic: Problem with compact tracer Rad + Nud boundaries
Replies: 2
Views: 2093

Problem with compact tracer Rad + Nud boundaries

In a post back in April... https://www.myroms.org/forum/viewtopic.php?f=19&t=3326&hilit=compact ...I reported a problem when radiative+nudging boundary conditions were specified for Fennel biological tracers using the compact specification, for example: LBC(isTvar) == RadNud RadNud RadNud RadNud \ !...
by m.hadfield
Fri Oct 03, 2014 12:49 am
Forum: ROMS Ecosystem
Topic: PhyIS units in Fennel
Replies: 5
Views: 3346

Re: PhyIS units in Fennel

I agree. I noticed this a month ago and intended to report it, but never got around to it. :(
by m.hadfield
Wed Oct 01, 2014 8:53 pm
Forum: ROMS Installation
Topic: make file problem
Replies: 8
Views: 6176

Re: make file problem

You don't need to edit the makefile. You can override the NC_CONFIG make variable by setting an environment variable with the same name before running make, eg:

Code: Select all

export NC_CONFIG=nf-config
Perhaps the make variable should now be renamed NF_CONFIG and point to nf-config by default.
by m.hadfield
Sun Sep 07, 2014 9:41 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Hi Mark and Bene, Unless things have changed, the NC_CONFIG macro is not very smart, and doesn't actually search for installed versions of NetCDF...it just assumes the netCDF files are in the location associated with the NC_CONFIG macro. Thus, if you have multiple netCDF installations, or have just...
by m.hadfield
Fri Sep 05, 2014 12:43 am
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Good :D , but you shouldn't need to define NETCDF_INCDIR if NC_CONFIG is set correctly.
by m.hadfield
Fri Aug 01, 2014 2:17 am
Forum: ROMS Bugs
Topic: Why floats solution behave with anti-parallel speed-up?
Replies: 5
Views: 2402

Re: Why floats solution behave with anti-parallel speed-up?

AlexisEspinosa wrote:If a particle leaves the partition domain to go into another, then the particle information would be sent into the receiving partition.
I think this is the tricky bit. :wink:
by m.hadfield
Fri Aug 01, 2014 1:12 am
Forum: ROMS Bugs
Topic: Why floats solution behave with anti-parallel speed-up?
Replies: 5
Views: 2402

Re: Why floats solution behave with anti-parallel speed-up?

Is OpenMP an option for you? In my experience, this is much better for parallel runs with floats than MPI. I presume this is because the overhead that Kate describes is absent or greatly reduced.
by m.hadfield
Thu Jul 24, 2014 8:44 pm
Forum: ROMS Adjoint
Topic: TLM: forrtl: severe(174): SIGSEGV, segmentation fault occur
Replies: 4
Views: 3015

Re: TLM: forrtl: severe(174): SIGSEGV, segmentation fault oc

I think it's crashing at some code in distribute.f90 (is 2674 the line number??), which is called from some code in wrt_gst.f90 (line 186??). I would attack this by inserting WRITE statements at the relevant locations to print out relevant variables, rebuilding and rerunning (repeat as necessary). I...
by m.hadfield
Wed Jul 09, 2014 10:47 pm
Forum: ROMS Discussion
Topic: roms river temperature problem
Replies: 7
Views: 2118

Re: roms river temperature problem

When you set LtracerSrc to false, what is your TS advection scheme? Sometimes TS_U3HADVECTION, sometimes TS_MPDATA, but I may have to back down on my reassurances about LtracerSrc = F. As I said, I've used this setting before now with no problems I have been aware of, but right I'm now looking at a...
by m.hadfield
Tue Jul 08, 2014 12:46 am
Forum: ROMS Discussion
Topic: roms river temperature problem
Replies: 7
Views: 2118

Re: roms river temperature problem

You have to set those LtracerSrc to True and provide tracer values for the incoming river flow. Otherwise you have a "downwind" advection scheme, known to be unstable. The only time it makes sense to turn LtracerSrc to False is on outflow from the domain (which could argue for LtracerSrc to be on f...
by m.hadfield
Tue Jul 01, 2014 3:32 am
Forum: ROMS Discussion
Topic: Direction of swflux
Replies: 0
Views: 985

Direction of swflux

Surface tracer fluxes in ROMS are stored in FORCES(ng)%stflx, with the convention that this is positive down , i.e. that a positive flux causes the amount of the tracer in the water column to increase. (Incidentally, the same is true of momentum fluxes: a positive value of sustr, say, tends to accel...
by m.hadfield
Fri Jun 27, 2014 2:24 am
Forum: ROMS Bugs
Topic: nesting issues
Replies: 6
Views: 2868

Re: nesting issues

My voice may not count for much, but I intend shortly to get into serious use of the nested ROMS (having been forced to abandon such an attempt about a year ago because of a looming project deadlines and the threat to my mental health--I am not entirely joking). I would very much like to see John an...
by m.hadfield
Tue Apr 15, 2014 4:42 am
Forum: ROMS Bugs
Topic: Problem with compact Fennel Rad+Nud boundaries
Replies: 1
Views: 1459

Re: Problem with compact Fennel Rad+Nud boundaries

I recently set up a simulation with the simple, 7-component Fennel model and--being an adventurous but trusting soul--specified Rad+Nud boundary conditions all round with the compact form, thus: LBC(isTvar) == RadNud RadNud RadNud RadNud \ ! idbio(*) Hmmm. I wonder if the trailing backslash on that...
by m.hadfield
Tue Apr 15, 2014 4:13 am
Forum: ROMS Bugs
Topic: Problem with compact Fennel Rad+Nud boundaries
Replies: 1
Views: 1459

Problem with compact Fennel Rad+Nud boundaries

These days, boundary conditions for biological tracers (Fennel model) are set in a file like ROMS/External/bio_Fennel.in, which has the following comment ! NOTICE: It is possible to specify the lateral boundary conditions for ! ====== all biological tracers in a compact form with a single entry. ! I...
by m.hadfield
Mon Apr 07, 2014 2:07 am
Forum: ROMS Problems
Topic: Error while processing Climatology multi-files:
Replies: 8
Views: 3614

Re: Error while processing Climatology multi-files:

Thank you very much for your reply,kunlv! The log file include all the info ROMS output.I am confused of the model blowing up. So am I, but can we please be clear about the status of the error you originally pointed out? On my reading of the log file you have asked ROMS to read temperature and sali...
by m.hadfield
Thu Apr 03, 2014 8:45 pm
Forum: ROMS Bugs
Topic: Beware of netCDF STRINGs
Replies: 6
Views: 4225

Beware of netCDF STRINGs

This isn't actually a ROMS bug at all (or even a picture of one) but for 6 hours on Wednesday I thought it was. I ran into a problem where ROMS was not reading the units attribute of a time variable in an input netCDF file. In fact it wasn't correctly reading any string attributes at all. The files ...
by m.hadfield
Mon Mar 17, 2014 8:42 pm
Forum: ROMS Bugs
Topic: OpenMP problem with restart from file
Replies: 4
Views: 2332

Re: OpenMP problem with restart from file

Thanks, Hernan!
by m.hadfield
Thu Mar 13, 2014 8:46 pm
Forum: ROMS Tools and Techniques
Topic: Tools for generating ATLANTIS flux data from ROMS output?
Replies: 0
Views: 917

Tools for generating ATLANTIS flux data from ROMS output?

ATLANTIS is a spatially compartmentalised ecosystem model (Link et al 2010; van Putten et al. 2013) that requires data on time-varying horizontal and vertical fluxes between the compartments from a hydrodynamic model like ROMS or HYCOM. The preparation of the fluxes is conceptually simple (provided ...
by m.hadfield
Fri Mar 07, 2014 1:15 am
Forum: ROMS Bugs
Topic: OpenMP problem with restart from file
Replies: 4
Views: 2332

Re: OpenMP problem with restart from file

See also the discussion on this thread:

viewtopic.php?t=3265
by m.hadfield
Thu Mar 06, 2014 9:16 pm
Forum: ROMS Problems
Topic: Inconsistent timestep reporting after restart under OpenMP?
Replies: 4
Views: 1883

Re: Inconsistent timestep reporting after restart under Open

Yes, MPI does work and is the best choice for most situations. OpenMP is generally not used as much and is therefore less well-tested. However OpenMP is much faster than MPI for floats simulations, in my experience. I don't think this bug will be too hard to fix, but don't have time to look at it fu...
by m.hadfield
Mon Mar 03, 2014 5:01 am
Forum: ROMS Problems
Topic: Inconsistent timestep reporting after restart under OpenMP?
Replies: 4
Views: 1883

Re: Inconsistent timestep reporting after restart under Open

It's a bug in the current ROMS when restarting under OpenMP, not specific to any specific compiler or platform. See this thread https://www.myroms.org/forum/viewtopic.php?f=19&t=3260 AS far as I am aware, there has been no solution posted. You may be able to work around it by reverting to an earlier...
by m.hadfield
Tue Feb 25, 2014 1:22 am
Forum: ROMS Discussion
Topic: Input Sources/Sinks forcing file
Replies: 4
Views: 1460

Re: Input Sources/Sinks forcing file

antoinemarie wrote:For instance, I make a source, and I want this source has the same temperature has a particular point of my model.
Is the particular point the point at which the source is being applied? If so, you can just set LtraceSrc(1) to F in the input file.
by m.hadfield
Mon Feb 24, 2014 10:35 pm
Forum: ROMS Bugs
Topic: OpenMP problem with restart from file
Replies: 4
Views: 2332

