[R] RMySQL connection very slow compared with PHP

Ernesto Jardim ernesto at ipimar.pt
Tue May 6 10:38:05 CEST 2003

On Mon, 2003-05-05 at 13:22, Laurent Faisnel wrote:
> Prof Brian Ripley wrote:
> >On Mon, 5 May 2003, Laurent Faisnel wrote:
> >
> >  
> >
> >>Thank you for your fast answer. I work on a 450MHz Pentium II with 192 
> >>MBytes RAM.
> >>    
> >>
> >
> >And Linux.  That's a rather old spec --  4-5 years?
> >
> >  
> >
> >>dbListTables() takes about 3 seconds. For direct use it's OK, but when 
> >>requests become included in programs, it makes very slow programs !
> >> I had to calculate an average score for each value of a column (i=1:12) 
> >>to fill an array, and so the operation (pretty simple) took more than 30 
> >>seconds (almost 3 seconds per "select avg(score)..." request).
> >>
> >>I don't think my dataset is huge enough to make it worth using ODBC, 
> >>which would cause other problems. I do not start R for each query. I 
> >>have the same slowness when sending the requests to R directly (without 
> >>using source code).
> >>
> >>What makes me hope for a solution is when you say "For me running a 
> >>query is instant". What could be the difference between our systems ? 
> >>The CPU speed does not explain all, in my opinion.
> >>    
> >>
> >
> >Well, I am using a dual Athlon 2600, 1Gb RAM and a fast local disc system,
> >so that is a considerable difference.  Maybe you need more RAM.
> >
> >  
> >
> OK. Clearly, I'm disadvantaged by my slow machine ! But there is another 
> element I have to give you to help you understand my scepticism. R is 
> called by PHP (which manages the web pages that  display amongst others 
> statistical results). The first version of our system did not use R. 
> Indeed PHP can access the database, and it did the work fine (and fast ! ).
> Now I want to use R for a better analysis (in a in evolutive view), but 
> I'm very disappointed to note how slow requests are treated. The problem 
> cannot be at MySQL's level since it was so fast with PHP (about 100x 
> faster I think). So I think there must be a problem with R/RMySQL. 
> However, isn't there fast C code in RMySQL ?
> Perhaps I do not use the best commands for the requests :
> /# beginning of R program (once only)
> library(DBI);
> library(RMySQL);
> con <- dbConnect("MySQL");
> # typical request
> dbGetQuery(con,"select avg(mark) from table1 where critere=1");
> # this takes 2 sec. (instant with PHP & MySQL)
> # table1 being a table without index, with 3 columns and only 500 rows/
> By the way, how should I close ResultSets to clean the workspace (I 
> tried dbSendQuery instead of dbGetQuery) ? Should I give an object name 
> to dbSendQuery's result (res) and then delete it (how ? seems to be a 
> problem with dbClearResult) ?
> Thanks again,
> Laurent
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Have you tried to run the commands inside R whithout php calling R ? Was
it slow ? Why are you making an average inside SQL if you're using R ?
Should it be better to select the dataset you want to work with and than
make the analysis inside R ?

Once again in my opinion you'll win a lot of speed if you index your



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