Displaying 20 results from an estimated 38 matches for "libmpi".
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2007 Apr 24
1
Problem installing Rmpi with lam on SGI SLES9
...message is about. Any help greatly appreciated.
thanks
Hendrik
behemoth:~/Rmpi # R CMD INSTALL /home/hfuss/build/Rmpi_0.5-3.tar.gz
--configure-args=--with-mpi=/usr/local/lam-mpi
* Installing *source* package 'Rmpi' ...
Try to find mpi.h ...
Found in /usr/local/lam-mpi/include
Try to find libmpi or libmpich ...
Found libmpi in /usr/local/lam-mpi/lib
Try to find liblam ...
Found liblam in /usr/local/lam-mpi/lib
checking for openpty in -lutil... no
checking for main in -lpthread... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/local/lib/R/incl...
2009 Aug 24
1
R with MPI
...n to use R with my cluster with OpenMPI.
I need the packaged 'snow' and 'Rmpi' for that, however, I get an error
while downloading and installing them:
When I do a:
install.packages("Rmpi", dependencies=T)
I get this error:
checking for mpi.h... no
Try to find libmpi.so or libmpich.a
checking for main in -lmpi... no
libmpi not found. exiting...
However, mpi.h is present via the openmpi-devel package on my RHEL 5.3.
Some of those packages need sprng 2.0 (rsprng, for instance, which is a
dependency for another MPI-related package). Sprng 2.0, however, i...
2015 Dec 17
2
boost-openmpi problems in 7.2
After the 7.2 upgrade?boost-openmpi-1.53.0-25 was installed, along
with?openmpi-1.10.0-10. ?The old openmpi was then replaced with?compat-
openmpi16-1.6.4-10. ?All fine.
Except boost-openmpi has a dependency on the old libmpi.so.1 and the
new openmpi has libmpi.so.12:
# ldd libboost_mpi-mt.so.1.53.0?
linux-vdso.so.1 =>??(0x00007ffe8c182000)
libboost_serialization-mt.so.1.53.0 => /lib64/libboost_serialization-mt.so.1.53.0 (0x00007f39da4d2000)
libmpi.so.1 => not found
libmpi_cxx.so.1 => /usr/lib64/openm...
2015 Dec 21
1
boost-openmpi problems in 7.2
...6-x86_64
Yes, but you can't load both mpi/openmpi-x86_64 and?mpi/compat-
openmpi16-x86_64 as they are labelled as conflicting.
As I said, if you load just mpi/compat-openmpi16-x86_64 it can't find
the boost-openmpi library; if you load just mpi/openmpi-x86_64 it can't
find the correct libmpi version.
P.
>
>
> Tony
>
> On Thu, Dec 17, 2015 at 10:57 AM, Pete Biggs <pete at biggs.org.uk> wrote:
>
> >
> > After the 7.2 upgrade boost-openmpi-1.53.0-25 was installed, along
> > with openmpi-1.10.0-10.??The old openmpi was then replaced with co...
2009 Mar 27
2
Installing openmpi & lam for use with R
I am trying to install the R package "Rmpi" which needs libmpi. I've
installed openmpi and lam in Centos 5.2:
[root at rab45-1 /]# rpm -qv openmpi
openmpi-1.2.5-5.el5
openmpi-1.2.5-5.el5
[root at rab45-1 /]# rpm -qv lam
lam-7.1.2-14.el5
lam-7.1.2-14.el5
But I get the following error message when trying to install Rmpi:
/usr/bin/ld: skipping incompatible...
2011 Mar 07
1
Rmpi fails to install
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=\"\" -DPACKAG...
2015 Dec 17
0
boost-openmpi problems in 7.2
...M, Pete Biggs <pete at biggs.org.uk> wrote:
>
> After the 7.2 upgrade boost-openmpi-1.53.0-25 was installed, along
> with openmpi-1.10.0-10. The old openmpi was then replaced with compat-
> openmpi16-1.6.4-10. All fine.
>
> Except boost-openmpi has a dependency on the old libmpi.so.1 and the
> new openmpi has libmpi.so.12:
>
> # ldd libboost_mpi-mt.so.1.53.0
> linux-vdso.so.1 => (0x00007ffe8c182000)
> libboost_serialization-mt.so.1.53.0 =>
> /lib64/libboost_serialization-mt.so.1.53.0 (0x00007f39da4d2000)
> libmpi.so.1 =...
2004 Nov 08
1
Problems with installing Rmpi on x86_64
Dear All,
I am trying to install Rmpi on AMD 64 with Fedora Core 2 for x86_64, but I
receive the following error:
/usr/bin/ld:
/usr/lib/gcc-lib/x86_64-redhat-linux/3.3.3/../../../../lib64/libmpi.a(abort.o):
relocation R_X86_64_32 can not be used when making a shared object;
recompile with -fPIC
/usr/lib/gcc-lib/x86_64-redhat-linux/3.3.3/../../../../lib64/libmpi.a:
could not read symbols: Bad value
Could anyone help me to solve this problem?
Thank you for your help,
Krzysiek
2011 Mar 14
1
Installing Rmpi on hpc
...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
I am here /usr/lib/lam and it is LAM
Trying to find mpi.h ...
Found in /usr/lib/lam/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib/lam/lib
Try to find liblam.so ...