Re: OpenMP problem with restart from file

A couple of extra data points: The problem I reported also occurs in the UPWELLING test case. It's not specific to float simulations (though float simulations are where I tend to use OpenMP). Contrary to what I said earlier, it does occur with Linux/Gfortran, as well as Cygwin/Gfortran and AIX/xlf.
by m.hadfield
Mon Feb 24, 2014 9:01 pm
Forum: ROMS Bugs
Topic: OpenMP problem with restart from file
Replies: 4
Views: 2332

OpenMP problem with restart from file

Attached are output files from two consecutive runs of the FLT_TEST case. In both cases ROMS (latest source) is run under OpenMP with 1x2 tiles, using Gfortran under Cygwin. The first run (rom001.log) proceeds as it should: the model is initialised analytically (NRREC=0) and runs to 1152 time steps,...
by m.hadfield
Sun Jan 12, 2014 8:11 pm
Forum: ROMS Adjoint
Topic: TLM: forrtl: severe(174): SIGSEGV, segmentation fault occur
Replies: 4
Views: 3015

Re: TLM: forrtl: severe(174): SIGSEGV, segmentation fault oc

wangzc wrote:Anyone know Why?
Not I. I suggest you build ROMS with the USE_DEBUG variable set to on (in build.bash) and try again. This *might* give you some useful extra information.
by m.hadfield
Wed Dec 04, 2013 3:25 am
Forum: ROMS Bugs
Topic: There's always a 1st time...1st time...1st time...1st time
Replies: 1
Views: 1256

There's always a 1st time...1st time...1st time...1st time

In a 4-thread OpenMP run of the UPWELLING case I'm getting the header line for the time stepping (the one that begins with "STEP") printed four times. The first occurrence is where it should be and the remaining 3 occur at irregular intervals, eg. STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG...
by m.hadfield
Thu Nov 21, 2013 2:21 am
Forum: ROMS Bugs
Topic: Initialisation of ANANAME
Replies: 3
Views: 1950

Re: Initialisation of ANANAME

Indeed but various compilers behave not the same in different computers. Therefore, I initialize it like this because debuggers will add junk characters if it is not initialized. This is primarily done as a safeguard to insure that file names are not padded with non blank characters. I have very ba...
by m.hadfield
Wed Nov 20, 2013 10:42 pm
Forum: ROMS Problems
Topic: How to force the model after QuickScat?
Replies: 2
Views: 1451

Re: How to force the model after QuickScat?

Sorry to revive an old thread, but it seems relevant. I want a reasonably high resolution (0.5 deg) surface stress dataset with global or Pacific Ocean coverage continuing to the present, more or less. (Aren't we all?) CCMP, as suggested by saulo above, does seem to be a good product, but currently ...
by m.hadfield
Mon Nov 18, 2013 10:29 pm
Forum: ROMS Bugs
Topic: Initialisation of ANANAME
Replies: 3
Views: 1950

Initialisation of ANANAME

In ROMS/Modules/mod_ncparam.F at line 487, ANANAME is declared with dimension 39 character (len=256), dimension(39) :: ANANAME but at lines 715-719 only the first 38 elements are initialised: DO i=1,38 DO j=1,LEN(ANANAME(1)) ANANAME(i)(j:j)=' ' END DO END DO This can lead to platform-dependent probl...
by m.hadfield
Mon Nov 04, 2013 9:14 pm
Forum: ROMS Bugs
Topic: Compilation errors in check_multifile
Replies: 3
Views: 2503

Re: Compilation errors in check_multifile

A minor remaining issue: looking at this...

https://www.myroms.org/svn/src/trunk/RO ... ultifile.F

...the variable lstr is still undeclared, and this is not picked up by the compiler because there is still no "implicit none".
by m.hadfield
Thu Oct 31, 2013 4:44 am
Forum: ROMS Bugs
Topic: Compilation errors in check_multifile
Replies: 3
Views: 2503

Compilation errors in check_multifile

With the multifile-checking code introduced a couple of days ago I'm getting compilation errors in check_multifile when the model is built in a configuration that requires the reading of forcing files: check_multifile.f90:68.33: ncname=BRY(ng)%files(Fcount) 1 Warning: Legacy Extension: REAL array in...
by m.hadfield
Mon Sep 23, 2013 12:57 am
Forum: ROMS Bugs
Topic: mpi and gfortran
Replies: 11
Views: 5432

Re: mpi and gfortran

The "n" in "build.bash -j n" has nothing to do with the number of processes in which you intend to run the model. It merely sets the number of processes (threads) that Gnu make can call on when it is compiling and building the model. There are two quite different concepts being referred to here. Par...
by m.hadfield
Wed Sep 18, 2013 12:45 am
Forum: ROMS Bugs
Topic: mpi and gfortran
Replies: 11
Views: 5432

Re: mpi and gfortran

Just backing up Kate: I have run ROMS+MPI+Gfortran using MPICH2 and OpenMPI at different times, no worries. Using mpif90 is definitely recommended: the mpif90 script ensures that environment variables & libraries are correctly set up for compiling and linking. It doesn't handle run-time environment ...
by m.hadfield
Fri Jun 07, 2013 1:07 am
Forum: ROMS Bugs
Topic: Possibly 3 nesting-related bugs
Replies: 16
Views: 5389

Re: Possibly 3 nesting-related bugs

Thanks for all your effort on this, Hernan. It's impressive looking stuff, but quite complicated, obviously.
by m.hadfield
Tue May 28, 2013 5:39 am
Forum: ROMS Bugs
Topic: The index of I,J in nesting.F (version 3.6) may be wrong.
Replies: 5
Views: 2189

Re: The index of I,J in nesting.F (version 3.6) may be wrong

The dogbone composite-grid case appears to work OK.
by m.hadfield
Tue May 28, 2013 1:46 am
Forum: ROMS Bugs
Topic: The index of I,J in nesting.F (version 3.6) may be wrong.
Replies: 5
Views: 2189

Re: The index of I,J in nesting.F (version 3.6) may be wrong

I have updated my code with this fix, but the dogbone-refined case is still not working properly. I have attached a couple of videos (gzipped AVIs) showing zeta in the outer and inner domains. In the outer domain, the positive-zeta wave moves in from the LH boundary and approaches the constriction, ...
by m.hadfield
Mon May 27, 2013 12:57 am
Forum: ROMS Problems
Topic: openmp, PBS and linking of netcdf library.
Replies: 2
Views: 1631

Re: openmp, PBS and linking of netcdf library.

Well, I guess the obvious thing to check is whether LD_LIBRARY_PATH is set correctly for ROMS when it is running inside the shell script. I haven't used PBS, but my impression is that batch scripting environments generally don't pass environment variables from the caller unless you specifically tell...
by m.hadfield
Mon May 27, 2013 12:53 am
Forum: ROMS Bugs
Topic: The index of I,J in nesting.F (version 3.6) may be wrong.
Replies: 5
Views: 2189

Re: The index of I,J in nesting.F (version 3.6) may be wrong

I don't know about that, but I do know that when I run the dogbone-refined case, the water level in the refined grid trends steadily downwards in a completely unphysical way. Perhaps these two problems are related.
by m.hadfield
Mon May 13, 2013 3:48 am
Forum: User Applications
Topic: LTRANS: Larval TRANSport Lagrangian model
Replies: 39
Views: 33092

Re: LTRANS: Larval TRANSport Lagrangian model

I trust you are running with bound checking, as I suggested a few posts ago.

When adding a line of code changes the results, it usually means you are doing something a bit dodgy, and writing or reading outside the bounds of an array is definitely dodgy.
by m.hadfield
Mon May 13, 2013 1:27 am
Forum: User Applications
Topic: LTRANS: Larval TRANSport Lagrangian model
Replies: 39
Views: 33092

Re: LTRANS: Larval TRANSport Lagrangian model

It looks like a bit of digging into the particle initialisation code might not go amiss!
by m.hadfield
Thu May 09, 2013 10:15 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

How can I check if usr/local/bin subdirectory is on my path? It looks like this directory is on your path, as you can call nc-config and nf-config without including the full name (which is what you want to happen, and the reason why I asked about the path). So, as Kate says, something else is telli...
by m.hadfield
Wed May 08, 2013 9:19 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Hi PedroMarques The configure command you gave several posts back specified an installation prefix of /usr/local. Is that where you installed netCDF and netCDF-Fortran? If so, why is ROMS looking for netcdf.mod under /opt? (I myself don't have a Cygwin /opt directory. All user-installed software goe...
by m.hadfield
Tue May 07, 2013 9:41 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

I'm stumped. I suspect configure is failing the first time it tries to link Fortran and C code together. But I don't know why that would happen. You're on Cygwin, right? On Linux you probably wouldn't want "--disable-shared". You could sort out what's happening by trying to reproduce the command tha...
by m.hadfield
Sun Feb 24, 2013 9:42 pm
Forum: ROMS Tools and Techniques
Topic: Cross Shelf Model
Replies: 3
Views: 1929

Re: Cross Shelf Model

Reduce Lm in the input file to a smaller number. As Kate said, the minimum is probably 3; whatever, 1 is not permitted. Whatever value of Lm you choose, the UPWELLING simulation is homogeneous in the xi direction, so you can do your analyses on any slice
by m.hadfield
Tue Feb 12, 2013 1:42 am
Forum: ROMS Discussion
Topic: fast currents in my roms model
Replies: 10
Views: 3631

