[MITgcm-support] MITgcm-support Digest, Vol 124, Issue 25
Jody Klymak
jklymak at uvic.ca
Tue Oct 29 12:44:47 EDT 2013
On Oct 28, 2013, at 21:12 PM, 李志远 <oceanlizy at 163.com> wrote:
>
>
> first, thanks for your advice ,but I tried "../../../tools/genmake2 -mods=../code -of=../../../OPTFILE"
> something is still wrong:
> Warning: ROOTDIR was not specified; try using a local copy of MITgcm found at "../../.. "
> getting OPTFILE information:
> Error : can't read OPTFILE="../../../OPTFILE"
"OPTFILE" is a file that has been modified from one of the ones in ../../../tools/build_options
Replace "OPTFILE" with the filename you use. For instance if your machine is linux intel processor using gnu Fortran 77 you might use -of ../../../tools/build_options/linux_ia64_g77
This is necessary for you to tell the Makefile where your libraries are and what compiler options you want.
Again, Sec. 3.5 of the manual is what you want....
Cheers, Jody
>
>
> I don't know what does it mean .
>
> many thanks!
>
>
>
>
> At 2013-10-29 11:45:57,mitgcm-support-request at mitgcm.org wrote:
> >Send MITgcm-support mailing list submissions to
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> >
> >
> >Today's Topics:
> >
> > 1. diagnosing numerical diffusion (Ryan Abernathey)
> > 2. diagnosing gmredi fluxes for tracers (Christoph Voelker)
> > 3. problems with specifying optfile (???)
> > 4. Re: problems with specifying optfile (Alexander Slavin)
> > 5. Re: problems with specifying optfile (Jody Klymak)
> >
> >
> >----------------------------------------------------------------------
> >
> >Message: 1
> >Date: Mon, 28 Oct 2013 12:01:11 -0400
> >From: Ryan Abernathey <ryan.abernathey at gmail.com>
> >To: mitgcm-support at mitgcm.org
> >Subject: [MITgcm-support] diagnosing numerical diffusion
> >Message-ID:
> > <CAJAZx5DbR2ue_KiQQJOCyxEOEmNbS6+Aa-bbUXtomqatLd1Lag at mail.gmail.com>
> >Content-Type: text/plain; charset="iso-8859-1"
> >
> >Hello,
> >
> >We are working on closing the tracer variance budget in a way that is
> >consistent with MITgcm numerics. In the variance budget, the distinction
> >between advection and diffusion is crucial, because diffusion leads to
> >dissipation, while advection does not. The biggest challenge is that the
> >nonlinear advection schemes introduce numerical diffusion even with
> >explicit diffusion set to zero, resulting in a dissipation of variance. We
> >would like to quantify this effect locally at each grid point.
> >
> >The idea we have come up with is to define a residual advective flux as the
> >difference between the advective flux estimated via naive centered
> >differences (i.e the way the diagnostics such as UVELTH are computed in
> >pkg/diagnostics/diagnostics_fill_state.F) and the "true" advective flux
> >calculated by the GAD package (i.e. the diagnostics such as ADVx_TH as
> >calculated in pkg/generic_advdiff/gad_calc_rhs.F). Our thinking is that
> >this will tell us something about the "extra" flux introduced by the
> >nonlinear scheme.
> >
> >I know that variance is not conserved exactly. We just want to do the best
> >we can. I am emailing the list to find whether you think this idea is sane
> >or not. If any of you numerical gurus has a better idea about how this can
> >be done, I would love to hear your suggestions.
> >
> >Best,
> >Ryan
> >-------------- next part --------------
> >An HTML attachment was scrubbed...
> >URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20131028/b119ede9/attachment-0001.htm>
> >
> >------------------------------
> >
> >Message: 2
> >Date: Mon, 28 Oct 2013 23:34:05 +0100
> >From: Christoph Voelker <christoph.voelker at awi.de>
> >To: <mitgcm-support at mitgcm.org>
> >Subject: [MITgcm-support] diagnosing gmredi fluxes for tracers
> >Message-ID: <526EE65D.2000206 at awi.de>
> >Content-Type: text/plain; charset="ISO-8859-1"
> >
> >Dear MITgcm'ers,
> >
> >I have a run of a biogeochemical model (i.e. with several additional
> >passive tracers) and I am trying to diagnose (and hopefully understand)
> >what the GMREDI eddy parameterization contributes to my tracer fluxes.
> >In doing so I got somewhat confused my the many options and parameter
> >settings that are possible in that package; I found it hard to follow
> >how the advective and diffusive fluxes are really calculated.
> >
> >My settings include
> >#define GM_VISBECK_VARIABLE_K
> >#define GM_BOLUS_ADVEC
> >in GMREDI_OPTIONS.h.
> >so, I am using the bolus velocity form, not the skew flux form, with
> >variable kappa_GM, a la Visbeck et al. '97. In addition I am using the
> >Large, Danabasoglu, Doney tapering scheme.
> >
> >My questions concern the diagnostics associated with the tracer fluxes.
> >
> >- Firstly, I assume that the explicit diffusive terms like DFrETr01
> >contain the Redi isopycnal diffusion, perhaps plus the additional
> >diffusion induced e.g. by the KPP sheme that I am using. Is this right?
> >
> >- Secondly, is the bolus advective flux part of the advective flux
> >diagnostics, like ADVrTr01? Or is this only the non-bolus advection?
