[visit-users] VisIt for Mac

Miller, Mark C. miller86 at llnl.gov
Wed Jul 15 13:06:31 EDT 2015


And, when I run the .dmg file on my Mac, 'Chombo' does appear in the list of available plugins.

Raymond, is there any chance you may have accidentically disabled chombo via the plugin manager? Can you run with -noconfig just to test to see if Chombo shoes up in the plugin list. Here is how I woud do that on my Mac with a mounted (but not installed) dmg file. . .

/Volumes/VisIt-2.9.2/VisIt.app/Contents/Resources/bin/visit -noconfig

Developers, is there a chance Chombo read options have changed in a way that makes some user's saved state (settings, session, config) incompatible with current plugin and VisIt is somehow deciding to then ignore it?

Mark


From: <Miller>, "Miller, Mark C." <miller86 at llnl.gov<mailto:miller86 at llnl.gov>>
Reply-To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Date: Wednesday, July 15, 2015 9:58 AM
To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Subject: Re: [visit-users] VisIt for Mac

Hmm. This is puzzling.

I just inspected *both the .dmg file and the .tar.gz file (as well as the builds) on my Mac that I gave to Eric to upload and Chombo *does* appear to be there in what I have.

[scratlantis:2.9.2/darwin-x86_64/plugins] miller86% cd databases/
[scratlantis:darwin-x86_64/plugins/databases] miller86% ls -1 | grep -i chombo
libEChomboDatabase_par.dylib
libEChomboDatabase_ser.dylib
libIChomboDatabase.dylib
libMChomboDatabase.dylib

[scratlantis:masonry/mbuild-visit-2.9.2-darwin-x86_64/build.release] miller86% gunzip < visit2_9_2 . darwin-x86_64 . tar . gz | tar tf - | grep -i chombo
visit2_9_2.darwin-x86_64/2.9.2/darwin-x86_64/plugins/databases/libEChomboDatabase_par.dylib
visit2_9_2.darwin-x86_64/2.9.2/darwin-x86_64/plugins/databases/libEChomboDatabase_ser.dylib
visit2_9_2.darwin-x86_64/2.9.2/darwin-x86_64/plugins/databases/libIChomboDatabase.dylib
visit2_9_2.darwin-x86_64/2.9.2/darwin-x86_64/plugins/databases/libMChomboDatabase.dylib

Mark


From: <Harrison>, "Cyrus D." <harrison37 at llnl.gov<mailto:harrison37 at llnl.gov>>
Reply-To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Date: Wednesday, July 15, 2015 8:39 AM
To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Subject: Re: [visit-users] VisIt for Mac

Hi Raymond,

Thanks for the detective work. We didn’t intend to disable Chombo support - something must have shifted to undermine our build of the plugin.
I’ll create a ticket so we can dive deeper into the issue.

-Cyrus

On Jul 14, 2015, at 11:05 PM, Raymond Fermo <rlf0010 at uah.edu<mailto:rlf0010 at uah.edu>> wrote:

Cyrus,
I think you're right... when I ssh into Blue Waters and run VisIt over X11, once again, Chombo is not an option among the listed file types, and I'm not able to open the file. The version number is 2.9.0. In contrast, the VisIt version running from my Linux desktop (which could open Chombo) is 2.8.2, and the one I just installed on my Macbook (which could not open Chombo) is the latest 2.9.2. Was support for Chombo files discontinued in v2.9 for some reason?

Platform            Version   Chombo?
Mac                   2.9.2       no
Linux (BW)        2.9.0       no
Linux (desktop) 2.8.2       yes

I tried installing the 2.8.2 version of VisIt on my Macbook just to see if that would work, but the application didn't even open properly on my Mac. (no error message, no log file, it simply doesn't open when I double-click it from my Applications menu.

By the way, thanks for responding, Cyrus, and for being helpful.

-Raymond

On Mon, Jul 13, 2015 at 11:41 AM, Harrison, Cyrus D. <harrison37 at llnl.gov<mailto:harrison37 at llnl.gov>> wrote:
Hi Raymond,

It sounds like there is a mismatch between your client and the remote instance.

When you are running over X11, which version of VisIt is launched? Is this a different version than the client you are running on your desktop?



-Cyrus

On Jul 11, 2015, at 4:48 AM, Raymond Fermo <rlf0010 at uah.edu<mailto:rlf0010 at uah.edu>> wrote:

Cyrus,
Thanks, I was able to open select Chombo as the file type while running VisIt locally, but not under all circumstances.

- When running VisIt locally on my Mac, the Chombo file type option was available.
- When running VisIt remotely through my Linux machine on the NCSA Blue Waters server (where the data is), the Chombo file type option was available. (This is how I was opening it before.)
- But when running Visit remotely through my Macbook on NCSA, the Chombo file type option disappears!