Re: fast currents in my roms model

An rx1 of 20 is too high. Somewhere in the vicinity of 5 to 8 should be OK. In my experience, the failure mode for large rx1 is that a large patch of the bottom layer decides, for no obvious reason, to move rapidly in one direction or other. This produces large velocities at the coastline, which cra...
by m.hadfield
Tue Feb 12, 2013 12:40 am
Forum: ROMS Discussion
Topic: fast currents in my roms model
Replies: 10
Views: 3631

Re: fast currents in my roms model

I believe you can get ROMS to output the surface stresses, which in your case should have been calculated by BULK_FLUXES. Do these look reasonable?
by m.hadfield
Thu Feb 07, 2013 8:16 pm
Forum: ROMS Installation
Topic: Compile ROMS problem via cygwin
Replies: 27
Views: 7838

Re: Compile ROMS problem via cygwin

Hi robjenkinsiii You could begin by reading all the posts in this thread. The linker is failing to find a netCDF Fortran routine, probably because the linker command is lacking a "-lnetcdff", and the most likely reason for that is that you have netcdf-4.x installed but have failed to define USE_NETC...
by m.hadfield
Tue Jan 29, 2013 9:24 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

I have not and I noticed this in your earlier posts. This might seem like a silly question (I'm very new to all of this), but does this require that I uninstall cygwin and reinstall with the appropriate packages or is there a simpler way to handle this? No you should not need to uninstall & reinsta...
by m.hadfield
Tue Jan 29, 2013 8:42 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Have you installed HDF5? It's available via the Cygwin setup utility. You need the hdf5 and libhdf5-devel packages, and also maybe libhdf5_7 (but I think that gets installed automatically with the other two.)
by m.hadfield
Wed Jan 23, 2013 9:34 pm
Forum: ROMS Bugs
Topic: PROBLEM INSTALLING ROMS IN WINDOWS 7
Replies: 1
Views: 1508

Re: PROBLEM INSTALLING ROMS IN WINDOWS 7

Hi jande023

Did you get this sorted out? I missed it back in November 2012.

Mark
by m.hadfield
Tue Jan 22, 2013 6:31 pm
Forum: ROMS Installation
Topic: Compile ROMS problem via cygwin
Replies: 27
Views: 7838

Re: Compile ROMS problem via cygwin

Hi Leo That's all as I expected. See the string that is returned by "nc-config --flibs" or "nf-config --flibs": -L/usr/local/lib -lnetcdff -lnetcdf -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl The ROMS build process needs to incorporate that string in the command used to link the ROMS e...
by m.hadfield
Mon Jan 21, 2013 8:27 pm
Forum: ROMS Discussion
Topic: How to add a 4-D variable into the Forcing file
Replies: 8
Views: 2919

Re: How to add a 4-D variable into the Forcing file

I have another potential use for a 4-D forcing field: to represent density of farmed mussels in order to calculate their effect on phytoplankton, nutrients, etc. The mussel density is a 3D (x,y,z) field that can vary in time.
by m.hadfield
Mon Jan 21, 2013 8:24 pm
Forum: ROMS Installation
Topic: Compile ROMS problem via cygwin
Replies: 27
Views: 7838

Re: Compile ROMS problem via cygwin

I think Mark's suggestion about adding the -lnetcdff library might have gotten lost in the noise. You have to do that. You can let nc-config(*) do that. You just need to ensure that nc-config is on the path and that USE_NETCDF4 is defined. Then the following lines (from the current CYGWIN_gfortran....
by m.hadfield
Thu Jan 17, 2013 9:28 pm
Forum: ROMS Installation
Topic: Compile ROMS problem via cygwin
Replies: 27
Views: 7838

Re: Compile ROMS problem via cygwin

Hello Mark Yes I´m using the netcdf-4.2.1.1 version and the netcdf-fortran-4.2 version. Anyway I guess my mistake is in here, I configured netcdf-4.2.1.1 with this: ./configure --prefix=/usr/local --disable-shared --enable-netcdf-4 --enable-dap --disable-dap-remote-tests and configured netcdf-fortr...
by m.hadfield
Wed Jan 16, 2013 8:33 pm
Forum: ROMS Discussion
Topic: What to correct to keep ROMS from blowing up?
Replies: 23
Views: 8845

Re: What to correct to keep ROMS from blowing up?

Personally, I would lay out the grid for an area like yours on a domain that's rectangular on a suitable (possibly rotated) map projection, with maybe some stretching towards the boundaries. I would do the whole thing in IDL (similar to Matlab) code. To my mind the benefit you're getting from warpin...
by m.hadfield
Wed Jan 16, 2013 8:22 pm
Forum: ROMS Installation
Topic: Compile ROMS problem via cygwin
Replies: 27
Views: 7838

Re: Compile ROMS problem via cygwin

Yes, Kate is on the right track. The command that triggers the error is /usr/bin/gfortran-4 -frepack-arrays -O3 -ffast-math /home/Usuario/roms/Projects/Upwelling/Build/esmf_roms.o /home/Usuario/roms/Projects/Upwelling/Build/master.o /home/Usuario/roms/Projects/Upwelling/Build/ocean_control.o /home/U...
by m.hadfield
Tue Jan 15, 2013 9:48 pm
Forum: ROMS Discussion
Topic: What to correct to keep ROMS from blowing up?
Replies: 23
Views: 8845

Re: What to correct to keep ROMS from blowing up?

There are holes (white patches) in the plot of barotropic time step limit. How do they arise?
by m.hadfield
Tue Jan 15, 2013 8:29 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Thanks for the follow-up, Leo :)
by m.hadfield
Mon Jan 14, 2013 3:56 am
Forum: ROMS Installation
Topic: Error compiling INLET_TEST Case
Replies: 6
Views: 3309

Re: Error compiling INLET_TEST Case

OK. If you look at ROMS/Functionals/ana_grid.h, you'll see a block of code that looks like the following (with a lot of lines in the middle deleted) #if defined BASIN Xsize=3600.0E+03_r8 Esize=2800.0E+03_r8 depth=5000.0_r8 f0=1.0E-04_r8 beta=2.0E-11_r8 ... #elif defined WINDBASIN Xsize=2000.0_r8*REA...
by m.hadfield
Mon Jan 14, 2013 1:56 am
Forum: ROMS Discussion
Topic: What to correct to keep ROMS from blowing up?
Replies: 23
Views: 8845

Re: What to correct to keep ROMS from blowing up?

A maximum barotropic Courant number of 0.62 is fine. (I find 0.8 is usually optimal for robustness and performance.) I can't see anything wrong with those boundary conditions, with temperatures in the range 0-27 and salinities in the range 0-36. I suspect the 0 values shouldn't be in there, but I do...
by m.hadfield
Mon Jan 14, 2013 1:03 am
Forum: ROMS Installation
Topic: Error compiling INLET_TEST Case
Replies: 6
Views: 3309

Re: Error compiling INLET_TEST Case

I have no trouble compiling INLET_TEST with an up-to-date copy of the trunk code.

Did you clear out all the files generated during your first attempt before re-trying?
by m.hadfield
Sun Jan 13, 2013 10:35 pm
Forum: ROMS Installation
Topic: Compile ROMS problem via cygwin
Replies: 27
Views: 7838

Re: Compile ROMS problem via cygwin

A quick Google search on "bad reloc address" indicates that this message is usually preceded by other error messages, eg undefined reference, that give you a better indication of the problem. Please, if you can, reply on the forum attaching the *entire* output of your ROMS build, or at least the las...
by m.hadfield
Thu Jan 10, 2013 1:14 am
Forum: ROMS Installation
Topic: Compile ROMS problem via cygwin
Replies: 27
Views: 7838

Re: Compile ROMS problem via cygwin

Hello Everyone I´m installing ROMS via CYGWIN. I´ve followed the instructions of the Tutorial for Windows and I´ve got to the Compile ROMS process in order to get the executable oceanS file; when I do so, I get this message: ./build.bash: line 40: $'\r': command not found ./build.bash: line 43: $'\...
by m.hadfield
Tue Jan 08, 2013 1:26 am
Forum: User Applications
Topic: LTRANS: Larval TRANSport Lagrangian model
Replies: 39
Views: 33092

Re: LTRANS: Larval TRANSport Lagrangian model

Rebuild with bounds-checking enabled, maybe try a few different compilers, to establish the statement and array reference that triggers the bounds violation. Then use your preferred debugging technique (mine is WRITE statements inserted into the code) to establish why this is happening. This being l...
by m.hadfield
Sun Dec 23, 2012 8:42 pm
Forum: ROMS Installation
Topic: how to install roms on windows seven?
Replies: 1
Views: 1737

Re: how to install roms on windows seven?

There's just been a long discussion on installing netCDF on Cygwin on this thread: https://www.myroms.org/forum/viewtopic.php?f=31&t=2766 I have a couple of comments. The first is that it is impossible to determine how a make check failure occurred without the full output. Perhaps you could attach i...
by m.hadfield
Sun Dec 23, 2012 8:35 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Thanks, Leo.

It failed during an OpenDAP test with a "Cannot locate test server" error. However it had already run a series of OpenDAP tests. This is probably just an isolated connectivity problem. It is safe to ignore it and install netCDF.
by m.hadfield
Fri Dec 21, 2012 2:55 am
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Thanks for those warnings, Chris.

