Particle tracking - vertical adaptive grid

[Adriana Huerta-Casas]

Dear GETM users,

I have two questions:

1) is the particle tracking module already implemented in GETM? If so, how does it work?

2) Can I already make use of the vertical adaptive grid?

Thanks a lot!
adriana

[Ulf Gräwe]

On Thu, 2012-04-12 at 12:23 +0200, Adriana Huerta-Casas wrote:
>
> Dear GETM users,
>
> I have two questions:
>
> 1) is the particle tracking module already implemented in GETM? If so,
> how does it work?

Hi Adriana,
there is no particle-tracking implemented in GETM. However, you have to
compute the velocity fields, temperature, viscosity, ... and store these
fields with an high temporal resolution. Than you can use GITM, a
particle-tracking tool developed for GETM output fields. GITM is an
independent tool. Either you contact Johan van der Molen (CEFAS) or
Bianca Schippmann (IOW). They can help you to set up GITM.

>
> 2) Can I already make use of the vertical adaptive grid?
>

This is not a problem at all.

Cheers, ulf

> Thanks a lot!
> adriana
>

--
Ulf Gr�we

Leibniz Institute for Baltic Sea Research Warnemuende
Dept. for Physical Oceanography and Instrumentation
Seestrasse 15
D-18119 Rostock-Warnemuende
Germany

Pho. : +49 (381) 5197-358
Fax : +49 (381) 5197-440
Web : http://www.io-warnemuende.de/ulf-graewe-en.html
Room : 216

[Johan Van Der Molen (Cefas)]

> -----Original Message-----
> From: getm-...@googlegroups.com [mailto:getm-...@googlegroups.com]
> On Behalf Of Ulf Gräwe
> Sent: Thursday, April 12, 2012 12:14 PM
> To: getm-...@googlegroups.com
> Subject: Re: [getm-users: 1672] Particle tracking - vertical adaptive
> grid
>
> On Thu, 2012-04-12 at 12:23 +0200, Adriana Huerta-Casas wrote:
> >
> > Dear GETM users,
> >
> > I have two questions:
> >
> > 1) is the particle tracking module already implemented in GETM? If
> so,
> > how does it work?
>
> Hi Adriana,
> there is no particle-tracking implemented in GETM. However, you have to
> compute the velocity fields, temperature, viscosity, ... and store
> these
> fields with an high temporal resolution. Than you can use GITM, a
> particle-tracking tool developed for GETM output fields. GITM is an
> independent tool. Either you contact Johan van der Molen (CEFAS) or
> Bianca Schippmann (IOW). They can help you to set up GITM.
>

I can supply you with the latest version if you like.

> >
> > 2) Can I already make use of the vertical adaptive grid?
> >
>
> This is not a problem at all.
>

I don't think GITM will work by default with vertical adaptive coordinates, as it was created before that option was added to GETM. But it may do as it allows for vertical motion of a 'fixed' grid through changes in water level. I will have a look.

Best wishes,

Johan

> Cheers, ulf
>
> > Thanks a lot!
> > adriana
> >
>
>
> --

> Ulf Gräwe

>
> Leibniz Institute for Baltic Sea Research Warnemuende
> Dept. for Physical Oceanography and Instrumentation
> Seestrasse 15
> D-18119 Rostock-Warnemuende
> Germany
>
> Pho. : +49 (381) 5197-358
> Fax : +49 (381) 5197-440
> Web : http://www.io-warnemuende.de/ulf-graewe-en.html
> Room : 216
>

This email and any attachments are intended for the named recipient only. Its unauthorised use, distribution, disclosure, storage or copying is not permitted. If you have received it in error, please destroy all copies and notify the sender. In messages of a non-business nature, the views and opinions expressed are the author's own and do not necessarily reflect those of Cefas. Communications on Cefas’ computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes.

[Georges Djoumna]

Dear GETM users,

I have this error message when I compile the  stable version is 2.2.

halo_mpi.F90(624): error #6633: The type of the actual argument differs from the type of the dummy argument.   [SIZEOF_REALTYPE]

   call MPI_TYPE_EXTENT(MPI_DOUBLE_PRECISION,sizeof_realtype,ierr)

---------------------------------------------^

halo_mpi.F90(637): warning #6075: The data type of the actual argument does not match the definition.

   call MPI_TYPE_HVECTOR(2,1,x_size*sizeof_realtype,x_line,x_lines,ierr)

-----------------------------------^

I don't know how to fix the problem.

Thanks.

------------------------------------------------------------

Georges Djoumna, Ph.D. 

