<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Hi</div><div><br></div><div>Just writing to see how the compilation is coming. Did not want to pressure, just wanted to get a idea of expected release. Thank you very much for your valued assistance.</div><div><br></div><div>Best<br><br>Sent from my iPhone</div><div><br>On 29.01.2013., at 00.09, "Larour, Eric (385J)" <<a href="mailto:eric.larour@jpl.nasa.gov">eric.larour@jpl.nasa.gov</a>> wrote:<br><br></div><blockquote type="cite"><div>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<div>Derrick, </div>
<div><br>
</div>
<div>what version of ISSM are you running? Did you grab your version from the ISSM pre-compiled binary section, </div>
<div>as an installable windows package? I would need to know to fully understand what I need to do. Also, be </div>
<div>aware that I have never compiled a parallel version of the Windows build. This is something that I would </div>
<div>like to go forward with, but I cannot promise it will work. </div>
<div><br>
</div>
<div>In addition, John has indeed prepared an Shp2Exp module to do the translation. I am still testing. As soon as </div>
<div>we have it running, we'll push it through the svn repository. </div>
<div><br>
</div>
<div>Thanks!</div>
<div>Eric L.</div>
<div><br>
</div>
<div><br>
</div>
<span id="OLK_SRC_BODY_SECTION">
<div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span style="font-weight:bold">From: </span>Derrick Lampkin <<a href="mailto:djl22@psu.edu">djl22@psu.edu</a>><br>
<span style="font-weight:bold">Date: </span>Monday, January 28, 2013 8:00 AM<br>
<span style="font-weight:bold">To: </span>"Morlighem, Mathieu (334H-Affiliate)" <<a href="mailto:Mathieu.Morlighem@jpl.nasa.gov">Mathieu.Morlighem@jpl.nasa.gov</a>><br>
<span style="font-weight:bold">Cc: </span>larour <<a href="mailto:eric.larour@jpl.nasa.gov">eric.larour@jpl.nasa.gov</a>>, "Schiermeier, John E (385J)" <<a href="mailto:John.E.Schiermeier@jpl.nasa.gov">John.E.Schiermeier@jpl.nasa.gov</a>>, "<a href="mailto:issm-support@issm.ess.uci.edu">issm-support@issm.ess.uci.edu</a>"
<<a href="mailto:issm-support@issm.ess.uci.edu">issm-support@issm.ess.uci.edu</a>><br>
<span style="font-weight:bold">Subject: </span>Re: data format conversion question..<br>
</div>
<div><br>
</div>
<div>
<div dir="auto">
<div>Hi Mathieu,</div>
<div><br>
</div>
<div>Thanks so much for the help.</div>
<div>Let me know when the updated package is ready.</div>
<div><br>
</div>
<div>Thanks<br>
<br>
Sent from my iPhone</div>
<div><br>
On 28.01.2013., at 09.06, "Morlighem, Mathieu (334H-Affiliate)" <<a href="mailto:Mathieu.Morlighem@jpl.nasa.gov">Mathieu.Morlighem@jpl.nasa.gov</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Derrick,
<div><br>
</div>
<div>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).</div>
<div><br>
</div>
<div>Regards,</div>
<div>Mathieu<br>
<div><br>
<div class="BodyFragment"><font size="2">
<div class="PlainText">----------------------------------------------<br>
Mathieu Morlighem<br>
Assistant Project Scientist<br>
Department of Earth System Science<br>
University of California, Irvine<br>
<br>
(818) 354-4134 (JPL office)<br>
(949) 824-1353 (UCI office)<br>
(626) 429-5780 (cell)<br>
<a href="mailto:Mathieu.Morlighem@uci.edu">Mathieu.Morlighem@uci.edu</a></div>
</font></div>
</div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF754385" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> djl22 [<a href="mailto:djl22@psu.edu">djl22@psu.edu</a>]<br>
<b>Sent:</b> Sunday, January 27, 2013 10:49 PM<br>
<b>To:</b> Morlighem, Mathieu (334H-Affiliate)<br>
<b>Cc:</b> Larour, Eric (385J); Schiermeier, John E (385J); <a href="mailto:issm-support@issm.ess.uci.edu">
issm-support@issm.ess.uci.edu</a><br>
<b>Subject:</b> Re: data format conversion question..<br>
</font><br>
</div>
<div></div>
<div>
<div class="moz-cite-prefix">Thanks so much.<br>
That got the simulation going. It ran for about 40 minutes then bombed (see screen messaged below in red)<br>
Not sure if error is related to the md.cluster setting.<br>
I'm running on my laptop PC (windows) and did not intend to run under any parallel computing architecture.<br>
I initially used your line that prescribes the md.cluster setting:<br>
md.cluster=generic('name',oshostname (),'np',4);<br>
<br>
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...<br>
<br>
<font color="#ff0000">checking model consistency<br>
marshalling file Jakobshavn Basin Dilation.bin<br>
launching solution sequence (stayed at this message for 40 minutes)<br>
call computational core<br>
preparing initial solution<br>
control method step 1/20<br>
compute adjoint state<br>
computing velocities<br>
Error message: Allocating a Vec of size 0 as gsize=0 for configuration: DiagnosticHorizAnalysisError using GetSolutionFromInputs<br>
<br>
<br>
Error in solver_nonlinear (line 20)<br>
ug=GetSolutionFromInputs(femmodel.elements, femmodel.nodes, femmodel.vertices, loads,<br>
femmodel.materials, femmodel.parameters);<br>
<br>
Error in adjointdiagnostic_core (line 17)<br>
femmodel=solver_nonlinear(femmodel,conserve_loads);<br>
<br>
Error in control_core (line 50)<br>
eval(['femmodel=' adjointcore '(femmodel);']);</font><br>
<br>
<br>
On 1/27/2013 6:04 PM, Morlighem, Mathieu (334H-Affiliate) wrote:<br>
</div>
<blockquote type="cite">
<pre>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)
<a class="moz-txt-link-abbreviated" href="mailto:Mathieu.Morlighem@uci.edu" target="_blank">Mathieu.Morlighem@uci.edu</a>
________________________________________
From: djl22 [<a class="moz-txt-link-abbreviated" href="mailto:djl22@psu.edu" target="_blank">djl22@psu.edu</a>]
Sent: Sunday, January 27, 2013 2:15 PM
To: Larour, Eric (385J)
Cc: Schiermeier, John E (385J); <a class="moz-txt-link-abbreviated" href="mailto:issm-support@issm.ess.uci.edu" target="_blank">issm-support@issm.ess.uci.edu</a>; 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:
</pre>
<blockquote type="cite">
<pre>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" <a class="moz-txt-link-rfc2396E" href="mailto:djl22@psu.edu" target="_blank"><djl22@psu.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre>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:
</pre>
<blockquote type="cite">
<pre>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?
