Jin.Li at ga.gov.au
2008-Jan-23 23:08 UTC
[R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]
Dear All, I am currently using R in Windows PC with a 2 GB of RAM. Some pretty large datasets are expected soon, perhaps in an order of several GB. I am facing a similar situation like Ralph, either to get a new PC with a bigger RAM or else. I am just wondering if R is getting faster in other systems like UNIX or Linux. Any suggestions are appreciated. Regards, Jin -------------------------------------------- Jin Li, PhD Spatial Modeller/ Computational Statistician Marine & Coastal Environment Geoscience Australia Ph: 61 (02) 6249 9899 Fax: 61 (02) 6249 9956 email: jin.li at ga.gov.au -------------------------------------------- -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Prof Brian Ripley Sent: Thursday, 24 January 2008 12:05 To: Ralph79 Cc: r-help at r-project.org Subject: Re: [R] Problems with XP32-"3GB-patch"?/ Worth upgrading to Vista X64? On Wed, 23 Jan 2008, Ralph79 wrote:> > Dear R-Users, > > as I will start a huge simulation in a few weeks, I am about to buy a new > and fast PC. I have noticed, that the RAM has been the limiting factor in > many of my calculations up to now (I had 2 GB in my "old" system, but > Windows still used quite a lot of virtual memory), hence my new computer > will have 4 GB of fast DDR2-800 RAM. > > However, I know that 1.) Windows 32 bit cannot make use of more than about > 3,2 GB RAM and 2.) it is normally not allowed to allocate more than 2 GB of > RAM to one single application (at least under XP, I don't know if that has > changed under Vista?). > > I remember from the R-FAQ that you can manually adjust XP so that it > allocates up to 3 GB to one application ("the 3GB patch"), but I read in a > PC-magazine and some message boards that this may cause problems. Does > anybody of you successfully use this "trick" without any problems?Yes, many people: most 32-bit Exchange servers use it. Please don't rate the advice in the R documentation below tittle-tattle you read on the web.> Would it be wise to use a 64bit OS, as e.g. Vista X64? I think, under Vista > X64 it should be no problem to allocate 4 GB of RAM to R. Any experiences > with that?That's what the rw-FAQ says, and we do write answers based on experience!> Thanks in advance, > Ralph Wirth > > > ----- > Ralph Wirth > University Erlangen-Nuremberg, Chair of Statistics > GfK Group, Department of Methods and Product Development > >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Peter Dalgaard
2008-Jan-23 23:23 UTC
[R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]
Jin.Li at ga.gov.au wrote:> Dear All, > I am currently using R in Windows PC with a 2 GB of RAM. Some pretty large > datasets are expected soon, perhaps in an order of several GB. I am facing a > similar situation like Ralph, either to get a new PC with a bigger RAM or > else. I am just wondering if R is getting faster in other systems like UNIX > or Linux. Any suggestions are appreciated. > Regards, > Jin >It has always been faster in Linux than in Windows on the same hardware. In addition, the toolchain issues have been holding up 64 bit development on 64 bit Windows, whereas 64 bit build has been working on Linux for years.> -------------------------------------------- > Jin Li, PhD > Spatial Modeller/ > Computational Statistician > Marine & Coastal Environment > Geoscience Australia > Ph: 61 (02) 6249 9899 > Fax: 61 (02) 6249 9956 > email: jin.li at ga.gov.au > -------------------------------------------- > > > -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On > Behalf Of Prof Brian Ripley > Sent: Thursday, 24 January 2008 12:05 > To: Ralph79 > Cc: r-help at r-project.org > Subject: Re: [R] Problems with XP32-"3GB-patch"?