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Nanoengineer-1 Simulator

 
 
technologiclee
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      12-13-2009

This is from a thread started at the Open Manufacturing Group.

It is about the Nanoengineer-1 molecular modeling program.
It is released under GPL license. I would like to know if this project
can be forked and continued - as development seems to have ceased, but
it is still the best software of its kind that I can find. All the
details are in the thread.

http://groups.google.com/group/openm...f728b7182ebd44

Specifically, I would like to ask this community about an error trying
to use the simulator:

This is the error from Netbeans when I try to run the simulator. Any
suggestions?

error trying to import dylib sim: <type 'exceptions.ImportError'>: No
module
named sim
[runSim.py:787]
sim parameters used by NE1 read from:
[/home/lee/nesuite1.1.12./cad/plugins/NanoDynamics-1/sim-params.txt]
bug in simulator-calling code: <type 'exceptions.AttributeError'>:
SimRunner
instance has no attribute 'system_parameters_file'
[runSim.py:372] [runSim.py:970] [runSim.py:1089]
exception opening trace file
'/home/lee/Nanorex/Untitled.2009-12-13-00-18-10-trace.txt': <type
'exceptions.IOError'>: [Errno 2] No such file or directory:
'/home/lee/Nanorex/Untitled.2009-12-13-00-18-10-trace.txt'
[runSim.py:1936]

 
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technologiclee
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      12-14-2009
On Dec 13, 12:34*am, technologiclee <(E-Mail Removed)> wrote:
> This is from a thread started at the Open Manufacturing Group.
>
> It is about the Nanoengineer-1 molecular modeling program.
> It is released under GPL license. I would like to know if this project
> can be forked and continued - as development seems to have ceased, but
> it is still the best software of its kind that I can find. All the
> details are in the thread.
>
> http://groups.google.com/group/openm..._thread/thread...
>
> Specifically, I would like to ask this community about an error trying
> to use the simulator:
>
> This is the error from Netbeans when I try to run the simulator. Any
> suggestions?
>
> error trying to import dylib sim: <type 'exceptions.ImportError'>: No
> module
> named sim
> * [runSim.py:787]
> sim parameters used by NE1 read from:
> [/home/lee/nesuite1.1.12./cad/plugins/NanoDynamics-1/sim-params.txt]
> bug in simulator-calling code: <type 'exceptions.AttributeError'>:
> SimRunner
> instance has no attribute 'system_parameters_file'
> * [runSim.py:372] [runSim.py:970] [runSim.py:1089]
> exception opening trace file
> '/home/lee/Nanorex/Untitled.2009-12-13-00-18-10-trace.txt': <type
> 'exceptions.IOError'>: [Errno 2] No such file or directory:
> '/home/lee/Nanorex/Untitled.2009-12-13-00-18-10-trace.txt'
> * [runSim.py:1936]


For the benefit of all those searching for this answer, I am adding
this response to the post. Thanks Tim.

(sorry for replying off-list - the email I use on-list email isn't
sending at the moment - feel free to post any reply back on-list)

On Sat, 2009-12-12 at 22:34 -0800, technologiclee wrote:
> It is released under GPL license. I would like to know if this project
> can be forked and continued - as development seems to have ceased, but
> it is still the best software of its kind that I can find. All the
> details are in the thread.


Yes - as long as you release all your changes under GPL as well -
that's
the great thing about the GPL.

> Specifically, I would like to ask this community about an error trying
> to use the simulator:
>
> This is the error from Netbeans when I try to run the simulator. Any
> suggestions?


Looking at the code - the module "sim" is a C extension module - from
the setup.py file in the NanoEngineer directory:

{{{

extra_compile_args = [ "-DDISTUTILS", "-O" ]

setup(name = 'Simulator',
ext_modules=[Extension("sim", ["sim.pyx", ...
}}}

- so you'll need to build the setup.py to get that working.

But... I get compile errors when trying to build that library

% python setup.py build
running build
running build_ext
building 'sim' extension
creating build/temp.linux-x86_64-2.4
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -
Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c sim.c -o build/
temp.linux-x86_64-2.4/sim.o -DDISTUTILS -O
In file included from sim.c:30:
simhelp.c:30:21: error: version.h: No such file or directory
In file included from sim.c:30:
simhelp.c:39: error: ‘TRACE_PREFIX’ undeclared here (not in a
function)
simhelp.c:39: error: expected ‘,’ or ‘;’ before
‘TRACE_PREFIX_DISTUTILS’
error: command 'gcc' failed with exit status 1

- and at this point it's a general C issue to be honest

TRACE_PREFIX seems to be added at some point during automake -
i.e. you've got to run the full build tools for sim to be able to be
built.

- the other "trace file" errors seem to be related.

Hope that helps,

Tim
 
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