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Trouble with installing Rmpi package

4 messages · Dirk Eddelbuettel, Tena Sakai

Original
Tena Sakai
# 
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?

Thank you.

Tena Sakai
tsakai at gallo.ucsf.edu
On 1/7/11 3:49 PM, "Tena Sakai" <tsakai at gallo.ucsf.edu> wrote:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
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.  Here?s 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 ?Rmpi? ...
| >   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 ?Rmpi?
| >   * removing ?/usr/local/lib64/R/library/Rmpi?
| > 
| >   The downloaded packages are in
| >           ?/tmp/Rtmp1J1kDj/downloaded_packages?
| >   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]]
| > 
| 
| ______________________________________________
| 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.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      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: