Re: [Rd] arima() bug
No segfault with my r-patched version on linux-i686: > set.seed(1); x <- ts(20*sin((1:731)*2*pi/365) + 10 + rnorm(731, 0, 4), > freq=365) > arima(x, c(1, 0, 1), c(1, 0, 1)) Errore: cannot allocate vector of size 1010.9 Mb F. > R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status Patched major 2 minor 7.0 year 2008 month 05 day29 svn rev45820 language R version.string R version 2.7.0 Patched (2008-05-29 r45820) 2008/6/12 Ray Brownrigg <[EMAIL PROTECTED]>: > I guess this is more r-devel than r-help. > > Note, I am just the messenger - I have no idea what the user is trying to > model here. > > arima() crashes R (segfault) with Linux R-2.7.0, Solaris R-2.6.0: > > *** caught segfault *** > address 4240, cause 'memory not mapped' > > Traceback: > 1: .Call(R_getQ0, phi, theta) > 2: makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) > 3: arima(x, c(1, 0, 1), c(1, 0, 1)) > > Under rw-2.7.0 or R version 2.8.0 Under development (unstable) (2008-06-10 > r45893) > it gets: > Error: cannot allocate vector of size 1010.9 Mb > In addition: Warning messages: > 1: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : > Reached total allocation of 447Mb: see help(memory.size) > 2: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : > Reached total allocation of 447Mb: see help(memory.size) > 3: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : > Reached total allocation of 447Mb: see help(memory.size) > 4: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : > Reached total allocation of 447Mb: see help(memory.size) > > Reproduce by: > > # 2 years of daily temperature data > set.seed(1); x <- ts(20*sin((1:731)*2*pi/365) + 10 + rnorm(731, 0, 4), > freq=365) > arima(x, c(1, 0, 1), c(1, 0, 1)) > > Ray Brownrigg > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Antonio, Fabio Di Narzo Ph.D. student at Department of Statistical Sciences University of Bologna, Italy __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] arima() bug
On Thu, 12 Jun 2008, Antonio, Fabio Di Narzo wrote: No segfault with my r-patched version on linux-i686: set.seed(1); x <- ts(20*sin((1:731)*2*pi/365) + 10 + rnorm(731, 0, 4), freq=365) arima(x, c(1, 0, 1), c(1, 0, 1)) Errore: cannot allocate vector of size 1010.9 Mb Yes, you need a lot of memory to reproduce it. It's a nonsensical calculation but nevertheless we need to track down the cause. F. R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status Patched major 2 minor 7.0 year 2008 month 05 day29 svn rev45820 language R version.string R version 2.7.0 Patched (2008-05-29 r45820) 2008/6/12 Ray Brownrigg <[EMAIL PROTECTED]>: I guess this is more r-devel than r-help. Note, I am just the messenger - I have no idea what the user is trying to model here. arima() crashes R (segfault) with Linux R-2.7.0, Solaris R-2.6.0: *** caught segfault *** address 4240, cause 'memory not mapped' Traceback: 1: .Call(R_getQ0, phi, theta) 2: makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) 3: arima(x, c(1, 0, 1), c(1, 0, 1)) Under rw-2.7.0 or R version 2.8.0 Under development (unstable) (2008-06-10 r45893) it gets: Error: cannot allocate vector of size 1010.9 Mb In addition: Warning messages: 1: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : Reached total allocation of 447Mb: see help(memory.size) 2: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : Reached total allocation of 447Mb: see help(memory.size) 3: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : Reached total allocation of 447Mb: see help(memory.size) 4: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : Reached total allocation of 447Mb: see help(memory.size) Reproduce by: # 2 years of daily temperature data set.seed(1); x <- ts(20*sin((1:731)*2*pi/365) + 10 + rnorm(731, 0, 4), freq=365) arima(x, c(1, 0, 1), c(1, 0, 1)) Ray Brownrigg __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Antonio, Fabio Di Narzo Ph.D. student at Department of Statistical Sciences University of Bologna, Italy __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] 2.7.1 scheduled for November 26
This is to announce that we plan to release R version 2.7.1 on Monday, June 23, 2008. Release procedures start tomorrow, Friday June 13. The source tarballs will be made available daily (barring build troubles) by a cron job running at 4AM CET, and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Monday 16 at the latest. For the Core Team Peter Dalgaard -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] 2.7.1 scheduled for JUNE 23
