An ARM comparison: Raspberry Pi vs OpenRD Client

On November 22, 2012 By panoskrtIn hpc, Linux, services, systemsLeave a comment

Bellow there’s a comparison between Raspberry Pi (Model B) and OpenRD Client, two low-power ARM SoC (System on a Chip), running Linux (Rasbian and Fedora respectively). I used the EEMBC CoreMark benchmark with default settings for 100000, 1000000 and 2000000 iterations. For each set, each device keep its performance with the same rate of iterations per second. The difference between the devices is at, an average level of, 520 iterations per second. That translates to 1.4x faster in favour of the OpenRD Client.

While OpenRD Client performs better, in terms of efficiency, Raspberry Pi seems to doing much better. In terms of CPU, Raspbeery Pi uses a 700MHz (with the possibility of setting it up to 1GHz) ARMv11 processor while OpenRD Client an older 1.2GHz Marvell Sheeva (ARMv5TE). ARMv11 supports an FPU unlike ARMv5 and that is one of the reasons that Raspberry Pi performs quite well despite its lower specifications. In terms of memory, Raspberry Pi uses 256MB DDR2 800MHz (newer models have 512MB RAM), in share with its relatively powerful GPU, while OpenRD Client uses 512MB DDR2 800MHz. OpenRD Client also provides Gigabit Ethernet as well as many more I/O interfaces. Also, OpenRD has preloaded OS, unlike Raspberry Pi that boots from an SD card. During this benchmark, Raspberry Pi was running Rasbian “Wheezy” (unofficial Debian port to armhf) while OpenRD Client Fedora 8.

(Raspberry Pi diagram – http://www.raspberrypi.org/wp-content/uploads/2012/04/Raspi_Iso_Blue.png)

(OpenRD Client Hardware Block diagram – http://www.globalscaletechnologies.com/skins/skin_1/images/OpenRD-Client_back.PNG)

HPC-Europa2 Virtual Cluster liveDVD – milestone6 (final release)

On January 17, 2012 By panoskrtIn coding, hpc, internet, Linux, services, systemsLeave a comment

The JRA2 team is proud to announce the release of HPC-Europa2 live DVD milestone 6. You can download milestone 6 ISO image (compressed with size 1.7 GB) from the below links:

CINECA (Italy) – http://www.hpc-europa.eu/?q=node/142
EPCC (Scotland) – http://hpce2jra2.epcc.ed.ac.uk/milestone6.iso.gz
HLRS (Germany) – https://fs.hlrs.de/projects/live-ptd/iso/milestone6.iso.gz

Release Note for Milestone 6
============================
The Virtual Cluster liveDVD:
* provides tools and libraries that are installed and used at the partner sites.
* emaulates the environment of the platforms available at HPC-Europa centers.
* allows hands-on building of a virtual cluster.

The liveDVD contains training and dissemination material published by the
HPC-Europa2 project, including material from the partner centers such as slides,
video tutorials and example code. Optional access to a source code repository enables
the migration of code and data from the Virtual Cluster to the user account created
on the HPC-Europa machines.

The liveDVD is based on SliTaz GNU/Linux, a free operating system, working completely
in RAM and booting from a removable media. The file size of the SliTaz GNU/Linux
3.0 ISO image is 29 MB. Hence, it leaves plenty of space for adding tools, libraries
and training material into this liveDVD. The SliTaz system is quick, responsive, and clean.
A lightweight and elegant desktop is included as well in the 29MB ISO image.

The milestone 6 ISO image has roughly the size of 3.8 GB including several tools
and libraries, as well as training material. Moreover, it contains a documentation
of how to build a virtual cluster using VirtualBox, and HPC-Europa2's Science and
Supercomputing in Europe research highlights for 2009 and 2010. Finally, this milestone
release addresses several bug fixes, such as firefox with flash support and
build scripts for Torque.

Since the previous release (milestone 5), existing packages have been updated, such as:
* MPICH2 to version 1.4.1p1
* Firefox to version 9.0.1 with flash support.
* Paraver to support the updated version of MPICH2.

In addition, this release has added several new packages:
* lava-1.0.6: Platform Lava - an open source version of Platform Load Sharing Facility (LSF).
* info (texinfo-4.13a) and man pages (man-db-2.6.0.2 and man-pages-3.35) for Linux documentation.
* Abiword and Gnumeric for office word documents and spreadsheets.
* Compiler wrappers (based on gcc and gfortran) to emulate Intel, IBM and NEC SX compilers.

