259. Compiling firefox 16.0.1 in debian testing/wheezy

I actually mainly use chromium/chrome for my normal browsing needs, and have set up an ssh tunnel with an American university for iceweasel so I can access sites that filter on IP.

There's nothing particularly wrong with iceweasel, but it's nice to check out the latest and shiniest versions of different projects every now and again, so here's how to compile the latest firefox:

The source is just a hair under 90 Mb and the build takes around 40 minutes on a three-core AMD.

I've got so many -dev packages installed on my system that I don't really know what the dependencies are anymore, but here's a guess:

sudo apt-get install build-essential gfortran gawk libpango1.0-dev libgconf2-dev libgnomevfs2-dev libcogl-pango-dev libpangomm-1.4-dev libgconfmm-2.6-dev libnotify-dev libgnomeui-dev libdbus-1-dev libdbus-glib-1-dev 

Anyway:

cd ~/tmp
wget ftp://ftp.mozilla.org/pub/firefox/releases/16.0.1/source/firefox-16.0.1.source.tar.bz2
tar xvf firefox-16.0.1.source.tar.bz2
mkdir firefox_build
cd firefox_build/
../mozilla-release/./configure --prefix=$HOME/.firefox --disable-necko-wifi
make

make install

I'm getting tired of the clutter in my PATH, so

echo "alias firefox16='$HOME/.firefox/bin/firefox'" >> ~/.bashrc

Note that iceweasel puts a firefox in/usr/bin/, hence the use of firefox16

258. Briefly: Throttle CPU between certain hours on linux

Because university administrators apparently don't consider academics trustworthy enough, at my university each office has an AC unit which cannot be adjusted. Sure, we can set the temperature -- but the unit cannot be turned on or off. Instead it shuts itself off at 5 pm and goes back on at 8 am. Same goes for weekends -- the unit shuts itself off on Friday at 5 pm and turns itself back on on Monday morning.

Obviously all the windows are sealed shut.

Which is fair enough in terms of saving energy -- no administrator would be in their office over the weekend. But most academics are constantly fighting to keep themselves afloat in terms of work, and most of us are in on weekends too.

But this is Australia -- the winters get cold enough that it's unpleasant to sit in an unheated office (no insulation) and the summers hot enough that computers get unhappy.

And I'm running a cluster in my office, so on a warmish weekend (above 20 degrees) my tiny office gets really hot. Last night one of my nodes overheated and shut itself down.

So, in want of a better solution, I figure I will throttle the CPUs overnight to give the fans a fighting chance to keep the cpus cool when the aircon is off. In particular weekends, with no air-conditioning from 5 pm on Friday until 8 am on Monday, are a challenge.

---

Enough talking! 

Put the following files in /etc/cron.d

throttle.sh

#!/bin/bash
## minimise heating overnight
/usr/bin/cpufreq-set -c 0 -g powersave
/usr/bin/cpufreq-set -c 1 -g powersave
/usr/bin/cpufreq-set -c 2 -g powersave
/usr/bin/cpufreq-set -c 3 -g powersave
/usr/bin/cpufreq-set -c 4 -g powersave
/usr/bin/cpufreq-set -c 5 -g powersave

slowdown.sh

#!/bin/bash
## minimise heating overnight
/usr/bin/cpufreq-set -c 0 -g userspace
/usr/bin/cpufreq-set -c 1 -g userspace
/usr/bin/cpufreq-set -c 2 -g userspace
/usr/bin/cpufreq-set -c 3 -g userspace
/usr/bin/cpufreq-set -c 4 -g userspace
/usr/bin/cpufreq-set -c 5 -g userspace
/usr/bin/cpufreq-set -c 0 -f 2.2G
/usr/bin/cpufreq-set -c 1 -f 2.2G
/usr/bin/cpufreq-set -c 2 -f 2.2G
/usr/bin/cpufreq-set -c 3 -f 2.2G
/usr/bin/cpufreq-set -c 4 -f 2.2G
/usr/bin/cpufreq-set -c 5 -f 2.2G

unthrottle.sh

#!/bin/bash
## maximise performance during the day
/usr/bin/cpufreq-set -c 0 -g ondemand
/usr/bin/cpufreq-set -c 1 -g ondemand
/usr/bin/cpufreq-set -c 2 -g ondemand
/usr/bin/cpufreq-set -c 3 -g ondemand
/usr/bin/cpufreq-set -c 4 -g ondemand
/usr/bin/cpufreq-set -c 5 -g ondemand

Now edit /etc/crontab

00 08   * * 1-5 root    sh /etc/cron.d/unthrottle.sh

00 17   * * 1-4 root    sh /etc/cron.d/slowdown.sh
00 17   * * 5 root    sh /etc/cron.d/throttle.sh

And you're good to go.

257. Wine 1.5.15 on debian testing/wheezy --finally sorting out that annoying libjpeg

UPDATE 16 May 2013: See here for Wine 1.5.30: http://verahill.blogspot.com.au/2013/05/416-wine-1530-in-chroot.html

UPDATE (10th Jan 2013): See here for Wine 1.5.21 using the multiarch approach: http://verahill.blogspot.com.au/2013/01/308-compiling-wine-1521-on-debian.html

Pretty much just follow this post:
The big difference here is that it seems to compile ok with libjpeg.

And here are the release notes

Install the pre-requisites 
(haven't checked this list for a while -- there may be a few too many packages)

sudo apt-get install ia32-libs ia32-libs-dev bison flex gcc libc6-dev libfontconfig-dev libfreetype6-dev libglu-dev libgsm1-dev libice-dev libjpeg-dev libldap-dev libmpg123-dev libncurses5-dev libopenal-dev libpng-dev libsm-dev libssl-dev libusb-dev libx11-dev libxcomposite-dev libxcursor-dev libxext-dev libxi-dev libxinerama-dev libxml2-dev libxrandr-dev libxrender-dev libxslt-dev libxt-dev libxxf86vm-dev make libcapi20-dev liblcms-dev libsane-dev libhal-dev libdbus-1-dev valgrind prelink libcups2-dev opencl-dev lib32opencl1 oss4-dev gettext lib32v4l-dev lib32ncurses5-dev lib32asound2-dev libtiff4-dev libgphoto2-2-dev

Get new source:

cd ~/tmp
wget http://sourceforge.net/projects/wine/files/Source/wine-1.5.15.tar.bz2
tar xvf wine-1.5.15.tar.bz2
cd wine-1.5.15/

To avoid

configure: WARNING: libjpeg 32-bit development files not found, JPEG won't be supported.

edit /usr/include/jpeglib.h and delete

24   #ifndef JCONFIG_INCLUDED        /* in case jinclude.h already did */
25   #include "jconfig.h"            /* widely used configuration options */
26   #endif

Then do 

./configure

which yields

configure: libOSMesa 32-bit development files not found (or too old), OpenGL rendering in bitmaps won't be supported.
configure: OpenCL 32-bit development files not found, OpenCL won't be supported.
configure: gstreamer-0.10 base plugins 32-bit development files not found, gstreamer support disabled
configure: libgsm 32-bit development files not found, gsm 06.10 codec won't be supported.
configure: Finished.  Do 'make' to compile Wine.

Neither of these issues are fatal -- depending on what you use wine for.

Time to install:
make
sudo checkinstall --install=no
sudo dpkg -i wine-1.5.15-1_amd64.deb

And you're done!

256. Briefly: Setting up ganglia on a debian beowulf cluster

On all your nodes (e.g. using clusterssh):
sudo apt-get install ganglia-monitor

On your front node only:
sudo apt-get install ganglia-webfrontend
sudo cp /etc/ganglia-webfrontend/apache.conf /etc/apache2/sites-enabled/ganglia.conf
sudo service apache2 restart

Edit /etc/ganglia/gmetad.conf and at a minimum add

data_source "debiwolf" 10 beryllium tantalum boron neon

or

data_source "debiwolf" 10 192.168.1.1 192.168.1.131 192.168.1.150 192.168.1.120

You can also specify additional information

gridname "rupert"
authority "http://192.168.1.1/ganglia/"

Go to http://localhost/ganglia in your browser. If you get

There was an error collecting ganglia data (127.0.0.1:8652): fsockopen error: Connection refused

Then do
sudo service gmetad start

Otherwise you should see something like this:

On all your nodes:
You may want to do
sudo service ganglia-monitor restart

if some of your nodes aren't showing.

Customize:
Edit your /etc/ganglia/gmond.conf:

cluster {
        name = "Debiwolf"
        owner = "Me"
        latlong = "unspecified"
        url = "None"
}

254. Compiling Thunderbird 16 on Debian Wheezy

I've posted how to compile thunderbird (12 and 13) in the past. Here's v 16.0.1:

First you need to sort out the dependencies:

sudo apt-get install libdbus-glib-1-dev gir1.2-notify-0.7 libnotify-dev yasm checkinstall libzip-dev zip libgtk2.0-dev

As usual, I prefer to do the building in ~/tmp
If you have a ~/tmp/comm-release directory, make sure to delete it first:

rm ~/tmp/comm-release -rf

Now download the new source (106 Mb):

cd ~/tmp
wget ftp://ftp.mozilla.org/pub/mozilla.org/thunderbird/releases/16.0.1/source/thunderbird-16.0.1.source.tar.bz2

Untar it, and create a new directory for out-of-tree building:

tar xvf thunderbird-16.0.1.source.tar.bz2
mkdir thunderbird16

cd thunderbird16/

Time to configure:

../comm-release/./configure --disable-necko-wifi

And build (40 minutes on a triple core AMD II)

make -j4

where -j4 indicates that it's built in parallel on a 3 core (3+1=4) processor. Note that this has nothing to do with running the finished binaries in parallel -- it's just a way of speeding up the compilation.