Remember that the ROMS makefile uses a variable called NC_CONFIG to find nc-config. The default is "nc-config", but you can override it via an environment variable.
by m.hadfield
Thu Dec 20, 2012 7:05 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Incidentally, both Kate and I have said on this thread that if you are installing the netCDF C and Fortran libraries separately (which is how they're packaged nowadays) then the command that the ROMS make file needs to call to determine the location of libraries and include files is nf-config, not n...
by m.hadfield
Thu Dec 20, 2012 6:58 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Hi Leo

"make check" worked fine for me once I'd worked around the #elifdef bug.

I can't tell the cause of the error with the output you've shown. Could you please include the entire make check output as an attachment, or email it to me separately.

Mark
by m.hadfield
Tue Dec 18, 2012 7:19 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Hi Leo The compilation problem occurs because the file in question, oc/ocinternal.c, contains the preprocessor directive "elifdef", which is not valid. Here is the offending block of code /* Note: TMPPATH must end in '/' */ #ifdef __CYGWIN__ #define TMPPATH1 "/cygdrive/c/temp/" #define TMPPATH2 "./"...
by m.hadfield
Tue Dec 18, 2012 7:02 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Hi Leo

I get the same error with netdf-4.2.1.1. It also occurs with 4.2.1. I suggest you install netcdf-4.2. I will check this problem out further and report it to the netCDF developers.

"nice" is a utility that runs executables at a reduced priority.

Mark
by m.hadfield
Mon Dec 17, 2012 8:48 pm
Forum: ROMS Bugs
Topic: Out-of-bounds error in mod_ncparam.F, variable idTTav
Replies: 1
Views: 1290

Out-of-bounds error in mod_ncparam.F, variable idTTav

When I run the UPWELLING case with ECOSIM defined and with bounds-checking enabled, I get the following error 0: Subscript out of range for array idttav (mod_ncparam.f90: 1938) subscript=3, lower bound=1, upper bound=2, dimension=1 The error arises in this section of code: SELECT CASE (Vinfo(1)) CAS...
by m.hadfield
Thu Dec 13, 2012 8:20 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

Hi lalvarez Please don't hesitate to ask for further help if you need it. A few messages back you referred to an error you got from the configure command for the netCDF-Fortran package (because you misunderstood a comment by Kate and substituted nf-config for nc-config). But you should have only bee...
by m.hadfield
Thu Dec 13, 2012 8:00 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

...Anyway "$(nc-config --libs)" is not the correct syntax. It is saying that whole expression is a variable of some kind due to the "$". The configure command that I suggested, namely CC=gcc FC=gfortran LIBS="$(nc-config --libs)" CPPFLAGS="-I$(nc-config --includedir)" nice ./configure --disable-sha...
by m.hadfield
Thu Dec 13, 2012 12:59 am
Forum: ROMS Discussion
Topic: Question about particle tracking
Replies: 17
Views: 3661

Re: Question about particle tracking

Thanks. :)
by m.hadfield
Wed Dec 12, 2012 1:42 am
Forum: ROMS Discussion
Topic: Question about particle tracking
Replies: 17
Views: 3661

Re: Question about particle tracking

Hi Kate

Can you comment on the relationship between the Github link you gave

https://github.com/TRACMASS/

and this one

http://tracmass.org/

which has an SVN repository

http://svn.tracmass.org/trunk

Mark
by m.hadfield
Tue Dec 11, 2012 8:40 pm
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

What Kate says. But what may not be immediately clear from my last post is that the files for the C and Fortran libraries are unpacked into different directories, because the tar archives contain subdirectories that match the archive names (without the .tar.gz bit). This is why the 4th command in ea...
by m.hadfield
Tue Dec 11, 2012 2:58 am
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

OK, you install the C library then the Fortran library. The C library optionally depends on several other prerequisite packages. If you want to be able to produce files in netCDF-4 format then you need HDF5. If you want to use OpenDAP then you need Curl. Also, in recent versions of netCDF, building ...
by m.hadfield
Tue Dec 11, 2012 12:46 am
Forum: ROMS Installation
Topic: Netcdf downloading via Cygwin
Replies: 64
Views: 288371

Re: Netcdf downloading via Cygwin

I suggest you download the netCDF source code from the Unidata FTP site with your Web browser. You will need the C and Fortran libraries: ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.2.1.1.tar.gz ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.2.tar.gz If you want any help regarding prerequ...
by m.hadfield
Sun Dec 09, 2012 9:41 pm
Forum: ROMS Installation
Topic: Customizing the build script
Replies: 10
Views: 6026

Re: Customizing the build script

Hi ming

I have replied on the other thread relating to this issue.

Mark
by m.hadfield
Sun Dec 09, 2012 9:40 pm
Forum: ROMS Installation
Topic: makefile:32: error
Replies: 3
Views: 2296

Re: makefile:32: error

With my up-to-date installation of Cygwin, The make version is 3.82.90. The version-testing code in the make file is not very clever: it doesn't find "3.82.90" in the list of acceptable make versions, so it aborts. In fact, this version has no problems in building ROMS. Suggested solutions: either c...
by m.hadfield
Wed Nov 28, 2012 2:36 am
Forum: ROMS Information
Topic: NTSHIS??
Replies: 4
Views: 2460

Re: NTSHIS??

My advice is to follow Kate's first suggestion: run your model in segments; use a shell or Python script to generate the input files and scripts required.
by m.hadfield
Thu Oct 18, 2012 2:01 am
Forum: ROMS Problems
Topic: Oscillation in bottom stress for GLS_MIXING plus SSW_BBL
Replies: 6
Views: 2148

Re: Oscillation in bottom stress for GLS_MIXING plus SSW_BBL

Um, I think you're right! And setting Pwave_bot to 8s suppresses the oscillation.

Thank you. :oops:
by m.hadfield
Wed Oct 17, 2012 12:40 am
Forum: ROMS Problems
Topic: Oscillation in bottom stress for GLS_MIXING plus SSW_BBL
Replies: 6
Views: 2148

Re: Oscillation in bottom stress for GLS_MIXING plus SSW_BBL

You only need Pwave_bot if SEDIMENT is enabled. The original case where I saw this behaviour did have sediment, but I stripped it out in order to simplify things.
by m.hadfield
Mon Oct 15, 2012 11:01 pm
Forum: ROMS Problems
Topic: Oscillation in bottom stress for GLS_MIXING plus SSW_BBL
Replies: 6
Views: 2148

Re: Oscillation in bottom stress for GLS_MIXING plus SSW_BBL

Also attached FYI is the input file (which includes the GLS model coefficients)
by m.hadfield
Thu Oct 04, 2012 6:53 pm
Forum: ROMS Problems
Topic: Some problems about using MPICH2 compile ROMS
Replies: 8
Views: 2442

Re: Some problems about using MPICH2 compile ROMS

Hi s091334 I think your problem is with the -fno-second-underscore option. In the past I have recommended using this for building ROMS. (It controls symbol name-mangling. Try a Google search on "g95 -fno-second-underscore Hadfield" for some history.) However this recommendation comes with the provis...
by m.hadfield
Wed Sep 26, 2012 2:27 am
Forum: ROMS Problems
Topic: Some problems about using MPICH2 compile ROMS
Replies: 8
Views: 2442

Re: Some problems about using MPICH2 compile ROMS

I was inspired by your question to take another look at the status of MPI on my system (PC with dual-core Intel, Windows 7, Cygwin). I have MPICH2 1.4.1p1 installed. I did this by building from source. The commands were CC=gcc FC=gfortran ./configure --prefix=/usr/local nice make nice make install I...
by m.hadfield
Wed Sep 26, 2012 1:32 am
Forum: ROMS Problems
Topic: Some problems about using MPICH2 compile ROMS
Replies: 8
Views: 2442

Re: Some problems about using MPICH2 compile ROMS

This is more a MPICH2 on Windows problem than a ROMS problem. There might be an MPICH2 forum somewhere wher people could help you. That said, I have run MPI on Cygwin successfully in the past (though for the past year or two it seems to have been broken) so I can offer a few pieces of advice. The fi...
by m.hadfield
Thu Sep 20, 2012 5:33 am
Forum: ROMS Problems
Topic: Oscillation in bottom stress for GLS_MIXING plus SSW_BBL
Replies: 6
Views: 2148

Oscillation in bottom stress for GLS_MIXING plus SSW_BBL

Hello colleagues Preface: I don't know how big a problem the following really is in practice, but I've noticed some curious & spurious behaviour, so I thought I'd let the community know about it. Short version: A toy case with oscillating tidal flow shows pronounced, rapid oscillations in bottom str...
by m.hadfield
Sat Jun 02, 2012 4:57 am
Forum: ROMS Discussion
Topic: Add a passive tracer to the model which has run for one year
Replies: 5
Views: 2083

Re: Add a passive tracer to the model which has run for one

A couple more comments: If the initial dye field is simple, you can set it with ana_passive.h. Just #define ANA_PASSIVE in the header file, set DSTART in the input file to the time at which you want the dye introduced and set NRREC to 0. You will not get a perfect restart in this case: the model wil...
by m.hadfield
Thu May 10, 2012 1:39 am
Forum: ROMS Bugs
Topic: Station files: fill values but not _FillValue attribute
Replies: 3
Views: 1530

Re: Station files: fill values but not _FillValue attribute

Hi again Hernan At the moment, values of 1.E37 are written to lon_rho/x_rho, lat_rho/y_rho, h and zeta for points in the land mask. Are you saying that this should not happen? I am inclined to agree. However if it is happening, then it is appropriate to mark them as fill values via that variables _F...
by m.hadfield
Wed May 09, 2012 3:24 am
Forum: ROMS Bugs
Topic: Station files: fill values but not _FillValue attribute
Replies: 3
Views: 1530

