[visit-users] VisIt for Mac

Raymond Fermo rlf0010 at uah.edu
Wed Jul 15 02:05:23 EDT 2015


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>
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> 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>
> 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> 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:/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>
>> 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> 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.
>>>
>>>  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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