[mira_talk] Re: Mira mailing list
- From: Sandrine Moreira <sandrine.moreira@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 13 Jan 2011 09:08:16 -0500
From Jonathan:
Hi Bastien,
My Name is Jonathan and I am an Scientific computing analyst at RQCHP. My role
is to help scientist to do science using hpc platforms in Canada. So I will be
responsible of helping Sandrine with her project. I can provide help to
implement either parallelization or checkpoint restart, but in the present
situation, it makes more sense to go with checkpoint restart.
In order to help me catchup on that, could you resume where your CR
implementation stand, and what still need to be done? What kind of things are
missing, and what can I do to help?
Thanks,
Jonathan
Le 2011-01-10 à 6:44 PM, Sandrine Moreira a écrit :
>
> Le 2011-01-10 à 1:42 PM, Bastien Chevreux a écrit :
>
>> On Montag 10 Januar 2011 Sandrine Moreira wrote:
>>> The technical suport suggest they could either :
>>> - Work on the parallelization of the code
>>> - Implement the "checkpoint" functionnality (to stop and restart the
>>> assembly after 7 days)
>>
>> Is that a help offer?
>
> Well, if our development could help others ....
>
>> Whomever wants to add to MIRA is very welcome, though
>> I'll note that there's a reason these two functions are not fully
>> implemented
>> yet: they're not easy to implement and it'll at least a couple of weeks to
>> implement (and test!) either one.
>
> I'm sure that it's a tricky part, but we can still evaluate the feasability
> and the difficulty.
> We will certainly implement the checkpoint due to this time limitation on the
> cluster (jobs longer than 7 days are killed).
>
> For the parallelization, it's less probable but it was worth asking if
> somebody has already developed half of the code ;-)
>
>>
>>> Before investing too much time on one of these solutions, does anyone begin
>>> working on one (both ?!) of these points ? Bastien ?
>>> Bastien, I read on the doc that you are planning to work on these points,
>>> did you already do something in this direction ?
>>
>> Both points are currently on hold, I have a couple of other things with
>> higher
>> priority on my list atm. The basics for checkpointing are there (MAF is a
>> result of it), but then I needed to shift focus when I saw that there was
>> more
>> to it than I wanted.
>
> Ok, we will surely interact with you for some precise questions on the
> checkpoint, if you don't mind.
> Is there some code related to this part which is not commited on sourceforge ?
>
>
>>
>>> BTW, I would be also interested by a small dataset to test our
>>> developements. If you have one to suggest ...
>>
>> For that I suppose that any bacterial Sanger data set from the NCBI trace
>> archive should work pretty well. I'd have to search for one though, all the
>> ones I had I lost a couple of weeks ago.
>
> I would prefer 454 data to stay closer as possible as our own data.
> BTW, I perhaps found a mitochondrial genome for my test : small but complex
> enough, with high %AT and nice homopolymers errors.
> Still need to have a closer look to see if it's really convenient.
>
> SaM
>
>>
>> B.
>>
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>
> --
> Sandrine Moreira Rousseau
> Doctorante en Bio-informatique
>
> (514) 343-6111 poste 2842
>
> Centre Robert-Cedergren en Bio-informatique et Génomique
> Université de Montréal
> Montréal, Québec, Canada
>
>
>
>
>
>
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--
Sandrine Moreira Rousseau
Doctorante en Bio-informatique
(514) 343-6111 poste 2842
Centre Robert-Cedergren en Bio-informatique et Génomique
Université de Montréal
Montréal, Québec, Canada
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