Station files: fill values but not _FillValue attribute

OK, it's a bit of a stretch to call this a bug report, more a suggestion for a minor improvement. When a station is inside the land mask (or just outside it in the case of velocity variables) values of 1.0E37 get written to the station file. The netCDF variables in which these values are written inc...
by m.hadfield
Fri Apr 27, 2012 7:33 am
Forum: ROMS Bugs
Topic: Incorrect nesting of OpenMP directives: FLOAT_VWALK
Replies: 11
Views: 4999

Re: Incorrect nesting of OpenMP directives: FLOAT_VWALK

Hi Hernan The problem with ana_psource isn't a big issue for me and I know you are busy on other things, but I just can't let these things go unsolved! I think the issue is with the BARRIER directives inside ana_psource.h. According to IBM, the rules are Rules A BARRIER directive binds to the closes...
by m.hadfield
Thu Apr 26, 2012 9:37 pm
Forum: ROMS Bugs
Topic: Incorrect nesting of OpenMP directives: FLOAT_VWALK
Replies: 11
Views: 4999

Re: Incorrect nesting of OpenMP directives: FLOAT_VWALK

Yes, that works: it runs to completion with AIX/xlf+OpenMP, and gives identical results to a serial run. Thank you!
by m.hadfield
Thu Apr 26, 2012 3:40 am
Forum: ROMS Bugs
Topic: Incorrect nesting of OpenMP directives: FLOAT_VWALK
Replies: 11
Views: 4999

Re: Incorrect nesting of OpenMP directives: FLOAT_VWALK

I have done a little more investigation and now think that The use of the OpenMP SINGLE directive in ROMS is incorrect. The xlf compiler on AIX is correct in recognising this. The PGI and Gfortran compilers are incorrect in failing to do so. Consider the following OpenMP test program: module openmp ...
by m.hadfield
Fri Apr 20, 2012 4:36 am
Forum: ROMS Bugs
Topic: Incorrect nesting of OpenMP directives: FLOAT_VWALK
Replies: 11
Views: 4999

Re: Incorrect nesting of OpenMP directives: FLOAT_VWALK

So far, my conclusions for the floats vertical-walk code are the same as the one drews reported for the river source: There are no obvious violations of the OpenMP rules The simulation runs and appears to give correct results if you remove the PARALLEL directives in main3d Perhaps it's an AIX compil...
by m.hadfield
Wed Apr 18, 2012 8:17 pm
Forum: ROMS Bugs
Topic: Incorrect nesting of OpenMP directives: FLOAT_VWALK
Replies: 11
Views: 4999

Re: Incorrect nesting of OpenMP directives: FLOAT_VWALK

Thanks, Hernan. I'll look into it.
by m.hadfield
Wed Apr 18, 2012 4:41 am
Forum: ROMS Bugs
Topic: Incorrect nesting of OpenMP directives: FLOAT_VWALK
Replies: 11
Views: 4999

Re: Incorrect nesting of OpenMP directives: FLOAT_VWALK

Incidentally, I also get the same error message when I run the RIVERPLUME1 test case in OpenMP mode on the IBM. (I checked this out because the problem reported in the previous thread was related to ana_psource.) As before, the simulation runs to completion with Linux/gfortran/OpenMP.
by m.hadfield
Tue Apr 17, 2012 5:27 am
Forum: ROMS Bugs
Topic: Incorrect nesting of OpenMP directives: FLOAT_VWALK
Replies: 11
Views: 4999

Incorrect nesting of OpenMP directives: FLOAT_VWALK

Did you know that a search for "1587-114 Incorrect nesting of OpenMP directives" on Google returns only one match, namely the following thread on the ROMS Forum https://www.myroms.org/forum/viewtopic.php?t=1714 Shortly there should be a second one! I have run into the same error message, this time i...
by m.hadfield
Sun Feb 26, 2012 10:03 pm
Forum: ROMS Installation
Topic: Build.bash architecture x86_64 error
Replies: 1
Views: 1412

Re: Build.bash architecture x86_64 error

You have added the -m64 flag to C and Fortran compiler options when building netCDF, but I see no sign that it has been used when building ROMS. That might be your problem.
by m.hadfield
Wed Feb 15, 2012 1:03 am
Forum: ROMS Problems
Topic: Post-compilation problems with ROMS
Replies: 6
Views: 2157

Re: Post-compilation problems with ROMS

Hi Liz You say you have netCDF libraries here? NETCDF_INCDIR ?= /opt/intelsoft/netcdf4/include NETCDF_LIBDIR ?= /opt/intelsoft/netcdf4/lib Then nc-config should be in /opt/intelsoft/netcdf4/bin. To help the ROMS make system find it, you can put that directory on the path or specify the following in ...
by m.hadfield
Wed Feb 08, 2012 2:54 am
Forum: ROMS Installation
Topic: Compiler warnings since upgrade
Replies: 7
Views: 2800

Re: Compiler warnings since upgrade

Yes. It can be adjointed. But we have several modules in ROMS/Nonlinear that are used in the ROMS/Utility directory. This includes the bc2d.F , bc3d.F , exchange_2d.F , exchage_3d.F , scale_omega , and so on. I don't understand why uv_rotate.F has to be different. This cross-directory references ar...
by m.hadfield
Wed Feb 08, 2012 1:35 am
Forum: ROMS Problems
Topic: Compilation Problem
Replies: 21
Views: 4416

Re: Compilation Problem

+1 to changing your own makefile. Probably better than moving source files.

It's getting off topic, I know, but I have had good results with using Mercurial to manage my copies of ROMS. However I haven't made a video about it.
by m.hadfield
Wed Feb 08, 2012 1:12 am
Forum: ROMS Problems
Topic: Compilation Problem
Replies: 21
Views: 4416

Re: Compilation Problem

Hi simion123... I've just noticed this thread, which deals with the same issue https://www.myroms.org/forum/viewtopic.php?f=31&t=2530 There Hernan answers the questions I posted in my previous message on the current thread. ...we have several modules in ROMS/Nonlinear that are used in the ROMS/Utili...
by m.hadfield
Tue Feb 07, 2012 1:30 am
Forum: ROMS Problems
Topic: Compilation Problem
Replies: 21
Views: 4416

Re: Compilation Problem

I just ran into the problem reported by Entrapmen (with the Gfortran linker). I fixed it by moving uv_rotate.F from ROMS/Nonlinear to ROMS/Utility. Then I read this thread :roll: Is there any reason why uv_rotate.F should be in ROMS/Nonlinear and not in ROMS/Utility? Could the other circular depende...
by m.hadfield
Fri Feb 03, 2012 1:03 am
Forum: ROMS Bugs
Topic: Declaration errors in wrt_his.F with SOLVE3D undefined
Replies: 1
Views: 1096

Declaration errors in wrt_his.F with SOLVE3D undefined

With the recent addition of rotated velocity I/O, a couple of minor declaration bugs were introduced into wrt_his.F when SOLVE3D is undefined: The following symbols are undeclared:
  • The integer tile
  • The subroutine uv_rotate2d
A corrected version of the file is attached.
by m.hadfield
Sun Jan 29, 2012 8:34 pm
Forum: ROMS Bugs
Topic: The perils of floating-point time-step arithmetic
Replies: 14
Views: 5106

Re: The perils of floating-point time-step arithmetic

A potentially attractive alternative would be to specify "dt" and fast-time step "dtfast", and let the model figure out the mode-splitting ratio within the code (along with a slight adjustment to "dtfast", so ndtfast*dtfast=dt made by the model via a simple algorithm described above). +1 to that. I...
by m.hadfield
Thu Jan 26, 2012 7:57 pm
Forum: ROMS Bugs
Topic: The perils of floating-point time-step arithmetic
Replies: 14
Views: 5106

Re: The perils of floating-point time-step arithmetic

shchepet wrote:Counters should always be of an integer type.
Quite right. The quick fix should do for now. If it doesn't (I have some runs with a much larger number of time steps) I'll send Hernan some code for all the different drivers.
by m.hadfield
Tue Jan 24, 2012 5:09 am
Forum: ROMS Bugs
Topic: The perils of floating-point time-step arithmetic
Replies: 14
Views: 5106

The perils of floating-point time-step arithmetic

I have a simulation with the non-linear, forward model driven by the M2 tide only. Accordingly I have made the simulation length a multiple of the M2 period, which is 44714.1 s. The simulation ends by writing a record to the restart file. Parameters are: NTIMES = 23040 DT == 7.7628819D0 NDTFAST == 1...
by m.hadfield
Wed Nov 23, 2011 1:04 am
Forum: ROMS Problems
Topic: *** glibc detected ***
Replies: 6
Views: 2224

Re: *** glibc detected ***

Make sure you're looking at line 1187 of read_phypar.f90 (the preprocessed file) not read_phypar.F.
by m.hadfield
Fri Sep 30, 2011 3:21 am
Forum: ROMS Installation
Topic: netcdf-4.1.3
Replies: 4
Views: 2985

Re: netcdf-4.1.3

In the absence of any direction to the contrary, netCDF will have been built for the Gfortran compiler. To tell ROMS to use the right configuration, set the following environment variables (Bash style) export FORT=gfortran export USE_NETCDF4=on export NC_CONFIG=/usr/local/bin/nc-config
by m.hadfield
Fri Sep 30, 2011 12:50 am
Forum: ROMS Installation
Topic: netcdf-4.1.3
Replies: 4
Views: 2985

