[MITgcm-support] MITgcm-support Digest, Vol 124, Issue 27
李志远
oceanlizy at 163.com
Tue Oct 29 21:38:04 EDT 2013
thank you,Jody;
I do that as you told "../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_amd64_g77"
then it reveals :
processing options files and arguments
getting local config information: none found
warning:ROOTDIR was not specified ; try using a local copy of MITgcm found at "../../.. "
getting OPTFILE information:
using OPTFILE ="../../../tools/build_options/linux_amd64_g77"
I wonder is there something wrong ?
At 2013-10-30 00:45:03,mitgcm-support-request at mitgcm.org wrote:
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>Today's Topics:
>
> 1. Re: MITgcm-support Digest, Vol 124, Issue 25 (Jody Klymak)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 29 Oct 2013 09:44:47 -0700
>From: Jody Klymak <jklymak at uvic.ca>
>To: mitgcm-support at mitgcm.org
>Subject: Re: [MITgcm-support] MITgcm-support Digest, Vol 124, Issue 25
>Message-ID: <B4E2134D-6DF1-4385-9472-A191358B969F at uvic.ca>
>Content-Type: text/plain; charset="utf-8"
>
>
>On Oct 28, 2013, at 21:12 PM, ??? <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
>> > mitgcm-support at mitgcm.org
>> >
>> >To subscribe or unsubscribe via the World Wide Web, visit
>> > http://mitgcm.org/mailman/listinfo/mitgcm-support
>> >or, via email, send a message with subject or body 'help' to
>> > mitgcm-support-request at mitgcm.org
>> >
>> >You can reach the person managing the list at
>> > mitgcm-support-owner at mitgcm.org
>> >
>> >When replying, please edit your Subject line so it is more specific
>> >than "Re: Contents of MITgcm-support digest..."
>> >
>> >
>> >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
>> >-------------- next part --------------
>> >An HTML attachment was scrubbed...
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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/
>> >
>> >
>> >
>> >
>> >-------------- next part --------------
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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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>
>End of MITgcm-support Digest, Vol 124, Issue 27
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