From schnetter at cct.lsu.edu  Tue Jun 23 10:02:39 2009
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Tue, 23 Jun 2009 11:02:39 -0400
Subject: [Developers] Correct timing information on web pages
Message-ID: <37CD436D-E6F5-4890-9E7C-2C89088E38D5@cct.lsu.edu>

The enclosed patch corrects the code in HTTPDExtra which parses the  
schedule timing information.  Timers with names that do not follow the  
"usual" pattern are still output, but no attempt is made to break  
their names into thorn name/schedule group/function name.  This still  
outputs e.g. Carpet's timers for schedule groups.

Introduce a new function TI_decomposeTimerName instead of the three  
previous functions TI_thornName, TI_funcName, TI_schedName.

Also remove the unused function TI_printExtraTimerTypeField, and  
remove some unused variables.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/

My email is as private as my paper mail.  I therefore support encrypting
and signing email messages.  Get my PGP key from <http://pgp.mit.edu>.




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From knarf at cct.lsu.edu  Tue Jun 23 20:18:12 2009
From: knarf at cct.lsu.edu (Frank Loeffler)
Date: Tue, 23 Jun 2009 20:18:12 -0500
Subject: [Developers] Correct timing information on web pages
In-Reply-To: <37CD436D-E6F5-4890-9E7C-2C89088E38D5@cct.lsu.edu>
References: <37CD436D-E6F5-4890-9E7C-2C89088E38D5@cct.lsu.edu>
Message-ID: <20090624011811.GE4163@numrel07.cct.lsu.edu>

Hi,

On Tue, Jun 23, 2009 at 11:02:39AM -0400, Erik Schnetter wrote:
> The enclosed patch corrects the code in HTTPDExtra which parses the  
> schedule timing information.  Timers with names that do not follow the  
> "usual" pattern are still output, but no attempt is made to break  
> their names into thorn name/schedule group/function name.  This still  
> outputs e.g. Carpet's timers for schedule groups.
> 
> Introduce a new function TI_decomposeTimerName instead of the three  
> previous functions TI_thornName, TI_funcName, TI_schedName.
> 
> Also remove the unused function TI_printExtraTimerTypeField, and  
> remove some unused variables.

Thanks for the patch. It removes problems, especially with those
'non-standard' timer names. It also cleans up the code. I tested it with
PUGH and Carpet and it worked for those cases.

There is only one minor issue: strlen() returns size_t (not int), which
generates a compiler warning. There is a place in the patch, but also
another place in the old code which uses int. Could you please also
change those two types at this time?

I recommend to submit that patch.

From jco34 at cornell.edu  Thu Jun 25 15:04:32 2009
From: jco34 at cornell.edu (Jeremy Ong)
Date: Thu, 25 Jun 2009 16:04:32 -0400
Subject: [Developers] Carpet HDF5 to VTK convertor
Message-ID: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>

Dear Cactus Users/Developers/Maintainers,

I am interested in viewing HDF5 output from the Carpet thorns using
Paraview. Does any such module exist? If my understanding is correct,
the HDF5 output from Carpet cannot be converted via h5tovtk because of
the mesh refinements.

Thank you!

(I have tried to use Visit, which should have all the necessary
modules in principle, but encountered tremendous difficulty in
building it)


--
Jeremy Ong
Applied & Engineering Physics
Cornell University

From bentivegna at cct.lsu.edu  Thu Jun 25 15:29:58 2009
From: bentivegna at cct.lsu.edu (Eloisa Bentivegna)
Date: Thu, 25 Jun 2009 15:29:58 -0500
Subject: [Developers] Carpet HDF5 to VTK convertor
In-Reply-To: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>
References: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>
Message-ID: <4A43DE46.4000606@cct.lsu.edu>

Jeremy Ong ha scritto:
> Dear Cactus Users/Developers/Maintainers,
> 
> I am interested in viewing HDF5 output from the Carpet thorns using
> Paraview. Does any such module exist? If my understanding is correct,
> the HDF5 output from Carpet cannot be converted via h5tovtk because of
> the mesh refinements.
> 
> Thank you!

Hey Jeremy,

to the best of my knowledge, there isn't one such tool. What you can do, 
however, is to extract the refinement levels one by one using the -d 
flag for h5tovtk, e.g.:

h5tovtk -d "ADMBASE::alp it=$iteration tl=0 rl=$reflevel c=$processor" 
-a -v alp.file_$processor.h5

thereby creating a .vtk file for each component of each refinement level 
at each iteration. For large runs, this can easily turn into a 
nightmare... therefore I'd recommend VisIt and the corresponding plugin.

> (I have tried to use Visit, which should have all the necessary
> modules in principle, but encountered tremendous difficulty in
> building it)

On which architecture are you trying to install VisIt? For the most 
common ones, there are precompiled binaries that you can download from 
the VisIt pages, and my experience is that they usually work out of the 
box. Also, there are public VisIt installations on most Teragrid 
machines and many other supercomputers.

