[issm-support] data format conversion question..
Derrick Lampkin
djl22 at psu.edu
Mon Jan 28 22:08:42 PST 2013
Hi,
Yes. I downloaded the pre-compiled windows 7 version for 64 bit before the workshop.
derrick j lampkin
__________________
research professor
institute of arctic and alpine research
university of colorado-boulder
__________________
email: djl22 at psu.edu
On Jan 29, 2013, at 12:09 AM, "Larour, Eric (385J)" <eric.larour at jpl.nasa.gov> wrote:
> Derrick,
>
> what version of ISSM are you running? Did you grab your version from the ISSM pre-compiled binary section,
> as an installable windows package? I would need to know to fully understand what I need to do. Also, be
> aware that I have never compiled a parallel version of the Windows build. This is something that I would
> like to go forward with, but I cannot promise it will work.
>
> In addition, John has indeed prepared an Shp2Exp module to do the translation. I am still testing. As soon as
> we have it running, we'll push it through the svn repository.
>
> Thanks!
> Eric L.
>
>
> From: Derrick Lampkin <djl22 at psu.edu>
> Date: Monday, January 28, 2013 8:00 AM
> To: "Morlighem, Mathieu (334H-Affiliate)" <Mathieu.Morlighem at jpl.nasa.gov>
> Cc: larour <eric.larour at jpl.nasa.gov>, "Schiermeier, John E (385J)" <John.E.Schiermeier at jpl.nasa.gov>, "issm-support at issm.ess.uci.edu" <issm-support at issm.ess.uci.edu>
> Subject: Re: data format conversion question..
>
> Hi Mathieu,
>
> Thanks so much for the help.
> Let me know when the updated package is ready.
>
> Thanks
>
> Sent from my iPhone
>
> On 28.01.2013., at 09.06, "Morlighem, Mathieu (334H-Affiliate)" <Mathieu.Morlighem at jpl.nasa.gov> wrote:
>
>> Hi Derrick,
>>
>> this version of the code is very very very old... Eric, if you could update the windows package it would be nice, Derrick seems to be running in "serial mode", which does not exist anymore (and this mode was awfully slow).
>>
>> Regards,
>> Mathieu
>>
>> ----------------------------------------------
>> Mathieu Morlighem
>> Assistant Project Scientist
>> Department of Earth System Science
>> University of California, Irvine
>>
>> (818) 354-4134 (JPL office)
>> (949) 824-1353 (UCI office)
>> (626) 429-5780 (cell)
>> Mathieu.Morlighem at uci.edu
>> From: djl22 [djl22 at psu.edu]
>> Sent: Sunday, January 27, 2013 10:49 PM
>> To: Morlighem, Mathieu (334H-Affiliate)
>> Cc: Larour, Eric (385J); Schiermeier, John E (385J); issm-support at issm.ess.uci.edu
>> Subject: Re: data format conversion question..
>>
>> Thanks so much.
>> That got the simulation going. It ran for about 40 minutes then bombed (see screen messaged below in red)
>> Not sure if error is related to the md.cluster setting.
>> I'm running on my laptop PC (windows) and did not intend to run under any parallel computing architecture.
>> I initially used your line that prescribes the md.cluster setting:
>> md.cluster=generic('name',oshostname (),'np',4);
>>
>> There was an initial run-time error and I realized that this is likely not reasonable in my case as I'm not running in parallel. I then reran after commenting this line out...
>>
>> checking model consistency
>> marshalling file Jakobshavn Basin Dilation.bin
>> launching solution sequence (stayed at this message for 40 minutes)
>> call computational core
>> preparing initial solution
>> control method step 1/20
>> compute adjoint state
>> computing velocities
>> Error message: Allocating a Vec of size 0 as gsize=0 for configuration: DiagnosticHorizAnalysisError using GetSolutionFromInputs
>>
>>
>> Error in solver_nonlinear (line 20)
>> ug=GetSolutionFromInputs(femmodel.elements, femmodel.nodes, femmodel.vertices, loads,
>> femmodel.materials, femmodel.parameters);
>>
>> Error in adjointdiagnostic_core (line 17)
>> femmodel=solver_nonlinear(femmodel,conserve_loads);
>>
>> Error in control_core (line 50)
>> eval(['femmodel=' adjointcore '(femmodel);']);
>>
>>
>> On 1/27/2013 6:04 PM, Morlighem, Mathieu (334H-Affiliate) wrote:
>>> Hi Derrick,
>>>
>>> just before you solve, make sure you have md.geometry.thickness consistent with the surface and bed:
>>>
>>> md.geometry.surface = md.geonetry.bed + md.geometry.thickness;
>>>
>>> John is almost done with a module that converts shape files to exp.