> >
> >- And finally, is there a way to diagnose the advective tracer fluxes
> >from the bolus velocity alone, i.e. separate it from the background
> >velocity advection, in a diagnostic variable, or does one have to write
> >out the bolus stream function terms GM_PsiX and GM_PsiY, and then
> >compute the induced additional advection offline?
> >
> >Sorry if my questions are daft, but I really first tried to understand
> >all this from the code,
> >
> >Thanks, Christoph
> >
> >--
> >Christoph Voelker
> >Alfred Wegener Institute for Polar and Marine Research
> >Am Handelshafen 12
> >27570 Bremerhaven, Germany
> >e: Christoph.Voelker at awi.de
> >t: +49 471 4831 1848
> >
> >
> >
> >
> >------------------------------
> >
> >Message: 3
> >Date: Tue, 29 Oct 2013 09:58:19 +0800 (CST)
> >From: ??? <oceanlizy at 163.com>
> >To: MITgcm <mitgcm-support at mitgcm.org>
> >Subject: [MITgcm-support] problems with specifying optfile
> >Message-ID: <739dc92.2e93.14201eed88c.Coremail.oceanlizy at 163.com>
> >Content-Type: text/plain; charset="utf-8"
> >
> > Dear all;
> > I started running with MITgcm recently, so I?m pretty new to the model . However,when I start with the Barotropic Gyre tutorial ,something goes wrong. I do it as follows:
> >
> > cd MITgcm/verification/tutorial-barotropic_gyre/build
> > ../../../tools/genmake2 -mods=../code
> >then it appeared warning: NO OPTFILE specified
> > searching for possible setting for optfile
> >
> >
> >
> >
> >I don't know how to specify optfile , someone can help me ?
> >
> >
> >
> >
> > many thanks !
> >-------------- next part --------------
> >An HTML attachment was scrubbed...
> >URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20131029/1c74f2f3/attachment-0001.htm>
> >
> >------------------------------
> >
> >Message: 4
> >Date: Mon, 28 Oct 2013 20:05:55 -0700
> >From: Alexander Slavin <aslavin at mun.ca>
> >To: mitgcm-support at mitgcm.org
> >Subject: Re: [MITgcm-support] problems with specifying optfile
> >Message-ID: <526F2613.20707 at mun.ca>
> >Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> >
> >Hello,
> >
> >You need to specify OPTFILE manually, for example like this:
> >../../../tools/genmake2 -mods=../code -of=../../../OPTFILE
> >You can find example OPT files here:
> >\MITgcm\tools\build_options
> >
> >Good luck!
> >
> >Alexander
> >
> >On 28/10/2013 6:58 PM, ??? wrote:
> >> Dear all;
> >> I started running with MITgcm recently, so I?m pretty new to the
> >> model . However,when I start with the Barotropic Gyre tutorial
> >> ,something goes wrong. I do it as follows:
> >> cd MITgcm/verification/tutorial-barotropic_gyre/build
> >> ../../../tools/genmake2 -mods=../code
> >> then it appeared warning: NO OPTFILE specified
> >> searching for possible setting for optfile
> >>
> >>
> >> I don't know how to specify optfile , someone can help me ?
> >>
> >>
> >> many thanks !
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org
> >> http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
> >
> >This electronic communication is governed by the terms and conditions at
> >http://www.mun.ca/cc/policies/electronic_communications_disclaimer_2012.php
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> >
> >------------------------------
> >
> >Message: 5
> >Date: Mon, 28 Oct 2013 20:45:42 -0700
> >From: Jody Klymak <jklymak at uvic.ca>
> >To: mitgcm-support at mitgcm.org
> >Subject: Re: [MITgcm-support] problems with specifying optfile
> >Message-ID: <96942482-B229-47A5-84A3-EBCE96604778 at uvic.ca>
> >Content-Type: text/plain; charset="utf-8"
> >
> >Hi,
> >
> >Have a look at Sec 3.5 of the manual, but you probably want to add "-opt=../../../tools/build_options/YourMachine" to your "genmake2"
> >
> >Where YourMachine is modified from one of the files already in that directory.
> >
> >Cheers, Jody
> >
> >
> >On Oct 28, 2013, at 18:58 PM, ??? <oceanlizy at 163.com> wrote:
> >
> >> Dear all;
> >> I started running with MITgcm recently, so I?m pretty new to the model . However,when I start with the Barotropic Gyre tutorial ,something goes wrong. I do it as follows:
> >>
> >> cd MITgcm/verification/tutorial-barotropic_gyre/build
> >> ../../../tools/genmake2 -mods=../code
> >> then it appeared warning: NO OPTFILE specified
> >> searching for possible setting for optfile
> >>
> >>
> >> I don't know how to specify optfile , someone can help me ?
> >>
> >>
> >> many thanks !
> >>
> >>
> >> _______________________________________________
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org
> >> http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
> >--
> >Jody Klymak
> >http://web.uvic.ca/~jklymak/
> >
> >
> >
> >
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> >
> >------------------------------
> >
> >_______________________________________________
> >MITgcm-support mailing list
> >MITgcm-support at mitgcm.org
> >http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
> >
> >End of MITgcm-support Digest, Vol 124, Issue 25
> >***********************************************
>
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
--
Jody Klymak
http://web.uvic.ca/~jklymak/
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