[MITgcm-support] Hello

Martin Losch martin.losch at awi.de
Fri Nov 11 03:48:10 EST 2016


First of all, you shouldn’t use "linux_amd64_gfortran+mpi_generic”. This mean that you either use very old code, that we cannot really help you with or you that you have copied it from the “tools/build_options/unsupported” directory, where again the directory name implies that we don’t support these files anymore. 

I suggest you use recent code with
-of ../../../tools/build_options/linux_amd64_gfortran
if you want to use gfortran. If you want to use MPI, then use the option -mpi and before you run genmake2 again, set the environment variable MPI_INC_DIR to point to you mpi-include directory (the one that contains “mpif.h”), ask your system admin where that is.

Martin



> On 10 Nov 2016, at 20:24, smaeilpour <saeid_gal at yahoo.com> wrote:
> 
> My command as:
> 
> ../../../tools/genmake2 -mods=../code -mpi -of=../../../tools/build_options/linux_amd64_gfortran+mpi_generic
> 
> 
> 
> 
> 
> 
> 
> 
> --------------------------------------------
> On Thu, 11/10/16, Matthew Mazloff <mmazloff at ucsd.edu> wrote:
> 
> Subject: Re: [MITgcm-support] Hello
> To: mitgcm-support at mitgcm.org
> Date: Thursday, November 10, 2016, 10:36 PM
> 
> What is the command you
> compile with
> 
> do you give a
> 
> -of 
> option? This should
> point to a file that has paths in it, and these paths should
> point to the compiler you are using. 
> typing
> which ifort 
> will tell you the path to the compiler in your
> environment
> 
> mpif.h is for
> parallel computing — are you trying to run multi-core?
> 
> Matt
> 
> 
> 
>> On Nov
> 10, 2016, at 10:55 AM, smaeilpour <saeid_gal at yahoo.com>
> wrote:
>> 
>> Very
> thanks for your help,
>> 
>> could you tell me how to changes in my
> paths? 
>> 
>> 
>> 
> --------------------------------------------
>> On Thu, 11/10/16, Matthew Mazloff <mmazloff at ucsd.edu>
> wrote:
>> 
>> Subject:
> Re: [MITgcm-support] Hello
>> To: mitgcm-support at mitgcm.org
>> Date: Thursday, November 10, 2016, 9:28
> PM
>> 
>> This is likely
> a platform
>> issue. Most likely your path
> to your ifort compiler is
>> wrong.  
>> 
>> You need to
>> change your optfile to point to the
> correct path. If all was
>> working fine
> and now it is not then it is likely that
>> someone updated the fortran compilers on
> your machine and
>> the paths have
> changed.
>> 
>> Clean
> out your build folder. Fix your paths.
>> 
> Try again
>> 
>> Hope
> this
>> helps
>> 
>> -Matt
>> 
>> 
>> 
>>> On Nov 10, 2016, at 9:39 AM,
> smaeilpour
>> <saeid_gal at yahoo.com>
>> wrote:
>>> 
>>> Hi, 
>>> 
>>> I have been having
>> some problem compiling my code today,
> after doing 
>>> 
>>>> make depend
>>> 
>>> I get the
> following
>> error
>>> 
>>> 
>> 
> ../../../tools/cyrus-imapd-makedepend/makedepend: warning
>> :
>>> 
> mdsio_readfield.F (reading SUPPORT.h,
>> 
> line 179): cannot find include
>>> 
> file
>> "mpif.h"  
>>> 
>>>        
>     not in mpif.h
>>>          
>   not in mpif.h
>>>            
> not in   
>> 
> opt/ifort/8.0.044/include/mpif.h
>>> 
> 
>> 
> ../../../tools/f90makedepend>>makefile
>>> 
>>> 
>>> and as a result I cannot compile
> the
>> code.
>>> I am
> sure i have overlooked
>> something quite
> simple.
>>> 
>>> 
> any Idea
>>> 
>>> 
> thanks a lot in advance
>>> saeid
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>> 
> --------------------------------------------
>>> 
>>> 
>>> 
>> 
> ----------------------------------------------------------------------------------------
>>> On Thu, 11/10/16, Jean-Michel
> Campin
>> <jmc at mit.edu> wrote:
>>> 
>>> Subject:
> Re:
>> [MITgcm-support] river runoff
>>> To: mitgcm-support at mitgcm.org
>>> Date: Thursday, November 10, 2016,
> 10:42
>> AM
>>> 
>>> Hi,
>>> 
>>> There are few
>> 
> available options for including
>>> 
>> run-off:
>>> 
>>> 1) the
>> most
>>> commonly used is to include just
>> in the surface level,
>>>    as part of
>> surface forcing (substracted to EmP
>>> 
>> into EmPmR).
>>>    Obviously this
> approach
>> is not
>>> great for deep estuary with
>> high
>>>    vertical
>>> 
>> resolution
> (small dz).
>>>    And the
> effect
>> on
>>> 
> sea-level is accounted for with
>>> 
> useRealFreshWaterFlux=.TRUE.,
>>>    and in a
>>> consistent
>> way
> for any tracers when Non-Lin Freee-surface
>>> is
>>>    used.
>>>    In this case, the
>>> 
>> run-off can be
> provide as part of EmPmR or
>>> 
>>> separately (e.g.,
>> 
> using pkg/exf), but only the run-off that