>>> Let us know if you have other questions
>>>
>>> Best,
>>> Mathieu
>>> ----------------------------------------------
>>> Mathieu Morlighem
>>> Assistant Project Scientist
>>> Department of Earth System Science
>>> University of California, Irvine
>>>
>>> (818) 354-4134 (JPL office)
>>> (949) 824-1353 (UCI office)
>>> (626) 429-5780 (cell)
>>> Mathieu.Morlighem at uci.edu
>>> ________________________________________
>>> From: djl22 [djl22 at psu.edu]
>>> Sent: Sunday, January 27, 2013 2:15 PM
>>> To: Larour, Eric (385J)
>>> Cc: Schiermeier, John E (385J); issm-support at issm.ess.uci.edu; Morlighem, Mathieu (334H-Affiliate)
>>> Subject: Re: data format conversion question..
>>>
>>> Greetings,
>>>
>>> Seem close to getting inversion stage of model running. Keep getting
>>> this error and not sure what the source might be as I have used the
>>> gridded versions of the CRESIS data (GEOTIFFS) over Jakobshavn and they
>>> already compute ice thickness. I also tried recomputing the ice
>>> thickness from their imported surface and bed grids. Both computed and
>>> imported as identical and after setting md.geometry.thickness to either
>>> I keep getting this error:
>>>
>>> model not consistent: equality thickness=surface-bed violated
>>> Error using ismodelselfconsistent (line 39)
>>>
>>>
>>>
>>> I also forwarded the link to my dropbox folder holding the shapefile for
>>> the import test.
>>>
>>> Thank you for all your valued assistance.
>>> Best
>>>
>>> On 1/16/2013 12:55 AM, Larour, Eric (385J) wrote:
>>>> I'm going to bounce that one to John Schiermeier, who wrote converters
>>>> from shape
>>>> files to kml, and from kml to exp. Theoretically, it should be possible to
>>>> use our
>>>> code to do this.
>>>>
>>>> John?
>>>>
>>>> Eric L.
>>>>
>>>>
>>>> On 1/15/13 9:51 PM, "djl22" <djl22 at psu.edu> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I had a small question about data format conversion. I actually have a
>>>>> shapefile created in ARCGIS that defines a regions bounded by polygons.
>>>>> I know I can get them imported into matlab, but I want to use them in a
>>>>> similar way as you did in your Jakobshavn example where you create an
>>>>> Argus file to define regions for shear margin softening.
>>>>> The issue is converting my shapefile into the Argus format without
>>>>> retracing the shapefile using exptool (which is possible, the primary
>>>>> reservation is that some of my polygon geometry is a bit complex in
>>>>> spots), or without having to buy ARGUS ONE personally.
>>>>>
>>>>> Any ideas?
>>>>>
>>>>> Thank you very much.
>>>>> Best
>>>>>
>>>>> On 12/31/2012 5:18 PM, Larour, Eric (385J) wrote:
>>>>>> Derrick,
>>>>>>
>>>>>> I ran your example and everything went fine. So the only thing right now
>>>>>> I can think
>>>>>> of is that your model is not in sync with svelint (i.e. svelint is not a
>>>>>> vertex based vector of
>>>>>> size (md.mesh.numberofvertices,1)). To check on that, could you send me
>>>>>> the results of the following?
>>>>>>
>>>>>>
>>>>>>>> md.mesh
>>>>>>>> whos x y svelocity svelint
>>>>>> Thanks!
>>>>>>
>>>>>> Eric L.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 12/31/12 1:53 PM, "Larour, Eric (385J)" <eric.larour at jpl.nasa.gov>
>>>>>> wrote:
>>>>>>
>>>>>>> Derrick,
>>>>>>>
>>>>>>> I'm also puzzled as to why bang is giving you an error. I am right now
>>>>>>> working
>>>>>>> on reproducing the bug from your procedure document. Will keep you
>>>>>>> posted
>>>>>>> as soon
>>>>>>> as I find the bug. Should not be long.