Department of Applied Mathematics 

University of Waterloo 

Office MC 5135 

Waterloo, Ontario 

Canada N2L 3G1 

E-mail        :  gdjo...@math.uwaterloo.ca 

Office Phone  :  1 519 888 4567 Ext 36648

[Knut]

Hi Georges,

Ilja reported something similar and Karsten fixed the devel version.
Can you please try with the devel version and report back.
Probably we have to fix the stable then as well.

Regards,
Knut

> <mailto:gdjo...@math.uwaterloo.ca>

[Karsten Bolding]

I'll do a back-port.

Karsten

PS: For the I don't know what time - please start a new thread when
raising a new issue.

--
http://www.getm.eu

[Karsten Bolding]

can you try the updated stable version now?

You are using a 64 bit system - right?

Karsten

On Tue, Apr 17, 2012 at 11:56:42 -0400, Georges Djoumna wrote:

--
http://www.getm.eu

[Georges Djoumna]

Hi,

I have try the updated stable version, but I still have the same error.

I am using a 64 bit system.

Georges

[Knut]

Hi Georges,

please excuse my question, but sometimes users are not familar with git
and I do not know your experience... :-)

Did you make a "git pull"? Do you see Karstens commit with "git log"?

Knut

>>> <mailto:gdjo...@math.uwaterloo.ca>

[Georges Djoumna]

Hi Knut,

I am not familiar with git. I just use 

git clone git://getm.git.sourceforge.net/gitroot/getm/getm getm-git 

to download the code and then compiles it.

I did not make a "git pull"

Thanks

Georges

[Georges Djoumna]

Hi Knut,

I make a "git pull" and recompile the code. The same error appears.

Georges

[Knut]

Dear Georges,

> Hi Knut,
> I am not familiar with git. I just use
> git clone git://getm.git.sourceforge.net/gitroot/getm/getm getm-git
>
> to download the code and then compiles it.
>
> I did not make a "git pull"

ok. please be aware that the default version you get after a clone is
the devel version. for the stable version you have to do (after the clone):

git checkout -b stable origin/stable

But this does not solve the problem... :-)

can you please try to compile the branch you get with:

git branch v2.2.0 origin/stable^1
git checkout v2.2.0

Regards,
Knut

[Knut]

> git branch v2.2.0 origin/stable^1
In case your mail client tries to be intelligent:
The command should of course not be a "superscript1", but a "hat1"!!!

[Georges Djoumna]

Hi Knut,

By using 

git branch v2.2.0 origin/stable^1

git checkout v2.2.0

I successfully compile the code.

Should I use these command every time I want to compile the stable version v2.2.0?

Thanks

Georges

[Knut]

Dear Georges,

thanks for your fast test and reply.

>
> By using
> git branch v2.2.0 origin/stable^1
> git checkout v2.2.0
>
> I successfully compile the code.

very interesting. Karsten and Ilja, can you sort that out?

>
> Should I use these command every time I want to compile the stable
> version v2.2.0?

This is only necessary if you clone again a new getm-git.
With the 1st command you created the branch v2.2.0 in you local
getm-git. With the 2nd command you switched to that branch. If you are
fine with continueing to work with that branch, you do not need to
execute any git commands.

Hope this helps,
Knut

[Ilja Maljutenko]

On Wed, Apr 18, 2012 at 9:06 PM, Knut <knut...@gmx.net> wrote:

Dear Georges,

thanks for your fast test and reply.

By using git branch v2.2.0 origin/stable^1
git checkout v2.2.0

I successfully compile the code.

very interesting. Karsten and Ilja, can you sort that out?

Tested same thing ...

> git clone git://getm.git.sourceforge.net/gitroot/getm/getm getm-git

and compiled without errors.
Then swiched into stable version ..

> git branch v2.2.0 origin/stable^1
> git checkout v2.2.0

And the old warning #6075 reappeared (Geroges seems to have error #6633 that i did not have ).

Link to that old thread is here 
http://groups.google.com/group/getm-users/browse_thread/thread/a0864d240363df7a

Best I could think is study the difference of two files with  diff command.  
 But I doubt there is anything else other than the change that Karsten did with the size_of_realtype. 

  

BR,

--
~ Ilja 

Ps: I can't find any leads that would put me back on a deafult devel branch with git :(, can someone help me with that?  

[Knut]

Hi Ilja,

>
> Ps: I can't find any leads that would put me back on a deafult devel
> branch with git :(, can someone help me with that?

git checkout master ?

[Ilja Maljutenko]

Thanks!  
 
--
~ Ilja 

[Karsten Bolding]

Hello

On a 64 bit system I can do:

cd GETM/getm-git/
git checkout stable
git log - shows a message from Apr 18 10:01:27

cd ~/getm-setups/git/box_cartesian
make mpi - compiles OK - for testing I add a print statement to show the
size of 'sizeof_realtype' and I get 8.

