[apbs-users] mergedx2 resolution

[Lane Votapka]

Hello APBS users/developers,

I believe that there is a bug in the mergedx2 program when the -r (resolution) argument is used.

When I type this command:

mergedx2 -r 0.5 -o gridmerged2.dx *_-PE0.dx

I recieve this error:

# main:   Reading Headers...
WARNING: The specified output resolution is greater than the
         resolution of the input DX files. Upsampling.......
# main:   Dimensions of the merged grid
# main:   nx = 2261, ny = -2147483648, nz = -2147483648
# main:   hx = 0.499895, hy = 0.000001, hz = 0.000001
# main:   xmin = -575.530000, ymin = -560.902000, zmin = -589.033000
# main:   xmax = 554.232005, ymax = 548.614121, zmax = 594.511896
VASSERT: ASSERTION FAILURE!  filename vmem.c, line 241, ((num > 0) && (size > 0))
Aborted

The program will even fail if I use -r 1.0 (the default). I'll bet it's somethin to do with the ny, and nz parameters output near the top.

mergedx2 without the -r argument works just fine, but that does me no good since I do want to change the resolution of my grid.

Best,
-Lane

[Baker, Nathan]

Hello --

Yes, that sounds like a bug. Would you be willing to share the OpenDX files that you were trying this with?

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
Phone: +1-509-375-3997
http://nabaker.me

From: Lane Votapka <lvota...@gmail.com<mailto:lvota...@gmail.com>>
Date: Friday, February 15, 2013 4:04 PM
To: APBS-USERS mailing list <apbs-...@lists.sourceforge.net<mailto:apbs-...@lists.sourceforge.net>>
Subject: [apbs-users] mergedx2 resolution

Hello APBS users/developers,

I believe that there is a bug in the mergedx2 program when the -r (resolution) argument is used.

When I type this command:

mergedx2 -r 0.5 -o gridmerged2.dx *_-PE0.dx

I recieve this error:

# main: Reading Headers...
WARNING: The specified output resolution is greater than the
resolution of the input DX files. Upsampling.......
# main: Dimensions of the merged grid

# main: nx = 2261, ny = -2147483648<tel:2147483648>, nz = -2147483648<tel:2147483648>

# main: hx = 0.499895, hy = 0.000001, hz = 0.000001
# main: xmin = -575.530000, ymin = -560.902000, zmin = -589.033000

# main: xmax = 554.232005, ymax = 548.614121, zmax = 594511896

VASSERT: ASSERTION FAILURE! filename vmem.c, line 241, ((num > 0) && (size > 0))
Aborted

The program will even fail if I use -r 1.0 (the default). I'll bet it's somethin to do with the ny, and nz parameters output near the top.

mergedx2 without the -r argument works just fine, but that does me no good since I do want to change the resolution of my grid.

Best,
-Lane

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[Lane Votapka]

It's a set of rather large .dx files (hence maybe why the problem was happening). I can probably get those to you after this weekend

-Lane

[Kelly Tran]

Hi,

Are there any new updates on this?  I believe I may be having a similar problem.

Thank you,

Kelly

[Baker, Nathan]

Hi Kelly --

I think Andrew is still working on this problem. Andrew, can you please provide an update?

Thanks!

--
Nathan Baker
Pacific Northwest National Laboratory

+1-509-375-3997
http://nabaker.me

From: Kelly Tran <trank...@gmail.com<mailto:trank...@gmail.com>>
Date: Wednesday, June 19, 2013 10:52 AM
To: APBS-USERS mailing list <apbs-...@googlegroups.com<mailto:apbs-...@googlegroups.com>>
Cc: Lane Votapka <lvota...@gmail.com<mailto:lvota...@gmail.com>>, APBS-USERS mailing list <apbs-...@lists.sourceforge.net<mailto:apbs-...@lists.sourceforge.net>>, "Libby, Steven" <Steven...@pnnl.gov<mailto:Steven...@pnnl.gov>>, "Stevens, Andrew J (PNNL)" <Andrew....@pnnl.gov<mailto:Andrew....@pnnl.gov>>, Nathan Baker <nathan...@pnnl.gov<mailto:nathan...@pnnl.gov>>
Subject: Re: [apbs-users] mergedx2 resolution

Hi,

Are there any new updates on this? I believe I may be having a similar problem.

Thank you,

Kelly

On Saturday, February 16, 2013 9:48:17 PM UTC-5, Baker, Nathan wrote:
Hello --

Yes, that sounds like a bug. Would you be willing to share the OpenDX files that you were trying this with?

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
Phone: +1-509-375-3997
http://nabaker.me

apbs-...@lists.sourceforge.net<javascript:>
https://lists.sourceforge.net/lists/listinfo/apbs-users

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[Tomek Wlodarski]

Hi Nathan,

Are there any new updates on that problem?
I am using mergedx2 from apbs 1.4 and still I have the same error:

"WARNING: The specified output resolution is greater than the
         resolution of the input DX files. Upsampling......."

Even with r =10....
Thanks!
Best,

tomek

[Nathan Baker]

Hello --

Can you please send me some example files that are causing this problem and I will investigate it?

Thank you and my apologies for the delay.

Sincerely,

Nathan Baker

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