On Jul 13, 2011, at 3:50 PM, Steven McKinney wrote: > > > >> -----Original Message----- >> From: [email protected] >> [mailto:[email protected]] On Behalf Of Wayne Gray >> Sent: July-13-11 12:25 PM >> To: [email protected] >> Subject: [R-SIG-Mac] R run time question >> >> All, >> >> We are doing ANOVAs that take a long time (> 3 hrs) to run in 64-bit mode on >> an Intel MacPro with 8 >> gbytes and 2.66 GHZ Intel Core i7 machine. >> >> We have just tried running these on our server where we don't care as much >> how long it takes. The >> server is a Mac "2 x 3 GHz Dual-Core Intel Xeon" with 13 GB 667 MHz DDR2 >> FB-DIMM. >> >> We have installed R "R 2.10.1 GUI 1.31-np Tiger build 32-bit (5538)" on the >> server. > > Why are you installing a 32 bit R? And why an older version of R? > > Can you not install a 64 bit version of the latest R? > >> >> The data.frame is composed of the following observations, factors, and >> numerals: >> >>> str(e1jit41blkAll) >> 'data.frame': 21648 obs. of 6 variables: >> $ subjectid: Factor w/ 22 levels "1379","1744",..: 1 1 1 1 1 1 1 1 1 1 ... >> $ cond : Factor w/ 2 levels "Visual","Auditory": 1 1 1 1 1 1 1 1 1 1 ... >> $ block : Factor w/ 8 levels "2","3","4","5",..: 1 1 1 1 1 1 1 1 1 1 ... >> $ cbtime : Factor w/ 41 levels "1","2","3","4",..: 1 10 11 12 13 14 15 16 >> 17 18 ... >> $ dirtime : Ord.factor w/ 3 levels "Early"<"Middle"<..: 1 1 1 1 1 1 1 1 1 1 >> ... >> $ jitter : num 7.78 7.33 5.56 5 6.11 ... >> >> When we run the following ANOVA on this dataframe: >> >>> anova.ALL.e1jit41.blkAll <- with(e1jit41blkAll, aov(jitter ~ >>> cond*block*dirtime*cbtime + >> error(subjectid/(block*dirtime*cbtime)), data = e1jit41blkAll)) >> >> We get the following feedback: >> >> Error: cannot allocate vector of size 3.5 Gb > > Running the ANOVA requires more than 4GB of RAM, which can not be done > with 32 bit versions of software. So you will need 64 bit R to do this > analysis. > >> >>> >> R(29720,0xa000d000) malloc: *** vm_allocate(size=3749089280) failed (error >> code=3) >> R(29720,0xa000d000) malloc: *** error: can't allocate region >> R(29720,0xa000d000) malloc: *** set a breakpoint in szone_error to debug >> R(29720,0xa000d000) malloc: *** vm_allocate(size=3749089280) failed (error >> code=3) >> R(29720,0xa000d000) malloc: *** error: can't allocate region >> R(29720,0xa000d000) malloc: *** set a breakpoint in szone_error to debug >>> >> >> So two categories of questions for all of you Mac-R wizards out there. >> >> First category of question: can this analysis be run faster (and if so, how) >> on our laptop Intel Macs? >> >> Second category of question: is there anything that can be done to the Apple >> Server or to our analysis >> so that the analysis runs on our server? > > What OS version is on your server? If it's an old 32 bit version, upgrading > the server > to a recent 64 bit OS will help. Then install a recent 64 bit version of R. >
FWIW: you can run R in 64-bit on Tiger as well, you just have to disable Quartz and the GUI since Tiger doesn't have 64-bit Cocoa. Cheers, Simon > If you can do this, you can better assess whether this analysis can be done > faster on the 8GB laptops. > > R runs entirely in RAM, so if the analysis needs more than 8GB of RAM, you may > be experiencing "swapping" on the laptops. The operating system allocates > as much memory as the job needs - if that amount of memory exceeds the amount > of RAM you have, then the rest is allocated to "virtual memory" which is > on the disk drive. Swapping occurs when part of the virtual memory of your > job > that is on disk is needed - the OS has to copy a chunk of what is in RAM out > to > disk, so it can copy the other chunk on disk back into RAM. > > Monitor the laptop with a shell command line process such as "top" > and you will be able to determine how much virtual memory your R job > is using, and how many "swaps" are involved. Swapping really slows things > down as reading and writing from the disk is slow. If your job is swapping > on the laptop, but uses less than 13GB of memory in total, it will run faster > on the server. If the job is not swapping at all on the laptop, it will not > run appreciably faster on the server. > > > HTH > > Steve McKinney > > >> >> Many thanks, >> >> Wayne Gray >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