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre>md.mesh
whos x y svelocity svelint
</pre>
</blockquote>
</blockquote>
<pre>Thanks!
Eric L.
On 12/31/12 1:53 PM, "Larour, Eric (385J)" <a class="moz-txt-link-rfc2396E" href="mailto:eric.larour@jpl.nasa.gov" target="_blank"><eric.larour@jpl.nasa.gov></a>
wrote:
</pre>
<blockquote type="cite">
<pre>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 <a class="moz-txt-link-abbreviated" href="mailto:issm-support@issm.ess.uci.edu" target="_blank">issm-support@issm.ess.uci.edu</a> in
your reply
all, so other ISSM folks can also help you :)
Eric L.
On 12/31/12 12:17 AM, "djl22" <a class="moz-txt-link-rfc2396E" href="mailto:djl22@psu.edu" target="_blank"><djl22@psu.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre>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:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre>info=geotiffinfo(filename);From
[x,y] = pixcenters(info);
</pre>
</blockquote>
</blockquote>
<pre>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:
</pre>
<blockquote type="cite">
<pre>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" <a class="moz-txt-link-rfc2396E" href="mailto:djl22@psu.edu" target="_blank"><djl22@psu.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre>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: <a class="moz-txt-link-abbreviated" href="mailto:djl22@psu.edu" target="_blank">djl22@psu.edu</a>
_______________________________________________
issm-support mailing list
<a class="moz-txt-link-abbreviated" href="mailto:issm-support@issm.ess.uci.edu" target="_blank">issm-support@issm.ess.uci.edu</a><a class="moz-txt-link-freetext" href="http://issm.ess.uci.edu/cgi-bin/mailman/listinfo/issm-support" target="_blank">http://issm.ess.uci.edu/cgi-bin/mailman/listinfo/issm-support</a></pre>
</blockquote>
</blockquote>
<pre>--
derrick j lampkin
__________________
research professor
institute of arctic and alpine research
university of colorado-boulder
adjunct
department of geoscience
pennsylvania state university
__________________
email: <a class="moz-txt-link-abbreviated" href="mailto:djl22@psu.edu" target="_blank">djl22@psu.edu</a>
web: <a class="moz-txt-link-freetext" href="http://www.geosc.psu.edu/academic-faculty/lampkin-derrick" target="_blank">http://www.geosc.psu.edu/academic-faculty/lampkin-derrick</a></pre>
</blockquote>
<pre>_______________________________________________
issm-support mailing list
<a class="moz-txt-link-abbreviated" href="mailto:issm-support@issm.ess.uci.edu" target="_blank">issm-support@issm.ess.uci.edu</a><a class="moz-txt-link-freetext" href="http://issm.ess.uci.edu/cgi-bin/mailman/listinfo/issm-support" target="_blank">http://issm.ess.uci.edu/cgi-bin/mailman/listinfo/issm-support</a></pre>
</blockquote>
</blockquote>
<pre>--
derrick j lampkin
__________________
research professor
institute of arctic and alpine research
university of colorado-boulder
adjunct
department of geoscience
pennsylvania state university
__________________
email: <a class="moz-txt-link-abbreviated" href="mailto:djl22@psu.edu" target="_blank">djl22@psu.edu</a>
web: <a class="moz-txt-link-freetext" href="http://www.geosc.psu.edu/academic-faculty/lampkin-derrick" target="_blank">http://www.geosc.psu.edu/academic-faculty/lampkin-derrick</a></pre>
</blockquote>
</blockquote>
<pre>--
derrick j lampkin
__________________
research professor
institute of arctic and alpine research
university of colorado-boulder
adjunct
department of geoscience
pennsylvania state university
__________________
email: <a class="moz-txt-link-abbreviated" href="mailto:djl22@psu.edu" target="_blank">djl22@psu.edu</a>
web: <a class="moz-txt-link-freetext" href="http://www.geosc.psu.edu/academic-faculty/lampkin-derrick" target="_blank">http://www.geosc.psu.edu/academic-faculty/lampkin-derrick</a></pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
derrick j lampkin
__________________
research professor
institute of arctic and alpine research
university of colorado-boulder
adjunct
department of geoscience
pennsylvania state university
__________________
email: <a class="moz-txt-link-abbreviated" href="mailto:djl22@psu.edu" target="_blank">djl22@psu.edu</a>
web: <a class="moz-txt-link-freetext" href="http://www.geosc.psu.edu/academic-faculty/lampkin-derrick" target="_blank">http://www.geosc.psu.edu/academic-faculty/lampkin-derrick</a> </pre>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</span>
</div></blockquote></body></html>