/ Worth upgrading to Vista > X64? > > On Wed, 23 Jan 2008, Ralph79 wrote: > > >> Dear R-Users, >> >> as I will start a huge simulation in a few weeks, I am about to buy a new >> and fast PC. I have noticed, that the RAM has been the limiting factor in >> many of my calculations up to now (I had 2 GB in my "old" system, but >> Windows still used quite a lot of virtual memory), hence my new computer >> will have 4 GB of fast DDR2-800 RAM. >> >> However, I know that 1.) Windows 32 bit cannot make use of more than about >> 3,2 GB RAM and 2.) it is normally not allowed to allocate more than 2 GB of >> RAM to one single application (at least under XP, I don't know if that has >> changed under Vista?). >> >> I remember from the R-FAQ that you can manually adjust XP so that it >> allocates up to 3 GB to one application ("the 3GB patch"), but I read in a >> PC-magazine and some message boards that this may cause problems. Does >> anybody of you successfully use this "trick" without any problems? >> > > Yes, many people: most 32-bit Exchange servers use it. Please don't rate > the advice in the R documentation below tittle-tattle you read on the web. > > >> Would it be wise to use a 64bit OS, as e.g. Vista X64? I think, under Vista >> X64 it should be no problem to allocate 4 GB of RAM to R. Any experiences >> with that? >> > > That's what the rw-FAQ says, and we do write answers based on experience! > > >> Thanks in advance, >> Ralph Wirth >> >> >> ----- >> Ralph Wirth >> University Erlangen-Nuremberg, Chair of Statistics >> GfK Group, Department of Methods and Product Development >> >> >> > >-- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
Jin.Li at ga.gov.au
2008-Jan-24 23:11 UTC
[R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]
Hi Peter, Thank you for the quick answer. Given that we have UNIX system available here in Geoscience Australia, I am wondering if UNIX is also faster and with 64 bit build. Perhaps they may be kind enough to let me have a Linux system. As I only have experience in using Windows PC, what kind of challenges are there for using R in other systems like UNIX and Linux? Thanks again, Jin -----Original Message----- From: Peter Dalgaard [mailto:p.dalgaard at biostat.ku.dk] Sent: Thursday, 24 January 2008 10:23 To: Li Jin Cc: r-help at r-project.org Subject: Re: [R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED] Jin.Li at ga.gov.au wrote:> Dear All, > I am currently using R in Windows PC with a 2 GB of RAM. Some pretty large > datasets are expected soon, perhaps in an order of several GB. I am facinga> similar situation like Ralph, either to get a new PC with a bigger RAM or > else. I am just wondering if R is getting faster in other systems like UNIX > or Linux. Any suggestions are appreciated. > Regards, > Jin >It has always been faster in Linux than in Windows on the same hardware. In addition, the toolchain issues have been holding up 64 bit development on 64 bit Windows, whereas 64 bit build has been working on Linux for years.> -------------------------------------------- > Jin Li, PhD > Spatial Modeller/ > Computational Statistician > Marine & Coastal Environment > Geoscience Australia > Ph: 61 (02) 6249 9899 > Fax: 61 (02) 6249 9956 > email: jin.li at ga.gov.au > -------------------------------------------- > > > -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On > Behalf Of Prof Brian Ripley > Sent: Thursday, 24 January 2008 12:05 > To: Ralph79 > Cc: r-help at r-project.org > Subject: Re: [R] Problems with XP32-"3GB-patch"?/ Worth upgrading to Vista > X64? > > On Wed, 23 Jan 2008, Ralph79 wrote: > > >> Dear R-Users, >> >> as I will start a huge simulation in a few weeks, I am about to buy a new >> and fast PC. I have noticed, that the RAM has been the limiting factor in >> many of my calculations up to now (I had 2 GB in my "old" system, but >> Windows still used quite a lot of virtual memory), hence my new computer >> will have 4 GB of fast DDR2-800 RAM. >> >> However, I know that 1.) Windows 32 bit cannot make use of more than about >> 3,2 GB RAM and 2.) it is normally not allowed to allocate more than 2 GBof>> RAM to one single application (at least under XP, I don't know if that has >> changed under Vista?). >> >> I remember from the R-FAQ that you can manually adjust XP so that it >> allocates up to 3 GB to one application ("the 3GB patch"), but I read in a >> PC-magazine and some message boards that this may cause problems. Does >> anybody of you successfully use this "trick" without any problems? >> > > Yes, many people: most 32-bit Exchange servers use it. Please don't rate > the advice in the R documentation below tittle-tattle you read on the web. > > >> Would it be wise to use a 64bit OS, as e.g. Vista X64? I think, underVista>> X64 it should be no problem to allocate 4 GB of RAM to R. Any experiences >> with that? >> > > That's what the rw-FAQ says, and we do write answers based on experience! > > >> Thanks in advance, >> Ralph Wirth >> >> >> ----- >> Ralph Wirth >> University Erlangen-Nuremberg, Chair of Statistics >> GfK Group, Department of Methods and Product Development >> >> >> > >-- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