Do I need to discuss this problem with someone at Blue Waters about getting installed? Is that odd? Does NCSA have different library plugins for VisIt installed depending on the version of VisIt running remotely?

Sincerely,
Raymond

On Fri, Jul 10, 2015 at 11:36 AM, Harrison, Cyrus D. <harrison37 at llnl.gov<mailto:harrison37 at llnl.gov>> wrote:
Hi Raymond
Yes, I was looking for which file format is used (sorry for the VisIt vernacular, we call our readers “database plugins” in most parts of the interface)

>From your error message on the mac before, it doesn’t appear combo was tried:

----
VisIt tried using the following file format readers to open the file: Tetrad, Silo
----

There are many plugins that can handle hdf5 data - it could be that:

* The Chombo plugin isn’t available on the mac version of Visit (unlikely)
or
* The auto detection for Chombo failed.

To avoid problems with the auto detection, you can explicitly select Chombo as an option:

In the File Open Window:

"Open file as Type”: Guess from name/extension

to

“Chombo"

Then try oping your hdf5 file.


If this works, you can set Chombo as a “Preferred Database Plugin”, which will make sure it tries Chombo first during auto detection.

You can do this in:
Options Menu->Plugin Manager-> Database Tab

After this, make sure to save your settings
Options Menu->Save Settings.


Hope this helps,

-Cyrus


On Jul 10, 2015, at 12:38 AM, Raymond Fermo <rlf0010 at uah.edu<mailto:rlf0010 at uah.edu>> wrote:

Cyrus,
Are you asking about the file format? That would be Chombo 1.0, but here's the rest of the text in that textbox, in the event that you're asking about something else.

Thanks,
Raymond

File = h2ologin . ncsa . illinois . edu<hxxp://h2ologin.ncsa.illinois.edu/>:/mnt/a/u/sciteam/fermo/scratch/Jacob_new/cycle.c.v4.*.3d.hdf5 database
==============================================================================
Database: /mnt/a/u/sciteam/fermo/scratch/Jacob_new/cycle.c.v4.29700.3d.hdf5
Simulation: No
Database comment:
File format: Chombo_1.0
Num Time States: 3
MetaData IS repopulated on state changes
useCatchAllMesh: 0
Format  cannot do its own domain decomposition
The temporal extents are not set.
All Times are ***NOT*** Accurate
Times:
2065.37, 0, 0
All Cycles are Accurate
Cycles:
29700, 32000, 33450

Database is virtual
Timesteps are located in /mnt/a/u/sciteam/fermo/scratch/Jacob_new/
Timesteps:
cycle.c.v4.29700.3d.hdf5
cycle.c.v4.32000.3d.hdf5
cycle.c.v4.33450.3d.hdf5

Meshes:
Name = Mesh
Number of blocks = 49525
Block origin = 0
Cell origin = 0 (origin within one block of the cells).
Node origin = 0 (origin within one block of the nodes).
Group origin = 0
Title for domain hierarchy is patches
Title for individual piece in domain hierarchy is patch
Number of groups = 5
Group ids are: 0, ...
Title for group hierarchy is levels
Title for individual piece in group hierarchy is level
Mesh type is AMR Mesh.
Spatial Dimension = 3
Spatial extents are: ((0, 1800), (0, 1800), (0, 1800))
Topological Dimension = 3


On Thu, Jul 9, 2015 at 11:00 PM, Harrison, Cyrus D. <harrison37 at llnl.gov<mailto:harrison37 at llnl.gov>> wrote:
Hi Raymond,

It’s possible the two installations of VisIt could have different plugins available.

After you open the file successfully using the Linux version, can you look at "File Menu->File Information”, to see what database plugin was used?


-Cyrus

On Jul 8, 2015, at 2:31 PM, Raymond Fermo <rlf0010 at uah.edu<mailto:rlf0010 at uah.edu>> wrote:

Hi,
I am trying to open a .hdf5 file using VisIt. I have no problems looking at the files from a Linux version of VisIt, but when I attempt to open the same files from my Macbook, I receive the error below. Are there differences in the implementations of the two versions of VisIt?

Sincerely,
Raymond

VisIt could not read from the file "/mnt/a/u/sciteam/fermo/scratch/Jacob_new/cycle.c.v4.*.3d.hdf5 database" on hosth2ologin . ncsa . illinois . edu<hxxp://h2ologin.ncsa.illinois.edu/>.

The generated error message was:

There was an error opening /mnt/a/u/sciteam/fermo/scratch/Jacob_new/cycle.c.v4.*.3d.hdf5 database. It may be an invalid file.
VisIt tried using the following file format readers to open the file: Tetrad, Silo

If you know the specific format reader VisIt should use to
read this data, you can use Open As... (GUI) or
'-o <file>,<plugin> (CL arg.) and identify that specific reader
for VisIt to try. This will possibly give more information on
the exact error.
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