[R] Rmpi fails to install
Juergen Rose
rose at rz.uni-potsdam.de
Thu Jun 30 17:40:21 CEST 2011
Hi Hugo,
I tried your patch. The first 'R CMD INSTALL --preclean
Rmpi_0.5-9a.tar.gz' failed with:
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
[inspironM12:22936] *** Process received signal ***
[inspironM12:22936] Signal: Segmentation fault (11)
[inspironM12:22936] Signal code: Address not mapped (1)
[inspironM12:22936] Failing at address: 0xb5f5480c
* DONE (Rmpi)
[inspironM12:22936] *** End of error message ***
The second 'R CMD INSTALL --preclean Rmpi_0.5-9a.tar.gz' works like a
charm:
root at inspironM12:/usr/src(26)# R CMD INSTALL --preclean
Rmpi_0.5-9a.tar.gz
* installing to library ‘/usr/lib/R/library’
* installing *source* package ‘Rmpi’ ...
checking for gcc... i686-pc-linux-gnu-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 i686-pc-linux-gnu-gcc -std=gnu99 accepts -g... yes
checking for i686-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
i686-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib/R/include -DPACKAGE_NAME=
\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2 -DOPENMPI
-I/usr/local/include -fpic -O2 -march=core2 -mtune=generic
-fomit-frame-pointer -pipe -c RegQuery.c -o RegQuery.o
i686-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib/R/include -DPACKAGE_NAME=
\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2 -DOPENMPI
-I/usr/local/include -fpic -O2 -march=core2 -mtune=generic
-fomit-frame-pointer -pipe -c Rmpi.c -o Rmpi.o
i686-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib/R/include -DPACKAGE_NAME=
\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2 -DOPENMPI
-I/usr/local/include -fpic -O2 -march=core2 -mtune=generic
-fomit-frame-pointer -pipe -c conversion.c -o conversion.o
i686-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib/R/include -DPACKAGE_NAME=
\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2 -DOPENMPI
-I/usr/local/include -fpic -O2 -march=core2 -mtune=generic
-fomit-frame-pointer -pipe -c internal.c -o internal.o
i686-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/lib/R/lib -lR
installing to /usr/lib/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
* DONE (Rmpi)
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.
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