search for: mpich

.... I take care of it's general-purpose research cluster, and have recently been asked to provide access to a parallelized R platform. I do not have any previous experience using R, and have only ever had to do anything more then 'yum -y install R'. We have a myrinet MPI network, and use mpich1 as our standard compiling environment which will link programs with libmyriexpress.so as well as libmpich.so Our myrinet driver package is Myrinet Express (MX) 1.2.12big. (I believe it was custom-built for us by myricom) The R package that my predecessor built was version 2.6.1. I have since ins...

...39;s what it says: ===================== [snip] --> Finished Dependency Resolution --> Running transaction check ---> Package kernel.x86_64 0:2.6.32-431.23.3.el6.centos.plus will be erased ---> Package kernel-devel.x86_64 0:2.6.32-431.23.3.el6.centos.plus will be erased ---> Package mpich2.x86_64 0:1.2.1-2.3.el6 will be obsoleted --> Processing Dependency: libmpich.so.1.2()(64bit) for package: hdf5-mpich2-1.8.5.patch1-7.el6.x86_64 --> Processing Dependency: libmpichf90.so.1.2()(64bit) for package: hdf5-mpich2-1.8.5.patch1-7.el6.x86_64 --> Processing Dependency: mpich2 for p...

...59d70f7c8445b38f096d7da99a457a707dc222f32458341513161de0558d8f66 boost-filesystem-1.41.0-25.el6.centos.i686.rpm 9ff07e5431c6b441f75d75f49ad8de98b58cfbcd7313fcdf1d9a748acb5cac4d boost-graph-1.41.0-25.el6.centos.i686.rpm 1236439492e10f87a653a0bcbfb586489ef26a889daee4a5725006963bac942f boost-graph-mpich-1.41.0-25.el6.centos.i686.rpm 7e1b63820423893fea7fe878a6192b316ce21e0c3fb688791fbe97a66ce9ab9a boost-graph-openmpi-1.41.0-25.el6.centos.i686.rpm 89c9f6f5c2efa34deabec09fcde997a2153e85b919f559fce4497da48bfd5526 boost-iostreams-1.41.0-25.el6.centos.i686.rpm c4c1e8d676e00a0b802b6d02a2cd306109758b375...

Hello everybody, I am trying to install Rmpi on 64-bit HP-Proliant server. I am facing the following error: * Installing *source* package 'Rmpi' ... Try to find mpi.h ... Found in /usr/local/mpich-1.2.7p1/include Try to find libmpi or libmpich ... Found libmpich in /usr/local/mpich-1.2.7p1/lib Try to find liblam ... checking for main in -llam... no liblam not found. Probably not LAM-MPI checking for openpty in -lutil... no checking for main in -lpthread... no configure: creating ./config.sta...

...he ./config.cache checking how to run the C preprocessor... grep: can't open conftest.out cc -E checking for main in -lz... no updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include -fPIC -g -O2 -c fread_functions.c -o fread_functions.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include -fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/...

Hi everyone As I couldn't succeed with manual installation of Rmpi I decided to start again from the beginning. I removed R and MPICH in my Ubuntu Hardy installation. Then, to avoid any dependencies problems I have installed MPICH and R from synaptic, not from sources. But now I can't install Rmpi. An error message appears when trying to install Rmpi, you can find in http://ubuntuone.com/p/71x/ Is it the time to upgrade...

...59d70f7c8445b38f096d7da99a457a707dc222f32458341513161de0558d8f66 boost-filesystem-1.41.0-25.el6.centos.i686.rpm 9ff07e5431c6b441f75d75f49ad8de98b58cfbcd7313fcdf1d9a748acb5cac4d boost-graph-1.41.0-25.el6.centos.i686.rpm 1236439492e10f87a653a0bcbfb586489ef26a889daee4a5725006963bac942f boost-graph-mpich-1.41.0-25.el6.centos.i686.rpm 7e1b63820423893fea7fe878a6192b316ce21e0c3fb688791fbe97a66ce9ab9a boost-graph-openmpi-1.41.0-25.el6.centos.i686.rpm 89c9f6f5c2efa34deabec09fcde997a2153e85b919f559fce4497da48bfd5526 boost-iostreams-1.41.0-25.el6.centos.i686.rpm c4c1e8d676e00a0b802b6d02a2cd306109758b375...

.... I have written to the package author but have not heard back as of yet. I have read the README in the package, as well, but it didn't give me enough detail to diagnose the problems that I am having. (I did edit out the LAM-MPI check in zzz.R.in.) I am working to install Rmpi on top of MPICH on a beowulf cluster. Below is the output of the install command (which seems to go OK and then the start of the R session, which fails. I was hoping someone with some experience installing Rmpi on MPICH could give me some help with doing so. Any help would be greatly appreciated.... Sean...

....wav=00;32: LD_LIBRARY_PATH=/opt/openmpi/lib:/opt/sge/lib/lx24-amd64 XNLSPATH=/usr/X11R6/lib/X11/nls HOSTTYPE=x86_64 PAGER=less XDG_CONFIG_DIRS=/usr/local/etc/xdg/:/etc/xdg/:/etc/opt/gnome/xdg/ C3_PATH=/opt/c3-4 MINICOM=-c on MAIL=/var/mail/pearman PATH=/opt/openmpi/bin:/opt/sge/bin/lx24-amd64:/opt/mpich/1.2.6..14b/x86_64/gcc//bin:/opt/gm/2.1 .21/2.6.11-21smp/bin:/opt/c3-4:/home/pearman/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/u sr/games:/opt/gnome/bin:/opt/kde3/bin:/opt/pathscale/bin CPU=x86_64 JAVA_BINDIR=/usr/lib/jvm/java/bin INPUTRC=/etc/inputrc PWD=/home/pearman JAVA_HOME=/usr/lib/jvm/...