Re: netcdf-4.1.3

gfortran
by m.hadfield
Mon Sep 19, 2011 9:49 am
Forum: ROMS Discussion
Topic: Can we have only passive tracers in rivers/point sources?
Replies: 40
Views: 9282

Re: Can we have only passive tracers in rivers/point sources

Mark, I had the same problem until I restricted the inflow to the top bin or few bins (I forget just now). I would be interested to know the outcome if you were to try this (top bin only). But what if inflow is at or near the bottom, like the brine from a desal plant. Has someone sorted this out? I...
by m.hadfield
Fri Sep 16, 2011 4:06 am
Forum: ROMS Discussion
Topic: Can we have only passive tracers in rivers/point sources?
Replies: 40
Views: 9282

Re: Can we have only passive tracers in rivers/point sources

So what is wrong with Q_PSOURCE ? This is not in my list of ROMS problems. This type of source is complicated because involves the continuity equations of ROMS. I am always uneasy messing around with the 2D and 3D continuity equations. It may explains why this is broken. This is very delicate stuff...
by m.hadfield
Fri Sep 16, 2011 3:50 am
Forum: ROMS Discussion
Topic: ROMS restart and floats
Replies: 25
Views: 7280

Re: ROMS restart and floats

The reason I use both PERFECT_RESTART and RST_SINGLE is because I am trying to emulate a very large, real-life ROMS application. I that application, we have to continue the ROMS simulations by breaking them in to segments (as we only get 4-hours of time on the supercomputer at a time) and the PERFE...
by m.hadfield
Fri Sep 16, 2011 3:43 am
Forum: ROMS Discussion
Topic: Can we have only passive tracers in rivers/point sources?
Replies: 40
Views: 9282

Re: Can we have only passive tracers in rivers/point sources

Mark, All of those scenarios would best be represented - in ROMS - as a rho-point-centered source of tracer. Not as a horizontal flux at the vertical face of a grid cell in the middle of the water column. Several of those scenarios could very sensibly be represented as surface or bottom fluxes of t...
by m.hadfield
Thu Sep 15, 2011 2:27 am
Forum: ROMS Discussion
Topic: Can we have only passive tracers in rivers/point sources?
Replies: 40
Views: 9282

Re: Can we have only passive tracers in rivers/point sources

But even this seems ill conceived - what sort of physical source to you envision acts this way in the middle of the water column? Usually sources like this are intended to represent the footprint on the model-resolved scale of some subgrid process. A wastewater pipe? A cloud of sediment stirred up ...
by m.hadfield
Thu Sep 15, 2011 2:03 am
Forum: ROMS Wish List
Topic: ROMS Wish List
Replies: 6
Views: 3724

Re: ROMS Wish List

Perhaps the word "wish" isn't quite what we need here! :twisted: Here's a wish, in the sense of something I have thought about and may well implement but would appreciate feedback on: an interior tracer point-source option (M_SOURCE?), each source to be defined in terms of its position, vertical sha...
by m.hadfield
Thu Sep 15, 2011 1:51 am
Forum: ROMS Discussion
Topic: ROMS restart and floats
Replies: 25
Views: 7280

Re: ROMS restart and floats

When I run the floats with my modified test problem without the PERFECT_RESTART and RST_SINGLE CPP options, the serial and parallel (MPI) outputs are the same. However, when I include these two CPP options, the parallel ROMS outputs has zero X, Y values upon carrying out a restart and the problems ...
by m.hadfield
Thu Sep 15, 2011 1:40 am
Forum: ROMS Discussion
Topic: Can we have only passive tracers in rivers/point sources?
Replies: 40
Views: 9282

Re: Can we have only passive tracers in rivers/point sources

However, now the problem is how to fix this and allow for point sources in the middle of the ocean (e.g. to simulate a broken pipe underwater which is pumping contaminants in to the ocean, etc.). My post of 8 September (which did not seem to draw any reaction at the time) refers to this issue: I re...
by m.hadfield
Thu Sep 15, 2011 12:19 am
Forum: ROMS Discussion
Topic: Can we have only passive tracers in rivers/point sources?
Replies: 40
Views: 9282

Re: Can we have only passive tracers in rivers/point sources

Could someone please let me know how I can include a point source/river in my ROMS simulations which only generates a passive tracer and not any T or S? This used to be so easy to do in the older ROMS like version 3.4, 3.6, etc.! To implement a point source for selected tracers, use LtracerSrc in t...
by m.hadfield
Wed Sep 14, 2011 1:36 am
Forum: ROMS Discussion
Topic: ROMS restart and floats
Replies: 25
Views: 7280

Re: ROMS restart and floats

I re-ran the two-segment run (for which I posted the files a couple of messages back) with MPI enabled and it worked correctly, i.e. the floats released at 0.1 days made it through the restart at 0.8 days and were joined by those from the next release at 0.9 days. That's with SOLVE3D turned off. PS:...
by m.hadfield
Sun Sep 11, 2011 7:32 pm
Forum: ROMS Discussion
Topic: ROMS restart and floats
Replies: 25
Views: 7280

Re: ROMS restart and floats

Attached are input files for a two-segment float simulation using the built-in FLT_TEST (SOLVE3D off). The segments are 0.8 days long and floats are released (successfully) at 0.1 days and 0.9 days.
by m.hadfield
Thu Sep 08, 2011 9:54 pm
Forum: ROMS Discussion
Topic: ROMS restart and floats
Replies: 25
Views: 7280

Re: ROMS restart and floats

lanerolle wrote:Really? I thought the times in the floats.in file (in units of days) have to be relative to the initialization time which is 0.0!
That's what I expected, too :roll:. But experience did not confirm my expectation :wink:.

When all else fails, read the source.
by m.hadfield
Thu Sep 08, 2011 9:27 pm
Forum: ROMS Discussion
Topic: ROMS restart and floats
Replies: 25
Views: 7280

Re: ROMS restart and floats

One possibility: release times in the floats-input file need to be relative to DSTART.
by m.hadfield
Thu Sep 08, 2011 2:35 am
Forum: ROMS Discussion
Topic: Can we have only passive tracers in rivers/point sources?
Replies: 40
Views: 9282

Re: Can we have only passive tracers in rivers/point sources

I recently needed to introduce passive tracer sources into the interior of a ROMS simulation. I couldn't get the point source system to do what I wanted in a toy simulation (it seems to generate a dipole when the point source is not adjacent to the land mask) so I added appropriate terms to the RHS ...
by m.hadfield
Thu Sep 08, 2011 12:02 am
Forum: ROMS Discussion
Topic: ROMS restart and floats
Replies: 25
Views: 7280

Re: ROMS restart and floats

Yes, I believe that's how it's supposed to work. The only way to know for 100% sure is to try it, though. So it does. I found a toy run I set up several years ago to confirm that ROMS does handle float locations and float releases in the second and subsequent runs of a series seamlessly. But I had ...
by m.hadfield
Wed Sep 07, 2011 12:46 am
Forum: ROMS Discussion
Topic: ROMS restart and floats
Replies: 25
Views: 7280

Re: ROMS restart and floats

As I understand it, if you choose to read float locations from the restart file, then you don't read the floats.in file, which means you can't release any more floats. In some cases, this is a significant restriction. Edit: Sorry, I didn't read the original post very carefully and I seem to have poi...
by m.hadfield
Sun Aug 21, 2011 7:41 pm
Forum: ROMS Installation
Topic: error with inlet_test example
Replies: 14
Views: 7056

Re: error with inlet_test example

The model coupling code has allocated 2 processors (numbers 0 and 1) to ROMS and 2 processors (numbers 2 and 3) to SWAN. However your ROMS input file evidently has NtileI and NtileJ both equal to 1. Set one of them to 2.
by m.hadfield
Fri Aug 19, 2011 1:59 am
Forum: ROMS Installation
Topic: error with inlet_test example
Replies: 14
Views: 7056

Re: error with inlet_test example

Nma, your undefined references are from the Fortran-90 interface and I suspect you are missing a "-lnetcdff" on your link command. NetCDF-4 has a script called nc-config that should provide the right linker options. Now that g77 is long gone, these problems are never (well hardly ever) related to th...
by m.hadfield
Fri Aug 19, 2011 1:53 am
Forum: ROMS Installation
Topic: Netcdf installation
Replies: 4
Views: 2030

Re: Netcdf installation

What were you doing wrong? It's always nice to know about new ways to break netCDF installation.
by m.hadfield
Tue Aug 16, 2011 12:58 am
Forum: ROMS Discussion
Topic: Missing input files for test cases? ie estuary_test, weddell
Replies: 4
Views: 1850

Re: Missing input files for test cases? ie estuary_test, wed

Hi Oceansifter Are you referring to the ROMS source area https://www.myroms.org/svn/src/trunk/ or the test cases https://www.myroms.org/svn/src/test/ If the latter, then I have successfully run a bunch of these, including estuary_test, though not yet weddell. Your estuary_test failure occurs at comp...
by m.hadfield
Tue Aug 09, 2011 12:41 am
Forum: ROMS Bugs
Topic: ROMS I/O bug when using floats
Replies: 2
Views: 1408

Re: ROMS I/O bug when using floats

Interesting. You shouldn't be seriously stressing the memory on your machine with 43,000 floats, let along, 2000.