>>>>>>>
>>>>>>> For further reference, please include issm-support at issm.ess.uci.edu in
>>>>>>> your reply
>>>>>>> all, so other ISSM folks can also help you :)
>>>>>>>
>>>>>>> Eric L.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 12/31/12 12:17 AM, "djl22" <djl22 at psu.edu> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I think I found a way through it. I tried working with the original
>>>>>>>> data, which provides surface velocity over the entire Greenland ice
>>>>>>>> sheet projected in polar stereographic. I used geotiffread to import
>>>>>>>> the
>>>>>>>> GEOTIFF image. I used exptool to draw my domain as a sub-region
>>>>>>>> (Jakobshavn area) from the imported image and set the initial
>>>>>>>> resolution
>>>>>>>> of my mesh at 2km (2000m). The output mesh looks about right. I then
>>>>>>>> extract the pixel center coordinates using the pixcenters command:
>>>>>>>>>> info=geotiffinfo(filename);From
>>>>>>>>>> [x,y] = pixcenters(info);
>>>>>>>> This gets my coordinates for pixel centers. I then have to flip my (y)
>>>>>>>> coordinates because the InterpFromGridToMesh command complains that
>>>>>>>> the
>>>>>>>> values should be decreasing. After doing so I run the
>>>>>>>> InterpFromGridToMesh command and here things get odd. I notice that in
>>>>>>>> your examples the velx and vely variables in your Searise and
>>>>>>>> jakobshavn
>>>>>>>> examples are entered in the InterpFromGridToMesh command as the
>>>>>>>> transpose of these variables, is this correct? (i.e.
>>>>>>>> vx=InterpFromGridToMesh(x1,y1,velx',md.mesh.x,md.mesh.y,0);).
>>>>>>>> If I enter my velocity grid as such then I get an error. if I enter
>>>>>>>> without the transpose the command seems to work, but then I get an odd
>>>>>>>> message when I use the output from the Interp command in the following
>>>>>>>> bamg command. I get:
>>>>>>>>
>>>>>>>> Anisotropic mesh adaptation
>>>>>>>> Error message: 'field' should have 930 rowsError using BamgMesher
>>>>>>>>
>>>>>>>> At this point I'm lost as to why its not working. When I attempted to
>>>>>>>> run your Searise example as indicated, I ended up with the same exact
>>>>>>>> error in running bamg (I ran the lines of code provided directly from
>>>>>>>> the example). I also go tthis error when I ran the Searise example:
>>>>>>>> Error message: Input parameter of class single not supported yetError
>>>>>>>> using InterpFromGridToMesh
>>>>>>>>
>>>>>>>> when I ran
>>>>>>>> vx=InterpFromGridToMesh(x1,y1,velx',md.mesh.x,md.mesh.y,0);...in this
>>>>>>>> case I converted the input variables x1, y1 and velx, vely to double
>>>>>>>> (x1=double(x1), etc...) was this necessary to get it to work? The
>>>>>>>> command worked after doing this which means ISSM could not recognize
>>>>>>>> the
>>>>>>>> data type "single" as oppose to "double"
>>>>>>>>
>>>>>>>> at any rate, i'm now stuck at bamg where I'm attempting to use the
>>>>>>>> velocity i assume were interpolated to my initial mesh within my
>>>>>>>> custom
>>>>>>>> domain to refine my initial mesh which would ideally create finer mesh
>>>>>>>> grids near the margins of Jakobshavn than outside of the margins....
>>>>>>>>
>>>>>>>> Thanks so much for the assistance....
>>>>>>>>
>>>>>>>>
>>>>>>>> On 12/29/2012 3:04 AM, Larour, Eric (385J) wrote:
>>>>>>>>> Dear Derrick,
>>>>>>>>>
>>>>>>>>> I think the issue is that when you plotted your surface velocities in
>>>>>>>>> matlab (before calling exptool
>>>>>>>>> on it), you did not specify the x and y coordinates of your image.
>>>>>>>>>
>>>>>>>>> Typically, in matlab, one does:
>>>>>>>>>
>>>>>>>>> imagesc(velocity) where velocity is a matrix. This will get you
>>>>>>>>> coordinates in scene coordinates.
>>>>>>>>>
>>>>>>>>> For your example, what you need to do is:
>>>>>>>>> imagesc(x,y,velocity),
>>>>>>>>> where x=0:(xmax-xmin)/m:xmax and
>>>>>>>>> y=0:(ymax-ymin)/n:ymax
>>>>>>>>>
>>>>>>>>> and m,n is the size of the velocity matrix.
>>>>>>>>>
>>>>>>>>> If you do this, you will recover from exptools the true vertex
>>>>>>>>> coordinates.
