[visit-users] Launching Visit on Syrah

Converse, Mark C. converse3 at llnl.gov
Tue Jul 21 19:58:30 EDT 2015


Mark,

Do you have the new version that has this error fixed in it?  I am talking with the Boxlib people and they want me to try some things.

Thanks,
Mark
________________________________
From: Miller, Mark C. [miller86 at llnl.gov]
Sent: Tuesday, July 21, 2015 11:58 AM
To: VisIt software users community
Subject: Re: [visit-users] Launching Visit on Syrah

FYI, I have found and fixed a tiny bug in VisIt that allowed a mesh with zero domains to cause a malloc for negative size which is why VisIt was crashing with this file. However, that doesn't fix VisIt's ability to display this file. It only means that VisIt no longer cores trying to read the file.

When Visit reads the file, it finds stuff like this. . .

All Times are Accurate
Times:
        5.57624e-06
All Cycles are Accurate
Cycles:
        100
Meshes:
        Name = Mesh
        Number of blocks = 0
        Block origin = 1
        Cell origin = 0 (origin within one block of the cells).
        Node origin = 0 (origin within one block of the nodes).
        Group origin = 1
        Title for domain hierarchy is patches
        Title for individual piece in domain hierarchy is patch
        The name scheme is: @level1,patch%d at n+1:
        Number of groups = 1
        Group ids are: 0: 0--1,
        Title for group hierarchy is levels
        Title for individual piece in group hierarchy is level
        Mesh type is AMR Mesh.
        Spatial Dimension = 3
        The spatial extents are not set.
        Topological Dimension = 3
        Block names:
        Disjoint elements No
        Contains ghost zones Maybe
        Contains original cells No
        Contains original nodes No
        Units =  x: "", y: "", z: "".
        Labels =  x: "X-Axis", y: "Y-Axis", z: "Z-Axis".
        Mesh coord type is XY
        Mesh is primarily cell-based
        Unit cell vector #0 is 1 0 0
        Unit cell vector #1 is 0 1 0
.
.
.
Scalars:
        Name = "density"
        Mesh is = "Mesh"
        Centering = node centered.
        The extents are not set.
        This variable does not contain enumerated values.

        Name = "xmom"
        Mesh is = "Mesh"
        Centering = node centered.
        The extents are not set.
        This variable does not contain enumerated values.

        Name = "ymom"
        Mesh is = "Mesh"
        Centering = node centered.
        The extents are not set.
        This variable does not contain enumerated values.

        Name = "zmom"
        Mesh is = "Mesh"
        Centering = node centered.
        The extents are not set.
        This variable does not contain enumerated values.

        Name = "eden"
        Mesh is = "Mesh"
        Centering = node centered.
        The extents are not set.
        This variable does not contain enumerated values.


The problem is VisIt thinks the mesh has zero blocks.

Mark



From: Gunther Weber <ghweber at lbl.gov<mailto:ghweber at lbl.gov>>
Reply-To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Date: Tuesday, July 21, 2015 11:25 AM
To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Subject: Re: [visit-users] Launching Visit on Syrah

Hi,

1) The fact that AmrVis can read the file is promising and indicates that the file is ok.

2) However, are you writing ghost zones into the file? The error message "Would like to have issued warning "Reader does not currently support ghostzones.", but no callback was registered.” seems to indicate that the file has ghost zones in it, while the reader currently does not support that, as indicated by its notes:

//   -> Ghost zones are currently not supported, and a warning is issued
//      if a dataset is found to have ghost zones. This is due to lack
//      of sample datasets, and should be removed once appropriate data
//      is avaliable.

3) BoxLib itself does not seem to have a release number itself. CCSE’s Marc Day maintains tar balls that are something like a release for a collaborating projects and a while back I migrated VisIt to use one of these TAR balls at hxxps://ccse.lbl.gov/Software/tarfiles/. VisIt uses 1.0.7, while the most recent release seems to be 1.3.0. It’s always a bit of a hassle to update, so I haven’t done it in a while. The BoxLib file format tends to be very stable, but I can check if there were any recent changes.

I would check the ghost zone issue first and then take things from there.

