FAQ

This page tries to answer to the Frequently Asked Questions related to GOTM. All questions, comments and suggestions are warmly welcome by sending an e-mail to devel@gotm.net.
Q: Why can I not compile GOTM ? (this is a VFAQ, very frequently asked question)

A: Unfortunately Makefiles and Fortran are not as standardized as they should be :-). However concerning Makefiles there is a viable solution. We strongly encourage users to install the GNU make (http://www.gnu.org/software/make/make.html). Especially with make on Sun's we have experienced problems with the Makefiles we supply - both with the stable and developers version. Installing GNU's make has always solved the problem. Concerning the Fortran compiler - it's more tricky. Unlike with C - Fortran (and especially fortran compiler flags) are very non-standardised. We only have access to a limited number of architectures and fortran compilers and can therefore not provide information for all compilers. In the Makefile (stable version) and Rules.make (developers version) information concerning the compiler has to be specified - please consult your local Fortran manuals for information. Next step - write to users@gotm.net - somebody might have a solution for your compiler. When it works please send info to devel@gotm.net and it will be included in the release. (Karsten Bolding)

Q: What is NetCDF and why do GOTM use it (VFAQ as well). ?

A: NetCDF is an effort by the University Corporation for Atmospheric Research sponsered by the National Science Foundation to create a machine independent self-describing format for storing scientific data. Today NetCDF is widely used in meteorology and oceanography (as well as many other fields) both for storing observations and model results. One of the advantages with NetCDF is that it is supported be many free and commercial graphical packages. Further information about NetCDF can be found in here. Finally NetCDF is much, much more flexible than e.g. ascii output. (Karsten Bolding)

Q: What is the best platform OS and compiler to use with GOTM ? (David Ciochetto, Halifax)

A: We have tried to make GOTM platform independent - using standard Fortran 90/95 and the machine independent file format, NetCDF. The authors of GOTM have compiled and run GOTM on the following OS'es/compilers - both stable and developers versions.
  • 1: Linux 2.2.17 - NAG version 1.0 of NAGWaref95
  • 2: Linux 2.2.17 - Fujitsu Fortran Compiler
  • 3: OSF1 V5.0 (Alpha) - Compaq Fortran 90/95
  • 4: SunOS 5.7 - FORTRAN 90 2.0
  • 5: SGI ?? - SGI Fortran 90 compiler.
  • 6: Windows: The stable version of GOTM has been run successfully under windows using the Compaq Visual Fortran (different versions including 6.5 and superior). The developpers version of GOTM with the precompiling instructions have not been adapted to run with a make and a fortran compiler under Windows. WeŽd be happy to know about any experience in this sense.

  • In all cases - except 6 - we have used GNU's version of 'make'. My personal favorite is the Compaq Fortran F90/F95 on the alpha. The best compiler on the fastest processor :-) - but most development is done on Linux machines using both compilers mentioned for this platform. (Karsten Bolding)


    Q: I had a question regarding the salinity surface boundary condition. Is this boundary condition coded in the model for fresh water flux? I had the impression from reading the GOTM Report that only a relaxation to a prescribed profile had been coded for salinity at the surface. I find in the namelist.inp link that there is an option for setting a switch called p_e_method and a file called p_e_flux_file for the salinity boundary condition at the surface. If you have something in the works for fresh water flux modeling I would be interested in the new code before I went in re-invented the wheel. (Luis Montenegro, New York)?

    A: It will be in the newest GOTM release. (Hans Burchard) NEW: Freshwater fluxes have been not fully tested in GOTM, mainly because they have not been used in the existing test cases. Apart from the relaxation of salinity at the surface (already implemented), GOTM structure is prepared to read precipitation - evaporation fluxes (see p_e_flux in airsea.F90), but this flux is not yet introduced in salinity.F90 in the release version, but only in an unstable version (Manuel Ruiz)

    Q: I have coded an interface of GOTM and HOPE (a global ocean model developed at the Max Plank Institut for Meteorology, Hamburg). The coupling has worked fine in some ideal test cases, but it does not seem to work properly in large scale simulations, apparently not enough mixing appears. As usually in global models, we are using a coarse resolution near the surface (Raimon Hernandez-Roura, Hamburg)

