[MITgcm-support] Hello
smaeilpour
saeid_gal at yahoo.com
Fri Nov 11 12:32:31 EST 2016
Hi Martin,
Thank you so much for your help, I acted exactly like your advice but after running a test case again error.,,
this time the errors were as fallows:
make [1]: *** [all_proc_dio.o] Error 1
make: *** [fwd_exe_target] Error 2
How do i fix these errors? any idea? I am grateful for your guidance
Best
saeid
--------------------------------------------
On Fri, 11/11/16, Martin Losch <martin.losch at awi.de> wrote:
Subject: Re: [MITgcm-support] Hello
To: "MITgcm Support" <mitgcm-support at mitgcm.org>
Date: Friday, November 11, 2016, 3:48 AM
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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>>
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>>
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