From babiuc at marshall.edu Mon Apr 6 09:34:52 2009 From: babiuc at marshall.edu (Babiuc-Hamilton, Maria) Date: Mon, 6 Apr 2009 10:34:52 -0400 Subject: [Users] generating output for VisIt Message-ID: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861B@MUXC09.marshall.edu> Hello, I would really appreciate if somebody will walk me through the process of obtaining a viable output that can be visualized with the VisIt software. I looked over the http://www.cactuscode.org/Visualization/VisIt/ web page and I am not sure: is visitCarpetHDF5 what I need? Can I have acces to a sample parameter file/ best, Maria From bentivegna at cct.lsu.edu Mon Apr 6 09:56:30 2009 From: bentivegna at cct.lsu.edu (Eloisa Bentivegna) Date: Mon, 06 Apr 2009 09:56:30 -0500 Subject: [Users] generating output for VisIt In-Reply-To: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861B@MUXC09.marshall.edu> References: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861B@MUXC09.marshall.edu> Message-ID: <49DA181E.8040700@cct.lsu.edu> Babiuc-Hamilton, Maria ha scritto: > Hello, > > I would really appreciate if somebody will walk me through the process of obtaining a viable output that can be visualized with the VisIt software. I looked over the http://www.cactuscode.org/Visualization/VisIt/ web page and I am not sure: is visitCarpetHDF5 what I need? Can I have acces to a sample parameter file/ Hi! VisIt recognizes the HDF5 format, so you could use, say, CarpetIOHDF5, specifying the corresponding parameters as it's usually done for other sorts of output: IOHDF5::out_every = 32 IOHDF5::out_vars = " ADMBase::lapse " This produces a number of .h5 files, which will be readable by VisIt. As for visitCarpetHDF5, this is not a Cactus component, but a plugin that helps VisIt parse the mesh structure and other metadata from your simulation. There should be instructions on how to include this plugin in your VisIt installation on the page you mentioned. Hope this helps! Eloisa From babiuc at marshall.edu Mon Apr 6 13:16:24 2009 From: babiuc at marshall.edu (Babiuc-Hamilton, Maria) Date: Mon, 6 Apr 2009 14:16:24 -0400 Subject: [Users] generating output for VisIt In-Reply-To: <49DA181E.8040700@cct.lsu.edu> References: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861B@MUXC09.marshall.edu>, <49DA181E.8040700@cct.lsu.edu> Message-ID: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861C@MUXC09.marshall.edu> Hello, Thank you. I generated files of the type gxy.file_0.h5 and tried to visualize it with Visit, as mesh or volume, but I did not have too much of a success. Could you please let me know if I'm doing it right? Thanks, Maria ________________________________________ From: users-bounces at cactuscode.org [users-bounces at cactuscode.org] On Behalf Of Eloisa Bentivegna [bentivegna at cct.lsu.edu] Sent: Monday, April 06, 2009 10:56 AM To: Cactus users mailing list Subject: Re: [Users] generating output for VisIt Babiuc-Hamilton, Maria ha scritto: > Hello, > > I would really appreciate if somebody will walk me through the process of obtaining a viable output that can be visualized with the VisIt software. I looked over the http://www.cactuscode.org/Visualization/VisIt/ web page and I am not sure: is visitCarpetHDF5 what I need? Can I have acces to a sample parameter file/ Hi! VisIt recognizes the HDF5 format, so you could use, say, CarpetIOHDF5, specifying the corresponding parameters as it's usually done for other sorts of output: IOHDF5::out_every = 32 IOHDF5::out_vars = " ADMBase::lapse " This produces a number of .h5 files, which will be readable by VisIt. As for visitCarpetHDF5, this is not a Cactus component, but a plugin that helps VisIt parse the mesh structure and other metadata from your simulation. There should be instructions on how to include this plugin in your VisIt installation on the page you mentioned. Hope this helps! Eloisa _______________________________________________ Users mailing list Users at cactuscode.org http://www.cactuscode.org/mailman/listinfo/users From bentivegna at cct.lsu.edu Mon Apr 6 13:37:12 2009 From: bentivegna at cct.lsu.edu (Eloisa Bentivegna) Date: Mon, 06 Apr 2009 13:37:12 -0500 Subject: [Users] generating output for VisIt