Try to run a lots of chips: 32 bits vs 64 bits
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 6.3 years ago
I'm trying to follow up on the discussions by Laurent and Issac, b/c we're also trying to run a lots of arrays (~200 133A) with Bioconductors. We tried with R on our 32 bits Linux server with 2G ram and it failed. So, my questions are: 1) now what is the highest number of chips you can process with Bioconductor? 2) How do you know if your R is 32 bits or 64 bits and how do you build 64 bits R under a 32 bits architecture? Our system administrator mentioned to me that the only mention in the administration manual is for Sparc systems (64-bit arch). 3) For specific analyses, for example, quantile normalization and RMA, is there a way around it? Many thanks in advance, ...Tao --------------------------------- [[alternate HTML version deleted]]
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Shi, Tao ▴ 70
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It was simply out of memory.=20=20 What's your estimate on the number of 133A chips we can handle under our sy= stem setup? ...Tao Robert Gentleman <rgentlem@jimmy.harvard.edu> wrote: On Mon, Mar 03, 2003 = at 02:33:31PM -0800, Shi, Tao wrote:> > I'm trying to follow up on the disc= ussions by Laurent and Issac, b/c we're also trying to run a lots of arrays= (~200 133A) with Bioconductors. We tried with R on our 32 bits Linux serve= r with 2G ram and it failed. So, my questions are:Could you perhaps say a b= it more than "failed", it is rather hard tounderstand what the problem migh= t be, given that amount ofinformation. > 1) now what is the highest number = of chips you can process with Bioconductor?> 2) How do you know if your R i= s 32 bits or 64 bits and how do you build 64 bits R under a 32 bits archite= cture? Our system administrator mentioned to me that the only mention in th= e administration manual is for Sparc systems (64-bit> arch).> 3) For specif= ic analyses, for example, quantile normalization and RMA, is there a way ar= ound it?> Many thanks in advance,> ...Tao > > > > > -----------------------= ----------> > > [[alternate HTML version deleted]]> > _____________________= __________________________> Bioconductor mailing list> Bioconductor@stat.ma= th.ethz.ch> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor-- +-= ---------------------------------------------------------------------- ----+= | Robert Gentleman phone : (617) 632-5250 || Associate Professor fax: (617)= 632-2444 || Department of Biostatistics office: M1B20 || Harvard School of= Public Health email: rgentlem@jimmy.dfci.harvard.edu |+-------------------= --------------------------------------------------------+ [[alternate HTML version deleted]]
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 6.3 years ago
ReadAffy() Ben Bolstad <bolstad@stat.berkeley.edu> wrote:On Mon, 2003-03-03 at 15:04, Tao Shi wrote: > It was simply out of memory. After which command did you get the out of memory error? ReadAffy()? rma()? Ben --------------------------------- [[alternate HTML version deleted]]
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rgentleman ★ 5.5k
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On Mon, Mar 03, 2003 at 02:33:31PM -0800, Shi, Tao wrote: > > I'm trying to follow up on the discussions by Laurent and Issac, b/c we're also trying to run a lots of arrays (~200 133A) with Bioconductors. We tried with R on our 32 bits Linux server with 2G ram and it failed. So, my questions are: Could you perhaps say a bit more than "failed", it is rather hard to understand what the problem might be, given that amount of information. > 1) now what is the highest number of chips you can process with Bioconductor? > 2) How do you know if your R is 32 bits or 64 bits and how do you build 64 bits R under a 32 bits architecture? Our system administrator mentioned to me that the only mention in the administration manual is for Sparc systems (64-bit > arch). > 3) For specific analyses, for example, quantile normalization and RMA, is there a way around it? > Many thanks in advance, > ...Tao > > > > > --------------------------------- > > > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+
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rgentleman ★ 5.5k
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Hi, sorry, but really, there are ways to ask questions that get answers and there are ways to ask questions that get no answers. You seem not to want to give us any information at all and from there it is pretty hard for anyone to help fix the problem. You shouldn't be running out of memory and we certainly cannot figure out why you did if you insist on giving one word answers. Robert On Mon, Mar 03, 2003 at 04:40:31PM -0800, Shi, Tao wrote: > > ReadAffy() > Ben Bolstad <bolstad@stat.berkeley.edu> wrote:On Mon, 2003-03-03 at 15:04, Tao Shi wrote: > > It was simply out of memory. > > After which command did you get the out of memory error? > > ReadAffy()? > rma()? > > > Ben > > > > --------------------------------- > > > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+