>>>>>>>>>
>>>>>>>>> Tell me how it goes!
>>>>>>>>>
>>>>>>>>> Thanks!
>>>>>>>>> Eric L.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 12/28/12 11:58 PM, "Derrick Lampkin" <djl22 at psu.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Greetings,
>>>>>>>>>>
>>>>>>>>>> I recently attended the ISSM workshop and found it useful. I'm
>>>>>>>>>> attempting
>>>>>>>>>> to use the system to model a system in the Jakobshavn outlet basin.
>>>>>>>>>> I
>>>>>>>>>> have been using your Jakobshavn example as a template. The exception
>>>>>>>>>> is
>>>>>>>>>> I'm using a base of surface velocity data derived from NSIDC
>>>>>>>>>> (Joughin
>>>>>>>>>> data set). I have imported a surface velocity grid as GEOTIFF into
>>>>>>>>>> matlab
>>>>>>>>>> and I use the exptool to draw the outline of my domain on top of
>>>>>>>>>> this
>>>>>>>>>> base map. The map is in the polar stereo graphic projection but
>>>>>>>>>> when I
>>>>>>>>>> create the initial mesh using triangle at the nominal resolution of
>>>>>>>>>> the
>>>>>>>>>> data (500 m), the grid spacing was not nearly as dense as expected.
>>>>>>>>>> I
>>>>>>>>>> inspected the domain file I created and the vertices coordinates are
>>>>>>>>>> in
>>>>>>>>>> scene coordinates (row/column) values and not the projected
>>>>>>>>>> coordinates ,
>>>>>>>>>> therefore the mesh spacing are not reasonable and do not correspond
>>>>>>>>>> to
>>>>>>>>>> the specified resolution I indicate in the triangle command. How
>>>>>>>>>> might
>>>>>>>>>> I
>>>>>>>>>> fix this issue?
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> derrick j lampkin
>>>>>>>>>> __________________
>>>>>>>>>> research professor
>>>>>>>>>>
>>>>>>>>>> institute of arctic and alpine research
>>>>>>>>>>
>>>>>>>>>> university of colorado-boulder
>>>>>>>>>>
>>>>>>>>>> __________________
>>>>>>>>>>
>>>>>>>>>> email: djl22 at psu.edu
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> issm-support mailing list
>>>>>>>>>> issm-support at issm.ess.uci.eduhttp://issm.ess.uci.edu/cgi-bin/mailman/listinfo/issm-support
>>>>>>>> --
>>>>>>>> derrick j lampkin
>>>>>>>> __________________
>>>>>>>> research professor
>>>>>>>>
>>>>>>>> institute of arctic and alpine research
>>>>>>>> university of colorado-boulder
>>>>>>>> adjunct
>>>>>>>> department of geoscience
>>>>>>>> pennsylvania state university
>>>>>>>> __________________
>>>>>>>>
>>>>>>>> email: djl22 at psu.edu
>>>>>>>> web: http://www.geosc.psu.edu/academic-faculty/lampkin-derrick
>>>>>>> _______________________________________________
>>>>>>> issm-support mailing list
>>>>>>> issm-support at issm.ess.uci.eduhttp://issm.ess.uci.edu/cgi-bin/mailman/listinfo/issm-support
>>>>> --
>>>>> derrick j lampkin
>>>>> __________________
>>>>> research professor
>>>>>
>>>>> institute of arctic and alpine research
>>>>> university of colorado-boulder
>>>>> adjunct
>>>>> department of geoscience
>>>>> pennsylvania state university
>>>>> __________________
>>>>>
>>>>> email: djl22 at psu.edu
>>>>> web: http://www.geosc.psu.edu/academic-faculty/lampkin-derrick
>>> --
>>> derrick j lampkin
>>> __________________
>>> research professor
>>>
>>> institute of arctic and alpine research
>>> university of colorado-boulder
>>> adjunct
>>> department of geoscience
>>> pennsylvania state university
>>> __________________
>>>
>>> email: djl22 at psu.edu
>>> web: http://www.geosc.psu.edu/academic-faculty/lampkin-derrick
>>
>>
>> --
>> derrick j lampkin
>> __________________
>> research professor
>>
>> institute of arctic and alpine research
>> university of colorado-boulder
>> adjunct
>> department of geoscience
>> pennsylvania state university
>> __________________
>>
>> email: djl22 at psu.edu
>> web: http://www.geosc.psu.edu/academic-faculty/lampkin-derrick
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