In-Reply-To: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861C@MUXC09.marshall.edu> References: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861B@MUXC09.marshall.edu>, <49DA181E.8040700@cct.lsu.edu> <31D46DC505870A4C980A8F38BB2DBD0E6350B3861C@MUXC09.marshall.edu> Message-ID: <49DA4BD8.7000009@cct.lsu.edu> Babiuc-Hamilton, Maria ha scritto: > Hello, > > Thank you. I generated files of the type gxy.file_0.h5 and tried to visualize it with Visit, as mesh or volume, but I did not have too much of a success. > Could you please let me know if I'm doing it right? Sure. Could you say more on your system and where exactly the visualization fails? In particular: 1) Does the visualization machine have HDF5 installed (if this is the same machine where you're running your simulation, I suppose the answers is yes)? 2) Was VisIt built with HDF5 support? 3) Are you or are you not using visitCarpetHDF5 in the end? 4) What happens when you try to open the .h5 file with VisIt? Eloisa From babiuc at marshall.edu Mon Apr 6 16:18:40 2009 From: babiuc at marshall.edu (Babiuc-Hamilton, Maria) Date: Mon, 6 Apr 2009 17:18:40 -0400 Subject: [Users] generating output for VisIt In-Reply-To: <49DA4BD8.7000009@cct.lsu.edu> References: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861B@MUXC09.marshall.edu>, <49DA181E.8040700@cct.lsu.edu> <31D46DC505870A4C980A8F38BB2DBD0E6350B3861C@MUXC09.marshall.edu>, <49DA4BD8.7000009@cct.lsu.edu> Message-ID: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861D@MUXC09.marshall.edu> Hello, 1) Does the visualization machine have HDF5 installed (if this is the same machine where you're running your simulation, I suppose the answers is yes)? I am running on a MAC OS, a Scientific Linux and a PSC supercomputer. Yes, I have HDF5 installed and cactus using it on all three operation systems. 2) Was VisIt built with HDF5 support? I installed VisIt from the script on the Mac OS. I assume it was build with HDF5 support. 3) Are you or are you not using visitCarpetHDF5 in the end? No, I am not using it. I tried, but I am not sure how to modify the Makefile tab for the Mac OS. 4) What happens when you try to open the .h5 file with VisIt? I can open the plot. I tried a mesh, volume and contour plot. I do not see anything inside the cube, though. What are the best plot options that I should use? Thanks, Maria ________________________________________ From: users-bounces at cactuscode.org [users-bounces at cactuscode.org] On Behalf Of Eloisa Bentivegna [bentivegna at cct.lsu.edu] Sent: Monday, April 06, 2009 2:37 PM To: Cactus users mailing list Subject: Re: [Users] generating output for VisIt Babiuc-Hamilton, Maria ha scritto: > Hello, > > Thank you. I generated files of the type gxy.file_0.h5 and tried to visualize it with Visit, as mesh or volume, but I did not have too much of a success. > Could you please let me know if I'm doing it right? Sure. Could you say more on your system and where exactly the visualization fails? In particular: 1) Does the visualization machine have HDF5 installed (if this is the same machine where you're running your simulation, I suppose the answers is yes)? 2) Was VisIt built with HDF5 support? 3) Are you or are you not using visitCarpetHDF5 in the end? 4) What happens when you try to open the .h5 file with VisIt? Eloisa _______________________________________________ Users mailing list Users at cactuscode.org http://www.cactuscode.org/mailman/listinfo/users From bentivegna at cct.lsu.edu Mon Apr 6 17:23:30 2009 From: bentivegna at cct.lsu.edu (Eloisa Bentivegna) Date: Mon, 06 Apr 2009 17:23:30 -0500 Subject: [Users] generating output for VisIt In-Reply-To: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861D@MUXC09.marshall.edu> References: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861B@MUXC09.marshall.edu>, <49DA181E.8040700@cct.lsu.edu> <31D46DC505870A4C980A8F38BB2DBD0E6350B3861C@MUXC09.marshall.edu>, <49DA4BD8.7000009@cct.lsu.edu> <31D46DC505870A4C980A8F38BB2DBD0E6350B3861D@MUXC09.marshall.edu> Message-ID: <49DA80E2.1010309@cct.lsu.edu> Babiuc-Hamilton, Maria ha scritto: > 3) Are you or are you not using visitCarpetHDF5 in the end? > No, I am not using it. I tried, but I am not sure how to modify the Makefile tab for the Mac OS. This will depend on your paths. In general, adding the compiler flags for the include/ and