[Rd] Call for participation: Comparative Methods in R Hackathon
NESCent Hackathon on Comparative Methods in R Call for Participation and Input The R statistical analysis package has emerged as a popular platform for implementation of powerful comparative phylogenetic methods to understand the evolution of organismal traits. The National Evolutionary Synthesis Center (NESCent) is organizing a hackathon focused on the integration of comparative phylogenetic methods within R. The event will take place on Dec 10-14, 2007, at NESCent in Durham, North Carolina. We are broadly soliciting applications for participation as well as comments and suggestions from the community. More information about the event is available at http://hackathon.nescent.org/R_Hackathon_1. A hackathon is an event at which a group of programmers who otherwise do not have the opportunity to interact on a routine basis meet to collaboratively develop working code that is of utility to the community as a whole. This event will bring together different groups of developers and users of comparative methods to work towards a common set of objectives centering on common challenges of data exchange, interoperability, and usability. CALL FOR INPUT We are soliciting input from the community at large regarding the priorities and objectives of the hackathon. If you are a user of comparative phylogenetic software and have any ideas that you would like the community of developers to be aware of, please submit your input directly through the hackathon wiki (http://hackathon.nescent.org; click on 'Forum') or by email to [EMAIL PROTECTED] CALL FOR PARTICIPATION We invite all individuals interested in attending to respond by email to the questions below. We are specifically encouraging applications from: * Members of underrepresented groups, specifically women and members of minorities. * Those with skills and interests in documentation or visualization, as both are currently underrepresented among the initial set of attendees * Biologists familiar with comparative phylogenetic methods who are interested in working face-to-face with developers to help prioritize needs, document and test the code being developed, provide feedback regarding usability, and ensure the community value of the code being written at the event. * Graduate students and postdocs. Please read the detailed description on the website (http://hackathon.nescent.org/R_Hackathon_1) prior to applying. Email your responses and, if possible, a CV to [EMAIL PROTECTED] by October 14. 1. Please indicate if you would be available for all or only for part of the Dec 10-14 time period. 2. All code produced at the event is to be made available immediately under an OSI-approved open-source license (specifically, the GPL for any code in R). Please indicate whether this would pose any difficulty for your participation. 3. Briefly describe your qualifications (e.g. your familiarity with comparative phylogenetic methods and/or R programming). 4. Please state what you would most like to accomplish at the hackathon. If you would not be writing software at the event, please state how you would like to contribute and how you would expect to benefit. 5. Please indicate if you are a member of an underrepresented group (including women, persons with disabilities, and any of the following minorities: African American, Hispanic, American Indian, Alaska Native, Native Hawaiian, and Pacific Islander). Please be aware that the funds, as well as the space, for this event are limited, and the organizers need to balance the skills of the attendees, so not all qualified applicants can be guaranteed acceptance. The Organizing Committee From NESCent: Hilmar Lapp, Brian O'Meara, Samantha Price, Todd Vision, Amy Zanne From UC Berkeley: Steven Kembel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Rmpi_0.5-4 and OpenMPI questions
Many thanks to Dr Yu for updating Rmpi for R 2.6.0, and for starting to make
the changes to support Open MPI.
I have just built the updated Debian package of Rmpi (i.e. r-cran-rmpi) under
R 2.6.0 but I cannot convince myself yet whether it works or not. Simple
tests work. E.g. on my Debian testing box, with Rmpi installed directly
using Open Mpi 1.2.3-2 (from Debian) and using 'r' from littler:
[EMAIL PROTECTED]:~> orterun -np 3 r -e 'library(Rmpi); print(mpi.comm.rank(0))'
[1] 0
[1] 1
[1] 2
[EMAIL PROTECTED]:~>
but I basically cannot get anything more complicated to work yet. R / Rmpi
just seem to hang, in particular snow and and getMPIcluster() just sit there:
> cl <- makeSOCKcluster(c("localhost", "localhost"))
> stopCluster(cl)
> library(Rmpi)
> cl <- makeMPIcluster(n=3)
Error in makeMPIcluster(n = 3) : no nodes available.
>
I may be overlooking something simple here, in particular the launching of
apps appears to be different for Open MPI than it was with LAM/MPI (or maybe
I am just confused because I also look at LLNL's slurm for use with Open MPI ?)
Has anybody gotten Open MPI and Rmpi to work on simple demos? Similarly, is
anybody using snow with Rmpi and Open MPI yet?
Also, the Open MPI FAQ is pretty clear on their preference for using mpicc
for compiling/linking to keep control of the compiler and linker options and
switches. Note that e.g. on my Debian system
[EMAIL PROTECTED]:~> mpicc --showme:link
-pthread -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm
-ldl
whereas Rmpi built with just the default from R CMD:
gcc-4.2 -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o
internal.o -L/usr/lib -lmpi -lpthread -fPIC -L/usr/lib/R/lib -lR
Don't we need libopen-rte and libopen-pal as the MPI FAQ suggests?
Many thanks, Dirk
--
Three out of two people have difficulties with fractions.
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[Rd] Rexcelpoi
I was experimenting with Rexcelpoi from Armstrong Whit. I was able to
compile the package in my Redhat linux machine with a few warnings but
no errors. I was not able to get the package built on my windows xp
computer, but that is for another post.
I load R on the linux computer and type in the library call to Rexcelpoi
the receive the following error.
library(Rexcelpoi)
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: dyn.load(file, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source)
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(ca ll[[1]],
quote(doTryCatch))) call <- sys.call(-4)dcall <-
deparse(call)[1]prefix <- paste ("Error in", dcall, ": ")
LONGCALL <- 30if (nchar(dcall) > LONGCALL)
prefix <- paste(prefi x, "\n\t", 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({ns <- loadNamespace(package, c(which.lib.loc, lib.loc),
keep.source = keep.source)dataPath <- file.p
ath(which.lib.loc, package, "data")env <- attachNamespace(ns, pos =
pos, dataPath = dataPath)})
9: library(Rexcelpoi)
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:
Some things I can figure out, but this one is beyond my capabilities.
Any thoughts or suggestions are greatly appreciated. If you think the
build warnings are important, I can rebuild the package and post those.
Everyone have a wonderful day.
Thank you
Joe
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