Found liblam in /usr/lib/lam/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/bs/R_h...
2006 May 09
1
Rmpi instlation problem (PR#8846)
...R CMD INSTALL Rmpi_0.5-2.tar.gz
But occurred this error:
gcc -shared -L/usr/local/lib64 -o Rmpi.so conversion.o internal.o RegQuery.o
Rmpi.o -lmpi -llam -lutil -lpthread -L/usr/local/lib64/R/lib -lR
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin
/ld: /usr/local/lib/libmpi.a(infoset.o): relocation R_X86_64_32 can not be
used when making a shared object; recompile with -fPIC
/usr/local/lib/libmpi.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [Rmpi.so] Error 1
chmod: cannot access `/usr/local/lib64/R/library/Rmpi/libs/*': No suc...
2014 Mar 12
1
2 versions of same library loaded
Can anyone help me understand how I got 2 versions of the same library
loaded, how to prevent it, and what the consequences are? Running under
Debian GNU/Linux squeeze.
lsof and /proc/xxx/map both show 2 copies of several libraries loaded:
/home/ross/install/lib/libmpi.so.1.3.0
/home/ross/install/lib/libopen-pal.so.6.1.0
/home/ross/install/lib/libopen-rte.so.7.0.0
/home/ross/Rlib-3.0.1/Rmpi/libs/Rmpi.so
/usr/lib/openmpi/lib/libmpi.so.0.0.2
/usr/lib/openmpi/lib/libopen-pal.so.0.0.0
/usr/lib/openmpi/lib/libopen-rte.so.0.0.0
/usr/lib/R/lib/libR.so
The system has t...
2007 Apr 24
2
Error in clusterApply(): recursive default argument reference
Hi,
I want to compute a distribution of the intersection of a graph and
'randomized' graphs induced by the permutations of node labels (to
preserve the graph topology).
Since I ll have many permutations to perform, I was thinking of using
the snow package and in particular "parSapply" to divide the work
between my 4 CPUs.
But I get the following error message :
Error in
2012 Oct 10
1
Rmpi installation trouble
...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
I am here /usr/local and it is OpenMPI
Trying to find mpi.h ...
Found in /usr/local/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/local/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
-DPACKAGE_TAR...
2012 Nov 21
2
installing Rmpi on centos 6 with mpich
...re using the GNU C compiler... yes
> checking whether gcc -m64 -std=gnu99 accepts -g... yes
> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
> I am here /usr/local and it is OpenMPI
> Trying to find mpi.h ...
> Found in /usr/local/include
> Trying to find libmpi.so or libmpich.a ...
> checking for main in -lmpi... no
> libmpi not found. exiting...
> ERROR: configuration failed for package ‘Rmpi’
> * removing ‘/usr/lib64/R/library/Rmpi’
> The downloaded source packages are in
> ‘/tmp/RtmpBvTTqc/downloaded_packages’
> Updating HTML index...
2008 Jan 16
3
Rmpi on Linux x86_64 GNU/Linux
...uffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
Try to find mpi.h ...
Found in /import/home/u1/uaf/ogorman/lam/include
Try to find libmpi.so or libmpich.a
checking for main in -lmpi... yes
Try to find liblam.so ...
checking for main in -llam... yes
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/local/pkg...
2007 Mar 28
4
Rmpi and OpenMPI ?
Has anybody tried to use Rmpi with the OpenMPI library instead of LAM/MPI?
LAM appears to be somewhat hardcoded in the Rmpi setup. Before I start to
experiment with changing this, has anybody else tried Rmpi with non-LAM MPI
implementations?
Dirk
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
2007 Aug 27
2
Rmpi and x86
Dear R Gurus:
Is there a problem with Rmpi on x86 with SUSE 10.1, please?
I've tried everything and it still won't load.
Has anyone else dealt with this please?
Thanks,
Edna Bell
2007 Jul 06
1
Rmpi installation
Hi R Gurus.
I'm trying to install the Rmpi package.
Here are the errors:
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
Try to find libmpi or libmpich ...
checking for main in -lmpi... no
libmpi not found. exiting...
ERROR: configuration failed for package 'Rmpi'
** Removing '/home/Desktop/R-2.5.1/library/Rmpi'
The downloaded packages are in
/tmp/Rtmp90H1Vp/downloaded_packages
Warning messages:
1: installation...
2011 Sep 09
1
R CMD INSTALL configure.args and CC customization
...r suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
Trying to find mpi.h ...
Found in /usr/lib64/openmpi/1.2.7-gcc/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib64/openmpi/1.2.7-gcc/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
-DPAC...
2005 Oct 27
2
installing Rmpi
...is an interface (wrapper) to MPI APIs
with interactive R slave functionalities.
See `library (help=Rmpi)' for details.
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/home/apps/R-2.2.0/lib/R/library/Rmpi/libs/Rmpi.so':
libmpi.so.0: cannot open shared object file: No such file or directory
Error in dyn.unload(x) : dynamic/shared library
'/home/apps/R-2.2.0/lib/R/library/Rmpi/libs/Rmpi.so' was not loaded
Error in makeMPIcluster(spec, ...) : the `Rmpi' package is needed for
MPI clusters.
The Rmpi.so exists and...