Hope this helps!
Eloisa

From Werner.Benger at aei.mpg.de  Thu Jun 25 16:35:18 2009
From: Werner.Benger at aei.mpg.de (Werner Benger)
Date: Thu, 25 Jun 2009 16:35:18 -0500
Subject: [Developers] Carpet HDF5 to VTK convertor
In-Reply-To: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>
References: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>
Message-ID: <op.uv3nk1snwhv95t@tardis.lsu.edu>

Jeremy,

 depending on your usage scenario, you could also give Vish a try.
This is yet software in development state, but has some support for
visualizing scalar, vector and tensor fields on AMR grids as provided
by Carpet. Project overview page can be found here:

	http://sciviz.cct.lsu.edu/projects/vish/

For Windows we have a installer.exe, under Linux you would need to
sign up at our source code hoster http://vish.origo.ethz.ch/ to get
the source via SVN and compile it yourself. There are some AMR 
screenshots at http://vish.origo.ethz.ch/wiki/screenshots to give you
an impression what might be possible, just be aware that it's still
at work and not as bugfree as visit or paraview.

The native carpet HDF5 format is not supported, but another flavor
of HDF5 provided by the "F5" library as available from 

	http://www.fiberbundle.net/

(website under construction, but it contains a link from where to
download it, including documentation). There exist converters from
the Carpet HDF5 format into F5, as well as a Carpet Thorn that natively
produces F5 files.

However, many things here are in development and/or have not been
tested for a while, though it has worked at least once. Nevertheless,
building F5 and Vish is very easy, only requirement for Vish is the
Qt 4.5 library. The build process certainly is not tremendously
difficult.

Cheers,
	Werner


On Thu, 25 Jun 2009 15:04:32 -0500, Jeremy Ong <jco34 at cornell.edu> wrote:

> Dear Cactus Users/Developers/Maintainers,
>
> I am interested in viewing HDF5 output from the Carpet thorns using
> Paraview. Does any such module exist? If my understanding is correct,
> the HDF5 output from Carpet cannot be converted via h5tovtk because of
> the mesh refinements.
>
> Thank you!
>
> (I have tried to use Visit, which should have all the necessary
> modules in principle, but encountered tremendous difficulty in
> building it)
>
>
> --
> Jeremy Ong
> Applied & Engineering Physics
> Cornell University
> _______________________________________________
> Developers mailing list
> Developers at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/developers
> 



-- 


From jshalf at lbl.gov  Thu Jun 25 19:42:45 2009
From: jshalf at lbl.gov (John Shalf)
Date: Fri, 26 Jun 2009 02:42:45 +0200
Subject: [Developers] Carpet HDF5 to VTK convertor
In-Reply-To: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>
References: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>
Message-ID: <F8CDC6ED-329B-490D-A2D0-AF00731DFA15@lbl.gov>

I created an AMR-to-VTK convertor that does grid-stitching of AMR  
meshes to enable viewing of multi-resolution AMR hierarchies. The  
resulting "stitched' mesh is represented as a Finite Element/ 
Unstructured Mesh to Paraview and VISIT.

Currently the code is written for the Chombo HDF5 file format, but I  
can provide the source to you so that you might be able to modify the  
reader to accept files in the H5/Carpet format if you would like.

-john

On Jun 25, 2009, at 10:04 PM, Jeremy Ong wrote:
> Dear Cactus Users/Developers/Maintainers,
>
> I am interested in viewing HDF5 output from the Carpet thorns using
> Paraview. Does any such module exist? If my understanding is correct,
> the HDF5 output from Carpet cannot be converted via h5tovtk because of
> the mesh refinements.
>
> Thank you!
>
> (I have tried to use Visit, which should have all the necessary
> modules in principle, but encountered tremendous difficulty in
> building it)
>
>
> --
> Jeremy Ong
> Applied & Engineering Physics
> Cornell University
> _______________________________________________
> Developers mailing list
> Developers at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/developers


From schnetter at cct.lsu.edu  Thu Jun 25 20:37:20 2009
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Thu, 25 Jun 2009 21:37:20 -0400
Subject: [Developers] Carpet HDF5 to VTK convertor
In-Reply-To: <4A43DE46.4000606@cct.lsu.edu>
References: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>
	<4A43DE46.4000606@cct.lsu.edu>
Message-ID: <015C9B98-BA7E-4A37-AEE6-1450A7F6AFE8@cct.lsu.edu>

On Jun 25, 2009, at 16:29:58, Eloisa Bentivegna wrote:

