Displaying 20 results from an estimated 400 matches similar to: "boost-openmpi problems in 7.2"
2015 Dec 21
1
boost-openmpi problems in 7.2
Sorry to take so long to reply ...
On Thu, 2015-12-17 at 11:53 -0500, Tony Schreiner wrote:
> Did you load the compat-openmpi environment module?
>
> module load mpi/compat-openmpi16-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
2015 Dec 17
0
boost-openmpi problems in 7.2
Did you load the compat-openmpi environment module?
module load mpi/compat-openmpi16-x86_64
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 compat-
> openmpi16-1.6.4-10. All fine.
>
> Except
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
2007 Oct 04
1
Rmpi_0.5-4 and OpenMPI questions
Many thanks to Dr Yu for updating Rmpi for R 2.6.0, and for starting to make
the changes to support Open MPI.
I have just built the updated Debian package of Rmpi (i.e. r-cran-rmpi) under
R 2.6.0 but I cannot convince myself yet whether it works or not. Simple
tests work. E.g. on my Debian testing box, with Rmpi installed directly
using Open Mpi 1.2.3-2 (from Debian) and using 'r' from
2009 Aug 24
1
R with MPI
Hello, I plan 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.
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 /usr/lib/lam/lib/libmpi.so
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...
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 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
2011 Mar 14
1
Installing Rmpi on hpc
Hi,
I was trying to install the package Rmpi on a hpc cluster running SGE. The
command, and the sessionInfo() is as follows:
===========================================
> install.packages("Rmpi",dependencies=TRUE)
also installing the dependency ‘rsprng’
trying URL '
http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/rsprng_1.0.tar.gz'
Content type
2013 Jun 07
1
cannot load pbdMPI package after compilation
Hello,
I try to install pbdMPI.
Compilation successful, but load fails with segfault.
Is anyone can help me?
R version 3.0.0
pbdMPI version 0.1-6
Intel compiler version 13.1.1
OpenMPI version 1.6.4-1
CPU Intel x86_64
# R CMD INSTALL pbdMPI_0.1-6.tar.gz
..
....
checking for gcc... icc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name...
2011 Sep 09
1
R CMD INSTALL configure.args and CC customization
I am running into the following issue that has been previously
reported on the R-devel mailing list. The short version is that I'm
writing a package for MPI, and I'd like to change CC and SHLIB_LD to
"mpicc". Trying to change them in Makevars.in has no effect, because
the values are clobbered by /etc/R/Makeconf. Will the following
changes to Makeconf.in introduce any problems?
2012 Nov 21
2
installing Rmpi on centos 6 with mpich
Hello everyone
im trying to install Rmpi library on centos 6. I have already installed
mpich2 1.4
[root@localhost ~]# R --version
> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-redhat-linux-gnu (64-bit)
[root@localhost ~]# mpich2version
> MPICH2 Version:
2012 Aug 29
2
Problem installing Rmpi with Open MPI
Hi guys,
I've spent a few days trying to install Rmpi with no luck. I originally
tried using mpich, moved on to mpich2, and then to openmpi. I've gotten
the furthest with openmpi, though am still running into this problem and
can't figure it out. Can someone help!? Thanks so much in advanced.
I'm using an HP Envy laptop with Ubuntu 12.04. Output is below, with the
error at the
2009 Feb 06
2
Rmpi Segmentation fault
Dear all,
I have used the Rmpi package many times before however this time I've
installed it as I always do with openMPI tar.gz file direct from the
website. I'm installing on my ubuntu 8.10.
Linux 2.6.27-11-generic #1 SMP Thu Jan 29 19:28:32 UTC 2009 x86_64 GNU/Linux
All i get is:
> library(Rmpi)
Segmentation fault
:~$
Which dumps me back into the shell, and doens't give me much
2012 Oct 10
1
Rmpi installation trouble
Dear R People:
I'm trying to install Rmpi (latest version) on Ubuntu.
However, I'm getting the following error:
erin at erin-Y480:~$ R
R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are
2007 Apr 24
1
Problem installing Rmpi with lam on SGI SLES9
Hi,
I've been trying here to install Rmpi on an SGI IA-64 machine with 64
processors, running SuSE Linux Enterprise Server 9, R 2.4.0 and
lam-mpi 7.1.3. While I've read of similar problems on this list, I
think I've got an entirely new set of error messages to contribute
(see below). I'm not sure what the actual error is and what the @gprel
relocation message is about. Any help
2008 May 06
1
trouble installing Rmpi on 64-bit Ubuntu 8.04 with openmpi
Subject pretty much says it all. I am running 64-bit Ubuntu 8.04, i.e. Hardy
Heron, have openmpi installed, and get the following error message with
attempted install of Rmpi. sessionInfo() follows.
Mark
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
2023 Feb 01
2
dyn.load(now = FALSE) not actually lazy?
On Linux, if I have a .so file that has a dependency on another .so, and I
`dyn.load(now=FALSE)` the first one, R seems to try to resolve the symbols
immediately, causing the load to fail.
For example, I have `libtorch` installed on my HPC. Note that it links to
various libs such as `libcudart.so` and `libmkl_intel_lp64.so.2` which
aren't currently in my library path:
? ~ ldd
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