(Resent, now with correct date in subject. Doh!) This is to announce that we plan to release R version 2.7.1 on Monday, June 23, 2008. Release procedures start tomorrow, Friday June 13. The source tarballs will be made available daily (barring build troubles) by a cron job running at 4AM CET, and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Monday 16 at the latest. For the Core Team Peter Dalgaard -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] arima() bug
I get the same behaviour on R version 2.7.0 Patched (2008-06-05 r45857), Opensuse 10.3 x86_64 (32 Gb RAM) > set.seed(1); x <- ts(20*sin((1:731)*2*pi/365) + 10 + rnorm(731, 0, 4), freq=365) > arima(x, c(1, 0, 1), c(1, 0, 1)) *** caught segfault *** address 0x2aafb83e9f50, cause 'memory not mapped' Traceback: 1: .Call(R_getQ0, phi, theta) 2: makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) 3: arima(x, c(1, 0, 1), c(1, 0, 1)) the problem seems to show up when the seasonal AR part is included > arima(x, c(2, 1, 3), c(0, 0, 0)) Call: arima(x = x, order = c(2, 1, 3), seasonal = c(0, 0, 0)) Coefficients: ar1 ar2 ma1 ma2 ma3 0.0363 0.9477 -0.9434 -0.9468 0.9060 s.e. 0.0291 0.0289 0.0258 0.0397 0.0233 sigma^2 estimated as 18.41: log likelihood = -2100.79, aic = 4213.59 > arima(x, c(0, 0, 0), c(0, 0, 1)) Call: arima(x = x, order = c(0, 0, 0), seasonal = c(0, 0, 1)) Coefficients: sma1 intercept 0. 9.9293 s.e. 0.0724 0.5674 sigma^2 estimated as 78.47: log likelihood = -2832.41, aic = 5670.81 > arima(x, c(0, 0, 0), c(1, 0, 0)) *** caught segfault *** address 0x2b00bf41eae0, cause 'memory not mapped' Traceback: 1: .Call(R_getQ0, phi, theta) 2: makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) 3: arima(x, c(0, 0, 0), c(1, 0, 0)) > arima(x, c(0, 0, 0), c(2, 0, 0)) Errore in makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : cannot allocate memory block of size 137438953465.2 Gb > arima(x, c(0, 0, 0), c(3, 0, 0)) Errore in optim(init[mask], armaCSS, method = "BFGS", hessian = FALSE, : initial value in 'vmmin' is not finite > R.version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status Patched major 2 minor 7.0 year 2008 month 06 day05 svn rev45857 language R version.string R version 2.7.0 Patched (2008-06-05 r45857) On Thu, Jun 12, 2008 at 9:27 AM, Antonio, Fabio Di Narzo < [EMAIL PROTECTED]> wrote: > No segfault with my r-patched version on linux-i686: > > > set.seed(1); x <- ts(20*sin((1:731)*2*pi/365) + 10 + rnorm(731, 0, 4), > freq=365) > > arima(x, c(1, 0, 1), c(1, 0, 1)) > Errore: cannot allocate vector of size 1010.9 Mb > > F. > > > R.version > _ > platform i686-pc-linux-gnu > arch i686 > os linux-gnu > system i686, linux-gnu > status Patched > major 2 > minor 7.0 > year 2008 > month 05 > day29 > svn rev45820 > language R > version.string R version 2.7.0 Patched (2008-05-29 r45820) > > > 2008/6/12 Ray Brownrigg <[EMAIL PROTECTED]>: > > I guess this is more r-devel than r-help. > > > > Note, I am just the messenger - I have no idea what the user is trying to > model here. > > > > arima() crashes R (segfault) with Linux R-2.7.0, Solaris R-2.6.0: > > > > *** caught segfault *** > > address 4240, cause 'memory not mapped' > > > > Traceback: > > 1: .Call(R_getQ0, phi, theta) > > 2: makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) > > 3: arima(x, c(1, 0, 1), c(1, 0, 1)) > > > > Under rw-2.7.0 or R version 2.8.0 Under development (unstable) > (2008-06-10 r45893) > > it gets: > > Error: cannot allocate vector of size 1010.9 Mb > > In addition: Warning messages: > > 1: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : > > Reached total allocation of 447Mb: see help(memory.size) > > 2: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : > > Reached total allocation of 447Mb: see help(memory.size) > > 3: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : > > Reached total allocation of 447Mb: see help(memory.size) > > 4: In makeARIMA(trarma[[1]], trarma[[2]], Delta, kappa) : > > Reached total allocation of 447Mb: see help(memory.size) > > > > Reproduce by: > > > > # 2 years of daily temperature data > > set.seed(1); x <- ts(20*sin((1:731)*2*pi/365) + 10 + rnorm(731, 0, 4), > freq=365) > > arima(x, c(1, 0, 1), c(1, 0, 1)) > > > > Ray Brownrigg > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > > -- > Antonio, Fabio Di Narzo > Ph.D. student at > Department of Statistical Sciences > University of Bologna, Italy > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- __ Simone Giannerini Dipartimento di Scienze Statistiche "Paolo Fortunati" Universita' di Bologna Via delle belle arti 41 - 40126 Bologna, ITALY Tel: +39 051 2098262 Fax: +39 051 232153 http://www2.stat.unibo.it/giannerini/ __ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list htt
