[R] Problem with R on dual core under Linux - can not execute mpi.spawn.Rslaves()
Rainer M Krug
r.m.krug at gmail.com
Mon Sep 29 15:46:50 CEST 2008
On Mon, Sep 29, 2008 at 3:05 PM, Luke Tierney <luke at stat.uiowa.edu> wrote:
> Look at the configure output below: configure is finding mpi.h in
> /usr/lib/mpich/include, soit is using mpich, not lam. You may be able
> to tell Rmpi specifically where to look for LAM stuff or you may need
> to uninstall mpich (almost surely that can be avoided but it may be
> easier if you don't really need mpich).
OK - I don't mind if I am using lam or mpich, so which one should I use?
I am confused.
If it helps, I am using Ubuntu Hardy
Rainer
>
> Best,
>
> luke
>
> On Mon, 29 Sep 2008, Rainer M Krug wrote:
>
>> On Mon, Sep 29, 2008 at 12:19 AM, Martin Morgan <mtmorgan at fhcrc.org>
>> wrote:
>>>
>>> "Rainer M Krug" <r.m.krug at gmail.com> writes:
>>>
>>>> Hi
>>>>
>>>> I am trying to utilize my dual core processor (and later a
>>>> High-performance clusters (HPC) ) by using the Rmpi, snow, snowfall,
>>>> ... packages, but I am struggling at the beginning, i.e. to initialise
>>>> the "cluster" on my dual core computer. Whenever I try to initialize
>>>> it (via sfInit(parallel=TRUE, cpus=2) or mpi.spawn.Rslaves(nslaves=2)
>>>> ), I get an error message:
>>>>
>>>>> sfInit(parallel=TRUE, cpus=2)
>>>>
>>>> Forced parallel. Using session: XXXXXXXXR_rkrug_143706_092708
>>>>
>>>> Error in mpi.comm.spawn(slave = mpitask, slavearg = args, nslaves =
>>>> count, :
>>>> MPI_Comm_spawn is not supported.
>>>> Error in sfInit(parallel = TRUE, cpus = 2) :
>>>> Starting of snow cluster failed! Error in mpi.comm.spawn(slave =
>>>> mpitask, slavearg = args, nslaves = count, :
>>>> MPI_Comm_spawn is not supported.
>>>>
>>>> and
>>>>
>>>>> mpi.spawn.Rslaves(nslaves=2)
>>>>
>>>> Error in mpi.spawn.Rslaves(nslaves = 2) :
>>>> You cannot use MPI_Comm_spawn API
>>>
>>> This error comes from Rmpi,
>>>
>>>> head(mpi.spawn.Rslaves, 6)
>>>
>>> 1 function (Rscript = system.file("slavedaemon.R", package = "Rmpi"),
>>> 2 nslaves = mpi.universe.size(), root = 0, intercomm = 2, comm = 1,
>>> 3 hosts = NULL, needlog = TRUE, mapdrive = TRUE)
>>> 4 {
>>> 5 if (!is.loaded("mpi_comm_spawn"))
>>> 6 stop("You cannot use MPI_Comm_spawn API")
>>>
>>> and occurs when the compiler variable MPI2 is undefined when your
>>
>>> package is installed. Likely this means that your mpi installation is
>>> either old (unlikely?) or that your Rmpi installation failed to
>>> properly detect the installed mpi version. It's difficult to know
>>> which, without more information on how the mpi and Rmpi installations
>>> went, at a minimum the result of R's sessionInfo() command and mpirun
>>> --version but likely including the output of Rmpi's installation.
>>
>> Version:
>> lamboot -V
>>
>> LAM 7.1.2/MPI 2 C++/ROMIO - Indiana University
>>
>> Arch: i486-pc-linux-gnu
>> Prefix: /usr/lib/lam
>> Configured by: buildd
>> Configured on: Sun Mar 23 08:07:16 UTC 2008
>> Configure host: rothera
>> SSI rpi: crtcp lamd sysv tcp usysv
>>
>> Below find the session info and the info from the instalaltion of Rmpi.
