[R] Trouble with installing Rmpi package
edd at debian.org
Sat Jan 8 06:19:30 CET 2011
On 7 January 2011 at 19:57, Tena Sakai wrote:
| I made a bit of progress. I went to open-mpi.org and downloaded
| mpi software and installed it, which went smoothly. Then I re-
| > install.packages( 'Rmpi' )
| which worked, except this time it complained about rsprng. I went
| to sprng.cs.fsu.edu and downloaded sprng4 and tried installing it.
| went fine, but make failed. Here's the the failure:
| mpif77 -DHAVE_CONFIG_H -I. -I. -I../.. -I../../include -I../../include
| -DSPRNG_MPI -g -O2 -c -o sprngf_simple_mpi_tmp-sprngf-simple_mpi.o `test -f
| 'sprngf-simple_mpi.F' || echo './'`sprngf-simple_mpi.F
| mpif77 -g -O2 -o sprngf-simple_mpi.tmp --showme:link -I/usr/local/include
| -pthread sprngf_simple_mpi_tmp-sprngf-simple_mpi.o -L../../lib -lsprng -lm
| -lstdc++ -lm
| -g -O2 -o sprngf-simple_mpi.tmp -I/usr/local/include -pthread
| sprngf_simple_mpi_tmp-sprngf-simple_mpi.o -L../../lib -lsprng -lm -lstdc++
| -lm -pthread -L/usr/local/lib -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl
| -Wl,--export-dynamic -lnsl -lutil -lm -ldl
| mv: cannot stat `sprng-simple_mpi.tmp': No such file or directory
| make: *** [sprng_mpi_test] Error 1
| I issued:
| > library( 'Rmpi' )
| which didn't complain. I don't want to ignore the failure of rsprng package
| install, however.
| Can somebody please assist me as to how I can get sprng4 installed?
You may not need it. I maintain Rmpi for Debian and for building that I only
rely on Open MPI and R.
But I also maintain the rsprng package for Debian, and therefore also the
sprng library. This is a difficult package; I looked briefly at sprng4 and
didn't bother upgrading. Try out patched version of sprng2. Start eg here
The parallel suites can use either Rsprng or the rlecuyer package for
parallel RNGs. The latter one may be a good alternative.
| Thank you.
| Tena Sakai
| tsakai at gallo.ucsf.edu
| On 1/7/11 3:49 PM, "Tena Sakai" <tsakai at gallo.ucsf.edu> wrote:
| > Hi,
| > I am having a problem with installing Rmpi package on redhat linux machine.
| > The R I am using is version 2.10.1. Here¹s what happens.
| >> install.packages( 'Rmpi' )
| > --- Please select a CRAN mirror for use in this session ---
| > Loading Tcl/Tk interface ... done
| > trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/Rmpi_0.5-9.tar.gz'
| > Content type 'application/x-gzip' length 87953 bytes (85 Kb)
| > opened URL
| > ==================================================
| > downloaded 85 Kb
| > * installing *source* package âRmpiâ ...
| > checking for gcc... gcc -std=gnu99
| > 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 -std=gnu99 accepts -g... yes
| > checking for gcc -std=gnu99 option to accept ISO C89... none needed
| > checking how to run the C preprocessor... gcc -std=gnu99 -E
| > checking for grep that handles long lines and -e... /bin/grep
| > checking for egrep... /bin/grep -E
| > checking for ANSI C header files... yes
| > checking for sys/types.h... yes
| > checking for sys/stat.h... yes
| > checking for stdlib.h... yes
| > checking for string.h... yes
| > checking for memory.h... yes
| > checking for strings.h... yes
| > checking for inttypes.h... yes
| > checking for stdint.h... yes
| > checking for unistd.h... yes
| > checking mpi.h usability... no
| > checking mpi.h presence... no
| > checking for mpi.h... no
| > configure: error: "Cannot find mpi.h header file"
| > ERROR: configuration failed for package âRmpiâ
| > * removing â/usr/local/lib64/R/library/Rmpiâ
| > The downloaded packages are in
| > â/tmp/Rtmp1J1kDj/downloaded_packagesâ
| > Updating HTML index of packages in '.Library'
| > Warning message:
| > In install.packages("Rmpi") :
| > installation of package 'Rmpi' had non-zero exit status
| >> library ('Rmpi' )
| > Error in library("Rmpi") : there is no package called 'Rmpi'
| > I think it is upset because the file mpi.h is missing. Am I right? If so,
| > How would I cure this problem? And if not, what must I do?
| > Please help. Thank you.
| > Tena Sakai
| > tsakai at gallo.ucsf.edu
| > [[alternative HTML version deleted]]
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Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
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