Re: [Rd] arima() bug
On Thu, 12 Jun 2008, Ray Brownrigg wrote:
> arima() crashes R (segfault) with Linux R-2.7.0, Solaris R-2.6.0:
>
> Reproduce by:
>
> # 2 years of daily temperature data
> set.seed(1); x <- ts(20*sin((1:731)*2*pi/365) + 10 + rnorm(731, 0, 4),
> freq=365)
> arima(x, c(1, 0, 1), c(1, 0, 1))
I put a breakpoint in Rf_allocVector when its length argument
was more than 10 million and it stopped when library/stats/src/arima.c:getQ0
asked for a vector of nrbar=132497980 doubles, a number proportional
to the 4th power of max(length(phi),length(theta)) from the R arima():upARIMA()
function:
SEXP getQ0(SEXP sPhi, SEXP sTheta)
{
...
int p = LENGTH(sPhi), q = LENGTH(sTheta);
...
int r = max(p, q + 1), np = r * (r + 1) / 2, nrbar = np * (np - 1) / 2;
...
rbar = (double *) R_alloc(nrbar, sizeof(double));
(gdb) print nrbar
$1 = 132497980
(gdb) print np
$2 = 67528
(gdb) print r
$3 = 367
(gdb) print q
$4 = 366
Trying to recover from running out of memory probably
causes the crash.
rbar is a scratch array.
Bill Dunlap
Insightful Corporation
bill at insightful dot com
"All statements in this message represent the opinions of the author and do
not necessarily reflect Insightful Corporation policy or position."
__
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Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Dirk, Configure concluded without errors. I am not running this on the HPC cluster with icc, rather a separate local box used for testing and learning. Its just an 64-bit Ubuntu 8.04 install on a 4-core machine. LAM is not installed (I checked to make sure). So, that leaves me with you last two options. Before I make my first foray into using the R-debugger, I'd like to try you suggestion to "Check ldd on Rmpi.so" but don't have a clue how to do so. Could you instruct me? Thanks to all for the helpful comments. Mark On Wed, Jun 11, 2008 at 8:22 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: > > On 11 June 2008 at 00:46, Mark Kimpel wrote: > | I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and using the > | following without errors: > | "R CMD INSTALL Rmpi_0.5-5.tar.gz > --configure-args=--with-mpi=/usr/lib64/openmpi" > > And it concluded without warnings or errors? Configure found all the right > files? > > As Paul suggested, make sure you're not getting it mixed with > exisiting LAM headers or MPICH2 headers or, say, that you're getting your gcc > and icc experiemenst mixed up or ... ? > > I control this by locally re-building the Debian packages for Open MPI. That > way I only keep one -dev package for MPI and can ensure that I do not get > mixups with other MPI installation. But then I do buy into the Package > Management mantra, but not everybody does... > > | Immediately at library(Rmpi) I get the segfault displayed in my > | complete output below. My first thought is that perhaps I used the > | wrong library for openmpi, but with my 64 bit install it seemed like a > | logical choice and the install went without a hitch. > > Check ldd on Rmpi.so to ensure that you linked against what you thought you > should link against. > > And if everything else fails, debug the compiled code and run R under the > debuggger. See the 'R Extensions' manual. > > | Two other general comments: > | 1. Am I addressing this to the correct list or should I use R-help? As > | I read the posting guide, I'm not sure. > | 2. Has anyone considered an R-SIG-HPC list? Anyone besides me interested? > > I'd join. > > Dirk > > -- > Three out of two people have difficulties with fractions. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
