OpenMP vs OpenMPI

For beginner "computationalist" like me, it's quite hard to understand the difference between OpenMP and OpenMPI. At first, I thought both of them tackles the same problem in the same way, namely parallel execution. However, after studying them both further, it's clear that OpenMPI uses a distributed-memory architecture while OpenMP uses shared-memory model. Both of the memory architecture can be explained as follows:

• In a distributed-memory architecture, each process doesn't share the same address space as the other process (which very possibly run on different machine). This means each process cannot "see" the other process variable(s). The process must "send a message" to the other process to change variable in the other process. Hence, the "Massage Passing Interface (MPI)". The MPI library such as OpenMPI basically is a sort of "middleware" to facilitate the massage passing between the processes, the process migration, initialization and tear-down.
• In a shared-memory architecture, there is usually one process which contains couple of threads which share the same memory address space, file handles and so on. Hence, the shared memory name. In this architecture, each threads can modify a "precess" global data. Therefore, a semaphore mechanism must be in use. OpenMP simplify the programming for shared memory architeture by providing compiler "extensions" in the form of various standardized "pragma"s. 

Upon reading both of the simplified explanation above, it's obvious that we can combine OpenMPI and OpenMP for paralel execution of code. Say, use OpenMP for "local execution within a machine" and use OpenMPI for inter-machine process communication. 

OpenMPI Slackbuild Script for Slamd64 12.1

I've just got OpenMPI to work on my Slamd64 12.1 system. I really hate cluttering the system. Therefore, I just build the package to ease removing it when I want to upgrade to a newer OpenMPI version later. This is the slackbuild script:

#!/bin/sh

# Slackware build script for Open MPI

# Written by Aleksandar Samardzic 
# Modified for Slamd64 12.1 by Darmawan Salihun  

PRGNAM=openmpi
VERSION=${VERSION:-1.3.3}
ARCH=${ARCH:-x86_64}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}

CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}

if [ "$ARCH" = "i486" ]; then
  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
elif [ "$ARCH" = "i686" ]; then
  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
elif [ "$ARCH" = "x86_64" ]; then
  SLKCFLAGS="-O2 -fPIC"
fi

set -e

rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $PRGNAM-$VERSION
tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2
cd $PRGNAM-$VERSION
chown -R root:root .
find . \
 \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
 -exec chmod 755 {} \; -o \
 \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
 -exec chmod 644 {} \;


CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
  --prefix=/usr \
  --libdir=/usr/lib64 \
  --mandir=/usr/man \
  --sysconfdir=/etc \
  --localstatedir=/var \
  --docdir=/usr/doc/$PRGNAM-$VERSION \
  --enable-static \
  --enable-mpirun-prefix-by-default \
  --build=$ARCH-slamd64-linux

make -j4
make install DESTDIR=$PKG

find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \
  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true

( cd $PKG/usr/man
  find . -type f -exec gzip -9 {} \;
  for i in $(find . -type l) ; do ln -s $(readlink $i).gz $i.gz ; rm $i ; done
)

# Let's not clobber config files
mv $PKG/etc/openmpi-totalview.tcl $PKG/etc/openmpi-totalview.tcl.new
mv $PKG/etc/openmpi-mca-params.conf $PKG/etc/openmpi-mca-params.conf.new
mv $PKG/etc/openmpi-default-hostfile $PKG/etc/openmpi-default-hostfile.new

mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a AUTHORS INSTALL LICENSE NEWS README VERSION examples \
  $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild

mkdir -p $PKG/install
cat $CWD/slack-desc > $PKG/install/slack-desc

cd $PKG
/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.tgz

That's it. Now, I can upgrade the package easily later. Anyway, I used OpenMPI 1.3.3 for my current experimental side projects.

AMI BIOS Reverse Engineering Article

AMI BIOS Reverse Engineering article is up. Check out the details here.

Booting OS Installed on Different Physical Drive in LILO

Booting an OS installed on other physical hard drive could be daunting at times.
However, one LILO keyword could prove very helpful:

master-boot

This keyword means (taken straight from LILO's repertoire):

'master-boot This flag (LILO version 22.5) indicates a DOS/Windows/OS2 or other system which will only boot from BIOS device 0x80, the "C:" drive, or BIOS device 0, the A: drive. When this flag is specified, if this drive is not assigned device code 0x80 or 0 by the BIOS, then the chain loader will dynamically swap the device code actually assigned with device code 0x80 or 0 to make this drive appear to be the first hard or floppy drive, "C:" or "A:".'


In my setup, the default boot drive is sda1 while M$ Windoze XP SP2 is installed on hda1. It seems to be M$ Windoze XP SP2 cannot boot unless its drive appear to be the first hard drive. This is the relevant excerpt from my /etc/lilo.conf:

# LILO configuration file
# generated by 'liloconfig'
#
# Start LILO global section
boot = /dev/sda
#compact        # faster, but won't work on all systems.
lba32
...
# Linux bootable partition config begins
image = /boot/vmlinuz
  root = /dev/sda1
  label = Slamd64-12.1
  read-only  # Partitions should be mounted read-only for checking
...
# Linux bootable partition config ends

# Windows bootable partition config begins
other = /dev/hda1
  label = Windows
  table = /dev/hda
  master-boot
# Windows bootable partition config ends

That's it. You should be able to boot from Windoze or other "insane" OS from other hard drive with LILO.