lib/ paths for hdf5 should suffice (notice that you'll need the cpp versions too). > I can open the plot. I tried a mesh, volume and contour plot. I do not see anything inside the cube, though. > What are the best plot options that I should use? OK, so you can see an entry for the variable you're trying to plot (I think it was gxy) in the "Plot" menu? In this case, I'd suggest using the "Spreadsheet" style, which will open a spreadsheet window with your data, so you can take a look and figure what's wrong. Sometimes the defaults for the other styles may not be appropriate for your data range (although you should always be able to the see the mesh); scanning your data in the spreadsheet, and taking a look at the defaults for each style on the "Plot Attributes" menu, should tell you if that is the case. Eloisa From ian.hinder at aei.mpg.de Wed Apr 8 03:22:55 2009 From: ian.hinder at aei.mpg.de (Ian Hinder) Date: Wed, 8 Apr 2009 10:22:55 +0200 Subject: [Users] generating output for VisIt In-Reply-To: <49DA80E2.1010309@cct.lsu.edu> References: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861B@MUXC09.marshall.edu>, <49DA181E.8040700@cct.lsu.edu> <31D46DC505870A4C980A8F38BB2DBD0E6350B3861C@MUXC09.marshall.edu>, <49DA4BD8.7000009@cct.lsu.edu> <31D46DC505870A4C980A8F38BB2DBD0E6350B3861D@MUXC09.marshall.edu> <49DA80E2.1010309@cct.lsu.edu> Message-ID: <992331C4-300B-402D-9671-28830CA5BD76@aei.mpg.de> On 7 Apr 2009, at 00:23, Eloisa Bentivegna wrote: > Babiuc-Hamilton, Maria ha scritto: > >> 3) Are you or are you not using visitCarpetHDF5 in the end? >> No, I am not using it. I tried, but I am not sure how to modify the >> Makefile tab for the Mac OS. > > This will depend on your paths. In general, adding the compiler flags > for the include/ and lib/ paths for hdf5 should suffice (notice that > you'll need the cpp versions too). > >> I can open the plot. I tried a mesh, volume and contour plot. I do >> not see anything inside the cube, though. >> What are the best plot options that I should use? > > OK, so you can see an entry for the variable you're trying to plot (I > think it was gxy) in the "Plot" menu? In this case, I'd suggest using > the "Spreadsheet" style, which will open a spreadsheet window with > your > data, so you can take a look and figure what's wrong. Sometimes the > defaults for the other styles may not be appropriate for your data > range > (although you should always be able to the see the mesh); scanning > your > data in the spreadsheet, and taking a look at the defaults for each > style on the "Plot Attributes" menu, should tell you if that is the > case. The plot style that I find most useful is "Pseudocolor", which gives you a 2D plot of a slice of your data, with the colours in the plot representing the data values. This is useful for figuring out what is going on in a run, and for debugging. Create a pseudocolor plot, and then in that plot, add a "slice" operator (as you can't do a 2D plot of 3D data). In the slice operator options, choose the plane you want to look at (I usually use the xy plane at z = 0). In the pseudocolor options, you can set the min and max data ranges, and the colour scheme you want to use. I have found volume rendering to be very tricky, though you can make nice movies if you are willing to spend a LOT of time on it. -- Ian Hinder ian.hinder at aei.mpg.de From babiuc at marshall.edu Fri Apr 10 12:11:41 2009 From: babiuc at marshall.edu (Babiuc-Hamilton, Maria) Date: Fri, 10 Apr 2009 13:11:41 -0400 Subject: [Users] generating output for VisIt In-Reply-To: <992331C4-300B-402D-9671-28830CA5BD76@aei.mpg.de> References: <31D46DC505870A4C980A8F38BB2DBD0E6350B3861B@MUXC09.marshall.edu>, <49DA181E.8040700@cct.lsu.edu> <31D46DC505870A4C980A8F38BB2DBD0E6350B3861C@MUXC09.marshall.edu>, <49DA4BD8.7000009@cct.lsu.edu> <31D46DC505870A4C980A8F38BB2DBD0E6350B3861D@MUXC09.marshall.edu> <49DA80E2.1010309@cct.lsu.edu>, <992331C4-300B-402D-9671-28830CA5BD76@aei.mpg.de> Message-ID: <31D46DC505870A4C980A8F38BB2DBD0E6350B3863B@MUXC09.marshall.edu> Hello, Thank you for the tip. I tried all the possibilities, and what ended up working for me was the contour plot. It would be great if on the Cactus Code Visualization web page will be posted some information on the same way Erik did with