Jin.Li at ga.gov.au
2008-Jan-27 22:57 UTC
[R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]
Thank you very much for the explanation and clarification, Patrick. It is a great help. Best regards, Jin -----Original Message----- From: Patrick Burns [mailto:pburns at pburns.seanet.com] Sent: Friday, 25 January 2008 9:48 To: Li Jin Cc: p.dalgaard at biostat.ku.dk; r-help at r-project.org Subject: Re: [R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED] Perhaps there are other opinions, but from my point of view R is spectacularly similar in Linux and Windows (and will be virtually identical in Linux and Unix). As long as you are doing "R" things, you should be in home territory. I regularly transfer R objects between 64-bit Linux and Windows, and have never had any problems. Patrick Burns patrick at burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and "A Guide for the Unwilling S User") Jin.Li at ga.gov.au wrote:>Hi Peter, >Thank you for the quick answer. >Given that we have UNIX system available here in Geoscience Australia, I am >wondering if UNIX is also faster and with 64 bit build. Perhaps they may be >kind enough to let me have a Linux system. >As I only have experience in using Windows PC, what kind of challenges are >there for using R in other systems like UNIX and Linux? >Thanks again, >Jin > >-----Original Message----- >From: Peter Dalgaard [mailto:p.dalgaard at biostat.ku.dk] >Sent: Thursday, 24 January 2008 10:23 >To: Li Jin >Cc: r-help at r-project.org >Subject: Re: [R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED] > >Jin.Li at ga.gov.au wrote: > > >>Dear All, >>I am currently using R in Windows PC with a 2 GB of RAM. Some pretty large >>datasets are expected soon, perhaps in an order of several GB. I am facing >> >> >a > > >>similar situation like Ralph, either to get a new PC with a bigger RAM or >>else. I am just wondering if R is getting faster in other systems like UNIX >>or Linux. Any suggestions are appreciated. >>Regards, >>Jin >> >> >> >It has always been faster in Linux than in Windows on the same hardware. >In addition, the toolchain issues have been holding up 64 bit >development on 64 bit Windows, whereas 64 bit build has been working >on Linux for years. > > > >>-------------------------------------------- >>Jin Li, PhD >>Spatial Modeller/ >>Computational Statistician >>Marine & Coastal Environment >>Geoscience Australia >>Ph: 61 (02) 6249 9899 >>Fax: 61 (02) 6249 9956 >>email: jin.li at ga.gov.au >>-------------------------------------------- >> >> >>-----Original Message----- >>From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On >>Behalf Of Prof Brian Ripley >>Sent: Thursday, 24 January 2008 12:05 >>To: Ralph79 >>Cc: r-help at r-project.org >>Subject: Re: [R] Problems with XP32-"3GB-patch"?/ Worth upgrading to Vista >>X64? >> >>On Wed, 23 Jan 2008, Ralph79 wrote: >> >> >> >> >>>Dear R-Users, >>> >>>as I will start a huge simulation in a few weeks, I am about to buy a new >>>and fast PC. I have noticed, that the RAM has been the limiting factor in >>>many of my calculations up to now (I had 2 GB in my "old" system, but >>>Windows still used quite a lot of virtual memory), hence my new computer >>>will have 4 GB of fast DDR2-800 RAM. >>> >>>However, I know that 1.) Windows 32 bit cannot make use of more than about >>>3,2 GB RAM and 2.) it is normally not allowed to allocate more than 2 GB >>> >>> >of > > >>>RAM to one single application (at least under XP, I don't know if that has >>>changed under Vista?). >>> >>>I remember from the R-FAQ that you can manually adjust XP so that it >>>allocates up to 3 GB to one application ("the 3GB patch"), but I read in a >>>PC-magazine and some message boards that this may cause problems. Does >>>anybody of you successfully use this "trick" without any problems? >>> >>> >>> >>Yes, many people: most 32-bit Exchange servers use it. Please don't rate >>the advice in the R documentation below tittle-tattle you read on the web. >> >> >> >> >>>Would it be wise to use a 64bit OS, as e.g. Vista X64? I think, under >>> >>> >Vista > > >>>X64 it should be no problem to allocate 4 GB of RAM to R. Any experiences >>>with that? >>> >>> >>> >>That's what the rw-FAQ says, and we do write answers based on experience! >> >> >> >> >>>Thanks in advance, >>>Ralph Wirth >>> >>> >>>----- >>>Ralph Wirth >>>University Erlangen-Nuremberg, Chair of Statistics >>>GfK Group, Department of Methods and Product Development >>> >>> >>> >>> >>> >> >> >> > > > >
