Nanoengineer-1 Simulator

Discussion in 'Python' started by technologiclee, Dec 13, 2009.

  1. 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/openmanufacturing/browse_thread/thread/aff728b7182ebd44

    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]
    technologiclee, Dec 13, 2009
    #1
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  2. On Dec 13, 12:34 am, technologiclee <> 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/openmanufacturing/browse_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
    technologiclee, Dec 14, 2009
    #2
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