simply cd to $R_HOME/library/Rmpi/libs and do on the command line ldd -r Rmpi.so this will display you a list of dependencies of Rmpi.so and you can see if you find there the libraries that you expected to link against, or there will be some libraries from unexpected paths or missing ones Mark Kimpel wrote: Dirk, Configure concluded without errors. I am not running this on the HPC cluster with icc, rather a separate local box used for testing and learning. Its just an 64-bit Ubuntu 8.04 install on a 4-core machine. LAM is not installed (I checked to make sure). So, that leaves me with you last two options. Before I make my first foray into using the R-debugger, I'd like to try you suggestion to "Check ldd on Rmpi.so" but don't have a clue how to do so. Could you instruct me? Thanks to all for the helpful comments. Mark On Wed, Jun 11, 2008 at 8:22 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: On 11 June 2008 at 00:46, Mark Kimpel wrote: | I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and using the | following without errors: | "R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi" And it concluded without warnings or errors? Configure found all the right files? As Paul suggested, make sure you're not getting it mixed with exisiting LAM headers or MPICH2 headers or, say, that you're getting your gcc and icc experiemenst mixed up or ... ? I control this by locally re-building the Debian packages for Open MPI. That way I only keep one -dev package for MPI and can ensure that I do not get mixups with other MPI installation. But then I do buy into the Package Management mantra, but not everybody does... | Immediately at library(Rmpi) I get the segfault displayed in my | complete output below. My first thought is that perhaps I used the | wrong library for openmpi, but with my 64 bit install it seemed like a | logical choice and the install went without a hitch. Check ldd on Rmpi.so to ensure that you linked against what you thought you should link against. And if everything else fails, debug the compiled code and run R under the debuggger. See the 'R Extensions' manual. | Two other general comments: | 1. Am I addressing this to the correct list or should I use R-help? As | I read the posting guide, I'm not sure. | 2. Has anyone considered an R-SIG-HPC list? Anyone besides me interested? I'd join. Dirk -- Three out of two people have difficulties with fractions. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Oleg Sklyar wrote: simply cd to $R_HOME/library/Rmpi/libs and do on the command line ldd -r Rmpi.so I think you'll want to R CMD ldd $R_HOME/library/Rmpi/libs/Rmpi.so which picks up the R configuration environment, e.g., compare BLAS below: [EMAIL PROTECTED]:~/> R CMD ldd $R_HOME/library/stats/libs/stats.so libRblas.so => /home/mtmorgan/arch/x86_64/R-devel/lib/libRblas.so (0x2b543f98b000) libgfortran.so.2 => /usr/lib64/libgfortran.so.2 (0x2b543fc09000) libm.so.6 => /lib64/libm.so.6 (0x2b543fec4000) libc.so.6 => /lib64/libc.so.6 (0x2b5440118000) /lib64/ld-linux-x86-64.so.2 (0x4000) [EMAIL PROTECTED]:~/s> ldd $R_HOME/library/stats/libs/stats.so libRblas.so => not found libgfortran.so.2 => /usr/lib64/libgfortran.so.2 (0x2aeabd923000) libm.so.6 => /lib64/libm.so.6 (0x2aeabdbde000) libc.so.6 => /lib64/libc.so.6 (0x2aeabde32000) /lib64/ld-linux-x86-64.so.2 (0x4000) Martin this will display you a list of dependencies of Rmpi.so and you can see if you find there the libraries that you expected to link against, or there will be some libraries from unexpected paths or missing ones Mark Kimpel wrote: Dirk, Configure concluded without errors. I am not running this on the HPC cluster with icc, rather a separate local box used for testing and learning. Its just an 64-bit Ubuntu 8.04 install on a 4-core machine. LAM is not installed (I checked to make sure). So, that leaves me with you last two options. Before I make my first foray into using the R-debugger, I'd like to try you suggestion to "Check ldd on Rmpi.so" but don't have a clue how to do so. Could you instruct me? Thanks to all for the helpful comments. Mark On Wed, Jun 11, 2008 at 8:22 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: On 11 June 2008 at 00:46, Mark Kimpel wrote: | I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and using the | following without errors: | "R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi" And it concluded without warnings or errors? Configure found all the right files? As Paul suggested, make sure you're not getting it mixed with exisiting LAM headers or MPICH2 headers or, say, that you're getting your gcc and icc experiemenst mixed up