similar to: centos 5, openmpi and alternatives

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

Dear R Debian Users: I wrote a quick C program (eventually to become R code) and compiled it as: mpicc -o greet greet.c So far so good. Now when I run mpirun, this happens: erin at erin-laptop:~$ mpirun -np 2 greet ----------------------------------------------------------------------------- It seems that there is no lamd running on the host erin-laptop. This indicates that the LAM/MPI

Hi, everybody. I hope the new year is treating you well. In a Rocks Cluster Linux system (that's Centos 5.2 based), I have built R-2.10 and it runs well. While fiddling with MPI libraries and R packages, I've noticed a few little wrinkles. This comes as no surprise to the veteran R programmers, but let me share to the new guys the following gem: There is a difference between . and -

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?

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

1.I have a library fpmpi . I made the shared library fpmpi.so from this library.I am using ubuntu . 2.Now, I want to use in my R package .My R package has src folder the there is makevars.in file ### Setup R source code and objects. PKG_CPPFLAGS = @PKG_CPPFLAGS@ PKG_LIBS = -L/home/g/Desktop/Project -fpmpip ### For user configuration. USER_CONF = Makeconf ### Start making here. all:

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

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

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...

Hello, I'm using R on a 10 blade dual quad core Rocks Cluster, and trying to use Rpmi and snow. I basically wondered if at the moment I ought to install Rmpi against another form of mpi (not openmpi) and wondered whether anyone could pass on any experience. I'm mainly worried about (a) the R server taking up 100% cpu time (I think this is a known issue with Rmpi and openmpi) and (b)

Just wondering if anyone can shed some light into an issue we are having with compat-openmpi after upgrading CentOS to version 6.5 Some of our cluster applications are dependent on an older version of OpenMPI, so we are using compat-openmpi. Up to CentOS 6.4 this was version 1.4.3: % /usr/lib64/compat-openmpi/bin/mpirun -V mpirun (Open MPI) 1.4.3 but after the upgrade to CentOS 6.5 it

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 =>

Greetings. I see a warning message while compiling OpenMPI and would appreciate it if you tell me what it means. This warning happens with any OpenMPI > 1.6.5. Even before starting a cluster, just "sessionInfo" triggers this warning. I'm pasting in the message from R-3.3.2 (this is MRO). Do the R parallel package cluster functions violate the warnings described here? >

Hello, We have recently added a 64-bit 2 x Dual-Core Athlon server running Red Hat Enterprise Linux AS release 3 to allow for processing of large data sets (>4GB) in R. To integrate this server into our Linux cluster, I have been trying (unsuccessfully) to use Rmpi/lam-mpi to parallel process some of our scripts. While I have successfully compiled R 2.4.0 and lam-mpi 7.1.2 on this server using

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

Dear knowledgeable experts :-), I am trying to get openmpi, Rmpi and SNOW running on a Myrinet/GM cluster. I'm not an IT expert, but I surely could use a working installation of Rmpi and SNOW. I try to load the Rmpi library and get the following: > library(Rmpi) [master:07230] mca: base: component_find: unable to open osc pt2pt: file not found (ignored)

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

Hello, I'd like to take a look at how the taskPR package performs on our computational cluster, and this morning I've spend some time trying to do a test install of this package on one of our linux machines. Unfortunately I've been unsuccessful in completing the install, and I wondered if someone could please advise me. As I've noted I working on a linux machine, and it's

Guys, I'm having troubles with Rmpi on Linux. I got it to work on windows, but on Linux (SuSE 64 bit), using OpenMPI, I can't seem to get it to work :( When I do library(Rmpi) I get the warning: mca: base: component_find: unable to open osc pt2pt: file not found (ignored) Interestingly enough all the examples from the snow tutorial ( http://www.sfu.ca/~sblay/R/snow.html) work despite

Whas missing the R in the command line: "mpirun -n --hostfile /home/hostfile R --no-save -f rtest.R" Hope this helps mario On 13-Jan-11 22:08, Justin Moriarty wrote: > Hi, > Just wanted to share a working example of doSNOW and foreach for an openMPI cluster. The function eddcmp() is just an example and returns some inocuous warnings. The