Gabor Grothendieck
2008-Jan-28 00:38 UTC
[R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]
On the PC there is a builtin GUI but not on UNIX and there are some packages that are OS specific in which case you might get more or less selection but probably more. Also depending on the specific system you may have greater difficulty installing certain packages due to the need to compile them on UNIX and the possibility exists that you don't quite have the right libraries. On Windows you get binaries so this is not a problem. I have repeatedly found that common packages that I took for granted on Windows had some problem with installation on UNIX and I had to hunt around and figure out what the problem was with my UNIDX libraries or possibly some other problem. For all R packages this won't be a problem but for packages that use C and FORTRAN this can be. Although I am lumping all UNIX systems together I think this varies quite a bit from one particular type/distro of UNIX/Linux to another and I suspect if you are careful in picking out the right one (if you have a choice) you will actually have zero problems. On Jan 23, 2008 6:08 PM, <Jin.Li at ga.gov.au> wrote:> Dear All, > I am currently using R in Windows PC with a 2 GB of RAM. Some pretty large > datasets are expected soon, perhaps in an order of several GB. I am facing a > similar situation like Ralph, either to get a new PC with a bigger RAM or > else. I am just wondering if R is getting faster in other systems like UNIX > or Linux. Any suggestions are appreciated. > Regards, > Jin > -------------------------------------------- > Jin Li, PhD > Spatial Modeller/ > Computational Statistician > Marine & Coastal Environment > Geoscience Australia > Ph: 61 (02) 6249 9899 > Fax: 61 (02) 6249 9956 > email: jin.li at ga.gov.au > -------------------------------------------- > > > -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On > Behalf Of Prof Brian Ripley > Sent: Thursday, 24 January 2008 12:05 > To: Ralph79 > Cc: r-help at r-project.org > Subject: Re: [R] Problems with XP32-"3GB-patch"?/ Worth upgrading to Vista > X64? > > On Wed, 23 Jan 2008, Ralph79 wrote: > > > > > Dear R-Users, > > > > as I will start a huge simulation in a few weeks, I am about to buy a new > > and fast PC. I have noticed, that the RAM has been the limiting factor in > > many of my calculations up to now (I had 2 GB in my "old" system, but > > Windows still used quite a lot of virtual memory), hence my new computer > > will have 4 GB of fast DDR2-800 RAM. > > > > However, I know that 1.) Windows 32 bit cannot make use of more than about > > 3,2 GB RAM and 2.) it is normally not allowed to allocate more than 2 GB of > > RAM to one single application (at least under XP, I don't know if that has > > changed under Vista?). > > > > I remember from the R-FAQ that you can manually adjust XP so that it > > allocates up to 3 GB to one application ("the 3GB patch"), but I read in a > > PC-magazine and some message boards that this may cause problems. Does > > anybody of you successfully use this "trick" without any problems? > > Yes, many people: most 32-bit Exchange servers use it. Please don't rate > the advice in the R documentation below tittle-tattle you read on the web. > > > Would it be wise to use a 64bit OS, as e.g. Vista X64? I think, under Vista > > X64 it should be no problem to allocate 4 GB of RAM to R. Any experiences > > with that? > > That's what the rw-FAQ says, and we do write answers based on experience! > > > Thanks in advance, > > Ralph Wirth > > > > > > ----- > > Ralph Wirth > > University Erlangen-Nuremberg, Chair of Statistics > > GfK Group, Department of Methods and Product Development > > > > > > -- > Brian D. Ripley, ripley at stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >
Jin.Li at ga.gov.au
2008-Feb-11 23:27 UTC
[R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]