Make sure that you don't have an older version of thunderbird install via dpkg i.e.

aptitude search thunderbird|grep ^i

should come up blank. If not, uninstall that package.

Finally, install your new binaries:

sudo make install

And you're done.

253. Leadtek DTV 1000s in kernel 3.6 (debian wheezy)

My Leadtek DTV 1000s has been working fine for a long time after the initial set-up, but when upgrading from kernel 3.4.0 to 3.6.0 on my tv computer' it suddenly stopped working.

me-tv 1.3.7-3

lspci shows

01:06.0 Multimedia controller: Philips Semiconductors SAA7130 Video Broadcast Decoder (rev 01)

but

 lsmod|grep saa 

returns nothing and there's nothing that looks right in /dev

Finally

sudo modprobe saa7134
FATAL: Module saa7134 not found.

 ls /lib/modules/3.4.0-amd64/kernel/drivers/media

common  dvb  media.ko  radio  rc  video

but

ls /lib/modules/3.6.0-amd64/kernel/drivers/media

common  dvb

Basically, saa7134.ko is never built.

I installed kernel 3.6 from deb files compiled on another computer. My first step was to uninstall linux-headers-3.6.0-amd64 and linux-image-3.6.0-amd64

---

Next, to get the saa7134 module-- roughly follow this post we get

wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.6.tar.bz2
tar xvf linux-3.6.tar.bz2
cd linux-3.6/
cat /boot/config-`uname -r`>.config
make oldconfig

Make sure to answer in the affirmative here:

* Multimedia support
*
Multimedia support (MEDIA_SUPPORT) [M/n/y/?] Y
*
* Multimedia core support
*
Cameras/video grabbers support (MEDIA_CAMERA_SUPPORT) [N/y/?] (NEW) Y
Analog TV support (MEDIA_ANALOG_TV_SUPPORT) [N/y/?] (NEW)
Digital TV support (MEDIA_DIGITAL_TV_SUPPORT) [N/y/?] (NEW) Y
AM/FM radio receivers/transmitters support (MEDIA_RADIO_SUPPORT) [N/y/?] (NEW)
Remote Controller support (MEDIA_RC_SUPPORT) [N/y/?] (NEW) Y

Then build as usual
time fakeroot make-kpkg -j2 --initrd --revision=3.6.0 --append-to-version=-amd64 kernel_image kernel_headers

You can check that it built by

me@lithium:~/tmp/linux-3.6$ ls drivers/media/video/saa7134/*.ko -lah
drivers/media/video/saa7134/saa6752hs.ko
drivers/media/video/saa7134/saa7134-alsa.ko
drivers/media/video/saa7134/saa7134-dvb.ko
drivers/media/video/saa7134/saa7134-empress.ko
drivers/media/video/saa7134/saa7134.ko

All that's left now is to install the kernel:
mv ../linux*3.6*.deb . 
sudo dpkg -i *.deb

and you're done (see the original post for loading the driver: i.e. put options saa7134 tuner=48 card=175 in your /etc/modules) -- unless you have an nvidia graphics card, in which case

me@lithium:~/tmp/linux-3.6$ sudo dpkg-reconfigure nvidia-kernel-dkms

-------- Uninstall Beginning --------
Module:  nvidia
Version: 304.48
Kernel:  3.4.0-amd64 (x86_64)
-------------------------------------

Status: Before uninstall, this module version was ACTIVE on this kernel.

nvidia.ko:
 - Uninstallation
   - Deleting from: /lib/modules/3.4.0-amd64/updates/dkms/
 - Original module
   - No original module was found for this module on this kernel.
   - Use the dkms install command to reinstall any previous module version.

depmod.......

DKMS: uninstall completed.

-------- Uninstall Beginning --------
Module:  nvidia
Version: 304.48
Kernel:  3.6.0-amd64 (x86_64)
-------------------------------------

Status: Before uninstall, this module version was ACTIVE on this kernel.

nvidia.ko:
 - Uninstallation
   - Deleting from: /lib/modules/3.6.0-amd64/updates/dkms/
 - Original module
   - No original module was found for this module on this kernel.
   - Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed.

------------------------------
Deleting module version: 304.48
completely from the DKMS tree.
------------------------------
Done.
Loading new nvidia-304.48 DKMS files...
Building for 3.4.0-amd64 and 3.6.0-amd64
Building initial module for 3.4.0-amd64
Done.

nvidia:
Running module version sanity check.
 - Original module
   - No original module exists within this kernel
 - Installation
   - Installing to /lib/modules/3.4.0-amd64/updates/dkms/

depmod....

DKMS: install completed.
Building initial module for 3.6.0-amd64
Done.

nvidia:
Running module version sanity check.
 - Original module
   - No original module exists within this kernel
 - Installation
   - Installing to /lib/modules/3.6.0-amd64/updates/dkms/

depmod....

DKMS: install completed.

252. Molecular weight calculator in python

Here's the molecular weight part of the isotopic pattern calculator in a previous post.

Most people won't need a full molecular weight calculator with plotting of isotopic composition, so I'm publishing the molecular weight part as a separate program.

The actual algorithm is fairly simple and is more or less contained in the formulaExpander function below. It looks messy because of the definition of the PeriodicTable dictionary at the beginning, but it's simple.

Copy the code, past it into a file (call it e.g. molcalc), put it in e.g. /usr/local/bin and chmod +x it.

Usage:
molcalc 'Mg2(PO4)3'
returns

The mass of Mg2P3O12 is 333.524247 and the calculated charge is -5.

The charge is based on my default oxidation states -- depending on what kind of chemistry you do the oxidation states you encounter are likely to differ.

#!/usr/bin/python2.7
#########################################################################
# Principal author of current version: Me
# Isotopic abundances and masses were copied from Wsearch32.
#
#
# Dependencies:
# To be honest I'm not quite certain. At a minimum you will need python2.7,
# python-numpy
#
#########################################################################

import re #for regular expressions
import sys
from numpy import matrix,transpose # for molw calc
try:
 molecules=sys.argv[1]
except:
 quit()