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 Ve...

Dear All, I have created a virtual high performance computing (HPC) cluster of 6 compute nodes with MPICH2 using Xen-based Fedora 11 Linux 64-bit paravirtualized (PV) domU guests. Dom0 is Fedora 11 Linux 64-bit. My Intel Desktop Board DQ45CB has a single onboard Gigabit LAN network adapter. I am able to bring up the ring of mpd on the set of 6 compute nodes. However, I am consistently encountering the...

Dear All, I have created a virtual high performance computing (HPC) cluster of 6 compute nodes with MPICH2 using Xen-based Fedora 11 Linux 64-bit paravirtualized (PV) domU guests. Dom0 is Fedora 11 Linux 64-bit. My Intel Desktop Board DQ45CB has a single onboard Gigabit LAN network adapter. I am able to bring up the ring of mpd on the set of 6 compute nodes. However, I am consistently encountering the...

...e.php?id=100000750083982&v=app_2392950137 Mobile Phone (Starhub pre-paid): +65-8369-2618 Windows Live Messenger: teoenming-at-hotmail.com Location: Bedok Reservoir Road, Singapore ZIP: 470103 My Open Letter (Plea for Medical Help/Assistance) to World Leaders:- http://lists.mcs.anl.gov/pipermail/mpich-discuss/2010-August/007811.html http://mythtv.org/pipermail/mythtv-users/2010-August/295952.html http://archives.gentoo.org/gentoo-user/msg_f6a341d9623fda17880159b137c07335.xml Photo of Mr. Teo En Ming (Zhang Enming) 张恩鸣 of Singapore: http://img825.imageshack.us/img825/5052/mrteoenmingzhangenmingo....

...e.php?id=100000750083982&v=app_2392950137 Mobile Phone (Starhub pre-paid): +65-8369-2618 Windows Live Messenger: teoenming-at-hotmail.com Location: Bedok Reservoir Road, Singapore ZIP: 470103 My Open Letter (Plea for Medical Help/Assistance) to World Leaders:- http://lists.mcs.anl.gov/pipermail/mpich-discuss/2010-August/007811.html http://mythtv.org/pipermail/mythtv-users/2010-August/295952.html http://archives.gentoo.org/gentoo-user/msg_f6a341d9623fda17880159b137c07335.xml Photo of Mr. Teo En Ming (Zhang Enming) 张恩鸣 of Singapore: http://img825.imageshack.us/img825/5052/mrteoenmingzhangenmingo....

...amp;v=app_2392950137 Mobile Phone (Starhub pre-paid): +65-8369-2618 Windows Live Messenger: teoenming-at-hotmail.com Location: Bedok Reservoir Road, Singapore ZIP: 470103 My Open Letter (Plea for Medical Help/Assistance) to World Leaders (Updated 28 August 2010):- http://lists.mcs.anl.gov/pipermail/mpich-discuss/2010-August/007811.html http://mythtv.org/pipermail/mythtv-users/2010-August/295952.html http://archives.gentoo.org/gentoo-user/msg_f6a341d9623fda17880159b137c07335.xml Photo of Mr. Teo En Ming (Zhang Enming) ??? of Singapore: http://img543.imageshack.us/img543/5052/mrteoenmingzhangenmingo....

Dear All, I am doing a performance study on Xen, and we are deploying Charm++ parallel runtime library as part of our applications. However, we observed a 20% slow down in Xen kernel that was not observed with MPICH. It is very important for us to understand why this overhead is happening. I am guessing that is caused due to the higher cost of system calls like fork and exec, since Charm++ deploy a dynamic load-balancing algorithm that relocates jobs across the cluster, and thus using extensively the fork...

...oblem I believe might be related to the portland group compiler, and / or the libs on CentOS. Essentially what is happening is the primary executable I'm trying to run is failing under mpi. Here's the output from the command (which would be the same as the script calling it) $ /usr/local/mpich/bin/mpirun -machinefile machines.LINUX -np 2 ./wrf.exe /home/sam/WRFV2/run/./wrf.exe: /usr/pgi/linux86-64/6.0/lib/libpthread.so.0: version `GLIBC_2.3.3' not found (required by /lib64/tls/librt.so.1) Oddly enough, this same kernel environment works quite well with a previous version of the WRF...

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

...et the $R_LIBS variable correctly. The MPI libraries are available through the PGI compiler, but this R instance was compiled with GCC. The Rmpi package can be compiled and installed with %R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args="CC=pgcc --with-mpi=/shared/pgi725/linux86-64/7.2/mpi/mpich" But when entering R and loading the library, I get %R > library(Rmpi) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/<username>/.Rlib/Rmpi/libs/Rmpi.so': /home/<username>/.Rlib/Rmpi/libs/Rmpi.so: undefined symbol: __pgdbg_stu...

...;). Of course, they are much quicker with "normal-reference". To speed things up, I tried to use the "npRmpi" package. I had a lot of trouble installing it - but after appealing to google and finding the following page: http://webappl.blogspot.co.uk/2012/01/install-rmpi-with-mpich2-environment.html npRmpi was finally installed (basically I just added the flags "-lmpl -lopa" to the definition of PKG_LIBS in the configure script, and in the R CMD INSTALL call, I passed the configure.args as the correct paths to my MPICH2 installation). However, when I call the &...