Thanks to all for your kind suggestions. After some discussion with our IT staff, I was told the UNIX system we have is Solaris and installation of R is very time consuming because "Given that this software is not standard, and given the amount of time required to compile the software (and potentially it's dependencies), it will need to be resourced as a project ..." From my experience with IT staff, it may take quite a long time for them to set up such project, let alone the installation. Given that, I wonder if it is possible to install it myself. As I have mentioned before, I have no experience in using UNIX, but I will have an access to the UNIX system soon. Any suggestions and help are greatly appreciated. Regards, Jin -----Original Message----- From: Gabor Grothendieck [mailto:ggrothendieck at gmail.com] Sent: Monday, 28 January 2008 11:38 To: Li Jin Cc: r-help at r-project.org Subject: Re: [R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED] On the PC there is a builtin GUI but not on UNIX and there are some packages that are OS specific in which case you might get more or less selection but probably more. Also depending on the specific system you may have greater difficulty installing certain packages due to the need to compile them on UNIX and the possibility exists that you don't quite have the right libraries. On Windows you get binaries so this is not a problem. I have repeatedly found that common packages that I took for granted on Windows had some problem with installation on UNIX and I had to hunt around and figure out what the problem was with my UNIDX libraries or possibly some other problem. For all R packages this won't be a problem but for packages that use C and FORTRAN this can be. Although I am lumping all UNIX systems together I think this varies quite a bit from one particular type/distro of UNIX/Linux to another and I suspect if you are careful in picking out the right one (if you have a choice) you will actually have zero problems. On Jan 23, 2008 6:08 PM, <Jin.Li at ga.gov.au> wrote:> Dear All, > I am currently using R in Windows PC with a 2 GB of RAM. Some pretty large > datasets are expected soon, perhaps in an order of several GB. I am facinga> similar situation like Ralph, either to get a new PC with a bigger RAM or > else. I am just wondering if R is getting faster in other systems like UNIX > or Linux. Any suggestions are appreciated. > Regards, > Jin > -------------------------------------------- > Jin Li, PhD > Spatial Modeller/ > Computational Statistician > Marine & Coastal Environment > Geoscience Australia > Ph: 61 (02) 6249 9899 > Fax: 61 (02) 6249 9956 > email: jin.li at ga.gov.au > -------------------------------------------- > > > -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On > Behalf Of Prof Brian Ripley > Sent: Thursday, 24 January 2008 12:05 > To: Ralph79 > Cc: r-help at r-project.org > Subject: Re: [R] Problems with XP32-"3GB-patch"?/ Worth upgrading to Vista > X64? > > On Wed, 23 Jan 2008, Ralph79 wrote: > > > > > Dear R-Users, > > > > as I will start a huge simulation in a few weeks, I am about to buy a new > > and fast PC. I have noticed, that the RAM has been the limiting factor in > > many of my calculations up to now (I had 2 GB in my "old" system, but > > Windows still used quite a lot of virtual memory), hence my new computer > > will have 4 GB of fast DDR2-800 RAM. > > > > However, I know that 1.) Windows 32 bit cannot make use of more thanabout> > 3,2 GB RAM and 2.) it is normally not allowed to allocate more than 2 GBof> > RAM to one single application (at least under XP, I don't know if thathas> > changed under Vista?). > > > > I remember from the R-FAQ that you can manually adjust XP so that it > > allocates up to 3 GB to one application ("the 3GB patch"), but I read ina> > PC-magazine and some message boards that this may cause problems. Does > > anybody of you successfully use this "trick" without any problems? > > Yes, many people: most 32-bit Exchange servers use it. Please don't rate > the advice in the R documentation below tittle-tattle you read on the web. > > > Would it be wise to use a 64bit OS, as e.g. Vista X64? I think, underVista> > X64 it should be no problem to allocate 4 GB of RAM to R. Any experiences > > with that? > > That's what the rw-FAQ says, and we do write answers based on experience! > > > Thanks in advance, > > Ralph Wirth > > > > > > ----- > > Ralph Wirth > > University Erlangen-Nuremberg, Chair of Statistics > > GfK Group, Department of Methods and Product Development > > > > > > -- > Brian D. Ripley, ripley at stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code. >
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