> Jeremy Ong ha scritto:
>> Dear Cactus Users/Developers/Maintainers,
>>
>> I am interested in viewing HDF5 output from the Carpet thorns using
>> Paraview. Does any such module exist? If my understanding is correct,
>> the HDF5 output from Carpet cannot be converted via h5tovtk because  
>> of
>> the mesh refinements.
>>
>> Thank you!
>
> Hey Jeremy,
>
> to the best of my knowledge, there isn't one such tool. What you can  
> do,
> however, is to extract the refinement levels one by one using the -d
> flag for h5tovtk, e.g.:
>
> h5tovtk -d "ADMBASE::alp it=$iteration tl=0 rl=$reflevel c=$processor"
> -a -v alp.file_$processor.h5
>
> thereby creating a .vtk file for each component of each refinement  
> level
> at each iteration. For large runs, this can easily turn into a
> nightmare... therefore I'd recommend VisIt and the corresponding  
> plugin.
>
>> (I have tried to use Visit, which should have all the necessary
>> modules in principle, but encountered tremendous difficulty in
>> building it)
>
> On which architecture are you trying to install VisIt? For the most
> common ones, there are precompiled binaries that you can download from
> the VisIt pages, and my experience is that they usually work out of  
> the
> box. Also, there are public VisIt installations on most Teragrid
> machines and many other supercomputers.


Jeremy

We just gave a Cactus tutorial at the TeraGrid '09 conference.  For  
this tutorial, Eloisa prepared a VisIt executable on Queen Bee, one of  
the TeraGrid machines.  For testing, and to see that things will  
indeed work after you built or installed VisIt, you could copy your  
data and visualise them there.

You can use either VisIt's remote visualisation capabilities,  
installing a binary copy of VisIt 1.11.x on your laptop, and  
connecting to the VisIt on Queen Bee which has the Cactus file reader  
already installed.  Alternatively, you can run VisIt on Queen Bee  
directly, and use either X forwarding or VNC to view the result on  
your laptop or workstation.  Detailed instructions are on <http://www.cactuscode.org/Documentation/tutorials/cactustutorialtg2009 
 >.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/

My email is as private as my paper mail.  I therefore support encrypting
and signing email messages.  Get my PGP key from <http://pgp.mit.edu>.



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From jco34 at cornell.edu  Fri Jun 26 08:46:14 2009
From: jco34 at cornell.edu (Jeremy Ong)
Date: Fri, 26 Jun 2009 09:46:14 -0400
Subject: [Developers] Carpet HDF5 to VTK convertor
In-Reply-To: <4A43DE46.4000606@cct.lsu.edu>
References: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com> 
	<4A43DE46.4000606@cct.lsu.edu>
Message-ID: <b308fa0906260646v24cf6017w6b01af5d16d53434@mail.gmail.com>

@Eloisa

Thanks! Are the precompiled binaries built with hdf5 support enabled?

@Werner

Great I have not heard of this software before. I will certainly give it a try.

@John

Your code would indeed be of great help if I do decide to convert
Carpet HDF5 to Vtk. Perhaps others in the community would find such a
program useful too.

@Erik

Reading the tutorial now, thanks.

cheers
Jeremy


--
Jeremy Ong
Applied & Engineering Physics
Cornell University

From bentivegna at cct.lsu.edu  Fri Jun 26 10:21:30 2009
From: bentivegna at cct.lsu.edu (Eloisa Bentivegna)
Date: Fri, 26 Jun 2009 10:21:30 -0500
Subject: [Developers] Carpet HDF5 to VTK convertor
In-Reply-To: <b308fa0906260646v24cf6017w6b01af5d16d53434@mail.gmail.com>
References: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>
	<4A43DE46.4000606@cct.lsu.edu>
	<b308fa0906260646v24cf6017w6b01af5d16d53434@mail.gmail.com>
Message-ID: <4A44E77A.9070600@cct.lsu.edu>

Jeremy Ong ha scritto:
> @Eloisa
> 
> Thanks! Are the precompiled binaries built with hdf5 support enabled?

I believe so. You will also need the visitCarpetHDF5 plugin 
(instructions at <http://www.cactuscode.org/Visualization/VisIt/>).

> Your code would indeed be of great help if I do decide to convert
> Carpet HDF5 to Vtk. Perhaps others in the community would find such a
> program useful too.

Indeed. I would be very interested in learning about this solution. 
John, is the source publicly available?

Thanks,
Eloisa

From jshalf at lbl.gov  Sun Jun 28 03:39:53 2009
From: jshalf at lbl.gov (John Shalf)
Date: Sun, 28 Jun 2009 10:39:53 +0200
Subject: [Developers] Carpet HDF5 to VTK convertor
In-Reply-To: <4A44E77A.9070600@cct.lsu.edu>
References: <b308fa0906251304s22bbe2a2ie8787fbfe37cc1d4@mail.gmail.com>
	<4A43DE46.4000606@cct.lsu.edu>
	<b308fa0906260646v24cf6017w6b01af5d16d53434@mail.gmail.com>
	<4A44E77A.9070600@cct.lsu.edu>
Message-ID: <48465BAA-D79D-4896-A06E-C00F48E5C707@lbl.gov>


On Jun 26, 2009, at 5:21 PM, Eloisa Bentivegna wrote:
> Indeed. I would be very interested in learning about this solution.
> John, is the source publicly available?

It will be as soon as I get home from EU.

-john