#slowly changed to IUPAC 1997 isotopic compositions and IUPAC 2007 masses
# see http://pac.iupac.org/publications/pac/pdf/1998/pdf/7001x0217.pdf for
# natural variations in isotopic composition
PeriodicTable ={
   'H':[1,1,[1.0078250321,2.0141017780],[0.999885,0.0001157]], # iupac '97 in water
   'He':[2,0,[3.0160293097,4.0026032497],[0.00000137,0.99999863]], # iupac iso '97
   'Li':[3,1,[6.0151233,7.0160040],[0.0759,0.9241]], # iupac '97
   'Be':[4,2,[9.0121821],[1.0]], # iupac '97
   'B':[5,3,[10.0129370,11.0093055],[0.199,0.801]], # iupac' 97
                        'C':[6,4,[12.0,13.0033548378],[0.9893,0.0107]], # iupac '97
                        'N':[7,5,[14.0030740052,15.0001088984],[0.99632,0.00368]], # iupac '97
                        'O':[8,-2,[15.9949146221,16.99913150,17.9991604],[0.99757,0.00038,0.00205]], # iupac '97
                        'F':[9,-1,[18.99840320],[1.0]], # iupac '97
                        'Ne':[10,0,[19.9924401759,20.99384674,21.99138551],[0.9048,0.0027,0.0925]], # iupac '97 in air
                        'Na':[11,1,[22.98976967],[1.0]], #iupac '97
                        'Mg':[12,2,[23.98504190,24.98583702,25.98259304],[0.7899,0.10,0.1101]], #iupac '97
                        'Al':[13,3,[26.98153844],[1.0]], #iupac '97
                        'Si':[14,4,[27.9769265327,28.97649472,29.97377022],[0.92297,0.046832,0.030872]],#iupac '97
                        'P':[15,5,[30.97376151],[1.0]], #iupac '97
                        'S':[16,-2,[31.97207069,32.97145850,33.96786683,35.96708088],[0.9493,0.0076,0.0429,0.0002]], #iupac '97
                        'Cl':[17,-1,[34.96885271,36.96590260],[0.7578,0.2422]], #iupac '97
                        'Ar':[18,0,[35.96754628,37.9627322,39.962383123],[0.003365,0.000632,0.996003]],#iupac '97 in air
                        'K':[19,1,[38.9637069,39.96399867,40.96182597],[0.932581,0.000117,0.067302]], #iupac '97
                        'Ca':[20,2,[39.9625912,41.9586183,42.9587668,43.9554811,45.9536928,47.952534],[0.96941,0.00647,0.00135,0.02086,0.00004,0.00187]], #iupac '97
                        'Sc':[21,3,[44.9559102],[1.0]], #iupac '97
                        'Ti':[22,4,[45.9526295,46.9517638,47.9479471,48.9478708,49.9447921],[0.0825,0.0744,0.7372,0.0541,0.0518]], #iupac '97
                        'V':[23,5,[49.9471628,50.9439637],[0.00250,0.99750]], #iupac '97
                        'Cr':[24,2,[49.9460496,51.9405119,52.9406538,53.9388849],[0.04345,0.83789,0.09501,0.02365]], #iupac '97
                        'Mn':[25,2,[54.9380496],[1.0]], #iupac '97
                        'Fe':[26,3,[53.9396148,55.9349421,56.9353987,57.9332805],[0.05845,0.91754,0.02119,0.00282]], #iupac '97
                        'Ni':[27,3,[57.9353479,59.9307906,60.9310604,61.9283488,63.9279696],[0.680769,0.262231,0.011399,0.036345,0.009256]], #iupac '97
                        'Co':[28,2,[58.933195],[1.0]], #iupac '97
                        'Cu':[29,2,[62.9296011,64.9277937],[0.6917,0.3083]], #iupac '97
                        'Zn':[30,2,[63.9291466,65.9260368,66.9271309,67.9248476,69.925325],[0.4863,0.2790,0.0410,0.1875,0.0062]], #iupac '97
                        'Ga':[31,3,[68.925581,70.9247050],[0.60108,0.39892]], #iupac '97
                        'Ge':[32,2,[69.9242504,71.9220762,72.9234594,73.9211782,75.9214027],[0.2084,0.2754,0.0773,0.3628,0.0761]], #iupac '97
                        'As':[33,3,[74.9215964],[1.0]], #iupac '97
                        'Se':[34,4,[73.9224766,75.9192141,76.9199146,77.9173095,79.9165218,81.9167000],[0.0089,0.0937,0.0763,0.2377,0.4961,0.0873]], #iupac '97
                        'Br':[35,-1,[78.9183376,80.916291],[0.5069,0.4931]],#iupac '97
                        'Kr':[36,0,[77.920386,79.916378,81.9134846,82.914136,83.911507,85.9106103],[0.0035,0.0228,0.1158,0.1149,0.5700,0.1730]], #iupac '97 in air
                        'Rb':[37,1,[84.9117893,86.9091835],[0.7217,0.2783]], #iupac '97
                        'Sr':[38,2,[83.913425,85.9092624,86.9088793,87.9056143],[0.0056,0.0986,0.0700,0.8258]], #iupac '97
                        'Y': [39,3,[88.9058479],[1.0]], #iupac '97
                        'Zr': [40,4,[89.9047037,90.9056450,91.9050401,93.9063158,95.908276],[0.5145,0.1122,0.1715,0.1738,0.0280]],#iupac '97
                        'Nb':[41,5,[92.9063775],[1.0]], #iupac '97
                        'Mo':[42,6,[91.906810,93.9050876,94.9058415,95.9046789,96.9060210,97.9054078,99.907477],[0.1484,0.0925,0.1592,0.1668,0.0955,0.2413,0.0963]], #checked, iupac '97
                        'Tc': [43,2,[96.906365,97.907216,98.9062546],[1.0]], #no natural abundance
                        'Ru': [44,3,[95.907598,97.905287,98.9059393,99.9042197,100.9055822,101.9043495,103.905430],[0.0554,0.0187,0.1276,0.1260,0.1706,0.3155,0.1862]], #iupac '97
                        'Rh':[45,2,[102.905504],[1.0]], #iupac '97
                        'Pd':[46,2,[101.905608,103.904035,104.905084,105.903483,107.903894,109.905152],[0.0102,0.1114,0.2233,0.2733,0.2646,0.1172]], #iupac '97
                        'Ag':[47,1,[106.905093,108.904756],[0.51839,0.48161]], #iupac '97
                        'Cd':[48,2,[105.906458,107.904183,109.903006,110.904182,111.9027572,112.9044009,113.9033581,115.904755],[0.0125,0.0089,0.1249,0.1280,0.2413,0.1222,0.2873,0.0749]],#iupac '97
                        'In':[49,3,[112.904061,114.903878],[0.0429,0.9571]], #iupac '97
                        'Sn':[50,4,[111.904821,113.902782,114.903346,115.901744,116.902954,117.901606,118.903309,119.9021966,121.9034401,123.9052746],[0.0097,0.0066,0.0034,0.1454,0.0768,0.2422,0.0859,0.3258,0.0463,0.0579]], #iupac '97
                        'Sb':[51,3,[120.9038180,122.9042157],[0.5721,0.4279]], #iupac '97
                        'Te':[52,4,[119.904020,121.9030471,122.9042730,123.9028195,124.9044247,125.9033055,127.9044614,129.9062228],[0.0009,0.0255,0.0089,0.0474,0.0707,0.1884,0.3174,0.3408]],#iupac '97
                        'I':[53,-1,[126.904468],[1.0]], #iupac '97
                        'Xe':[54,0,[123.9058958,125.904269,127.9035304,128.9047795,129.9035079,130.9050819,131.9041545,133.9053945,135.907220],[0.0009,0.0009,0.0192,0.2644,0.0408,0.2118,0.2689,0.1044,0.0887]], #iupac '97
                        'Cs':[55,1,[132.905447],[1.0]], #iupac '97
   'Ba':[56,2,[129.906310,131.905056,133.904503,134.905683,135.904570,136.905821,137.905241],[0.00106,0.00101,0.02417,0.06592,0.07854,0.11232,0.71698]], #iupac '97
   'La':[57,3,[137.907107,138.906348],[0.00090,0.99910]],#iupac '97
   'Ce':[58,3,[135.907140,137.905986,139.905434,141.909240],[0.00185,0.00251,0.88450,0.11114]],#iupac '97
                        'Pr':[59,3,[140.907648],[1.0]], #iupac '97
   'Nd':[60,3,[141.907719,142.909810,143.910083,144.912569,145.913112,147.916889,149.920887],[0.272,0.122,0.238,0.083,0.172,0.057,0.056]],#iupac '97
   'Pm':[61,3,[144.91270],[1.0]], #no natural occurence
   'Sm':[62,3,[143.911995,146.914893,147.914818,148.917180,149.917271,151.919728,153.922205],[0.0307,0.1499,0.1124,0.1382,0.0738,0.2675,0.2275]], #iupac '97
   'Eu':[63,3,[150.919846,152.921226],[0.4781,0.5219]], #iupac '97
   'Gd':[64,3,[151.919788,153.920862,154.922619,155.922120,156.923957,157.924101,159.927051],[0.0020,0.0218,0.1480,0.2047,0.1565,0.2484,0.2186]],#iupac '97
                        'Tb':[65,4,[158.925343],[1.0]], #iupac '97
   'Dy':[66,3,[155.924278,157.924405,159.925194,160.926930,161.926795,162.928728,163.929171],[0.0006,0.0010,0.0234,0.1891,0.2551,0.2490,0.2818]], #iupac '97
   'Ho':[67,3,[164.930319],[1.0]], #iupac '97
   'Er':[68,3,[161.928775,163.929197,165.930290,166.932045,167.932368,169.935460],[0.0014,0.0161,0.3361,0.2293,0.2678,0.1493]], #iupac '97
   'Tm':[69,3,[168.934211],[1.0]], #iupac '97
                        'Yb':[70,3,[167.933894,169.934759,170.936322,171.9363777,172.9382068,173.9388581,175.942568],[0.0013,0.0304,0.1428,0.2183,0.1613,0.3183,0.1276]], #iupac '97
   'Lu':[71,3,[174.9407679,175.9426824],[0.9741,0.0259]],#iupac '97
   'Hf':[72,4,[173.940040,175.9414018,176.9432200,177.9436977,178.9458151,179.9465488],[0.0016,0.0526,0.1860,0.2728,0.1362,0.3508]], #iupac '97
   'Ta':[73,5,[179.947466,180.947996],[0.00012,0.99988]], #iupac '97
   'W':[74,6,[179.946704,181.9482042,182.9502230,183.9509312,185.9543641],[0.0012,0.2650,0.1431,0.3064,0.2843]], #iupac  '97
                        'Re':[75,2,[184.9529557,186.9557508],[0.3740,0.6260]],#iupac '97
   'Os':[76,4,[183.952491,185.953838,186.9557479,187.9558360,188.9581449,189.958445,191.961479],[0.0002,0.0159,0.0196,0.1324,0.1615,0.2626,0.4078]],#iupac '97
   'Ir':[77,4,[190.960591,192.962924],[0.373,0.627]], #iupac '97
   'Pt':[78,4,[189.959930,191.961035,193.962664,194.964774,195.964935,197.967876],[0.00014,0.00782,0.32967,0.33832,0.25242,0.07163]],#iupac '97
   'Au':[79,3,[196.966552],[1.0]], #iupac '97
                        'Hg':[80,2,[195.965815,197.966752,198.968262,199.968309,200.970285,201.970626,203.973476],[0.0015,0.0997,0.1687,0.2310,0.1318,0.2986,0.0687]], #iupac '97
   'Tl':[81,1,[202.972329,204.974412],[0.29524,0.70476]], #iupac '97
   'Pb':[82,2,[203.973029,205.974449,206.975881,207.976636],[0.014,0.241,0.221,0.524]],#
   'Bi':[83,3,[208.980383],[1.0]], #iupac '97
   'Po':[84,4,[209.0],[1.0]],
   'At':[85,7,[210.0],[1.0]],
                        'Rn':[86,0,[220.0],[1.0]],
   'Fr':[87,1,[223.0],[1.0]],
   'Ra':[88,2,[226.0],[1.0]],
   'Ac':[89,3,[227.0],[1.0]],
   'Th':[90,4,[232.0380504],[1.0]], #iupac '97
   'Pa':[91,4,[231.03588],[1.0]],
                        'U':[92,6,[234.0409456,235.0439231,236.0455619,238.0507826],[0.000055,0.007200,0.0,0.992745]], #iupac '97
   'Np':[93,5,[237.0],[1.0]],
   'Pu':[94,3,[244.0],[1.0]],
   'Am':[95,2,[243.0],[1.0]],
   'Cm':[96,3,[247.0],[1.0]],
   'Bk':[97,3,[247.0],[1.0]],
   'Cf':[98,0,[251.0],[1.0]],
                        'Es':[99,0,[252,.0],[1.0]],
   'Fm':[100,0,[257.0],[1.0]],
   'Md':[101,0,[258.0],[1.0]],
   'No':[102,0,[259.0],[1.0]],
   'Lr':[103, 0,[262.0],[1.0]],
   'Rf':[104, 0,[261.0],[1.0]],
   'Db':[105, 0,[262.0],[1.0]],
   'Sg':[106, 0,[266.0],[1.0]]
}