So in short - the stable code works on 64 bit machines with update code.

Karsten

On Tue, Apr 17, 2012 at 11:56:42 -0400, Georges Djoumna wrote:

--
http://www.getm.eu

[Georges Djoumna]

Thanks a lot.

Is there a tutorial or a test case available on how to use FABM with GETM v2.2?

I would like to do some biogeochemical run for Lakes.

Thanks

Georges

[Knut]

Hi Karsten and Georges,

in my opinion there seems to be still a problem.
Karsten had problems with the v2.2.0 stable and solved them with the
backport. For Georges it was the other way around...

Knut

>>> <mailto:gdjo...@math.uwaterloo.ca>

[Georges Djoumna]

Dear GETM users,

when  compiling the stable version  2.2 of GETM  with " export FABM=true", the following errors  appear.

It looks like I have to set a path fro GOTM_FABM?

 

make[1]: Entering directory `/RAID3/gdjoumna/GETM_git/getm-git/src/3d'

ifort -DIFORT -DFORTRAN95 -DREAL_4B=real\(kind=4\) -D_FABM_ -DNETCDF3 -DGETM_PARALLEL -DPRODUCTION  -O3 -i-static -mp1  -module /RAID3/gdjoumna/GETM_git/getm-git/modules/IFORT -I/RAID3/gdjoumna/GETM_git/getm-git/include -I/RAID3/gdjoumna/GETM_git/getm-git/modules/IFORT -I/home/gdjoumna/FABM/fabm-git/include -I/home/gdjoumna/FABM/fabm-git/modules/gotm/IFORT -I/home/gdjoumna/FABM/fabm-git/src/drivers/gotm -I/RAID3/gdjoumna/GOTM_git/gotm-git/modules/IFORT -w95  -c getm_fabm.F90

getm_fabm.F90(22): error #6580: Name in only-list does not exist.   [FABM_PEL]

   use variables_3d,only: fabm_pel,fabm_ben,fabm_diag,fabm_diag_hz

--------------------------^

getm_fabm.F90(22): error #6580: Name in only-list does not exist.   [FABM_BEN]

   use variables_3d,only: fabm_pel,fabm_ben,fabm_diag,fabm_diag_hz

-----------------------------------^

getm_fabm.F90(22): error #6580: Name in only-list does not exist.   [FABM_DIAG]

   use variables_3d,only: fabm_pel,fabm_ben,fabm_diag,fabm_diag_hz

--------------------------------------------^

getm_fabm.F90(22): error #6580: Name in only-list does not exist.   [FABM_DIAG_HZ]

   use variables_3d,only: fabm_pel,fabm_ben,fabm_diag,fabm_diag_hz

------------------------------------------------------^

getm_fabm.F90(30): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [GOTM_FABM]

   use gotm_fabm, only: init_gotm_fabm,set_env_gotm_fabm,do_gotm_fabm

-------^

getm_fabm.F90(31): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [GOTM_FABM]

   use gotm_fabm, only: fabm_calc, model, cc_col=>cc, cc_diag_col=>cc_diag, cc_diag_hz_col=>cc_diag_hz

-------^

getm_fabm.F90(32): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [FABM_TYPES]

   use fabm_types,only: time_treatment_last

-------^

Thanks

Georges

On 20-Apr-12, at 5:08 AM, Karsten Bolding wrote:

[Ilja Maljutenko]

Hi,

On Fri, May 11, 2012 at 7:50 PM, Georges Djoumna <gdjo...@uwaterloo.ca> wrote:

Dear GETM users,

when  compiling the stable version  2.2 of GETM  with " export FABM=true", the following errors  appear.

Try
export _FABM_=true
because in the script it reads
#ifdef _FABM_

BR,

--
~ Ilja 

[Ilja Maljutenko]

Sorry, ignore the last post.
Seems you allready had " -D_FABM_"  tag. 
The error was similar with the one i had some times ago, thats why I thought that this could be the case.

--
~ Ilja 

[Georges Djoumna]

Hi 

I 've done a make distclean  and set  export _FABM_=true

 I receive  a different error message.

getm_fabm.F90(30): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [GOTM_FABM]

   use gotm_fabm, only: init_gotm_fabm,set_env_gotm_fabm,do_gotm_fabm

-------^

getm_fabm.F90(31): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [GOTM_FABM]

   use gotm_fabm, only: fabm_calc, model, cc_col=>cc, cc_diag_col=>cc_diag, cc_diag_hz_col=>cc_diag_hz

-------^

How to set  GOTM_FABM path?

 

Thanks

Georges

[Ulf Gräwe]

Have you properly compiled FABM in $FABMDIR/src/ ?