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Sorry, I can provide any information, but I'm not very familiar with Linux system, so I don't know what specific information you guys need. The situation is like this: we have ~200 133A chips and want to use RMA to calculate the expression values. However, we couldn't even use ReadAffy() to read them in. (In details, I started R in the directory where .cel files are located and use command such as dat1<- ReadAffy(); and R told me something like"can't allocate ### kb vector....."). I only know our Linux server is 32 bits and has 2G ram. ...Tao Robert Gentleman <rgentlem@jimmy.harvard.edu> wrote:Hi, sorry, but really, there are ways to ask questions that get answers and there are ways to ask questions that get no answers. You seem not to want to give us any information at all and from there it is pretty hard for anyone to help fix the problem. You shouldn't be running out of memory and we certainly cannot figure out why you did if you insist on giving one word answers. Robert On Mon, Mar 03, 2003 at 04:40:31PM -0800, Shi, Tao wrote: > > ReadAffy() > Ben Bolstad wrote:On Mon, 2003-03-03 at 15:04, Tao Shi wrote: > > It was simply out of memory. > > After which command did you get the out of memory error? > > ReadAffy()? > rma()? > > > Ben > > > > --------------------------------- > > > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+ --------------------------------- [[alternate HTML version deleted]]
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Laurent Gautier ★ 2.3k
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(I've seen answers to this post by Robert & Ben) On Mon, Mar 03, 2003 at 02:33:31PM -0800, Shi, Tao wrote: > > I'm trying to follow up on the discussions by Laurent and Issac, b/c we're also trying to run a lots of arrays (~200 133A) with Bioconductors. We tried with R on our 32 bits Linux server with 2G ram and it failed. So, my questions are: > 1) now what is the highest number of chips you can process with Bioconductor? It depends on the type of the chips (they were not created equal, some are bigger than other). I recently processed 142 U95Av2 on a 2Gb linux box. ...but 200 133A appears a bit too much to me... > 2) How do you know if your R is 32 bits or 64 bits and how do you build 64 bits R under a 32 bits architecture? Our system administrator mentioned to me that the only mention in the administration manual is for Sparc systems (64-bit > arch). R can be built for 64 bits (Isaac did so). You may want to 'google' about your harware, linux and 64 bits.. > 3) For specific analyses, for example, quantile normalization and RMA, is there a way around it? for the moment, the only I can think of is to crank up your favorite editor and try to make your way through... sorry.. > Many thanks in advance, > ...Tao > > > > > --------------------------------- > > > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
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one way to get around it is to write a function that does RMA but reads only the PMs. If you learn R it wont be that hard. reading only the PMs will reduce the memory use by more than 1/2. RMA doesnt use MMs. if you decide to do this, email me and ill help as long as you contribute the final product. another, less satisfying, way is to run rma by parts (half and half) and then join the exprSets. On Tue, 4 Mar 2003, Laurent Gautier wrote: > (I've seen answers to this post by Robert & Ben) > > On Mon, Mar 03, 2003 at 02:33:31PM -0800, Shi, Tao wrote: > > > > I'm trying to follow up on the discussions by Laurent and Issac, b/c we're also trying to run a lots of arrays (~200 133A) with Bioconductors. We tried with R on our 32 bits Linux server with 2G ram and it failed. So, my questions are: > > 1) now what is the highest number of chips you can process with Bioconductor? > > It depends on the type of the chips (they were not created equal, > some are bigger than other). I recently processed 142 U95Av2 on > a 2Gb linux box. > > ...but 200 133A appears a bit too much to me... > > > 2) How do you know if your R is 32 bits or 64 bits and how do you build 64 bits R under a 32 bits architecture? Our system administrator mentioned to me that the only mention in the administration manual is for Sparc systems (64-bit > > arch). > > R can be built for 64 bits (Isaac did so). You may want to 'google' about your > harware, linux and 64 bits.. > > > 3) For specific analyses, for example, quantile normalization and RMA, is there a way around it? > > for the moment, the only I can think of is to crank up your favorite editor > and try to make your way through... sorry.. > > > > > Many thanks in advance, > > ...Tao > > > > > > > > > > --------------------------------- > > > > > > [[alternate HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > -------------------------------------------------------------- > currently at the National Yang-Ming University in Taipei, Taiwan > -------------------------------------------------------------- > Laurent Gautier CBS, Building 208, DTU > PhD. Student DK-2800 Lyngby,Denmark > tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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