[Primeusers] Release 1.0 of PrimeGSR

[Filipe Garrett]

Hi,

I've been running primeGSR (see below for command line arguments) with both trees (scaled at 0.5 and 
1.0) just to test and the 0.5 just crashed with a "Command terminated by signal 11" after 19300 
iterations. I think this signal means a "Segmentation Fault" occurred. So I think I'll take your 
advice and use trees with root scaled at 1.

thanks,
FG

primeGSR -o seqs.mcmc -c 350 -Bp 0.1 0.1 -i 100000 -t 100 -Sm JTT -Hi tree.nwk seqs.aln.fas 
seqs_0.5.gs &> seqs.log

Lars Arvestad wrote:
> This (0.5 vs 1.0) is probably a bug. We have consistently used 1.0 for 
> the root, so if you do too, you will be safe.
> 
> No, we do not have parallelized the program. It is on the todo-list. 
> There are many opportunities for parallelization, we just need someone 
> to do it.
> 
> Yes, we are planning to extend the manual! :-) I have not had time to do 
> much about it though. You are welcome to fire off questions however.
> 
>     Lars
> 
> 
> 
> Filipe Garrett skrev:
>> Yes, I was referring to the same tree but having the root at 0.5 instead of 1.
>> This tree only works in prime GSR with a "-c" option of, at least, 500 and this greatly increases 
>> time and memory usage. I suppose it can be because when scaling the tree some branches are just too 
>> small. I just thought it was strange....
>>
>> By the way, is it possible to execute primeGSR in parallel (threads, pvm, mpi, ....)?
>> Are you planning to add a chapter to the manual to explain the MCMC output?
>>
>> thanks a lot for your help and time,
>> FG
>>
>>
>> Lars Arvestad wrote:
>>   
>>> I am not sure what you mean by "branch lengths roughly half of the 
>>> branches of the 1.0 root tree".
>>>
>>> Do you mean the root is at 0.5?
>>>
>>> The number after -c affects the run time quadratically, but the actual 
>>> branchlengths should not affect memory.
>>>
>>>     Lars
>>>
>>>
>>>
>>> Filipe Garrett wrote:
>>>     
>>>> Scaling the tree to 1.0 at the root apparently works (still running) with both 90 ("-c 200") and 375 
>>>> ("-c 400") sequences; although with 375 sequences needs too much memory (around 11Gb).
>>>>
>>>> Changing the "-c" option greatly influences memory usage and speed. I've also tried a scaled tree 
>>>> with branch lengths roughly half of the branches of the 1.0 root tree, and it only works with "-c" 
>>>> equal to at least 500. Is it normal that a reduction in branch lengths to half leads to such an 
>>>> increase in memory usage and time (from 700Mb to 4Gb and approx. 10x slower)??
>>>>       
>>>     
>>   
> 
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-- 
Filipe G. Vieira
Departament de Genetica
Universitat de Barcelona
Av. Diagonal, 645
08028 Barcelona
SPAIN
Phone: +34 934 035 306
Fax: +34 934 034 420
fgarret at ub.edu
http://www.ub.edu/molevol/