search for: mpirun

Hello together! I've Debian 6.0.3 with OpenSSH_5.5p1 and problem with the execution of remote commands via ssh. It seems as if the first command isn't looked up in all "$PATH" dirs. Here normally I should get the version information of mpirun twice but the first one fails: $ ssh cluster2 mpirun --version ; mpirun --version bash: mpirun: command not found mpirun (Open MPI) 1.4.3 Here I should get the place of "mpirun" twice but the first "which" doesn't find an "mpirun" and prints nothing: $ ssh cluster...

...yone 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 suddenly reports version 1.5.3: % /usr/lib64/compat-openmpi/bin/mpirun -V mpirun (Open MPI) 1.5.3 But rpm/yum still reports that version 1.4.3 is installed: % rpm -qv compat-openmpi compat-openmpi-1.4.3-1.1.el6.x86_64 Is this del...

...machine "compute-0-12.local" "x86_64" [[3]] nodename machine "compute-0-13.local" "x86_64" > stopCluster(c1) [1] 1 > q() -------------------------------------- But on running the same script with mpirun i get the following error. *****************************************************************8 [srividya at cheaha ~]$ mpirun -np 3 R -slave R CMD BATCH TestSnow.R /home/srividya/R/library/snow/RMPInode.sh: line 9: 19431 Segmentation fault ${RPROG:-R} --vanilla >${OUT:-/dev/null} 2>&...

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 runtime environment is not operating. The LAM/MPI runtime environ...

Dear R People: I'm running Rmpi on a single machine and I have the following statement from the command line: mpirun -np 3 ./R --no-save < eek1.in >stuff4.out The stuff4.out file only contains the third result. Is there a way to fix this such that it shows all 3 sets, please Thanks in advance, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Housto...

...ode ---------------------------------------------------------------------------------------------------- #MSUB -l nodes=1:ppn=1 #MSUB -l walltime=100:00:00 #MSUB -m be #MSUB -V #MSUB -o /export/home/example/Runs/eg.out #MSUB -e /export/home/example/Runs/eg.err #MSUB -d /export/home/example/Runs mpirun --mca mpi_warn_on_fork 0 -np 1 /export/home/R-2.12.1/bin/R --slave -f /export/home/example/Runs/eg.r echo "DONE multiple run!" ---------------------------------------------------------------------------------------------------- ### UNIVERSITY OF CAPE TOWN This e-mail is subj...

...le for parallel computing via "foreach" + "doSNOW" to run on a computer cluster (Brutus from ETH Zurich). The minimal example is given below. It runs perfectly fine on my MacBook but when I submit it as a batch job via ... > bsub -n 3 -R "select[model==Opteron8380]" mpirun R --no-save -q -f doSNOW_minimal.R > ... it does not work. The output is also given below. The error is "Error in makeMPIcluster(spec, ...) : a cluster already exists 1". The only similar thing I found on the web is http://www.mail-archive.com/r-help at stat.math.ethz.ch/msg35501.html...

...ocesses running as I think I should. Rmpi version 0.5.5 Openmpi version 1.1 Viglen HPC with (effectively) 9 blades and 8 nodes on each blade. myhosts file contains details of the 9 blades, but specifies that there are 4 slots on each blade (to make sure I leave room for other users). When running mpirun -bynode -np 2 -hostfile myhosts R --slave --vanilla task_pull.R 1. I get as many R slaves as there slots defined in my myhosts file (there are 36 slots defined, and I get 36 slaves, regardless of the setting of -np, the master goes on the first machine in the myhosts file. 2. The .Rout file co...

...nt 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: $(SHLIB)@echo "MPIRUN = @MPIRUN@" > $(USER_CONF)@echo "MPIEXEC = @MPIEXEC@" >> $(USER_CONF)@echo "ORTERUN = @ORTERUN@" >> $(USER_CONF)@echo "TMP_INC = @TMP_INC@" >> $(USER_CONF)@echo "TMP_LIB = @TMP_LIB@" >> $(USER_CONF)@echo "MPI_ROOT = @MPI_R...

