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jsalvatier / multichain_mcmc

Multichain MCMC framework and algorithms based on PyMC.
pypi.python.org/pypi/multichain_mcmc
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most of the examples don't work out of the box #1

Open andyfaff opened 11 years ago

andyfaff commented 11 years ago

I have downloaded the multichain_mcmc package and have tried out the majority of samples in the multichain_mcmc dream_examples folder. All of them result in error messages:

Python 2.7.3 (v2.7.3:70274d53c1dd, Apr 9 2012, 20:52:43) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin numpy 1.7.0 pymc 2.2 multichain_mcmc 0.3

faffmatic:dream_examples andrew$ python example1.py Leopard libedit detected. Traceback (most recent call last): File "example1.py", line 13, in sampler.sample() File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 211, in sample File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/convergence.py", line 63, in update FloatingPointError: divide by zero encountered in log

faffmatic:dream_examples andrew$ python example2.py Leopard libedit detected. /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/multichain_mcmc-0.3-py2.7-macosx-10.6-intel.egg/multichain_mcmc/multichain.py:116: RuntimeWarning: overflow encountered in exp Traceback (most recent call last): File "example2.py", line 13, in sampler.sample(nChains = 5, ndraw = 1000) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 211, in sample File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/convergence.py", line 63, in update FloatingPointError: divide by zero encountered in log

faffmatic:dream_examples andrew$ python example3.py Leopard libedit detected. /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/multichain_mcmc-0.3-py2.7-macosx-10.6-intel.egg/multichain_mcmc/multichain.py:116: RuntimeWarning: overflow encountered in exp 0.0131135598072 Traceback (most recent call last): File "example3.py", line 13, in sampler.sample(nChains = 5, ndraw = 500, mConvergence = True,mAccept = True) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 211, in sample File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/convergence.py", line 63, in update FloatingPointError: divide by zero encountered in log

faffmatic:dream_examples andrew$ python example4.py Leopard libedit detected. 0.0 Traceback (most recent call last): File "example4.py", line 14, in sampler.sample(nChains = 10,adaptationRate = 'auto', mConvergence = True,mAccept = True) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 224, in sample FloatingPointError: divide by zero encountered in double_scalars

faffmatic:dream_examples andrew$ python example5.py Leopard libedit detected. /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/multichain_mcmc-0.3-py2.7-macosx-10.6-intel.egg/multichain_mcmc/multichain.py:116: RuntimeWarning: overflow encountered in exp 0.0065567799036 0.166164433169 Traceback (most recent call last): File "example5.py", line 14, in sampler.sample( mConvergence = True,mAccept = True) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 211, in sample File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/convergence.py", line 63, in update FloatingPointError: divide by zero encountered in log

faffmatic:dream_examples andrew$ python example6.py Leopard libedit detected. 0.0 Traceback (most recent call last): File "example6.py", line 14, in sampler.sample( nChains = 5, adaptationRate = 'auto', mConvergence = True,mAccept = True) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 224, in sample FloatingPointError: divide by zero encountered in double_scalars

jsalvatier commented 11 years ago

This is a dead project, I should probably remove it from pypi. However there is somewhat similar work ongoing in PyMC 3, see https://github.com/pymc-devs/pymc/tree/pymc3. Less of a focus on multiple chains and more on gradient based samplers, though I may reimplement DREAM since it does have its advantages.

On Mon, Apr 22, 2013 at 5:23 PM, andyfaff notifications@github.com wrote:

I have downloaded the multichain_mcmc package and have tried out the majority of samples in the multichain_mcmc dream_examples folder. All of them result in error messages:

Python 2.7.3 (v2.7.3:70274d53c1dd, Apr 9 2012, 20:52:43) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin numpy 1.7.0 pymc 2.2 multichain_mcmc 0.3

faffmatic:dream_examples andrew$ python example1.py Leopard libedit detected. Traceback (most recent call last): File "example1.py", line 13, in sampler.sample() File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 211, in sample File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/convergence.py", line 63, in update FloatingPointError: divide by zero encountered in log

faffmatic:dream_examples andrew$ python example2.py Leopard libedit detected. /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/multichain_mcmc-0.3-py2.7-macosx-10.6-intel.egg/multichain_mcmc/multichain.py:116: RuntimeWarning: overflow encountered in exp Traceback (most recent call last): File "example2.py", line 13, in sampler.sample(nChains = 5, ndraw = 1000) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 211, in sample File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/convergence.py", line 63, in update FloatingPointError: divide by zero encountered in log

faffmatic:dream_examples andrew$ python example3.py Leopard libedit detected. /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/multichain_mcmc-0.3-py2.7-macosx-10.6-intel.egg/multichain_mcmc/multichain.py:116: RuntimeWarning: overflow encountered in exp 0.0131135598072 Traceback (most recent call last): File "example3.py", line 13, in sampler.sample(nChains = 5, ndraw = 500, mConvergence = True,mAccept = True) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 211, in sample File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/convergence.py", line 63, in update FloatingPointError: divide by zero encountered in log

faffmatic:dream_examples andrew$ python example4.py Leopard libedit detected. 0.0 Traceback (most recent call last): File "example4.py", line 14, in sampler.sample(nChains = 10,adaptationRate = 'auto', mConvergence = True,mAccept = True) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 224, in sample FloatingPointError: divide by zero encountered in double_scalars

faffmatic:dream_examples andrew$ python example5.py Leopard libedit detected. /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/multichain_mcmc-0.3-py2.7-macosx-10.6-intel.egg/multichain_mcmc/multichain.py:116: RuntimeWarning: overflow encountered in exp 0.0065567799036 0.166164433169 Traceback (most recent call last): File "example5.py", line 14, in sampler.sample( mConvergence = True,mAccept = True) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 211, in sample File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/convergence.py", line 63, in update FloatingPointError: divide by zero encountered in log

faffmatic:dream_examples andrew$ python example6.py Leopard libedit detected. 0.0 Traceback (most recent call last): File "example6.py", line 14, in sampler.sample( nChains = 5, adaptationRate = 'auto', mConvergence = True,mAccept = True) File "build/bdist.macosx-10.6-intel/egg/multichain_mcmc/dream.py", line 224, in sample FloatingPointError: divide by zero encountered in double_scalars

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