You can download milestone 6 ISO image (compressed - size 1.7 GB) from the below link:
    http://www.hpc-europa.eu/?q=node/142

System Requirements
===================
* A laptop or computing with a DVD drive.
* Intel or AMD processor with a hardware virtualization support when using KVM
  and libvirt. Otherwise, this liveDVD can be run under VirtualBox or VMware or similar.

Known Issues
============
* PGI compilers require a license file in order to work (not included in this milestone).
* Totalview requires a license file in order to work (not included in this milestone).
  For requiring a demo license visit:
  http://www.roguewave.com/products/totalview-family/totalview.aspx
* On a MacBook Pro laptop, the mousepad does not work. Need to use an USB mouse
* Resizing video screen on VLC causes an unexpected exit of the program.
* VLC has no sound for viewing mkv videos.
* VLC cannot stream files or view incoming streams.

Acknowledgement
===============
This work was carried out under the HPC-EUROPA2 project (project number: 228398),
with the support of the European Community - Research Infrastructure Action of the FP7.

HPC-Europa2 Virtual Cluster liveDVD – milestone 5

On December 6, 2011December 6, 2011 By panoskrtIn hpc, Linux, services, systemsLeave a comment

The fifth release of the HPC-Europa2 Virtual Cluster liveDVD is available (milestone 5) for download:

CINCENA (ITA) - http://www.hpc-europa.eu/files/iso/milestone5.iso.gz
EPCC (UK) - http://hpce2jra2.epcc.ed.ac.uk/milestone5.iso.gz

Release Note for Milestone 5
============================
The Virtual Cluster liveDVD:
* provides tools and libraries that are installed and used at the partner sites.
* emulates the environment of the platforms available at HPC-Europa centers.
* allows hands-on building of a virtual cluster.

The liveDVD contains training and dissemination material published by the HPC-Europa2 project, including material from the partner centers such as slides, video tutorials and example code. Optional access to a source code repository enables the migration of code and data from the Virtual Cluster to the user account created on the HPC-Europa machines.

The liveDVD is based on SliTaz GNU/Linux, a free operating system, working completely in RAM and booting from a removable media. The file size of the SliTaz GNU/Linux 3.0 ISO image is 29 MB. Hence, it leaves plenty of space for adding tools, libraries and training material into this liveDVD. The SliTaz system is quick, responsive, and clean. A lightweight and elegant desktop is included as well in the 29MB ISO image.

The milestone 5 ISO images has roughly the size of 3.7 GB including several tools and libraries, as well as training material.

Since the previous release (milestone 4), existing packages have been updated, such as:

* Open MPI to version 1.5.4
* Midori with flash support
* Firefox to version 7.0.1

In addition, this release has added a new package to support EVO (http://evo.caltech.edu/)

System Requirements
===================
* A laptop or computing with a DVD drive.
* Intel or AMD processor with a hardware virtualization support when using KVM and libvirt. Otherwise, this liveDVD can be run under VirtualBox or VMware or similar.

Known Issues
============
* Totalview requires a license file, which is no included, in order to work.
For requiring a demo license visit:
http://www.roguewave.com/products/totalview-family/totalview.aspx
* On a MacBook Pro laptop, the mousepad does not work. Need to use an USB mouse
* Resizing video screen on VLC causes an unexpected exit of the program.
* VLC has no sound for viewing mkv videos.
* VLC cannot stream files or view incoming streams.
* Flash cannot be viewed under Firefox. Use Midori instead.

Acknowledgement
===============
This work was carried out under the HPC-EUROPA2 project (project number: 228398),
with the support of the European Community – Research Infrastructure Action of the FP7.

HPC-Europa2 Virtual Cluster liveDVD – milestone 4

On September 16, 2011September 27, 2011 By panoskrtIn hpc, Linux, servicesLeave a comment

The fourth release of the HPC-Europa2 Virtual Cluster liveDVD is available (milestone 4) for download:

CINCENA (ITA) - http://www.hpc-europa.eu/files/iso/milestone4.iso.gz
EPCC (UK) - http://hpce2jra2.epcc.ed.ac.uk/milestone4.iso.gz
HLRS (GER) - https://fs.hlrs.de/projects/live-ptd/milestone4.iso

Release Notes for milestone 4
============================
The Virtual Cluster liveDVD:
* provides tools and libraries that are installed and used at the partner sites.
* emulates the environment of the platforms available at HPC-Europa centers.
* allows hands-on building of a virtual cluster.