Try building the model with USE_DEBUG, then run it and look for any array bounds violations.
by m.hadfield
Mon Aug 01, 2011 11:52 pm
Forum: ROMS Installation
Topic: Netcdf 3.6.3 problem
Replies: 7
Views: 2245

Re: Netcdf 3.6.3 problem

If I were to update gfortran would I need to go through and redo the install on netcdf? I am very new to all of this and am teaching myself so I really appreciate the help. You're unlucky to have run into such an obscure problem so early in your learning curve. You probably wouldn't need to rebuild...
by m.hadfield
Mon Aug 01, 2011 9:56 pm
Forum: ROMS Installation
Topic: Netcdf 3.6.3 problem
Replies: 7
Views: 2245

Re: Netcdf 3.6.3 problem

That's not netCDF-related. The missing symbols are ROMS variables. For example to take the first two ld: warning: can't find atom for N_GSYM stabs rx0:G(0,3) in Build/libMODS.a(mod_scalars.o) ld: warning: can't find atom for N_GSYM stabs r0:G(0,158)=xsarray1_real8: in Build/libMODS.a(mod_scalars.o) ...
by m.hadfield
Sun Jul 31, 2011 10:39 pm
Forum: ROMS Installation
Topic: Netcdf 3.6.3 problem
Replies: 7
Views: 2245

Re: Netcdf 3.6.3 problem

Or if you're the sort of person who finds failed tests troubling, you could rebuild it without C++ support, using the --disable-cxx switch. From the INSTALL file: `--disable-cxx' This turns off the building of the C++ API. Setting the environment variable CXX to null for configure will have the same...
by m.hadfield
Thu Jul 28, 2011 9:27 pm
Forum: ROMS Installation
Topic: [SOLVED] netcdf configure using gfortran
Replies: 11
Views: 5640

Re: [SOLVED] netcdf configure using gfortran

That zlib issue is an odd one! I guess it shows that life isn't meant to be easy. I'm glad you got it sorted out. :D
by m.hadfield
Mon Jul 25, 2011 9:56 pm
Forum: ROMS Installation
Topic: [SOLVED] netcdf configure using gfortran
Replies: 11
Views: 5640

Re: netcdf configure using gfortran

Hi sbergman Have a look at the command that triggered those errors in building ROMS--post it here if you want. Does the linker command line have the options you expect? I would expect it to end with "-lnetcdff -lnetcdf". does it? I don't think you need to worry about "-fno-second-underscore" or any ...
by m.hadfield
Sun Jul 24, 2011 10:53 pm
Forum: ROMS FAQ
Topic: build.bash problem
Replies: 10
Views: 10939

Re: build.bash problem

I have a further suggestion: check out a copy of the test subdirectory https://www.myroms.org/svn/src/test/ Now go to the upwelling subdirectory, where you will find a build.bash script very similar to the one you ran before. Modify and run that script, leaving the files in your ROMS tree unmodified...
by m.hadfield
Sun Jul 24, 2011 10:47 pm
Forum: ROMS FAQ
Topic: build.bash problem
Replies: 10
Views: 10939

Re: build.bash problem

(Sorry about the raw BBCode tags in the following. For some reason BBCode processing is turned off.) [quote="huangxh"]Should I change something in the file build.bash or something?[/quote] Indeed you should. Line 397 of build.bash is [code] cd ${MY_ROMS_SRC}[/code] and the directory pointed to by MY...
by m.hadfield
Thu Jul 21, 2011 2:37 am
Forum: ROMS Installation
Topic: [SOLVED] netcdf configure using gfortran
Replies: 11
Views: 5640

Re: netcdf configure using gfortran

kate wrote:Thanks, Mark, my last build was way back at 4.1.1.
Ancient history. :wink:
by m.hadfield
Wed Jul 20, 2011 2:12 am
Forum: ROMS Installation
Topic: [SOLVED] netcdf configure using gfortran
Replies: 11
Views: 5640

Re: netcdf configure using gfortran

As ever, it depends. Here's what I used last (on Linux): configure FC=gfortran F77=gfortran F90=gfortran CXX=g++ --prefix=/u1/uaf/kate --enable-netcdf4 --enable-shared --with-hdf5=/u1/uaf/kate With the latest release of netCDF-4 (4.1.3) you don't use "--with-hdf5" to specify the location of the HDF...
by m.hadfield
Tue Jul 19, 2011 1:09 am
Forum: ROMS Installation
Topic: make file problem
Replies: 8
Views: 6176

Re: make file problem

By the way, if you're using netCDF4 (USE_NETCDF4=on) with an up-to-date copy of Rutgers ROMS, then the makefile should be able to infer the options required to link with netCDF. It does this by invoking a utility called nc-config, via the following lines in the platform-specific make file: ifdef USE...
by m.hadfield
Wed Jul 13, 2011 12:52 am
Forum: ROMS Discussion
Topic: ROMS Particle Tracking
Replies: 5
Views: 3214

Re: ROMS Particle Tracking

I do recall saying something like this: Re the vertical interpolation, the ROMS interpolation routines are low order (piecewise linear, I think) so I wouldn't be too surprised to see discrepancies of several centimetres when a depth is converted to a vertical grid coordinate and then back, particula...
by m.hadfield
Mon Jul 11, 2011 1:00 am
Forum: ROMS Installation
Topic: Compile specific files without optimization
Replies: 1
Views: 873

Re: Compile specific files without optimization

In the platform-specific make files in subdirectory Compilers, there are examples of the compiler flags being altered for specific targets, eg, this from Compilers/Linux-ifort.mk # # Set free form format in source files to allow long string for # local directory and compilation flags inside the code...
by m.hadfield
Wed Jun 29, 2011 1:27 am
Forum: ROMS Installation
Topic: Problem in installing Nedcdf with Cygwin
Replies: 4
Views: 4083

Re: Problem in installing Nedcdf with Cygwin

I have edited the tutorial as you suggest. The recommended GCC-related packages are now gcc4, gcc4-core and gcc4-fortran. (Not gcc4-g++, as this is the C++ compiler, which shouldn't be necessary.) I hope this is correct.
by m.hadfield
Wed Jun 29, 2011 1:03 am
Forum: ROMS Installation
Topic: pgf90-Error-Unknown switch: -M/opt/netcdf4/lib
Replies: 2
Views: 1617

Re: pgf90-Error-Unknown switch: -M/opt/netcdf4/lib

I think this is an issue with the output of netCDF's nc-config command, via these lines in the make file ifdef USE_NETCDF4 NC_CONFIG ?= nc-config ... LIBS := $(shell $(NC_CONFIG) --flibs) else ... You can confirm this by running "nc-config --flibs" at the command line, yourself. You shouldn't be usi...
by m.hadfield
Tue Jun 28, 2011 1:55 am
Forum: ROMS Problems
Topic: Headland test case hanging
Replies: 3
Views: 936

Re: Headland test case hanging

Never mind. I killed one of the jobs with Ctrl-C, at which point it emitted some additional, more helpful output: Output/Input Files: Output Restart File: ocean_rst.nc Output History File: ocean_his.nc Output Floats File: ocean_flt.nc Physical parameters File: ocean_test_head.in Input Grid File: Dat...
by m.hadfield
Tue Jun 28, 2011 1:48 am
Forum: ROMS Problems
Topic: Headland test case hanging
Replies: 3
Views: 936

Headland test case hanging

When I run the test_head case here https://www.myroms.org/svn/src/test/test_head/ it hangs indefinitely with the following output ... T Hout(idU3rs) Write out total 3D u-radiation stress. T Hout(idV3rs) Write out total 3D v-radiation stress. T Hout(idU3Sd) Write out 3D u-momentum stokes velocity. T ...
by m.hadfield
Tue Jun 28, 2011 1:18 am
Forum: ROMS Installation
Topic: Problem in installing Nedcdf with Cygwin
Replies: 4
Views: 4083

Re: Problem in installing Nedcdf with Cygwin

This is really a netCDF and/or Cygwin problem rather than a ROMS problem; perhaps you should send it to the netCDF or Cygwin mailing lists. That said, I have successfully built netCDF 3.6.x and 4.1.x many times without too many problems, so perhaps I can help. Your configure output suggests you have...
by m.hadfield
Tue Jun 28, 2011 12:47 am
Forum: ROMS FAQ
Topic: build.bash problem
Replies: 10
Views: 10939

Re: build.bash problem

The *best* solution, as has been reported elsewhere, is to download ROMS using Cygwin's svn command.
by m.hadfield
Tue Jun 28, 2011 12:02 am
Forum: ROMS Problems
Topic: Inlet test case blowing-up
Replies: 14
Views: 2613

Re: Inlet test case blowing-up

You're right. Perhaps I spoke too soon. The inlet_test case, as implemented in the ROMS test suite https://www.myroms.org/svn/src/test/inlet_test/ (with preprocessor options determined by a combination of build.bash and inlet_test.h) is characterised by large values of Cw at grid point (43,35,7) be...
by m.hadfield
Wed Jun 15, 2011 3:33 am
Forum: ROMS Problems
Topic: Inlet test case blowing-up
Replies: 14
Views: 2613

Re: Inlet test case blowing-up

thanks for continuing to look at this, but just because you change the viscosity does not mean the compiler issue is not still valid. In my opinion, you should not get a different answer if you use debug vs optimized. But you do, depending on the optimized flags chosen. For optimized mode, if you s...
by m.hadfield
Tue Jun 14, 2011 3:38 am
Forum: ROMS Problems
Topic: Inlet test case blowing-up
Replies: 14
Views: 2613

Re: Inlet test case blowing-up

I have repeated mmahone's experiment of turning off optimisation with Gfortran (via USE_DEBUG=on). I too find that the INLET_TEST case runs to completion. However I can also avoid a blow-up without turning off optimisation by increasing VISC2 from 1.0E-3 to 1.0E-2. This has very little effect on the...
by m.hadfield
Thu May 26, 2011 7:29 pm
Forum: ROMS Installation
Topic: Error installing mpi on cygwin
Replies: 8
Views: 2844