Dear R People: I'm having some trouble with mpiexec and Rmpi. I would like to be able to pass in the number of "children" via the mpiexec command (from the command line). this is in SUSE10.1, with R-2.7.1 Here are my files: cat eb.R library(Rmpi) mpi.remote.exec(paste("i am",mpi.comm.rank(),"of",mpi.comm.size())) mpi.quit() hodgesse at

Hello, I don't know if the question pertains to Rmpi, snow or snowfall. I run my job by: mpirun -np N -hostfile $PBS_NODEFILE RMPISNOW -f my-script.r --slave In the snowfall sfInit call I have to specify one less CPU respect to the mpirun call sfInit(parallel=TRUE, cpus=N-1, type="MPI") otherwise I receive an error similar to: "cluster size N-1 already running" (s...

Can someone please provide me with a little more information about this. It could be the source of some issues I am seeing with mpirun/mpiexec.hydra/ssh (post earlier today), and information about what it leads to (and any signatures) would be helpful. Thanks. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 "Research is to see what...

...5 ::ffff:10.30.1.15 22 PKG_CONFIG_PATH=/opt/gnome/lib64/pkgconfig LESSOPEN=lessopen.sh %s INFOPATH=/usr/local/info:/usr/share/info:/usr/info:/opt/gnome/share/info LESSCLOSE=lessclose.sh %s %s G_BROKEN_FILENAMES=1 JAVA_ROOT=/usr/lib/jvm/java COLORTERM=1 _=/usr/bin/env pearman at master:~> which mpirun /opt/openmpi/bin/mpirun Also note: mpich is also installed and is also in the PATH, after openmpi BTW. I have seen a number of posts concerning the pt2pt error message. Still, I was unable to understand how they might apply to fixing the current problem. Help would be greatly appreciated....

Hello, the package snow is not working on a windows cluster with MPICH2 and Rmpi. There is an error in makeCluster: launch failed: CreateProcess(/usr/bin/env "RPROG="C:\Programme\R\R-2.5.1\bin\R" "OUT=/dev/null" "R_LIBS=" C:/Programme/R/R-2.5.1/library/snow/RMPInode.sh) on 'cl1' failed, error 3 - Das System kann den angegbenen Pfad nicht finden. I

...suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether icc -std=gnu99 accepts -g... yes checking for icc -std=gnu99 option to accept ISO C89... none needed checking for mpirun... mpirun checking for mpiexec... mpiexec checking for orterun... orterun checking for sed... /bin/sed checking for mpicc... mpicc checking for ompi_info... ompi_info checking for mpich2version... F found sed, mpicc, and ompi_info ... >> TMP_INC_DIRS = /opt/openmpi/1.6.4-1/intel-13.1.1/includ...

Hello: Anybody knows how to run Rmpi through PBS (Portable Batch System) on a cluster computer. I'm using a supercomputer which require to submit jobs to PBS queue for dispatching. I tried use mpirun in my PBS script. But all my Rslaves are spawned to the same node. This is not desired. Any suggestions are welcome! Thanks in advance. ======================================== Shengqiao Li Research Associate The Department of Statistics PO Box 6330 West Virginia University Morgantown, WV 26506...

I'm running R/snow on a small cluster with opensuse, openmpi, and openshh. I start up R with "mpirun -n 1 R --no-save". That works but it strikes me how easily I get kicked out of R whenever I run into syntax errors. Is there a way to avoid this, for instance, by starting up a regular R session and invoking/activating(?) openmpi within R, e.g. by passing on extra arguments to the makeCluster...

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 examp...

Dear R People: I am having some trouble with the snow package. It requires MPICH2 and Rmpi. Rmpi is fine. However, I downloaded the MPICH2 package, and installed. There is no mpicc, mpirun, etc. Does anyone have any suggestions, please? Thanks in advance! Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: hodgess at gator.uhd.edu

Hi, I have a query regarding Lustre Throughput Numbers with mdtest benchmark.I am running mdtest benhmark with following options :- /home/meshram/mpich2-new/mpich2-1.4/mpich2-install/bin/mpirun -np 256 -hostfile ./hostfile ./mdtest -z 3 -b 10 -I 5 -v -d /tmp/l66 where , mdtest - is the standard benchmark to test metadata operations. [ https://computing.llnl.gov/?set=code&page=sio_downloads ] /tmp/l66 is my Lustre mount. I am using 1Gige Network with TCP transport. hostfile has 8 hos...