>>> fall
>>>    on ocean grid
>> cell (wet-cell) will be
>>> considered.
>>> 
> 
>>> 2) If you want
>>> to address the issue of deep
> estuaries,
>> you can 
>>>     try to prescribe
>> a 3-D run-off input (file:
>>> addMassFile
>> 
> loaded into 
>>>     model 2-D
>> array
>>> 
> "addMass") using
>> 
> selectAddFluid=1.
>>>     This
>> requires to compile with #define
>>> 
>> 
> ALLOW_ADDFLUID
>>> 
>>>     Note that
>>> the current code does not provide
> an
>> option to prescribe
>>>     time
>> 
> dependent "addMass" inflow
>>> 
>> (but should not
> be difficult to add).
>>> 
>> 
>>> 3) And the last
> option, as described
>> by Andrea,
>>> is to use OBCS. This enable
>> 
>>>     to
> account,
>>> in the momentum budget,
> for the speed of
>> the incoming
>>> run-off.
>>>    
> Probably useful at very high
>> to
>>> high resolution (bot horizontal and
>> vertical)
>>>    
> but may be not
>> so important at lower
>>> resolution.
>>> 
> 
>>> Cheers,
>>> 
> Jean-Michel
>>> 
>>> On
>>> Wed, Nov
> 09, 2016
>> at 08:31:34AM +0100, Andrea
> Cimatoribus
>>> 
>> 
> wrote:
>>>> Certainly not the
> most
>> expert
>>> 
> around here, but I have been
>> dealing
>>>> 
>>> with
>> this lately, so I can try an answer.
>>>> 
>>>> The
> neatest
>> way to
>>> 
> do it is with obcs package, that
>> is,
> the open
>>>> boundary package.
> In
>> data.obcs you can
>>> define the (vertical)
>> grid
>>>> faces
>>> 
>> through which
> you want to apply the discharge (see
>>> manual).
>>>> 
> Using
>> the correct grid metric,
>>> you can set
>> the
> discharge velocity to
>>>> 
>>> match the total volume discharge (and
> you
>> can easily check
>>> if you
>>>> 
> are doing it right using the
>>> 
> diagnostic output). The simplest way to
>>>> 
>>> impose
> a
>> time-variable discharge and
> temperature is via the
>>> exf
>>>> package, in a
>> 
> new namelist which is
>>> provided by
> the
>> OBCS package,
>>>> something
>>> 
> along these lines:
>>>>    
>>> 
>> 
> &EXF_NML_OBCS
>>>> # OBCS
>> prescribe
>>>>  
>   obcsEstartdate1   =
>>> 
> 20080101,
>>>>    
>>> obcsEstartdate2   =
> 010000,
>>>>    
> obcsEperiod   
>>     =
>>> 3600.,
>>>>  
>   obcsWstartdate1   =
>>> 
> 20080101,
>>>>    
>>> obcsWstartdate2   =
> 010000,
>>>>    
> obcsWperiod   
>>     =
>>> 3600.,
>>>>  
>   &
>>>> As
>>> far as I
>> 
> understand, the temperature of the discharge must
>>> span
>>>> 
> exactly the
>> same time interval and
>>> have the same
>> 
> periodicity as the
>>>> 
>>> velocity.
>>>> 
> The
>> file names containing the
>>> data are
>> defined
> in the data.obcs
>>>> 
>>> (again, see manual).
>>>> 
>>>> Hope
> this
>> helps, best,
>>>> 
>>>> 
> Andrea
>>> 
>> 
> Cimatoribus
>>>> postdoctoral
>> researcher
>>>> 
> EPFL ENAC IIE ECOL
>>>> https://people.epfl.ch/andrea.cimatoribus
>>>> 
>>>> On
> 09/11/16
>> 03:26,
>>> ????????? wrote:
>>>>> Hi
>>>>> 
>> 
>>>>> I am using
>>> mitgcm to simulate SST variation in
>> coastal area with
>>> 
> large
>>>>> runoff. Does anyone
> tell me
>>> how to set up the river?
> How mitgcm
>> deal
>>>>> with river mouth?
>>>> 
>>>> 
>>>>> I've known that the
> runoff
>>> should be added to the
> freshwater flux
>> EmPmR,
>>>>> but how to represent the
>> effect of a
>>> river
> by gridded runoff
>> data is not
>>>> 
>>>> 
> clear to me (should the river grid
>> 
> point be contacted
>>> with ocean
>>>>> interior or
>>> 
>> boundary?).
>>>>> 
>>>> 
> 
>>>> It seems
>> 
> that the test cases in mitgcm do not provide
>>> enough river
>>>>> 
>> 
> information.
>>>>> 
>>>>> I'd
>>> 
>> appreciate any
> help.
>>>>> 
>>>>> 
>>>> 
> 
>>>> ------------------
>>>>> Best
>>> 
> 
>> regards
>>>>> 
>>>> 
> 
>>>> Yu-Kun Qian
>> (?????????)
>>>>> Center
>>> for Monsoon and Environment
> Research
>>>> 
>>>> Department
>> of
> Atmospheric Sciences
>>>> 
>>>> School of Environmental Science
> and
>> Engineering
>>>>> Sun Yat-sen
>> University
>>>>> No. 135 Xingang West
>> Road, Haizhu
>>> 
> District
>>>>> Guangzhou, 510275,
> P.R.
>>> China
>>>>> Tel;
>> 
> 020-84115227
>>>>> Email: qianyk at mail3.sysu.edu.cn
>>> <mailto:qianyk at mail2.sysu.edu.cn>
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>> 
> 
>>>> 
>> 
> _______________________________________________
>>>>> MITgcm-support mailing list
>>>>> MITgcm-support at mitgcm.org
>>>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>> 
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>> 
>>> 
>> 
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