Re: Error installing mpi on cygwin

It's OK I have Ubuntu!! Now, I have some problem, when I try to compile build.bash for the first time I have the following error: /bin/sh: -c: not found make: *** [/home/antoine/Projects/Upwelling/Build/mod_kinds.o] Erreur 127 I have checked in /bin, and sh exists, so I don't understand why I have ...
by m.hadfield
Wed May 25, 2011 9:45 pm
Forum: ROMS Problems
Topic: Inlet test case blowing-up
Replies: 14
Views: 2613

Re: Inlet test case blowing-up

I have carried out a couple more runs of INLET_TEST: Rebuilt it with the PGI compiler (pgf90 7.1-6 64-bit target on x86-64 Linux -tp k8-64e): it crashes at the approximately the same point as the Gfortran run. Halved DT (and also NFAST since it's nowhere near the barotropic CFL limit): it crashes at...
by m.hadfield
Wed May 25, 2011 1:56 am
Forum: ROMS Installation
Topic: Error installing mpi on cygwin
Replies: 8
Views: 2844

Re: Error installing mpi on cygwin

I use Cygwin on my Windows desktop PC a lot and am happy with it, within limits. It's my preferred platform for testing, because I control it, I have fast access to local files and I can manage & edit files with Windows tools that I like. I do the serious work on Unix hosts. I have not had much luck...
by m.hadfield
Tue May 24, 2011 2:53 am
Forum: ROMS Problems
Topic: Inlet test case blowing-up
Replies: 14
Views: 2613

Re: Inlet test case blowing-up

The crash is associated with a spike of large negative temperatures (-2500 degC) extending from surface to bottom at location (43,35) on the rho grid (i.e. adjacent to the land mask on the eastern side of the mouth of the inlet). Temperature is the only variable that appears to have unreasonable val...
by m.hadfield
Mon May 23, 2011 10:02 pm
Forum: ROMS Problems
Topic: Inlet test case blowing-up
Replies: 14
Views: 2613

Re: Inlet test case blowing-up

My ROMS source is up-to-date, I think. (I last downloaded changes on 6 May. I can't check for more recent updates as the svn client on the machine with the ROMS source cannot connect to the server, though my Web browser and a client on another machine can. Odd :? ) I used Gfortran 4.1.2 on SUSE Linu...
by m.hadfield
Sun May 22, 2011 10:01 pm
Forum: ROMS Problems
Topic: Inlet test case blowing-up
Replies: 14
Views: 2613

Re: Inlet test case blowing-up

Hello, I am a new ROMS user. I have upgraded my code to ROMS 3.4 revision 550 lately on my CYGWIN. I have run successfully several cases both in serial and in parallel (canyon, test_chan, test_head)...until I have tried the inlet test case: mpirun -np 2 ./oceanM coupling_inlet_test.in The coupled m...
by m.hadfield
Thu May 05, 2011 9:07 pm
Forum: ROMS Bugs
Topic: Infinity=one/zero
Replies: 6
Views: 4818

Re: Infinity=one/zero

arango wrote:For now, we can have the following directive in mod_scalars.F until I find a more robust way to do this:

Code: Select all

#ifdef SWAN_COUPLING
      Infinity=one/zero
#endif
That looks like a sensible solution for the time being. Thanks.
by m.hadfield
Sun May 01, 2011 11:00 pm
Forum: ROMS Bugs
Topic: Infinity=one/zero
Replies: 6
Views: 4818

Infinity=one/zero

Ticket 497 introduced the following lines into mod_scalars.F, subroutine initialize_scalars: one=1.0_r8 zero=0.0_r8 Infinity=one/zero This is not a safe or standard-conforming way of initializing an IEEE infinity. I discovered this because when USE_DEBUG is in effect I normally turn on the compiler ...
by m.hadfield
Thu Apr 14, 2011 8:56 pm
Forum: ROMS Bugs
Topic: Omega confusion
Replies: 3
Views: 2305

Re: Omega confusion

However, omega, when output in an ocean_his.nc file, is in units of m/s, as is w. Does this mean that the output from the model for the vertical velocity in sigma coordinates is already multiplied by this Hz factor? Yes, I think that is the case. You should be able to verify this for yourself by re...
by m.hadfield
Wed Mar 30, 2011 12:45 am
Forum: ROMS Discussion
Topic: Spatially varying bottom friction
Replies: 1
Views: 1057

Re: Spatially varying bottom friction

The only problem seems to be that the old policy of allowing the user to activate several types of bottom friction simultaneously has been prohibited with this new option. It's been prohibited for the last year or two, since before the spatially varying option was introduced. (Or so I recall.) But ...
by m.hadfield
Sun Mar 27, 2011 10:46 pm
Forum: ROMS Information
Topic: Question about Pair
Replies: 4
Views: 2896

Re: Question about Pair

Dear Users, There are two different surface pressure variable from atmospheric model such as NCEP. The one is surface pressure and the other is sea level pressure. I was wondering which one should I use when I use 'Pair' in the bulk formulae. Regards, -Peter The variable I have used is surface pres...
by m.hadfield
Mon Feb 28, 2011 1:45 am
Forum: ROMS Installation
Topic: NCL Installation Problem
Replies: 5
Views: 4233

Re: NCL Installation Problem

ROMS needs to link to the curl library. You tell it to look for it in the build script or makefile by setting "USE_DAP = on". This sort of thing would be much easier if ROMS were to use the output of the nc-config command. Eg in my make files I have ifdef USE_NETCDF4 NC_CONFIG ?= nc-config NETCDF_I...
by m.hadfield
Sun Feb 20, 2011 1:08 am
Forum: ROMS Installation
Topic: Error while compiling ROMS - gfortran
Replies: 3
Views: 1694

Re: Error while compiling ROMS - gfortran

Hi, Thank you for the response. The gfortran version installed on my machine is gcc version 4.0.0 20041201 (experimental). I'll try to compile it without USE_DEBUG and update the gfortran compiler. Kamila That's old. I'm sure that's the problem. According to my records, Gfortran wouldn't compile RO...
by m.hadfield
Sat Feb 19, 2011 3:47 am
Forum: ROMS Installation
Topic: Error while compiling ROMS - gfortran
Replies: 3
Views: 1694

Re: Error while compiling ROMS - gfortran

The only significant disadvantage in using GFortran instead of Intel Fortran, in my opinion, is in the area of run-time performance, rather than ability to compile the code. I regularly use Gfortran, amongst other compilers. I have run into problems & glitches with all of them, but I wouldn't say Gf...
by m.hadfield
Thu Dec 23, 2010 2:29 am
Forum: ROMS Discussion
Topic: inverse barometer effect on a costal lagoon
Replies: 4
Views: 2247

Re: inverse barometer effect on a costal lagoon

I should think that in a coastal lagoon, the only way atmospheric pressure variations will affect the interior is by causing the sea level at the lagoon entrance(s) to vary, causing water to surge in and out. So what you need is a time series of sea level at the entrance(s), bearing in mind that if ...
by m.hadfield
Wed Dec 22, 2010 7:37 pm
Forum: ROMS Bugs
Topic: Omega confusion
Replies: 3
Views: 2305

Omega confusion

A forum post early last year called " units of omega " mentioned some confusion about the units of the netCDF output variable omega and appeared to clear it up, however it's more complicated and confusing than implied there. To recap, the vertical fluid velocity in s coordinates, ds/dt, is conventio...
by m.hadfield
Wed Nov 17, 2010 1:24 am
Forum: ROMS Bugs
Topic: FLOAT_VWALK scaling problem
Replies: 1
Views: 1352

Re: FLOAT_VWALK scaling problem

But I was thinking it may not be appropriate to use the predictor-corrector scheme at all with the VWALK on. After all, each random kick is, by the definition of "random walk," unrelated to the previous time steps. Indeed. This was why, when I first wrote the FLOAT_VWALK code many years ago, I used...
by m.hadfield
Tue Oct 19, 2010 1:09 am
Forum: ROMS Discussion
Topic: gmake errors: gmake: *** virtual memory exhausted. Stop. ..
Replies: 11
Views: 3997

Re: gmake errors: gmake: *** virtual memory exhausted. Stop. ..

kate wrote:Stolen straight from an NCAR IBM, the only one I have access to these days. See attached (just rename it back to gmake).
Thanks. Works a treat!
by m.hadfield
Mon Oct 18, 2010 10:27 pm
Forum: ROMS Discussion
Topic: gmake errors: gmake: *** virtual memory exhausted. Stop. ..
Replies: 11
Views: 3997

Re: gmake errors: gmake: *** virtual memory exhausted. Stop. ..

Just as what Kate said that gmake3.81 instead of gmake3.80 is necessary for the present version on IBM AIX. I am very lucky to get the gmake3.81 from Kate couple years ago and put it in my home directory. Everything goes pretty well. Can anyone suggest how I might obtain Gnu make 3.81 or 3.82 for A...
by m.hadfield
Mon Jul 19, 2010 10:01 pm
Forum: ROMS Problems
Topic: Restarting floats
Replies: 4
Views: 1939

Re: Restarting floats

I add floats to an existing run all the time. There are 1 or 2 gotchas (I'm not sure I remember what they all are) but basically it should work OK. As it says in the floats-file documentation, Ft0 is the "Time (days) of float release after model initialization." It will be less than the time printed...