#######################################
# Collect properties
#######################################
def getMass(x):
 atom=re.findall('[A-Z][a-z]*',x)
 number=re.findall('[0-9]+', x)
 if len(number) == 0:
  multiplier = 1
 else:
  multiplier = float(number[0])
 atomic_mass=float(matrix(PeriodicTable[atom[0]][2])*transpose(matrix(PeriodicTable[atom[0]][3])))
# That's right -- the molecular weight is based on the isotopes and ratios
 return (atomic_mass*multiplier)

def getCharge(x):
 atom=re.findall('[A-Z][a-z]*',x)
 number=re.findall('[0-9]+', x)
 if len(number) == 0:
  multiplier = 1
 else:
  multiplier = float(number[0])
 atomic_charge=float(PeriodicTable[atom[0]][1])
 return (atomic_charge*multiplier)


#####################################################
# Iterate over expanded formula to collect property
#####################################################
def molmass(formula):
 mass=0
 while (len(formula)>0):
  segments = re.findall('[A-Z][a-z]*[0-9]*',formula)
  for i in range(0, len(segments)):
   mass+=getMass(segments[i])
  formula=re.sub(formula, '', formula)
 return mass

def molcharge(formula):
 charge=0
 while (len(formula)>0):
  segments = re.findall('[A-Z][a-z]*[0-9]*',formula)
  for i in range(0, len(segments)):
   charge+=getCharge(segments[i])  
  formula=re.sub(formula, '', formula)
 return charge


################################################################################
#expands ((((M)N)O)P)Q to M*N*O*P*Q
################################################################################

def formulaExpander(formula):
 while len(re.findall('\(\w*\)',formula))>0:
  parenthetical=re.findall('\(\w*\)[0-9]+',formula)
  for i in parenthetical:
   p=re.findall('[0-9]+',str(re.findall('\)[0-9]+',i)))
   j=re.findall('[A-Z][a-z]*[0-9]*',i)
   oldj=j
   for n in range(0,len(j)):
    numero=re.findall('[0-9]+',j[n])
    if len(numero)!=0:
     for k in numero:
      nu=re.sub(k,str(int(int(k)*int(p[0]))),j[n])
    else:
     nu=re.sub(j[n],j[n]+p[0],j[n])
    j[n]=nu
   newphrase=""
   for m in j:
    newphrase+=str(m)
   formula=formula.replace(i,newphrase)
  if (len((re.findall('\(\w*\)[0-9]+',formula)))==0) and (len(re.findall('\(\w*\)',formula))!=0):
   formula=formula.replace('(','')
   formula=formula.replace(')','')
 return formula


#######
# main #
########
if __name__ == '__main__':
 molecules=molecules.split(',')
 for element in molecules:
  element=formulaExpander(element)
  print ('The mass of %(substance)s is %(Mass)f and the calculated charge is %(Charge)i.' % {'substance': \
   element, 'Mass': molmass(element), 'Charge': molcharge(element)})

251. Isotopic pattern and molecular weight calculator in Python for Linux

UPDATE: I've moved this code to https://sourceforge.net/projects/pyisocalc/

I'm not answering questions about this code -- it's a work in progress (updated every other day) and if you can't figure out how to use it  on your own, you're not the (currently) intended audience. For example, I've only had time to add a small subsection of the elements.

I originally implemented a very different solution -- a very exact and shiny one. The problem is that the number of permutations increases too rapidly, so that anything larger than e.g. B3(NO3)4 would use up 8 GB of RAM or more. 'Easy' molecules like C18 didn't use that much RAM, but still introduced a noticeable delay. Trimming the list of permutations introduces errors (small, hopefully) but speeds things up orders of magnitude.

In other words: this calculator is moderately fast (python), and very accurate (as far as I can tell). As I keep on looking at more and more complex examples for validation I find that I need to introduce various trimming functions to keep the matrices small.

Having said that, it's still kind of neat. Here's RuCl5^2- by my program and Matt Monroe's calculator (which I trust):

Monroe's output:

And plotting on top (scaled Monroe's by 1.08 to compensate for the error in scaling in Monroe's program which gives 108% abundance):

I removed the figures of W6O19^- since the error in the y axis scale in Monroe's program (went to 120%) made it a less good example, and the list of peaks is too long for easy comparison.
Here's another figure:

A hypothetical W6^- molecule

Anyway, here are a couple of syntax examples:

  Usage:
 ./isocalc 'Al2(NO3)3'
 ./isocalc 'Al2(NO3)3' -1
 ./isocalc 'Al2(NO3)3' -1 output.dat
 ./isocalc Al2N3O9 
  ./isocalc Al(NO3)3(OH)1
  ./isocalc Al(NO3)3(OH)
./isocalc Al

See here for the source code:
https://sourceforge.net/projects/pyisocalc/

250. Compiling Kernel 3.6 on Debian Testing/Wheezy

IMPORTANT: a lot of drivers need to be explicitly enabled now, in particular those related to video devices (e.g. saa*, uvcvideo)

Nothing difficult or weird about compiling your own kernel, and 3.6 is no exception. This post is pretty much identical to my previous kernel compile posts, but with 3.6 replacing 3.x.
I've successfully compiled 3.6.0, 3.6.2, 3.6.3 and 3.6.6 this way.

If you're wondering whether it's worth it, you can have a look here:
 http://www.h-online.com/open/features/What-s-new-in-Linux-3-6-1714690.html

If you've never compiled a kernel before you might need to:

sudo apt-get install kernel-package fakeroot build-essential

Then get on with it:

wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.6.3.tar.bz2
tar xvf linux-3.6.3.tar.bz2
cd linux-3.6/
cat /boot/config-`uname -r`>.config
make oldconfig

You'll get a whole bunch of questions about what to include. See the end of the post for a list.

Video device drivers
Chances are that you will want to do

make menuconfig

and enable the compilation of various video device drivers e.g. go to Device drivers, Multimedia support, star (*) Cameras/video grabbers support, which enables Video Capture Adapters. Go to Video Capture Adapters and enable e.g. V4L USB devices/USB Video Class (m) to get your webcam working. You may need to enable other things too.

 Next:

make-kpkg clean
time fakeroot make-kpkg -j3 --initrd --revision=3.6.3 --append-to-version=-amd64 kernel_image kernel_headers

Building takes a while -- about 39 minutes on an AMD II X3.

mv ../*3.6.3*.deb .
sudo dpkg -i *.deb

And you're done!

