failed to poll for a spawned proc

I am having problem running an openmpi program. It kept on giving me this error:

[opto023:31621] pls:tm: failed to poll for a spawned proc, return status = 17002
[opto023:31621] [0,0,0] ORTE_ERROR_LOG: In errno in file ../../../../../orte/mca/rmgr/urm/rmgr_urm.c at line 462
[opto023:31621] mpirun: spawn failed with errno=-11

I after I searched in the net, it might be due to OpenMPI and Torque problem.
check this forum.

The problem is solved by submitting the job using -S option

$qsub -S /bin/sh paralleljob.pbs

Compiling IT++ with MKL library

I downloaded it++ 4.0.6 and tried to compile using MKL library. To do that, I need first to set the environment path

export LDFLAGS=-L/opt/intel/Compiler/11.0/081/mkl/lib/32/

export CPPFLAGS=-I/opt/intel/Compiler/11.0/081/mkl/include

and then I run the configure with this option

./configure –prefix=$HOME/local F77=gfortran –with-blas=”-lmkl_intel -lmkl_sequential -lmkl_core -lpthread” –with-lapack=”-lmkl_lapack”

With this settings configure can detect my MKL library

UPDATE: though it can detect MKL, but it gives a compilation error. I haven’t managed to solve it. so I currently by passing the mkl library and install ATLAS instead.

./configure –prefix=/scratch/ihpcoka/local CPPFLAGS=’-I$(HOME)/DATA/Download/boost_1_36_0 -I/scratch/ihpcoka/local/include’ F77=gfortran LDFLAGS=’-L/usr/lib64 -L/scratch/ihpcoka/local/lib’ –with-fftw=’-lfftw3′ –with-blas=’-lf77blas -latlas’ –with-lapack=’-llapack’

Installing OpenDX 4.4.4 in Enterprise Linux from source

download the source code from this page.

untar the file with

% tar xzvf dx-4.4.4.tar.gz

cd to the directory and read the README file for detail installation steps. In short, simply type

% ./configure –prefix=<your directory to install>

% make

% make install

Installing Armadillo 0.4.0

I found a nice C++ linear algebra library called Armadillo by Conrad. I will write short posts to describe how to use it, and I will begin on how to install it.

First, download the source tarball from this link

untar the tar.gz file, and enter the directory.

The installation uses CMake, so if you don’t have, you can install it (in Ubuntu)
sudo apt-get install cmake

and then to install Armadillo, simply type:
cmake .
make
make install DESTDIR=$HOME/local

where I chose to install it in $HOME/local/usr/local. (NOTE: Somehow the installation folder will add “/usr/local”)

To compile a C++ code with armadillo, you need to include the header file
#include “armadillo”

and specify in the compiler option:
-I$HOME/local/usr/local/include -L$HOME/local/usr/local/lib -larmadillo

you can find an example in the “example” folder shipped with the source.