Re: [simuPOP-devel] test on simuPOP scalability.

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I have attached the modified patch. Please check it out. It can work after 2 or 3 times compile. That is weird.

Regards!
Chong

-----Original Message-----
From: Bo Peng [mailto:be...@gm...] 
Sent: Wednesday, June 29, 2011 1:04 PM
To: Wang,Chong
Cc: sim...@li...
Subject: Re: [simuPOP-devel] test on simuPOP scalability.

Why do you still have two setup calls? You are supposed to write one
setup call with common options, and different ones passed by
setup_params. Also, you do not do dict(), rather {a:b, ...}.

Cheers,
Bo

On Wed, Jun 29, 2011 at 1:00 PM, Wang,Chong <CW...@md...> wrote:
> This is one of the path, I think here no error in coding, but it can not run as what we expect
>
> -----Original Message-----
> From: Bo Peng [mailto:be...@gm...]
> Sent: Wednesday, June 29, 2011 12:53 PM
> To: Wang,Chong
> Cc: sim...@li...
> Subject: Re: [simuPOP-devel] test on simuPOP scalability.
>
> I do not understand, this is only a technical rewrite so as long as
> you pass the right parameters using the right syntax, everything
> should work as before. In the worst case, you can replace setup() by
>
> def mysetup(*argv,**kwargs):
>  print argv
>  print kwargs
>
> and check if everything is passed to the function correctly.
>
> Bo
>
>
> On Wed, Jun 29, 2011 at 12:18 PM, Wang,Chong <CW...@md...> wrote:
>> Unlucky, I have tested many ways of dictionary for setuptools parameters expressions and input as **setup_params. I have tested them all the morning, but the setup() seems not be able to execute with "install_requires=['distribute']"
>> So I guess we have to use the last patch
>>
>>
>> -----Original Message-----
>> From: Bo Peng [mailto:be...@gm...]
>> Sent: Wednesday, June 29, 2011 11:40 AM
>> To: sim...@li...
>> Subject: Re: [simuPOP-devel] test on simuPOP scalability.
>>
>> Great. Thank you very much. Now we should focus on the release of 1.0.6.
>>
>> Chong, do you have your setup.py patch ready? I will starting merging
>> the branch to trunk and test it on different systems.
>>
>> Thanks,
>> Bo
>>
>>
>> On Wed, Jun 29, 2011 at 10:49 AM, Charoenrattanaruk,Panitee
>> <PCh...@md...> wrote:
>>> I add more experiments and edit some part. You can review again at http://simupop.sourceforge.net/cookbook/pmwiki.php/Main/MiscScripts.
>>>
>>> Best Regards,
>>>
>>> Panitee
>>> ________________________________________
>>> From: Bo Peng [be...@gm...]
>>> Sent: Tuesday, June 28, 2011 11:54 AM
>>> To: Charoenrattanaruk,Panitee
>>> Cc: sim...@li...
>>> Subject: Re: [simuPOP-devel] test on simuPOP scalability.
>>>
>>> Very well-written. Just two comments:
>>>
>>> The first part is too technique. Perhaps we can give quick formulas
>>> how to calculate maximum population size using RAM and number of loci.
>>> E.g. 4000/48/nLoci .
>>>
>>> We can also fix population size and see how many loci can be
>>> simulated. Population size can be 1000 and 100,000.
>>>
>>> Thanks.
>>>
>>>
>>> On Tue, Jun 28, 2011 at 11:32 AM, Charoenrattanaruk,Panitee
>>> <PCh...@md...> wrote:
>>>> I wrote the scalability of simuPOP in http://simupop.sourceforge.net/cookbook/pmwiki.php/Main/MiscScripts. You can review and make a comment.
>>>>
>>>> Best Regards,
>>>> Panitee
>>>> ________________________________________
>>>> From: Peng,Bo [bp...@md...]
>>>> Sent: Thursday, June 23, 2011 2:23 PM
>>>> To: sim...@li...
>>>> Subject: [simuPOP-devel] test on simuPOP scalability.
>>>>
>>>> Hi, Panitee,
>>>>
>>>> The question about scalability of simuPOP has been asked quite a few times. Because we have been using 64 bit system for a while, could you do some tests on large simulations. More specifically, could you write a page on the simuPOP cook about the largest simulation simuPOP can run on a 64bit, 8 core, 16G RAM system (bp9), and how fast it can run? I would list, like http://simupop.sourceforge.net/Main/DevelopmentStories#toc3 , tables with things like
>>>>
>>>> Population size, number of loci, how long to run 10 generations etc.
>>>>
>>>> We could try this for the basic random mating model with three different modules, and 1 and 4 cores. You might want to use gcc because most users will use gcc.
>>>>
>>>> Thanks,
>>>> --
>>>> Bo Peng, Ph.D.
>>>> Instructor
>>>> Department of Epidemiology
>>>> The University of Texas
>>>> M. D. Anderson Cancer Center
>>>>
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>>>>
>>>>
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>>>
>>> ------------------------------------------------------------------------------
>>> All of the data generated in your IT infrastructure is seriously valuable.
>>> Why? It contains a definitive record of application performance, security
>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>> sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-d2d-c2
>>> _______________________________________________
>>> simuPOP-devel mailing list
>>> sim...@li...
>>> https://lists.sourceforge.net/lists/listinfo/simupop-devel
>>>
>>
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>> _______________________________________________
>> simuPOP-devel mailing list
>> sim...@li...
>> https://lists.sourceforge.net/lists/listinfo/simupop-devel
>>
>