---

---

What's new:

Expose hardware/virtual IRQ mapping via debugfs (IRQ_DOMAIN_DEBUG) [N/y/?] (NEW) *
Memory Resource Controller for Control Groups (MEMCG) [N/y/?] (NEW)
HugeTLB Resource Controller for Control Groups (CGROUP_HUGETLB) [N/y/?] (NEW)
Virtual (secure) IP: tunneling (NET_IPVTI) [N/m/?] (NEW)
NFQUEUE integration with Connection Tracking (NETFILTER_NETLINK_QUEUE_CT) [N/y/?] (NEW)
CAN Identifier (NET_EMATCH_CANID) [N/m/?] (NEW)     IPset (NET_EMATCH_IPSET) [N/m/?] (NEW)
Three-wire UART (H5) protocol support (BT_HCIUART_3WIRE) [N/y/?] (NEW)
Trace all mac80211 debug messages (MAC80211_MESSAGE_TRACING) [N/y/?] (NEW)   *
Driver for Broadcom BCM8706 and BCM8727 PHYs (BCM87XX_PHY) [N/m/?] (NEW) 
rt2800pci - Include support for rt3290 devices (EXPERIMENTAL) (RT2800PCI_RT3290) [Y/n/?] (NEW) 
MELFAS MMS114 touchscreen (TOUCHSCREEN_MMS114) [N/m/?] (NEW) 
EDT FocalTech FT5x06 I2C Touchscreen support (TOUCHSCREEN_EDT_FT5X06) [N/m/?] (NEW) 
Analog Devices AD-FMCOMMS1-EBZ SPI-I2C-bridge driver (SPI_XCOMM) [N/m/?] (NEW) 
BT8XX GPIO abuser (GPIO_BT8XX) [N/m/y/?] (NEW)   
AMD 8111 GPIO driver (GPIO_AMD8111) [N/m/y/?] (NEW)  
4096-Bit Addressable 1-Wire EEPROM with PIO (DS28E04-100) (W1_SLAVE_DS28E04) [N/m/?] (NEW)
Adaptive Voltage Scaling class support (POWER_AVS) [N/y/?] (NEW) *
Honeywell Humidicon HIH-6130 humidity/temperature sensor (SENSORS_HIH6130) [N/m/?] (NEW) 
BCMA Broadcom GBIT MAC COMMON core driver (BCMA_DRIVER_GMAC_CMN) [N/y/?] (NEW)
Support Wolfson Microelectronics Arizona platform with I2C (MFD_ARIZONA_I2C) [N/m/?] (NEW)
Support Wolfson Microelectronics Arizona platform with SPI (MFD_ARIZONA_SPI) [N/m/y/?] (NEW)
Cameras/video grabbers support (MEDIA_CAMERA_SUPPORT) [N/y/?] (NEW)  
Analog TV support (MEDIA_ANALOG_TV_SUPPORT) [N/y/?] (NEW) 
Digital TV support (MEDIA_DIGITAL_TV_SUPPORT) [N/y/?] (NEW)  
AM/FM radio receivers/transmitters support (MEDIA_RADIO_SUPPORT) [N/y/?] (NEW) 
Remote Controller support (MEDIA_RC_SUPPORT) [N/y/?] (NEW) 
Enable framebuffer console under vmwgfx by default (DRM_VMWGFX_FBCON) [N/y/?] (NEW)  
User-space I/O driver support for HID subsystem (UHID) [N/m/?] (NEW)  
Lenovo ThinkPad USB Keyboard with TrackPoint (HID_LENOVO_TPKBD) [N/m/?] (NEW) 
LED support for LM3556 Chip (LEDS_LM3556) [N/m/?] (NEW)  
LED support for the BlinkM I2C RGB LED (LEDS_BLINKM) [N/m/?] (NEW) 
LED One-shot Trigger (LEDS_TRIGGER_ONESHOT) [N/m/y/?] (NEW) 
EDAC legacy sysfs (EDAC_LEGACY_SYSFS) [Y/n/?] (NEW)  
VFIO Non-Privileged userspace driver framework (VFIO) [N/m/y/?] (NEW) *
Xen platform mcelog (XEN_MCE_LOG) [N/y/?] (NEW) *
Comedi misc drivers (COMEDI_MISC_DRIVERS) [N/y/?] (NEW) *
Comedi PCI drivers (COMEDI_PCI_DRIVERS) [N/y/?] (NEW) *
Comedi PCMCIA drivers (COMEDI_PCMCIA_DRIVERS) [N/y/?] (NEW) *
Comedi USB drivers (COMEDI_USB_DRIVERS) [N/y/?] (NEW) *
CSR wireless driver (CSR_WIFI) [N/m/?] (NEW) *
Pulse-Width Modulation (PWM) Support (PWM) [N/y/?] (NEW) *
Log kernel console messages (PSTORE_CONSOLE) [N/y/?] (NEW)   
Provide swap over NFS support (NFS_SWAP) [N/y/?] (NEW) 
Notifier error injection (NOTIFIER_ERROR_INJECTION) [N/m/y/?] (NEW)
Set upper limit of TLB entries to flush one-by-one (DEBUG_TLBFLUSH) [N/y/?] (NEW)
Serpent cipher algorithm (x86_64/AVX) (CRYPTO_SERPENT_AVX_X86_64) [N/m/y/?] (NEW) 
Twofish cipher algorithm (x86_64/AVX) (CRYPTO_TWOFISH_AVX_X86_64) [N/m/y/?] (NEW)   *
TCM_VHOST fabric module (EXPERIMENTAL) (TCM_VHOST) [N/m/?] (NEW) #

---

Links to this post:
http://forumubuntusoftware.info/viewtopic.php?f=117&t=8832
http://linux.org.ru/forum/linux-hardware/8339795
http://www.taringa.net/comunidades/ubuntuparataringeros/6513772/_ayuda_compilar-kernel-3_6-en-crunchbang.html
http://kenan.abdullahoglu.com/index.php/bilisim
http://crunchbang.org/forums/viewtopic.php?id=24484
http://forum.teneon.de/index.php?yshout&file=home&history&n=1000

246. Cluster network performance testing (very basic) on Debian Testing using a gigabit switch

Playing with hpcc got me thinking about my network connection.

My cluster looks like this:
I've got four nodes which are connected via two networks, 192.168.2.0/24 and 192.168.1.0/24. The 192.168.1.0/24 network is connected using a gigabit switch. Be (see below) acts as the gateway. The 192.168.2.0/24 network is connected via a crappy old netgear 10/100 router (dhcp) and provides access to the outside world (hello mac spoofing :) ). Each box shares a folder via nfs using a unique name.
_Nodes_
Be: AMD II X3, 8 GB ram (192.168.1.1): Ethernet controller: Realtek Semiconductor Co., Ltd. RTL-8169 Gigabit Ethernet (rev 10)
Ta: Intel i5-2400, 8 GB ram (192.168.1.150):  Intel Corporation 82579LM Gigabit Network Connection (rev 04)
B: AMD Phenom II X6, 8 GB ram (192.168.1.101): Realtek Semiconductor Co., Ltd. RTL8111/8168B PCI Express Gigabit Ethernet controller (rev 03)
Ne: AMD FX 8150 X8, 16 GB ram (192.168.1.120): Ethernet controller: Realtek Semiconductor Co., Ltd. RTL-8169 Gigabit Ethernet (rev 10)

So, time to test the network performance:
sudo apt-get install iperf

On all your boxes (e.g. using clusterssh) start the iperf daemon
iperf -s

Then on each of your nodes run:

iperf -c 192.168.1.1 && iperf -c 192.168.1.101 && iperf -c 192.168.1.150 && iperf -c 192.168.1.120

------------------------------------------------------------
Client connecting to 192.168.1.1, TCP port 5001
TCP window size: 45.7 KByte (default)
------------------------------------------------------------
[  3] local 192.168.1.101 port 37893 connected with 192.168.1.1 port 5001
[ ID] Interval       Transfer     Bandwidth
[  3]  0.0-10.0 sec   564 MBytes   473 Mbits/sec
------------------------------------------------------------
Client connecting to 192.168.1.101, TCP port 5001
TCP window size:  169 KByte (default)
------------------------------------------------------------
[  3] local 192.168.1.101 port 35926 connected with 192.168.1.101 port 5001
[ ID] Interval       Transfer     Bandwidth
[  3]  0.0-10.0 sec  15.5 GBytes  13.3 Gbits/sec
------------------------------------------------------------
Client connecting to 192.168.1.150, TCP port 5001
TCP window size: 22.9 KByte (default)
------------------------------------------------------------
[  3] local 192.168.1.101 port 48257 connected with 192.168.1.150 port 5001
[ ID] Interval       Transfer     Bandwidth
[  3]  0.0-10.0 sec   564 MBytes   473 Mbits/sec
------------------------------------------------------------
Client connecting to 192.168.1.120, TCP port 5001
TCP window size: 22.9 KByte (default)
------------------------------------------------------------
[  3] local 192.168.1.101 port 43236 connected with 192.168.1.120 port 5001
[ ID] Interval       Transfer     Bandwidth
[  3]  0.0-10.0 sec   617 MBytes   517 Mbits/sec

Overall, this is what I got
Client/Server (MBit/s)

     Be     B     Ta    Ne
Be   13.7G  310   308   316
B    564    15.5G 564   617
Ta   726    660   19.7G 936
Ne   882    484   917   19.4G

I'm not sure whether to expect a metric gigabit (1000 metric MBit) or a binary one (1024 binary MBit), but looking at our results our best is 936 Mbit/s and worst 308 Mbit/s. All of them should thus ideally reach at least 936 MBit/s. They all have gigabit network card.

And now, try to improve it:
I went through the whole shebang with
sudo ifconfig eth1 mtu 9000
sudo ifconfig eth1 mtu 8000
etc.
Anyway, I got the following MTUs that way:
Be  7100
B    7100
Ne  9000
Ta   9000

I then set the MTUs to 7100 on all the nodes and tried pinging from node to node, e.g.:
ping -s 7072 -M do 192.168.1.101

Well, that maxed out at 1472 i.e. about MTU 1500 which was the original value. So I'm a bit confused.