    A: Although GOTM boundary conditions on turbulence equations are prepared to work for coarse resolutions (see Burchard and Petersen, JPO 2000), enough resolution near the surface is necessary for describing the mixing layer with a differential model like GOTM. Otherwise, a non-realistic strong stratification may appear and inhibit mixing. After some experiences with GOTM and different resolutions near the surface in the Papa test case (mixed layers of meters in summer), weŽve seen that GOTM works with a fine resolution near the surface, with 10 m as a maximum orientative value for the first layer. (Manuel Ruiz)
    NOTE: This FAQ is the result of some cooperation between MPI Hamburg and the GOTM team. Ask Manuel Ruiz or Raimon Hernandez-Roura for further details.


    Q: I have integrated GOTM turbulence code into a 3D model (HAMSOM). I wish to simulate the mixing and stratification at a shelf sea, but the results can no simulate the upper mixing layer up a thermocline, the strength of the thermocline was reinforced and the thickness of the thermocline was lessened much. (Wu Yingyan, China).

    A: You should try to include the turbulence closure used in HAMSOM (the so-called Kochergin model) into GOTM. This should be done in completely the same way as it is done in HAMSOM. By doing so, you should compute the same results with the pure HAMSOM model and with the coupled HAMSOM-GOTM model (with Kochergin closure). In case the results are considerably different, it is quite likely that the coupling has not been done in a technically correct way. This construction will allow you to correct the coupling, and then - hopefully - also model runs with higher turbulence closure models such a sthe k-epsilon model should work. (Hans Burchard, Hamburg, Germany).

    Q: Were can we find the new turbulence closure by Canuto et al. (JPO 31, 1413-1426, 2001) in the GOTM model ? (Bob Wilson, Stony Brook, USA).

    A: Usually, our input (namelist) files are set up such that the Canuto et al. model is the default. If you have a look into the gotmturb.inp file of any scenario (e.g. OWS Papa) you would have to set stab_method to 3 or 4 for the full Canuto stability functions, as we (Burchard and Bolding, JPO 31, 1943-1968, 2001) call them. For stab_method=3 this has the consequence that cm0 has to be set to 0.527 and ce3 (if you have stratification) to -0.629. This is for the F90 version of GOTM. In case you use the F77 version (which is not further developed) some things might work slightly different. You find the coding for Canuto et al. stability functions in the file cmue_ca.F90 (version A) and cmue_cb.F90 (version B). Quasi-equilibrium versions are found in files cmue_caqe.F90 and cmue_cbqe.F90. (Hans Burchard, Hamburg, Germany).

    Q: Can you tell me where I can find the original data set (profiles and met data) for stations papa and november? The profile data are already available from the gotm release but what about the surface data. I am sure that there must be some Web site where I can find them. (Patrick Luyten, Brussels) ?

    A: The best would be to write an email to Paul Martin, and ask him. However, the GOTM Team can also provide you with the original data provided by Paul Martin. (Hans Burchard)

    Q: How does your water column model treat the bottom boundary condition? By specifying the roughness (for the current) or a drag coefficient (current friction factor) or something else? (Ole S. Madsen, Boston) ?

    A: In GOTM, the bottom boundary condition is hopefully imlemented in the correct way. Physically, the two velocity components are assumed to be zero at the boundary which we locate on top of an unresolved layer of thickness z0. Since we locate the discrete velocity points vertically in the center of the grid boxes, an extremely fine resolution would be needed for resolving the bottom boundary layer. In order to circumvent this problem, we assume a logarithmic behaviour of the velocity in the lowest discrete layer. This leads to the quadratic friction law with a friction coefficient depending on the height of the bootom layer, the bed roughness, the von Karman number and the friction velocity. I think that this approach is quite standard. (Hans Burchard)

    Q: I am very interested in having the output of GOTM 1.2.4, that is the Fortran 77 version, directly in NetCDF format, an option I have seen is not yet available. Therefore, I was wondering if it is possible to get the necessary subroutines somehow. Is it? (Raimon Hernandez-Roura, Hamburg)

    A: Karsten answered this

    Q: ?
    A:

    www.gotm.net updated: Fri Nov 23 17:50:32 2001