[R] Trouble with installing Rmpi package

[Tena Sakai]

Hi Dirk,

Many thanks for your reply and comments.

I have downloaded sprng2.0 from the link you mentioned
and am editing the make.CHOICES file.  For LIB_REL_DIR
directive, should I change this to (something like)
/usr/local/lib64 for R to know its existence?  Or should
I leave it alone to default (which would be sprng/lib)?

Thank you in advance.

Regards,

Tena Sakai
tsakai at gallo.ucsf.edu


On 1/7/11 9:19 PM, "Dirk Eddelbuettel" <edd at debian.org> wrote:

> 
> On 7 January 2011 at 19:57, Tena Sakai wrote:
> | Hi,
> | 
> | 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-
> | Executed
> |  > 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.
> |  .configure
> | 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[4]: *** [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
> 
>   http://packages.qa.debian.org/s/sprng.html
> 
> The parallel suites can use either Rsprng or the rlecuyer package for
> parallel RNGs. The latter one may be a good alternative.
> 
> Hth, Dirk
> 
>  
> | 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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