similar to: 001: RELIABILITY FIX: March 15, 2013

I have a slightly complicated question. I am using an mpi application (Intel impi) which uses ssh to launch applications. For about 0.1-0.2% of the ssh connections I end up with a zombie, i.e. ps will show [ssh] <defunct>. Something is going wrong with the ssh when it starts, perhaps a race condition, it is not disconnecting after some time, that I have been able to verify. The most obvious

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 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...

Attached is the very verbose ssh output. Just to be perverse, this time two nodes lost connectivity. The only thing I see is lines saying that the two connections are lost, although being honest I have no idea what everything else means. For reference, 8 ssh cinnections were being made at the same time for a 8x8mpi task. N.B., since the OS I am using does not have rsh, I am currently using the

I'd like someone familiar with the R options initialization to comment on a difference of behavior within/without mpiexec I have a (.NET) application with embedded R that is proven to run in a single process: ./Sample1.exe on a Debian Linux with R 3.0.2 Running the same code with mpiexec, it fails at the R engine initialization: mpiexec -n 1 ./Sample1.exe Fatal error: you must

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

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

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, I am working on a 64-bit rocks cluster and am relatively new to the R package. I am trying to get Snow working with R and Rmpi and have run into the following issue. R is able to load the Rmpi and snow libraries and is able to run simple commands both interactively and batch as follows: -------------------------------------------------------------------------------------------------------

Hello All, Does anyone happen to be running Quagga on CentOS 5 with SELinux in enforcing mode? Have you had to create SELinux policies or did it "just work" out of the box? (I'll get around to building this out on CentOS 6 as well.) I'm simply trying to write my config (for the zebra daemon) and it can't be written... Looks like this bug from Fedora 8 in 2008 [0] remains

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:

Dear all, I have a large dataset of randomly generated weighed sample for which I wish to compute a kernel density estimate. I have used the "np" package successfully for smaller datasets, however for the larger ones, they take too long when using the cross validation options for bandwidth selection ("cv.ls" or "cv.ml"). Of course, they are much quicker with

Hi all, Not sure if this is the best place to put this question since I'm not sure if it's a Libvirt issue but... I currently have two VMs up with networking and I can successfully ssh to and from each VM and I have confirmed that I can successfully download things from the internet. However, when trying to run mpiexec (which uses ssh), the connection fails and gives me the following

Hello, We have R working with Rmpi/openmpi, but I'm a little worried. Specifically, (a) the -np flag doesn't seem to override the hostfile (it works fine with fortran hello world) and (b) I appear to have twice as many processes 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

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi list, I have a weird (?) problem here on a setup running CentOS 5.3 x86_64 (and OpenVZ, and some home-brew L2TP daemons, RIPd, BGPd, etc). There's a (VE in OpenVZ speak) virtual machine that has two ethernet interfaces, seen as eth0 and eth1, respectively. Those live in VLANs, but it's not important here. The thing is that on eth1 the

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

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

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)

I have some problem with traffic shaping on debian testing. I actually posted a full config on the list a while ago but didn''t get any answers. The problem is that traffic doesn''t get into the user classes (~150) when I associate a class with a qdisc. I tried sfq, fifo but none works. If I dont''t associate a qdisc with a class classification occurs well.

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