[MITgcm-support] Hello
smaeilpour
saeid_gal at yahoo.com
Wed Nov 16 12:08:30 EST 2016
Hi,
I have gfortran compiler,,,
amgradmac203:~ smollaes$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin15.6.0/6.2.0/lto-wrapper
Target: x86_64-apple-darwin15.6.0
Configured with: ../gcc-6.2.0/configure --enable-languages=c++,fortran --with-gmp=/usr/local
Thread model: posix
gcc version 6.2.0 (GCC)
--------------------------------------------
On Wed, 11/16/16, Martin Losch <martin.losch at awi.de> wrote:
Subject: Re: [MITgcm-support] Hello
To: "MITgcm Support" <mitgcm-support at mitgcm.org>
Date: Wednesday, November 16, 2016, 11:57 AM
Hi Saeid,
if you already have a working installation of gfortran (this
means, that calling “gfortran -v” gives you some output
about the version of the compiler etc. I think I downloaded
mine from hpc.sourceforge.net, but my version 4.9.2 is in
fact very old), then you should be able to download and
compile the model without any specific measures. Just follow
the instructions on mitgcm.org:
# for example:
cvs co MITgcm
cd MITgcm/verification/internal_wave
../../../tools/genmake2 -mods ../code #(this will
automatically use
../../../tools/build_options/darwin_amd64_gfortran if
gfortran is the first compiler in your path, otherwise
specify it with -of)
make CLEAN
make depend
make
# then
cd ../run
ln -s ./input/* .
../build/mitgcmuv > output.txt
all of this can be found on http://mitgcm.org (Getting started)
Martin
> On 16 Nov 2016, at 17:18, smaeilpour <saeid_gal at yahoo.com>
wrote:
>
> Hi Martin
> would you explain what are the necessary compilers for
installing MITgcm Model on Mac OS X EI Capitan?
however i would like to use gfortran compiler and I
installed it on my Mac OS.
> and how Can I install Model on mac? so what are
instructions for that? and how can i put on directory (e.x.
internal wave) in it's right path for running of model?
>
> regards
> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>> _______________________________________________
>>>>> 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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