The milestone4 ISO images has roughly the size of 3.4GB including several tools and libraries, as well as training material.

Since the previous release (milestone3), existing packages have been updated. Moreover, new packages have been added, such as:

* Emacs version 23.1
* Firefox version 6.0.2
* covise-6.5.0: A collaborative visualization and simulation environment
* imagemagick-6.5.5: Imaging tools.
* libvirt-0.9.4: The virtualization API
* marmot-2.4.0: A tool for analysing and checking MPI applications
* modules-3.2.8: The modules environment.
* opennebula-2.2.1: A virtualization manager
* qcachegrind-0.6: A profile data visualization under Qt similar to KCachegrind.
* torque-3.0.0: Provides the binaries for the Torque Batch System.
* tcl-8.5.9, tcl-8.4: TCL scripting packages, dependencies for the modules environment.
* VampirTrace-5.11: Generates an OTF trace file, which can be analyzed and visualized by the visualisation tool Vampir.
* MPI and OpenMP training material has been added.
* Tutorial has been provided on how to set up the Virtual Cluster.

System Requirements
===================
* A laptop or computing with a DVD drive.
* Intel or AMD processor with a hardware virtualization support.

Known Issues
============
* Totalview requires a license file, which is no included, in order to work. For requiring a demo license visit: http://www.roguewave.com/products/totalview-family/totalview.aspx
* On a MacBook Pro laptop, the mousepad does not work. Need to use an USB mouse
* Resizing video screen on VLC causes an unexpected exit of the program.
* VLC has no sound for viewing mkv videos.
* VLC cannot stream files or view incoming streams.

Acknowledgement
===============
This work was carried out under the HPC-EUROPA2 project (project number: 228398), with the support of the European Community – Research Infrastructure Action of the FP7.

Simple and very basic PBS/Torque emulator

On June 22, 2011June 22, 2011 By panoskrtIn coding, hpc, Linux, services, systemsLeave a comment

PBS (Portable Batch System) is one of the common batch systems used across clusters. Unfortunately, proprietary piece of software. There used to be an open source version, OpenPBS which has been forked to Torque. Torque can be installed and configured to perform the basic operations within 15-20 minutes. Although, for evaluation purposes, I have wrote a *very simple* emulator for PBS/Torque. All it provides is three scripts:

– qsub -> submitting a job
– qstat -> displaying job list
– qdel -> removing job(s)

A virtual job can be submitted, without need of proper PBS or Torque-like submission script and other parameters. The parameters each script is accepting are:

– qsub – single virtual job: qsub test
– qstat – either username to list jobs of a user or none to list all jobs: qstat foobar
– qdel – single or list of job IDs to remove: qdel 1234 5678

Download: pbs-emu-0.1.tar.gz

Speedup and efficiency shell calculator

On June 17, 2011June 17, 2011 By panoskrtIn coding, hpc, Linux, os x, services, solaris, systemsLeave a comment

The following script can be used to calculate the speedup and efficiency of a parallel code when compared to its serial version. Pretty much straight forward process. This script can be used either individually or as part of another script to automate the process of generating the required results. It accepts three arguments: 1) serial execution time 2) parallel execution time 3) number of processors.

./SEcalc.sh <serial> <parallel> <procs>

Script:

############################################################################
# Copyright (C) 2011  Panagiotis Kritikakos <panoskrt@gmail.com>           #
#                                                                          #
#    This program is free software: you can redistribute it and/or modify  #
#    it under the terms of the GNU General Public License as published by  #
#    the Free Software Foundation, either version 3 of the License, or     #
#    (at your option) any later version.                                   #
#                                                                          #
#    This program is distributed in the hope that it will be useful,       #
#    but WITHOUT ANY WARRANTY; without even the implied warranty of        #
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         #
#    GNU General Public License for more details.                          #
#                                                                          #
#    You should have received a copy of the GNU General Public License     #
#    along with this program.  If not, see <http://www.gnu.org/licenses/>. #
############################################################################

#!/bin/bash

if [ "$#" -eq "3" ]; then
   runtime1proc=$1
   runtimeNproc=$2
   totalprocs=$3
   speedup=`echo "${runtime1proc}/${runtimeNproc}" | bc -l`;
   efficiency=`echo "${speedup}/${totalprocs}" | bc -l`;

   printf "\n Total processors: ${totalprocs}\n\n";
   printf " Runtime for serial code: ${runtime1proc}\n Runtime for parallel code: \
   ${runtimeNproc}\n\n";
   printf " Speedup: ${speedup}\n Efficiency: ${efficiency}\n\n";
else
   printf "\n Usage: SEcalc.sh   \n\n";
   printf " SEcalc.sh 0.350 0.494 2\n\n";
fi