gnuplot. best, Maria ________________________________________ From: users-bounces at cactuscode.org [users-bounces at cactuscode.org] On Behalf Of Ian Hinder [ian.hinder at aei.mpg.de] Sent: Wednesday, April 08, 2009 4:22 AM To: Cactus users mailing list Subject: Re: [Users] generating output for VisIt On 7 Apr 2009, at 00:23, Eloisa Bentivegna wrote: > Babiuc-Hamilton, Maria ha scritto: > >> 3) Are you or are you not using visitCarpetHDF5 in the end? >> No, I am not using it. I tried, but I am not sure how to modify the >> Makefile tab for the Mac OS. > > This will depend on your paths. In general, adding the compiler flags > for the include/ and lib/ paths for hdf5 should suffice (notice that > you'll need the cpp versions too). > >> I can open the plot. I tried a mesh, volume and contour plot. I do >> not see anything inside the cube, though. >> What are the best plot options that I should use? > > OK, so you can see an entry for the variable you're trying to plot (I > think it was gxy) in the "Plot" menu? In this case, I'd suggest using > the "Spreadsheet" style, which will open a spreadsheet window with > your > data, so you can take a look and figure what's wrong. Sometimes the > defaults for the other styles may not be appropriate for your data > range > (although you should always be able to the see the mesh); scanning > your > data in the spreadsheet, and taking a look at the defaults for each > style on the "Plot Attributes" menu, should tell you if that is the > case. The plot style that I find most useful is "Pseudocolor", which gives you a 2D plot of a slice of your data, with the colours in the plot representing the data values. This is useful for figuring out what is going on in a run, and for debugging. Create a pseudocolor plot, and then in that plot, add a "slice" operator (as you can't do a 2D plot of 3D data). In the slice operator options, choose the plane you want to look at (I usually use the xy plane at z = 0). In the pseudocolor options, you can set the min and max data ranges, and the colour scheme you want to use. I have found volume rendering to be very tricky, though you can make nice movies if you are willing to spend a LOT of time on it. -- Ian Hinder ian.hinder at aei.mpg.de _______________________________________________ Users mailing list Users at cactuscode.org http://www.cactuscode.org/mailman/listinfo/users From schnetter at cct.lsu.edu Fri Apr 17 10:51:23 2009 From: schnetter at cct.lsu.edu (Erik Schnetter) Date: Fri, 17 Apr 2009 10:51:23 -0500 Subject: [Users] Upcoming Cactus Tutorials Message-ID: <87A701DA-1E4E-4D48-8314-4DDC18C82CA8@cct.lsu.edu> We would like to draw your attention to three Cactus tutorials that we will be offering in the coming months. These tutorials do not assume prior knowledge of Cactus. The tutorial material will also be made available on the Cactus web site. May 24 in Baton Rouge, LA: A half-day tutorial for ICCS (International Conference on Computational Science) titled "Developing HPC Applications with the Cactus Framework". It will introduce the Cactus framework, how to write applications using Cactus, and how to use its adaptive mesh refinement infrastructure. Note that you can attend this tutorial without registering (and paying) for the conference, but you need to register for the tutorial itself. May 27 in Baton Rouge, LA: A two-hour beginner's tutorial as part of the LSU/LONI HPC training courses, to be announced at . It will introduce the Cactus framework and how to use it on the LSU/LONI HPC systems. June 22 in Arlington, VA: A half-day tutorial as part of TeraGrid '09 . This will be a hands-on tutorial introducing Cactus, building applications, running simulations, and visualising output. Note: "The deadline to submit to the TeraGrid '09 student program has been extended to April 20. Funding is available from the National Science Foundation to cover registration, travel, and lodging for participating high school, undergraduate, and graduate students." . -erik -- Erik Schnetter 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 . -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 194 bytes Desc: This is a digitally signed message part Url : http://www.cactuscode.org/pipermail/users/attachments/20090417/81abac7f/attachment-0001.bin