or ... ? I control this by locally re-building the Debian packages for Open MPI. That way I only keep one -dev package for MPI and can ensure that I do not get mixups with other MPI installation. But then I do buy into the Package Management mantra, but not everybody does... | Immediately at library(Rmpi) I get the segfault displayed in my | complete output below. My first thought is that perhaps I used the | wrong library for openmpi, but with my 64 bit install it seemed like a | logical choice and the install went without a hitch. Check ldd on Rmpi.so to ensure that you linked against what you thought you should link against. And if everything else fails, debug the compiled code and run R under the debuggger. See the 'R Extensions' manual. | Two other general comments: | 1. Am I addressing this to the correct list or should I use R-help? As | I read the posting guide, I'm not sure. | 2. Has anyone considered an R-SIG-HPC list? Anyone besides me interested? I'd join. Dirk -- Three out of two people have difficulties with fractions. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
On 12 June 2008 at 18:38, Mark Kimpel wrote: | Dirk, | | Configure concluded without errors. I am not running this on the HPC | cluster with icc, rather a separate local box used for testing and | learning. Its just an 64-bit Ubuntu 8.04 install on a 4-core machine. | LAM is not installed (I checked to make sure). | | So, that leaves me with you last two options. Before I make my first | foray into using the R-debugger, I'd like to try you suggestion to | "Check ldd on Rmpi.so" but don't have a clue how to do so. Could you | instruct me? ldd is a command so try 'man ldd'; or just use what Oleg and Martin showed you. You still told us where you got R, Rmpi, and Open MPI from. You could just do $ sudo apt-get install r-cran-rmpi and get Rmpi installed along with its dependencies (eg R and Open MPI). That just works on Debian. It also worked, as I recall, on Ubuntu 'Gutsy' aka 7.10. However, on Ubuntu 'Hardy' aka 8.04, this may be broken as I discovered during some testing for the HPC presentation I'll be giving at Use R. I filed an Ubuntu bug report at https://bugs.launchpad.net/ubuntu/+source/binutils/+bug/234837 but no follow-up has happened. That said, this still all works for me at a) at work which is x86 and all Ubuntu machines b) at home where it is x86 and a mix of Debian and Ubuntu machines _but_ only after I rebuilt openmpi_1.2.5 on an older Gutsy machine as detailed in the bugreport. Something on Hardy breaks it. I am not an Ubuntu maintainer, so I am not sure who to talk to. I'll forward a copy of this to the Ubuntu folks. As an aside, the Debian packages all work. Dirk | Thanks to all for the helpful comments. | Mark | | On Wed, Jun 11, 2008 at 8:22 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: | > | > On 11 June 2008 at 00:46, Mark Kimpel wrote: | > | I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and using the | > | following without errors: | > | "R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi" | > | > And it concluded without warnings or errors? Configure found all the right files? | > | > As Paul suggested, make sure you're not getting it mixed with | > exisiting LAM headers or MPICH2 headers or, say, that you're getting your gcc | > and icc experiemenst mixed up or ... ? | > | > I control this by locally re-building the Debian packages for Open MPI. That | > way I only keep one -dev package for MPI and can ensure that I do not get | > mixups with other MPI installation. But then I do buy into the Package | > Management mantra, but not everybody does... | > | > | Immediately at library(Rmpi) I get the segfault displayed in my | > | complete output below. My first thought is that perhaps I used the | > | wrong library for openmpi, but with my 64 bit install it seemed like a | > | logical choice and the install went without a hitch. | > | > Check ldd on Rmpi.so to ensure that you linked against what you thought you | > should link against. | > | > And if everything else fails, debug the compiled code and run R under the | > debuggger. See the 'R Extensions' manual. | > | > | Two other general comments: | > | 1. Am I addressing this to the correct list or should I use R-help? As | > | I read the posting guide, I'm not sure. | > | 2. Has anyone considered an R-SIG-HPC list? Anyone besides me interested? | > | > I'd join. | > | > Dirk | > | > -- | > Three out of two people have difficulties with fractions. | > | > __ | > R-devel@r-project.org mailing list | > https://stat.ethz.ch/mailman/listinfo/r-devel | > | | | | -- | Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry | Indiana University School of Medicine | | 15032 Hunter Court, Westfield, IN 46074 | | (317) 490-5129 Work, & Mobile & VoiceMail | (317) 663-0513 Home (no voice mail please) | | __ | R-devel@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-devel -- Three out of two people have difficulties with fractions. