Hello, Sorry if this question has been posted before but could't find out exactly an answer to the question.... I'm doing bioinformatics and doing small RNA sequencing that make use of packages such as DESeq and EDGE. For those familiar with this data you will notice that you end up having large matrices with millions of entries. So i guess many people might be facing the same problem of dealing with so big matrices. and vectors. I've heard of people using other math libraries (since the default R math lib is single core). to compile R and make it use several procs on the server. I'm not familiar with the different math libs availables (BLAS,..) Can i use faster math libraries so that R uses the full procs capacities of my server ? I'm running 2.12.2 on an linux server (16cpu with 32Gb ram). thanks for your tips, david
R and multithread
2 messages · David martin, Bert Gunter
How about googling it?!! "R multithread" " R Parallel processing" both got numerous apprently relevant hits. Also please familiarize yourself with CRAN's task views, where you will find HighPerformanceComputing. -- Bert
On Wed, Apr 6, 2011 at 5:27 AM, David martin <vilanew at gmail.com> wrote:
Hello, Sorry if this question has been posted before but could't find out exactly an answer to the question.... I'm doing bioinformatics and doing small RNA sequencing that make use of packages such as DESeq and EDGE. For those familiar with this data you will notice that you end up having large matrices with millions of entries. So i guess many people might be facing the same problem of dealing with so big matrices. and vectors. I've heard of people using other math libraries (since the default R math lib is single core). to compile R and make it use several procs on the server. I'm not familiar with the different math libs availables (BLAS,..) Can i use faster math libraries so that R uses the full procs capacities of my server ? I'm running 2.12.2 on an ?linux server (16cpu with 32Gb ram). thanks for your tips, david
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"Men by nature long to get on to the ultimate truths, and will often be impatient with elementary studies or fight shy of them. If it were possible to reach the ultimate truths without the elementary studies usually prefixed to them, these would not be preparatory studies but superfluous diversions." -- Maimonides (1135-1204) Bert Gunter Genentech Nonclinical Biostatistics