Gunther


On Jul 20, 2015, at 7:44 PM, Converse, Mark C. <converse3 at llnl.gov<mailto:converse3 at llnl.gov>> wrote:
Mark,
I'm not sure about the patches, but the AMR algorithm, can allow multiple mesh refinement levels.  This simulation only allows one though.
I have a contact I'm going to ask about the Boxlib in Visit.
Mark
From: Miller, Mark C. [miller86 at llnl.gov<mailto:miller86 at llnl.gov>]
Sent: Monday, July 20, 2015 5:39 PM
To: VisIt software users community
Subject: Re: [visit-users] Launching Visit on Syrah
Is there anything funky about the number of patches and/or levels here.
The VisIt plugin seems to think there is one level with zero patches.
From: <Converse>, "Mark C." <converse3 at llnl.gov<mailto:converse3 at llnl.gov>>
Reply-To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Date: Monday, July 20, 2015 5:26 PM
To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Subject: Re: [visit-users] Launching Visit on Syrah
Mark,
I have been using the AMRvis program that is produced by the same group as the Boxlib.  It reads the plot files and displays the data from them.  It works fine on those files.
It seems to be extremely limited however in how you can view, manipulate, overlay, etc. the variables, which is why I was looking into Visit.  Which seems much more powerful than this program.
Mark
From: Miller, Mark C. [miller86 at llnl.gov<mailto:miller86 at llnl.gov>]
Sent: Monday, July 20, 2015 5:07 PM
To: VisIt software users community
Subject: Re: [visit-users] Launching Visit on Syrah
Hi Mark,
Do you by chance have any other "evidence" or reason to believe the boxlib file is "good." I mean, are there any other tools out their that digest boxlib and believe the file is ok? I'd just like a sanity check before I dig into this further. Obviously, the boxlib library being used in the VisIt plugin doesn't like the file for some reason.
Mark
From: <Converse>, "Mark C." <converse3 at llnl.gov<mailto:converse3 at llnl.gov>>
Reply-To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Date: Monday, July 20, 2015 4:23 PM
To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Subject: Re: [visit-users] Launching Visit on Syrah
Mark,
That is a good question.  I'm using the latest version of Boxlib.  I just used git to grab it from the website a couple weeks ago.  In the documentation it says it is version  BoxLib Version 2014-02-28.  It's a little vague, but I assume probably not version 1?  Is there something we can do to update the plugin version?
Mark
From: Miller, Mark C. [miller86 at llnl.gov<mailto:miller86 at llnl.gov>]
Sent: Monday, July 20, 2015 11:28 AM
To: VisIt software users community
Subject: Re: [visit-users] Launching Visit on Syrah
I've tried opening plt00100/Header on two different machines and get
BoxLib::Error::Sorry, out of memory, bye ... !!!
Eventually, the engine hits a SIGBRT (abort).
Just prior to that, in the engine logs, I see this. . .
avtDatabaseFactory: specifically told to use Boxlib3D_1.0
Skipping already loaded database plugin Boxlib3D version 1.0
Trying to open the file with the Boxlib3D file format, strict mode is off
Would like to have issued warning "Reader does not currently support ghostzones.", but no callback was registered.
signalhandler_core: SIGBRT!
The file is only 25 Mb (compressed) so I assume Boxlib isn't really running out of memory and something else bad is happening.
VisIt seems to know enough to think this is a 3D boxlib file and not 2D as I tried both readers and the 2D reader failed due to incorrect dimension.
Has boxlib changed its file format recently? Are you maybe using a newer version of Boxlib than VisIt is using?
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: Friday, July 17, 2015 2:51 PM
To: VisIt software users community <visit-users at elist.ornl.gov<mailto:visit-users at elist.ornl.gov>>
Subject: Re: [visit-users] Launching Visit on Syrah
Hi Mark,
I am sorry I haven’t had a chance to dive in — I’ll be out of the office next week, but I forwarded your data to the other LLNL VisIt developers to look at next week.
-Cyrus
On Jul 16, 2015, at 1:45 PM, Converse, Mark C. <converse3 at llnl.gov<mailto:converse3 at llnl.gov>> wrote:
Cyrus,

Any luck with opening that file format?

Thanks,
Mark

From: Harrison, Cyrus D. [mailto:harrison37 at llnl.gov]
Sent: Friday, July 10, 2015 4:32 PM
To: VisIt software users community
Subject: Re: [visit-users] Launching Visit on Syrah

Mark,

Thanks for sending me the file, this crashes on my mac as well — so I don’t think the issue is related to Syrah.

I’ll look into it further.

-Cyrus

On Jul 10, 2015, at 10:31 AM, Converse, Mark C. <converse3 at llnl.gov<mailto:converse3 at llnl.gov>> wrote:
Cyrus,

Sure, how should I give it to you?  Email or give command on the LC machines?

Thanks,
Mark

From: Harrison, Cyrus D. [mailto:harrison37 at llnl.gov]
Sent: Thursday, July 09, 2015 8:21 PM
To: VisIt software users community
Subject: Re: [visit-users] Launching Visit on Syrah

Hi Mark,

Sorry, you are having so much trouble.

I don’t think we have a host-profile setup for syrah - this means it’s likely means you are running a serial engine.
Depending on the size of your dataset, that could explain why you are running out of memory.

Would it be possible for you to give us part of your data set so we can investigate more?

-Cyrus

On Jul 8, 2015, at 1:45 PM, Converse, Mark C. <converse3 at llnl.gov<mailto:converse3 at llnl.gov>> wrote:
I’ve been trying to launch visit on syrah . llnl . gov.  I got it to open a metadata server on syrah and went to the folder where the data was.  Then I opened the file, and it crashed saying that it couldn’t find a compute engine and that would try to start a new one.  Then I get a

BoxLib::Error::Sorry, out of memory, bye…!!!!

Any idea how I can make this work.  According to the Boxlib website, their output is compatible with Visit.

Regards,
Mark
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