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Dirk,
Did R CMD ldd $R_HOME/library/Rmpi/libs/Rmpi.so as suggested and
things looked okay. Not really wanting to mess with the debugger I
decided to use your prepackaged version. I completely uninstalled all
openmpi packages on my system using Synaptic and deleted my compiled
from source Rmpi from my site-library. Then I executed "sudo apt-get
install r-cran-rmpi" and things seemed to go smoothly. I put a soft
link from the library aptitude installed Rmpi into to my
~/R_HOME/site-library. I get exactly the same error as before. Does
the minimal debugging info below "options(error = recover) provide any
insight? Mark
> require(Rmpi)
Loading required package: Rmpi
*** caught segfault ***
address 0x2224008, cause 'memory not mapped'
Traceback:
1: .Call("mpi_initialize", PACKAGE = "Rmpi")
2: f(libname, pkgname)
3: firstlib(which.lib.loc, package)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) {call <- conditionCall(e)
if (!is.null(call)) {if (identical(call[[1]],
quote(doTryCatch))) call <- sys.call(-4)dcall <-
deparse(call)[1]prefix <- paste("Error in", dcall, ": ")
LONG <- 75msg <- conditionMessage(e)sm <-
strsplit(msg, "\n")[[1]]if (14 + nchar(dcall, type = "w") +
nchar(sm[1], type = "w") > LONG) prefix <-
paste(prefix, "\n ", sep = "")}else prefix <- "Error : "
msg <- paste(prefix, conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1]))if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {
cat(msg, file = stderr()).Internal(printDeferredWarnings())
}invisible(structure(msg, class = "try-error"))})
8: try(firstlib(which.lib.loc, package))
9: library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE, warn.conflicts = warn.conflicts,
keep.source = keep.source, version = version)
10: require(Rmpi)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 2
Save workspace image? [y/n/c]: n
[EMAIL PROTECTED]:~/R_HOME/site-library-2.7.0/Rmpi$ R
R version 2.7.0 Patched (2008-05-18 r45728)
#stuff deleted for brevity
__
> sessionInfo()
R version 2.7.0 Patched (2008-05-18 r45728)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] graph_1.18.1
loaded via a namespace (and not attached):
[1] cluster_1.11.10 tools_2.7.0
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
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Re: [Rd] significant digits (PR#9682)
Thanks Patrick, your function is a neat work-around to include trailing
zeroes when specifying significant digits.
It worked better with this modification to the "format" arguments: =20
else if (sigdigs<=3Dleft+right)
{out<-format(signum,nsmall=3Dsigdigs-left)}
Agree would be nice to include this in signif()
Regards, Scott.
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf=20
> Of Patrick Carr
> Sent: Tuesday, 3 June 2008 11:28 AM
> To: [EMAIL PROTECTED]
> Cc: Wilkinson, Scott (CLW, Townsville)
> Subject: Re: significant digits (PR#9682)
>=20
> To reply to my own message, that function wasn't quite right. I think
> this one works better:
>=20
> signif.string <- function(signum,sigdigs){
> test <- abs(signum)
> left <- nchar(trunc(test))
> right <- nchar(test)-left-1
> if (test<1) {left<-left-1}
> if (right<0) {right<-0}
> if (sigdigs else if (sigdigs=3D=3Dleft & trunc(signum) %% 10 =3D=3D 0)
> {out<-paste(round(signum),".",sep=3D"")}
> else if (sigdigs<=3Dleft+right) =
{out<-format(signum,digits=3Dsigdigs)}
> else {out<-sprintf(paste("%.",sigdigs-left,"f",sep=3D""),signum)}
> return(noquote(out))
> }
>=20
> But it should still have error checking and vector capability, yadda
> yadda. Also, I forgot what year it was, so sorry, Scott, for spamming
> you with something you're hopefully not still stuck on.
>=20
> Pat Carr
>=20
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