Have you also freshly compiled GOTM with:
export FABM=true ?

--
Ulf Gräwe

Leibniz Institute for Baltic Sea Research Warnemuende
Dept. for Physical Oceanography and Instrumentation
Seestrasse 15
D-18119 Rostock-Warnemuende
Germany

Tel. : +49 (381) 5197-358
Fax : +49 (381) 5197-440

[Georges Djoumna]

Hello Ulf,

Thanks for your suggestions: When
I properly compile FABM in $FABMDIR/src/
and compile GOTM with export FABM=true

I have this error

ifort -DIFORT -DFORTRAN95 -DREAL_4B=real\(kind=4\) -D_FABM_ -DNETCDF3
-DGETM_PARALLEL -DPRODUCTION -O3 -i-static -mp1 -module /RAID3/
gdjoumna/GETM_git/getm-git/modules/IFORT -I/RAID3/gdjoumna/GETM_git/
getm-git/include -I/RAID3/gdjoumna/GETM_git/getm-git/modules/IFORT -I/
home/gdjoumna/FABM/fabm-git/include -I/home/gdjoumna/FABM/fabm-git/
modules/gotm/IFORT -I/home/gdjoumna/FABM/fabm-git/src/drivers/gotm -I/
RAID3/gdjoumna/GOTM_git/gotm-git/modules/IFORT -w95 -c getm_fabm.F90

getm_fabm.F90(32): error #7002: Error in opening the compiled module
file. Check INCLUDE paths. [FABM_TYPES]
use fabm_types,only: time_treatment_last
-------^

getm_fabm.F90(32): error #6580: Name in only-list does not exist.
[TIME_TREATMENT_LAST]
use fabm_types,only: time_treatment_last
------------------------^
getm_fabm.F90(106): error #6406: Conflicting attributes or multiple
declaration of name. [TIME_TREATMENT_LAST]
model%info%diagnostic_variables(n)%time_treatment =
time_treatment_last
-------------------------------------------------------------^
getm_fabm.F90(109): error #6406: Conflicting attributes or multiple
declaration of name. [TIME_TREATMENT_LAST]
model%info%diagnostic_variables_hz(n)%time_treatment =
time_treatment_last


Thanks.

Georges

[Karsten Bolding]

do you have this directory:
/home/gdjoumna/FABM/fabm-git/include
or this:
/home/gdjoumna/FABM/fabm-git/src/drivers/gotm
?

The compiler actually write s a lot of usefull information that can be
used to check for errors.

You have chosen to install in non-staandard places - this makes it more
complicated but still doable.

Karsten

On Mon, May 14, 2012 at 02:40:48 -0400, Georges Djoumna wrote:
> Hello Ulf,
>
> Thanks for your suggestions: When
> I properly compile FABM in $FABMDIR/src/
> and compile GOTM with export FABM=true
>
> I have this error
>
> ifort -DIFORT -DFORTRAN95 -DREAL_4B=real\(kind=4\) -D_FABM_
> -DNETCDF3 -DGETM_PARALLEL -DPRODUCTION -O3 -i-static -mp1 -module

> /RAID3/gdjoumna/GETM_git/getm-git/modules/IFORT
> -I/RAID3/gdjoumna/GETM_git/getm-git/include
> -I/RAID3/gdjoumna/GETM_git/getm-git/modules/IFORT -I/home/gdjoumna/FABM/fabm-git/include
> -I/home/gdjoumna/FABM/fabm-git/modules/gotm/IFORT
> -I/home/gdjoumna/FABM/fabm-git/src/drivers/gotm -I/RAID3/gdjoumna/GOTM_git/gotm-git/modules/IFORT

> >Ulf Gr�we

> >
> >Leibniz Institute for Baltic Sea Research Warnemuende
> >Dept. for Physical Oceanography and Instrumentation
> >Seestrasse 15
> >D-18119 Rostock-Warnemuende
> >Germany
> >
> >Tel. : +49 (381) 5197-358
> >Fax : +49 (381) 5197-440
>
>

--
http://www.getm.eu

[Georges Djoumna]

Hello Karsten

I do have the directory

/home/gdjoumna/FABM/fabm-git/src/drivers/gotm.

I don't have 

/home/gdjoumna/FABM/fabm-git/include

How do i install FABM in standard places?

Thanks

Georges

Ulf Gräwe

Leibniz Institute for Baltic Sea Research Warnemuende

Dept. for Physical Oceanography and Instrumentation

Seestrasse 15

D-18119 Rostock-Warnemuende

Germany

Tel. : +49 (381) 5197-358

Fax  : +49 (381) 5197-440

-- 

http://www.getm.eu