---

Settings:
Be:

eth1      Link encap:Ethernet  HWaddr 00:f0:4d:83:0a:48  
          inet addr:192.168.1.1  Bcast:192.168.1.255  Mask:255.255.255.0
          inet6 addr: fe80::2f0:4dff:fe83:a48/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:24124966 errors:0 dropped:27064 overruns:0 frame:0
          TX packets:19569426 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000 
          RX bytes:25859945667 (24.0 GiB)  TX bytes:14200267703 (13.2 GiB)

B:

eth1      Link encap:Ethernet  HWaddr 02:00:8c:50:2f:6b  
          inet addr:192.168.1.101  Bcast:192.168.1.255  Mask:255.255.255.0
          inet6 addr: fe80::8cff:fe50:2f6b/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:14540970 errors:0 dropped:36651 overruns:0 frame:0
          TX packets:16801915 errors:0 dropped:2 overruns:0 carrier:0
          collisions:0 txqueuelen:1000 
          RX bytes:12347398135 (11.4 GiB)  TX bytes:18008416370 (16.7 GiB)

Ta:

eth1      Link encap:Ethernet  HWaddr 78:2b:cb:b3:a4:b7  
          inet addr:192.168.1.150  Bcast:192.168.1.255  Mask:255.255.255.0
          inet6 addr: fe80::7a2b:cbff:feb3:a4b7/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:14717233 errors:0 dropped:68232 overruns:0 frame:0
          TX packets:17769966 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000 
          RX bytes:13860096243 (12.9 GiB)  TX bytes:20207270880 (18.8 GiB)
          Interrupt:20 Memory:e1a00000-e1a20000 

Ne:

eth1      Link encap:Ethernet  HWaddr 90:2b:34:93:75:e6  
          inet addr:192.168.1.120  Bcast:192.168.1.255  Mask:255.255.255.0
          inet6 addr: fe80::922b:34ff:fe93:75e6/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:13567520 errors:0 dropped:0 overruns:0 frame:0
          TX packets:10710054 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000 
          RX bytes:13086635236 (12.1 GiB)  TX bytes:12381041605 (11.5 GiB)

245. Recompile debian's hpcc with other libs

I installed hpcc using apt-get, but -- and this is a first -- when trying to run it complained over missing libs.

---

Why compile?

hpcc

hpcc: error while loading shared libraries: libatlas.so.3gf: cannot open shared object file: No such file or directory

Doing
aptitude show hpcc 

Depends: libatlas3gf-base, libc6 (>= 2.7), libopenmpi1.3, mpi-default-bin

apt-cache search libatlas.so.3gf

libatlas3-base - Automatically Tuned Linear Algebra Software, generic shared
libatlas3gf-base - Transitional package to libatlas3-base

and doing

 aptitude search atlas|grep ^i

i   libatlas-dev                    - Automatically Tuned Linear Algebra Softwar
i A libatlas3gf-base                - Transitional package to libatlas3-base

but
locate libatlas.so.3gf
comes up empty.

---

So build your own:
sudo mkdir /opt/hpcc
sudo chown $USER /opt/hpcc
cd /opt/hpcc
wget http://ftp.de.debian.org/debian/pool/main/h/hpcc/hpcc_1.4.1.orig.tar.gz
tar xvf hpcc_1.4.1.orig.tar.gz
cd hpcc-1.4.1/
wget http://ftp.de.debian.org/debian/pool/main/h/hpcc/hpcc_1.4.1-2.debian.tar.gz
tar xvf hpcc_1.4.1-2.debian.tar.gz
patch -i debian/patches/add-Make.Debian.patch

Edit Make.Debian. For some reason LAdir is ignored, hence the -L option in LAlib

 78 # ----------------------------------------------------------------------
 79 # - MPI directories - library ------------------------------------------
 80 # ----------------------------------------------------------------------
 81 # MPinc tells the  C  compiler where to find the Message Passing library
 82 # header files,  MPlib  is defined  to be the name of  the library to be
 83 # used. The variable MPdir is only used for defining MPinc and MPlib.
 84 #
 85 MPdir        =/usr/lib/openmpi/lib/
 86 MPinc        =
 87 MPlib        =-lmpi
 88 #
 89 # ----------------------------------------------------------------------
 90 # - Linear Algebra library (BLAS or VSIPL) -----------------------------
 91 # ----------------------------------------------------------------------
 92 # LAinc tells the  C  compiler where to find the Linear Algebra  library
 93 # header files,  LAlib  is defined  to be the name of  the library to be
 94 # used. The variable LAdir is only used for defining LAinc and LAlib.
 95 #
 96 LAdir        = /opt/ATLAS/lib
 97 LAinc        =
 98 LAlib        = -L/opt/ATLAS/lib -ltatlas
 99 #

The above assumes that you've compiled your own openblas as shown elsewhere on this blog. You can use whatever math libs you want. Again, there are a couple described on this blog (acml, netlib blas/lapack, openblas, ATLAS). I've had success with the netlib blas/lapack and atlas (built with netlib lapack).

mv Make.Debian hpl/
make arch=Debian

Hopefully everything went well. Now you need an input file.
cp _hpccinf.txt hpccinf.txt

Edit hpccinf.txt:

HPLinpack benchmark input file
Innovative Computing Laboratory, University of Tennessee
HPL.out      output file name (if any)
8            device out (6=stdout,7=stderr,file)
1            # of problems sizes (N)
1000         Ns
1            # of NBs
80           NBs
0            PMAP process mapping (0=Row-,1=Column-major)
1            # of process grids (P x Q)
3            Ps
1            Qs
16.0         threshold
1            # of panel fact
2            PFACTs (0=left, 1=Crout, 2=Right)
1            # of recursive stopping criterium
4            NBMINs (>= 1)
1            # of panels in recursion
2            NDIVs
1            # of recursive panel fact.
1            RFACTs (0=left, 1=Crout, 2=Right)
1            # of broadcast
1            BCASTs (0=1rg,1=1rM,2=2rg,3=2rM,4=Lng,5=LnM)
1            # of lookahead depth
1            DEPTHs (>=0)
2            SWAP (0=bin-exch,1=long,2=mix)
64           swapping threshold
0            L1 in (0=transposed,1=no-transposed) form
0            U  in (0=transposed,1=no-transposed) form
1            Equilibration (0=no,1=yes)
8            memory alignment in double (> 0)
##### This line (no. 32) is ignored (it serves as a separator). ######
0                               Number of additional problem sizes for PTRANS
1200 10000 30000                values of N
0                               number of additional blocking sizes for PTRANS
40 9 8 13 13 20 16 32 64        values of NB

Launch by doing
mpirun -n X ./hpcc
where X=Ps times Qs (e.g. 3 in the example above).

I put the hpccinf.txt in a shared (nfs) folder (~/jobs), created a file called myhost

tantalum slots=2 max_slots=4
boron slots=2 max_slots=6
neon slots=2 max_slots=8

 and then launched using
mpirun -n 4 -hostfile myhost /opt/hpcc/hpcc-1.4.1/./hpcc

244. Molden on debian testing

Update: avogadro can write gamess input files, but seems to offer little in the way of showing detailed output from gamess output files. Also, some of the input files contain keywords which don't exist.

Original post:
Nothing beats a good GUI, so after butting heads with gabedit again (and losing - again. Although in this case I think I tried to make it do something it wasn't designed to) I've decided to try Molden.

To download, go here, make sure to be a good citizen and register yourself as a user (will help motivate funding for development) then download: http://www.cmbi.ru.nl/molden/howtoget.html

cd ~/tmp
wget ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.0.tar.gz
tar xvf molden5.0.tar.gz
cd molden5.0/

Edit makefile and remove -lXmu from line 20:

16 CC = cc
17 FC = gfortran
18 LIBS =  -lX11 -lm
19 LDR = ${FC} 
20 LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lX11 -lm

cd surf/

edit Makefile and change it from

 46 depend: $(DEPEND)
 47     @ echo making dependencies...
 48     @ echo ' ' > makedep
 49     @ makedepend $(INCLUDE) -f makedep $(DEPEND)

to

 46 depend: $(DEPEND)
 47     @ echo making dependencies...
 48     @ echo ' ' > makedep
 49     @ $(CC) $(INCLUDE) -M $(DEPEND) > makedep

Save and go back up one level, and run make:
 cd ../
 make

You're pretty much done.

I like putting things in /opt, so
sudo mkdir /opt/molden
sudo chown $USER /opt/molden
cp ~/tmp/molden5.0/* -R /opt/molden

stick

export PATH=$PATH:/opt/molden

in your ~/.bashrc

Type
molden
to run

Molden can read output files from gamess -- still exploring the exact capabilities, but e.g the convergence information can be accessed:

and you can get nifty contour plots of the electron density of orbitals etc.

