[R] Rmpi fails to install

[Juergen Rose]

Hi,

I was just able to install the patched Rmpi on the second system with
openmpi-1.5.3. What can we that Rmpi_0.5-9a.tar.gz becomes a standard
CRAN package?

Regards Juergen

Am Freitag, den 17.06.2011, 13:28 +0200 schrieb Hugo Mildenberger:
> Juergen,
> 
> > I try to install Rmpi as root with install.packages("Rmpi").
> > It fails with:
> > ...
> 
> I encountered a similar problem with openmpi-1.5.3 and 
> Rmpi_0.5-9.tar.gz. The reason was an unchecked call to 
> dlopen("libmpi.so.0").  At least openmpi-1.5.3 does not provide  
> "libmpi.so.0" anymore. The patch below corrects for this. 
> 
> According to man dlopen, this should work with all POSIX.1-2001 
> compliant systems. But possibly R already has an abstraction layer
> for loading shared objects?
> 
> Here is how to apply this patch locally:
> 
>    tar -xvzf Rmpi_0.5-9.tar.gz
>    patch -p1 < rmpi-check-dlopen-status.patch
>    tar -cvzf  Rmpi_0.5-9a.tar.gz
>    R CMD INSTALL --preclean Rmpi_0.5-9a.tar.gz
> 
> 
> Best 
> 
> Hugo  
> 
> ---- cut ----
> 
> diff -ru a/Rmpi/src/Rmpi.c b/Rmpi/src/Rmpi.c
> --- a/Rmpi/src/Rmpi.c   2010-11-30 20:38:01.000000000 +0100
> +++ b/Rmpi/src/Rmpi.c   2011-06-17 12:48:37.000000000 +0200
> @@ -68,7 +68,11 @@
>         else {
>  
>  #ifdef OPENMPI
> -       dlopen("libmpi.so.0", RTLD_GLOBAL | RTLD_LAZY);
> +       if (!dlopen("libmpi.so", RTLD_GLOBAL | RTLD_LAZY)) { 
> +            Rprintf("%s\n",dlerror());
> +            return AsInt(0);
> +       }
> +
>  #endif
>  
>  #ifndef MPI2
> 
> --- cut ----
> 
> 
> 
> 
> 
> 
> On Monday 07 March 2011 21:53:05 rose at uni-potsdam.de wrote:
> > I try to install Rmpi as root with install.packages("Rmpi").
> > It fails with:
> > ...
> > checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ISO
> > C89... none needed
> > I am here /usr and it is OpenMPI
> > Trying to find mpi.h ...
> > Found in /usr/include
> > Trying to find libmpi.so or libmpich.a ...
> > Found libmpi in /usr/lib
> > checking for openpty in -lutil... yes
> > checking for main in -lpthread... yes
> > configure: creating ./config.status
> > config.status: creating src/Makevars
> > ** libs
> > x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
> > -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
> > -DOPENMPI -I/usr/local/include    -fpic  -march=nocona -O2 -pipe
> > -fomit-frame-pointer -c RegQuery.c -o RegQuery.o
> > x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
> > -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
> > -DOPENMPI -I/usr/local/include    -fpic  -march=nocona -O2 -pipe
> > -fomit-frame-pointer -c Rmpi.c -o Rmpi.o
> > x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
> > -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
> > -DOPENMPI -I/usr/local/include    -fpic  -march=nocona -O2 -pipe
> > -fomit-frame-pointer -c conversion.c -o conversion.o
> > x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
> > -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
> > -DOPENMPI -I/usr/local/include    -fpic  -march=nocona -O2 -pipe
> > -fomit-frame-pointer -c internal.c -o internal.o
> > x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o
> > Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib -lmpi
> > -lutil -lpthread -L/usr/lib64/R/lib -lR
> > installing to /usr/lib64/R/library/Rmpi/libs
> > ** R
> > ** demo
> > ** inst
> > ** preparing package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices ...
> > ** testing if installed package can be loaded
> > /usr/lib64/R/bin/exec/R: symbol lookup
> > error: /usr/lib64/openmpi/mca_paffinity_linux.so: undefined symbol:
> > mca_base_param_reg_int
> > 
> > The downloaded packages are in
> >          ?/tmp/RtmpLvvl9R/downloaded_packages?
> > Updating HTML index of packages in '.Library'
> > Warning message:
> > In install.packages("Rmpi") :
> >    installation of package 'Rmpi' had non-zero exit status
> > 
> > The system is a gentoo system with openmpi-1.5.1. I am thankful for any
> > hint.
> > 
> > Juergen
> > 
> > ______________________________________________
> > 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.