It works for me without problems on python 2.7.2 on 64 bit ubuntu, in a
more humble machine (4 Gb of RAM), and the usage of RAM memory is not that
big (maybe 500 Mb or less for both executions together)
Adrià
2011/11/14 Arturo, Steven (SG) <[email protected]>
> Good day all. I understand that I use pybel to manipulate structures that
> are larger than what the code is intended to do. So I am testing the
> limits of this.****
>
> ** **
>
> I write because if I execute a ‘make3D’ function on a molecule that is too
> large, pybel (or openbabel) crashes python.****
>
> ** **
>
> Here is what a good execution looks like when I use ‘make3D’ on a large
> molecule.****
>
> ** **
>
> Python 2.7 (r27:82525, Jul 4 2010, 09:01:59) [MSC v.1500 32 bit (Intel)]
> on win32****
>
> Type "help", "copyright", "credits" or "license" for more information.****
>
> >>> import pybel****
>
> >>> smiles='O'+'CCO'*300****
>
> >>> mol=pybel.readstring('smi',smiles)****
>
> >>> mol.make3D()****
>
> >>> ^Z****
>
> ** **
>
> And here is what a bad execution looks like****
>
> ** **
>
> Python 2.7 (r27:82525, Jul 4 2010, 09:01:59) [MSC v.1500 32 bit (Intel)]
> on win32****
>
> Type "help", "copyright", "credits" or "license" for more information.****
>
> >>> import pybel****
>
> >>> smiles='O'+'CCO'*400****
>
> >>> mol=pybel.readstring('smi',smiles)****
>
> >>> mol.make3D()****
>
> ** **
>
> This application has requested the Runtime to terminate it in an unusual
> way.****
>
> Please contact the application's support team for more information.****
>
> ** **
>
> As you can see, I am running a 32-bit version of python on Windows. It is
> a 64-bit version of Windows 7 with 12 GB of memory.****
>
> ** **
>
> I investigated whether the error is memory-based. It seems that this
> error is shown when python asks for about 490 MB of memory. This is well
> below the limits of this machine, since I have run scripts on this same
> machine that fail when it is ~1.7 GB of memory, something more meaningful
> when I run a 32-bit application on Windows 7.****
>
> ** **
>
> Two questions… Why is this happening? And is there a more graceful way to
> fail, so that I can wrap the command with a try loop and execute the rest
> of my script if ‘make3D’ fails? ****
>
> ** **
>
> Thanks for your help.****
>
> ** **
>
> Steve****
>
> ** **
>
> Steven G. Arturo****
>
> Core R&D – E&PS****
>
> The Dow Chemical Company****
>
> 727 Norristown Road****
>
> Spring House, PA 19477****
>
> 7B/207P 979.238.5749****
>
> ** **
>
>
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--
*Adrià Cereto Massagué*
Universitat Rovira i Virgili
Languages: Català, Español, English, Français, Deutsch, Português, Esperanto
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