---

Error:

If you don't edit the surf/Makefile as shown above you'll get

make[1]: Leaving directory `/home/me/tmp/molden5.0/ambfor'
make -C surf depend
make[1]: Entering directory `/home/me/tmp/molden5.0/surf'
making dependencies...
make[1]: makedepend: Command not found
make[1]: *** [depend] Error 127
make[1]: Leaving directory `/home/me/tmp/molden5.0/surf'

234. CPMD with netlib lapack, blas and your own fftw on debian testing

This is a minor update to my previous post on CPMD. Back in the days I had issue linking to my Openblas libs (got a binary which would not run properly) but I've since had success with the netlib lapack and blas libs.

1. Compile the netlib lapack and blas libraries according to this post: http://verahill.blogspot.com.au/2012/09/compiling-netlibs-lapack-and-blas-on.html

2. Compile the fftw libraries according to this post (ignore the sections on Openblas and Gromacs):
http://verahill.blogspot.com.au/2012/05/gromacs-with-external-fftw3-and-blas-on.html

3. Compile CPMD. We'll be following this post in large parts.
Register with cpmd.org. Once you're approved download the cpmd source to ~/tmp.

sudo apt-get install libopenmpi-dev openmpi-bin

cd ~/tmp
tar -xvf cpmd-v3_15_3.tar.gz
cd CPMD/CONFIGURE

Create the file LINUX-x86_64-DEBIAN:

   
     IRAT=2
     CFLAGS='-c -O2 -Wall'
     CPP='/lib/cpp -P -C -traditional'
     CPPFLAGS='-D__Linux -D__PGI -D__GNU -DFFT_FFTW3 -DPARALLEL -DPOINTER8'
     FFLAGS='-c -O2 -fcray-pointer -fno-whole-file -fsecond-underscore'
     LFLAGS='-l:/opt/fftw/fftw-3.3.2/double/lib/libfftw3.a -l:/opt/fftw/fftw-3.3.2/double/lib/libfftw3_mpi.a -l:/opt/fftw/fftw-3.3.2/double/lib/libfftw3_threads.a -I/usr/include -l:/opt/netlib/blas/lib/libnetblas.so -l:/opt/netlib/lapack/lib/liblapack.so -lpthread -lmpi'
     FFLAGS_GROMOS='  $(FFLAGS)' 
      FC='mpif77 -fbounds-check'
      CC='mpicc'
      LD='mpif77 -fbounds-check'

Next edit ~/tmp/CPMD/wfnio.F and change the following lines:

 15       CHARACTER(len=*) TAG
 63         IF(TAG(1:2).EQ.'NI') THEN
201       IF(TAG(1:2).NE.'NI') THEN
271         IF(TAG(1:2).EQ.'NI') THEN

Now, in ~/tmp/CPMD, run

./mkconfig.sh LINUX-x86_64-DEBIAN > Makefile
make
sudo mkdir /opt/cpmd
sudo chown $USER /opt/cpmd
cp cpmd.x /opt/cpmd

And follow everything below 'Done! Almost.' in this post: http://verahill.blogspot.com.au/2012/07/not-solved-compiling-cpmd-on-debian.html

233. Compiling netlib's lapack and blas on Debian Testing (Wheezy)

In addition to specific BLAS/LAPACK libs such as ACML, MKL, and ATLAS netlib provides (what I understand to be) reference versions of BLAS and LAPACK. Presumably these are slower than optimised versions of blas/lapack, but it doesn't hurt being familiar with them.

Here's how to compile those versions.

---

BLAS

sudo mkdir /opt/netlib
sudo chown $USER /opt/netlib
mkdir /opt/netlib/blas/lib -p
wget http://www.netlib.org/blas/blas.tgz
tar xvf blas.tgz
cd BLAS/

Edit make.inc
OPTS = -O3 -shared -m64 -march=native -fPIC

make all
gfortran -shared -Wl,-soname,libnetblas.so -o libblas.so.1.0.1 *.o -lc
ln -s libblas.so.1.0.1 libnetblas.so
cp lib*blas* /opt/netlib/blas/lib

To see whether everything linked ok:
 ldd libnetblas.so 

        linux-vdso.so.1 =>  (0x00007ffff1bc6000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b42ec030000)
        libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00002b42ec3b8000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002b42ec6ce000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002b42ec950000)
        libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002b42ecb67000)
        /lib64/ld-linux-x86-64.so.2 (0x00002b42ebaf3000)

---

LAPACK
(inspired by this and this)
mkdir -p /opt/netlib/lapack
sudo apt-get install cmake-curses-gui
cd ~/tmp
wget http://www.netlib.org/lapack/lapack-3.4.1.tgz
tar xvf lapack-3.4.1.tgz
cd lapack-3.4.1/
mkdir build
cd build
ccmake ../

Hit 'c' to generate a configuration. Navigate with arrow keys and hit enter to change values. Change to the values in red:

 
 BUILD_COMPLEX                   *ON
 BUILD_COMPLEX16                 *ON
 BUILD_DOUBLE                    *ON
 BUILD_SHARED_LIBS               *ON
 BUILD_SINGLE                    *ON
 BUILD_STATIC_LIBS               *ON
 BUILD_TESTING                   *ON
 CMAKE_BUILD_TYPE                *     
 CMAKE_INSTALL_PREFIX            */opt/netlib/lapack
 LAPACKE                         *OFF
 LAPACKE_WITH_TMG                *OFF
 USE_OPTIMIZED_BLAS              *ON
 USE_XBLAS                       *OFF

Then hit 'c' which might give you (change the values in red) -- I got some errors about ACML/eula here, but don't worry about that.

NOTE: this will only work if you already have blas installed in a standard location. If you don't get the BLAS_FOUND etc. then you should hit 'c' again and then 'g'. Next edit your CMakeCache.txt and paste the variables (without line numbers) you find below this section, then do ccmake ../ again and make sure everything looks ok, and generate using 'g'.

 BLAS_FOUND                       TRUE
 BLAS_GENERIC_FOUND               ON
 BLAS_GENERIC_blas_LIBRARY        /opt/netlib/blas/lib/libnetblas.so
 BLAS_LIBRARIES                   /opt/netlib/blas/lib/libnetblas.so
 BLAS_LINKER_FLAGS
 BUILD_COMPLEX                   *ON
 BUILD_COMPLEX16                 *ON
 BUILD_DOUBLE                    *ON
 BUILD_SHARED_LIBS               *OFF
 BUILD_SINGLE                    *ON
 BUILD_STATIC_LIBS               *ON
 BUILD_TESTING                   *ON
 CMAKE_BUILD_TYPE                *     
 CMAKE_INSTALL_PREFIX            */usr/local 
 LAPACKE                         *OFF
 LAPACKE_WITH_TMG                *OFF
 USE_OPTIMIZED_BLAS              *ON
 USE_XBLAS                       *OFF

The hit 'c' again. If there were no issues, hit 'g' which writes the configuration and exits.


make

[100%] Building Fortran object TESTING/EIG/CMakeFiles/xeigtstz.dir/__/__/INSTALL/dsecnd_INT_ETIME.f.o
Linking Fortran executable ../../bin/xeigtstz
[100%] Built target xeigtstz

make install

Install the project...
-- Install configuration: ""
-- Installing: /opt/netlib/lapack/lib/pkgconfig/lapack.pc
-- Installing: /opt/netlib/lapack/lib/cmake/lapack-3.4.1/lapack-config.cmake
-- Installing: /opt/netlib/lapack/lib/cmake/lapack-3.4.1/lapack-config-version.cmake
-- Installing: /opt/netlib/lapack/lib/cmake/lapack-3.4.1/lapack-targets.cmake
-- Installing: /opt/netlib/lapack/lib/cmake/lapack-3.4.1/lapack-targets-noconfig.cmake
-- Installing: /opt/netlib/lapack/lib/liblapack.so
-- Removed runtime path from "/opt/netlib/lapack/lib/liblapack.so"
-- Installing: /opt/netlib/lapack/lib/libtmglib.so
-- Removed runtime path from "/opt/netlib/lapack/lib/libtmglib.so"

tree /opt/netlib/ -d
/opt/netlib/
|-- blas
|   `-- lib
`-- lapack
    `-- lib
        |-- cmake
        |   `-- lapack-3.4.1
        `-- pkgconfig

7 directories

---

CMakeCache.txt variables:

 16 
 17 BLAS_FOUND:STRING=TRUE
 18 
 19 //Whether not the GENERIC library was found and is usable
 20 BLAS_GENERIC_FOUND:BOOL=TRUE
 21 
 22 //Path to a library.
 23 BLAS_GENERIC_blas_LIBRARY:FILEPATH=/opt/netlib/blas/lib/libnetblas.so
 24 
 25 BLAS_LIBRARIES:PATH=/opt/netlib/blas/lib/libnetblas.so
 26 