>>
>> In the install log from Rmpi, it says:
>> checking whether MPICH2 is declared... no
>> checking whether MPICH2 is declared... (cached) no
>>
>> So what went wrong? Do I have to start the "cluster" on the dual-core
>> machine?
>> Can I set the compiler variable MPI2 manually?
>>
>>> version
>>
>> _
>> platform i486-pc-linux-gnu
>> arch i486
>> os linux-gnu
>> system i486, linux-gnu
>> status
>> major 2
>> minor 7.2
>> year 2008
>> month 08
>> day 25
>> svn rev 46428
>> language R
>> version.string R version 2.7.2 (2008-08-25)
>>>
>>> sessionInfo()
>>
>> R version 2.7.2 (2008-08-25)
>> i486-pc-linux-gnu
>>
>> locale:
>>
>> LC_CTYPE=en_ZA.UTF-8;LC_NUMERIC=C;LC_TIME=en_ZA.UTF-8;LC_COLLATE=en_ZA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_ZA.UTF-8;LC_PAPER=en_ZA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_ZA.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] snow_0.3-3 Rmpi_0.5-5 snowfall_1.53
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.7.2
>>>
>>> install.packages(c("Rmpi"), dep=TRUE, repo="http://cbio.uct.ac.za/CRAN/")
>>
>> Warning in install.packages(c("Rmpi"), dep = TRUE, repo =
>> "http://cbio.uct.ac.za/CRAN/") :
>> argument 'lib' is missing: using '/usr/local/lib/R/site-library'
>> trying URL 'http://cbio.uct.ac.za/CRAN/src/contrib/Rmpi_0.5-5.tar.gz'
>> Content type 'application/x-gzip' length 94643 bytes (92 Kb)
>> opened URL
>> ==================================================
>> downloaded 92 Kb
>>
>> * Installing *source* package 'Rmpi' ...
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> I am here /usr/lib/mpich and it is MPICH
>> Try to find mpi.h ...
>> Found in /usr/lib/mpich/include
>> Try to find libmpi.so or libmpich.a
>> Found libmpich in /usr/lib/mpich/lib
>> ##########################################
>> checking whether MPICH2 is declared... no
>> checking whether MPICH2 is declared... (cached) no
>> ##########################################
>> checking for openpty in -lutil... yes
>> checking for main in -lpthread... yes
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> ** libs
>> gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -DHAVE_DECL_MPICH2=0 -DHAVE_DECL_MPICH2=0
>> -I/usr/lib/mpich/include -DMPICH -fPIC -fpic -g -O2 -c
>> conversion.c -o conversion.o
>> gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -DHAVE_DECL_MPICH2=0 -DHAVE_DECL_MPICH2=0
>> -I/usr/lib/mpich/include -DMPICH -fPIC -fpic -g -O2 -c
>> internal.c -o internal.o
>> gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -DHAVE_DECL_MPICH2=0 -DHAVE_DECL_MPICH2=0
>> -I/usr/lib/mpich/include -DMPICH -fPIC -fpic -g -O2 -c
>> RegQuery.c -o RegQuery.o
>> gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -DHAVE_DECL_MPICH2=0 -DHAVE_DECL_MPICH2=0
>> -I/usr/lib/mpich/include -DMPICH -fPIC -fpic -g -O2 -c Rmpi.c -o
>> Rmpi.o
>> gcc -std=gnu99 -shared -o Rmpi.so conversion.o internal.o RegQuery.o
>> Rmpi.o -L/usr/lib/mpich/lib -lmpich -lutil -lpthread -fPIC
>> -L/usr/lib/R/lib -lR
>> ** R
>> ** demo
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> >>> Building/Updating help pages for package 'Rmpi'
>> Formats: text html latex example
>> hosts text html latex
>> internal text html latex
>> mpi.abort text html latex
>> mpi.apply text html latex example
>> mpi.barrier text html latex
>> mpi.bcast text html latex
>> mpi.bcast.Robj text html latex
>> mpi.bcast.cmd text html latex
>> mpi.cart.coords text html latex example
>> mpi.cart.create text html latex example