Compiling SPEC Benchmarks tools on ARM

On May 21, 2011May 21, 2011 By panoskrtIn hpc, Linux, services, systems11 Comments

Some of the SPEC benchmarks come for a variety of architectures but not for ARM, which is not surprising anyway. The easiest way to execute the benchmarks is by using the provided scripts, which is pretty much straight forward operation. The benchmarks come with pre-compiled tools and libraries that are needed by the benchmarks. Among them is Perl, which will fail to compile on ARM systems because of some invalid object definitions in its makefile. These definitions get in the makefile by the Configure script which is called before calling make. Instead of messing around with Configure, I added a couple of lines in the buildtools file, which is responsible for building the SPEC tools on a new architecture or after having modified the host system, in order to remove the unnecessary lines from the corresponding makefiles.

The buildtools script can be found under tools/src/ in the SPEC benchmarks directoy. What is needed is to go in the Perl building section, line 103, and replace the fist part of the building phase with the following oneliner:

(cd $PERLSRC; LD_LIBRARY_PATH=`pwd`; export LD_LIBRARY_PATH; 
./Configure -dOes $PERLFLAGS -Ddosuid=undef -Dprefix=$INSTALLDIR 
-Dd_bincompat3=undef; cat makefile | grep -v built-in 
| grep -v "command line" > makefile.new; cp makefile.new makefile; 
cat x2p/makefile | grep -v built-in | grep -v "command line" > x2p/makefile.new; 
cp x2p/makefile.new x2p/makefile; make; ./perl installperl ) 
|| die "Can't build perl"

Running Fortran on ARM

On May 15, 2011April 19, 2013 By panoskrtIn coding, hpc, Linux, solaris, systems4 Comments

Generally and very briefly, there is no official Fortran compiler available for the ARM architecture. The easiest way to get Fortran code (specifically Fortran 77) to run on the ARM architecture, or any other architecture that doesn’t have a Fortran compiler, is to convert the Fortran code to C. In order to do that efficiently, we can use Netlib’s f2c command line tool, available for Linux, Unix and Windows.

The steps that need to be followed are:

1) Compile the library – source at http://www.netlib.org/f2c/libf2c.zip
Rename makefile.u to makefile and do make. Copy the generated libf2c.a to /usr/lib and the f2c.h header under /usr/include.
2) Compile the binary – source at http://www.netlib.org/f2c/src/
Rename makefile.u to makefile and do make. Copy the binary f2c under /usr/local/bin.

Supposing we have the foo.f file we can generate the C version by running f2c foo.f, giving us foo.c. It can now be compiled using ‘gcc foo.c -o foo -lf2c‘.

In order to automate this process a while, the following script can be used. It accepts only one argument, the Fortran source file.

#!/bin/bash
fortranFile=$1
fileName=`echo $1 | sed 's/\(.*\)\..*/\1/'`
echo $fileName
f2c $fortranFile
gcc ${fileName}.c -o $fileName -lf2c

UPDATE: There is GCC Fortran compiler for ARM Fedora and Debian and I presume for other distros as well. The issue now is that these distributions are compiled for ARMv5, while the latest ARM processors (Cortex-A8, A9, A15) are of the ARMv7 architecture. The compilers, and the OS in general is therefore unable to make use of the additional instructions sets and FPU. Other distros, such as Slackware, are compiled on even older architecture, ARMv4.

The Case of Exascale

On March 17, 2011 By panoskrtIn hpc, services, systemsLeave a comment

http://insidehpc.com/2011/01/16/video-the-case-for-exascale/

Virtual Cluster liveDVD milestone 3 released

On February 21, 2011March 17, 2011 By panoskrtIn hpc, internet, Linux, services, systemsLeave a comment

The Virtual Cluster liveDVD milestone 3, an activity of the HPC-Europa2 project, is available from today for download.

“The “HPC-Europa2 Virtual Cluster Live DVD” is a SliTaz based Live Linux DVD. It boots and runs completely from DVD providing recent tools, compilers and libraries for the development of parallel applications. Further on the DVD includes training material, videos from past virtual surgeries and reports from past HPC-Europa visitors.”