>> mpi.cart.get text html latex example
>> mpi.cart.rank text html latex example
>> mpi.cart.shift text html latex example
>> mpi.cartdim.get text html latex example
>> mpi.comm text html latex example
>> mpi.comm.disconnect text html latex
>> mpi.comm.free text html latex
>> mpi.comm.inter text html latex
>> mpi.comm.set.errhandler text html latex
>> mpi.comm.spawn text html latex
>> mpi.const text html latex
>> mpi.dims.create text html latex example
>> mpi.exit text html latex
>> mpi.finalize text html latex
>> mpi.gather text html latex example
>> mpi.gather.Robj text html latex example
>> mpi.get.count text html latex
>> mpi.get.processor.name text html latex
>> mpi.get.sourcetag text html latex
>> mpi.info text html latex
>> mpi.init.sprng text html latex
>> mpi.intercomm.merge text html latex
>> mpi.parSim text html latex
>> mpi.parapply text html latex example
>> mpi.probe text html latex
>> mpi.realloc text html latex
>> mpi.reduce text html latex
>> mpi.remote.exec text html latex example
>> mpi.scatter text html latex example
>> mpi.scatter.Robj text html latex example
>> mpi.send text html latex example
>> mpi.send.Robj text html latex
>> mpi.sendrecv text html latex example
>> mpi.setup.rng text html latex
>> mpi.spawn.Rslaves text html latex example
>> mpi.universe.size text html latex
>> mpi.wait text html latex
>> ** building package indices ...
>> * DONE (Rmpi)
>>
>> The downloaded packages are in
>> /tmp/RtmpdX6zlZ/downloaded_packages
>>>
>>
>>>
>>> Dirk Eddelbuettel
>>> (https://stat.ethz.ch/pipermail/r-devel/2008-September/050665.html)
>>> suggested that snow's makeSOCKcluster is an easier starting point for
>>> single computer 'clusters' or other configurations where significant
>>> system administration is not desired -- these should work without
>>> additional software on most systems, even if more limiting in the long
>>> term (in my opinion). See, e.g., the examples on the help page for
>>> clusterApply for basic operation. A bit oddly, apparently the
>>> 'snowfall' package restricts snow's functionality to mpi clusters. So
>>> you might start with snow directly.
>>>
>>> Martin
>>>
>>>>
>>>> I followed the pdf "Developing parallel programs using snowfall" by
>>>> Jochen Knaus,. installed the relevant libraries and programs, but it
>>>> does not work.
>>>>
>>>> I am stuck.
>>>>
>>>> Any help appreciated,
>>>>
>>>> Rainer
>>>>
>>>>
>>>> --
>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
>>>> Biology, UCT), Dipl. Phys. (Germany)
>>>>
>>>> Centre of Excellence for Invasion Biology
>>>> Faculty of Science
>>>> Natural Sciences Building
>>>> Private Bag X1
>>>> University of Stellenbosch
>>>> Matieland 7602
>>>> South Africa
>>>>
>>>> ______________________________________________
>>>> 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.
>>>
>>> --
>>> 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
>>>
>>
>>
>>
>>
>
> --
> Luke Tierney
> Chair, Statistics and Actuarial Science
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa Phone: 319-335-3386
> Department of Statistics and Fax: 319-335-3017
> Actuarial Science
> 241 Schaeffer Hall email: luke at stat.uiowa.edu
> Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
>
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Faculty of Science
Natural Sciences Building
Private Bag X1
University of Stellenbosch
Matieland 7602
South Africa
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