---

Testing the libraries:
I built gromacs against the new libs to make sure they 'worked'

sudo mkdir /opt/gromacs
sudo chown ${USER} /opt/gromacs
cd ~/tmp
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz
tar xvf gromacs-4.5.5.tar.gz
cd gromacs-4.5.5/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/netlib/blas/lib:/opt/netlib/lapack/lib
export LDFLAGS="-l:/opt/netlib/blas/lib/libnetblas.so -l:/opt/netlib/lapack/lib/liblapack.so"
./configure --disable-mpi --enable-float --with-external-blas --with-external-lapack --program-suffix=_netlib --prefix=/opt/gromacs/gromacs-4.5.5
make

make install

Check that it linked ok:

ldd /opt/gromacs/gromacs-4.5.5/bin/grompp_netlib
        linux-vdso.so.1 =>  (0x00007fffb83f2000)
        libgmxpreprocess.so.6 => /opt/gromacs/gromacs-4.5.5/lib/libgmxpreprocess.so.6 (0x00002b6411cfa000)
        libmd.so.6 => /opt/gromacs/gromacs-4.5.5/lib/libmd.so.6 (0x00002b6411fcd000)
        libfftw3f.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3f.so.3 (0x00002b64123ad000)
        libxml2.so.2 => /usr/lib/x86_64-linux-gnu/libxml2.so.2 (0x00002b64127b0000)
        libgmx.so.6 => /opt/gromacs/gromacs-4.5.5/lib/libgmx.so.6 (0x00002b6412b10000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002b6412fe5000)
        libnetblas.so => /opt/netlib/blas/lib/libnetblas.so (0x00002b64131e9000)
        liblapack.so => /opt/netlib/lapack/lib/liblapack.so (0x00002b64134cc000)
        libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00002b6413ece000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002b64140e6000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00002b6414369000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b6414585000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00002b641490c000)
        liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00002b6414b24000)
        /lib64/ld-linux-x86-64.so.2 (0x00002b6411ad8000)
        libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00002b6414d47000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002b641505d000)
        libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002b6415274000)

Here are some input files (it's not a 'real' md run -- I just needed something small and quick to run):
step1.top:

#include "/opt/gromacs/gromacs-4.5.5/share/gromacs/top/ffoplsaa.itp"
#include "/opt/gromacs/gromacs-4.5.5/share/gromacs/top/oplsaa.ff/tip4p.itp"

[system]
test 

[molecules]

step1.mdp:

integrator = md
define      = -DFLEXIBLE
emtol      = 1000.0
emstep     = 0.001
nsteps     = 5000
nstlist    = 1
ns_type    = grid 
rlist      = 0.9
coulombtype= PME  
rcoulomb   = 0.9  
rvdw       = 1.0  
pbc        =  xyz

genbox_netlib -o step1.gro -cs /opt/gromacs/gromacs-4.5.5/share/gromacs/top/tip4p.gro -box 4x4x4 -p step1.top

grompp_netlib -f step1.mdp -po step2.mdp -p step1.top -pp step2.top -c step1.gro -o step2.tpr

mdrun_netlib -v -s step2.tpr -o step3.trr -x step3.xtc -cpo step3.cpt -c step3.gro -e step3.edr -g step3.log

On my old AMD II X3 I got about 7.7 GFLOPS with Openblas and 7.8 GFLOPS with the above libs. Note that the run is shorter than a minute so it's pretty useless for benchmarking. However, there's no obvious MAJOR penalty.

---

---

If you don't have cmake:
cp INSTALL/make.inc.gfortran make.inc

Edit make.inc

 15 FORTRAN  = gfortran
 16 OPTS     = -O2 -fPIC -m64
 17 DRVOPTS  = $(OPTS)
 18 NOOPT    = -O0 -fPIC -m64
 19 LOADER   = gfortran
 20 LOADOPTS =

Edit Makefile

 11 #lib: lapacklib tmglib
 12 lib: blaslib variants lapacklib tmglib

Run make

make

-->  Tests passed: 13176


   -->   LAPACK TESTING SUMMARY  <--
  Processing LAPACK Testing output found in the TESTING direcory
SUMMARY              nb test run  numerical error    other error  
================    =========== ================= ================  
REAL              1077227  0 (0.000%) 0 (0.000%) 
DOUBLE PRECISION 1078039  0 (0.000%) 0 (0.000%) 
COMPLEX           522814  0 (0.000%) 0 (0.000%) 
COMPLEX16          552410  0 (0.000%) 0 (0.000%) 

--> ALL PRECISIONS 3230490  0 (0.000%) 0 (0.000%) 

---

---

Older version:
In the oldest version of this post I did the blas compilation by hand:

gfortran -O2 -fPIC -m64 -march=native -funroll-all-loops -c *.f

To build a static library:
ar rvs libblas.a *.o

To build a shared/dynamic library:
gfortran -shared -Wl,-soname,libnetblas.so -o libblas.so.1.0.1 *.o -lc 

ldd libblas.so.1.0.1

        linux-vdso.so.1 =>  (0x00007fff301af000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002aeeac390000)
        libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00002aeeac718000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002aeeaca2e000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002aeeaccb0000)
        libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002aeeacec7000)
        /lib64/ld-linux-x86-64.so.2 (0x00002aeeabedd000)

Either way:
cp libblas* /opt/netlib/blas/lib

To test:
wget http://www.netlib.org/blas/sblat1
mv sblat1 sblat1.f

And EITHER
gfortran sblat1.f -l:libblas.a

OR
ln -s libblas.so.1.0.1 libnetblas.so
gfortran sblat1.f -l:libnetblas.so

THEN
./a.out

 
Real BLAS Test Program Results
Test of subprogram number  1             SDOT 
                                    ----- PASS -----

 Test of subprogram number  2            SAXPY 
                                    ----- PASS -----

 Test of subprogram number  3            SROTG 
                                    ----- PASS -----

 Test of subprogram number  4             SROT 
                                    ----- PASS -----

 Test of subprogram number  5            SCOPY 
                                    ----- PASS -----

 Test of subprogram number  6            SSWAP 
                                    ----- PASS -----

 Test of subprogram number  7            SNRM2 
                                    ----- PASS -----

 Test of subprogram number  8            SASUM 
                                    ----- PASS -----

 Test of subprogram number  9            SSCAL 
                                    ----- PASS -----

 Test of subprogram number 10            ISAMAX
                                    ----- PASS -----

232. Compile parallel (threaded) povray 3.7-rc6 on Debian Wheezy

Update 13 May 2013: This build won't work with v3.7-rc7 on debian wheezy if you have libjpeg62 installed. See http://verahill.blogspot.com.au/2013/05/413-povray-37-rc7-on-debian-wheezy.html.

Remove libjpeg62 and it works fine though.

Original post
Expanding my little cluster has got me thinking about additional uses for it. The primary purpose is obviously work i.e. MD simulations using gromacs and ab initio calcs using NWChem and Gaussian. I'm also testing it with John the Ripper to see how well the users of the linux box in the lab are choosing their passwords.

At that point I realised that it'd be sweet to have at least an OMP capable version of povray to speed things up when polishing figures for those elusive journal covers.

Debian testing currently uses v. 3.6.1 of povray but

  POV-Ray 3.6 does not support multithreaded rendering. POV-Ray 3.7 does.

So compile we will although v 3.7 is beta, so be aware.

sudo mkdir /opt/povray
sudo chown $USER /opt/povray

wget http://povray.org/redirect/www.povray.org/beta/source/povray-3.7.0.RC6.tar.gz
tar xvf povray-3.7.0.RC6.tar.gz
cd povray-3.7.0.RC6/
sudo apt-get install libboost-all-dev libpng-dev libjpeg-dev libtiff-dev build-essential libsdl-dev

Note: libboost-all-dev is big. It might be enough with libboost-thread-dev

./configure --prefix=/opt/povray --program-suffix=_3.7 COMPILED_BY="me@here"

===============================================================================
POV-Ray 3.7.0.RC5 has been configured.

Built-in features:
  I/O restrictions:          enabled
  X Window display:          disabled
  Supported image formats:   gif tga iff ppm pgm hdr png jpeg tiff
  Unsupported image formats: openexr

Compilation settings:
  Build architecture:  x86_64-unknown-linux-gnu
  Built/Optimized for: x86_64-unknown-linux-gnu (using -march=native)
  Compiler vendor:     gnu
  Compiler version:    g++ 4.7
  Compiler flags:      -pipe -Wno-multichar -Wno-write-strings -fno-enforce-eh-specs -s -O3 -ffast-math -march=native -pthread

Type 'make check' to build the program and run a test render.
Type 'make install' to install POV-Ray on your system.

The POV-Ray components will be installed in the following directories:
  Program (executable):       /opt/povray/bin
  System configuration files: /opt/povray/etc/povray/3.7
  User configuration files:   $HOME/.povray/3.7
  Standard include files:     /opt/povray/share/povray-3.7/include
  Standard INI files:         /opt/povray/share/povray-3.7/ini
  Standard demo scene files:  /opt/povray/share/povray-3.7/scenes
  Documentation (text, HTML): /opt/povray/share/doc/povray-3.7
  Unix man page:              /opt/povray/share/man
===============================================================================

The way it is configured we can keep our debian version of povray and install the newer version (povray_3.7)

make
make install

Seems like -geometry 1000x1000 doesn't work anymore. Instead use -H1000 -W1000

I've played around with it a little bit and it does parallel (threaded) execution nicely.

wget http://www.ms.uky.edu/~lee/visual05/povray/fourcube7.pov
./povray_3.7 -H1000 -W1000 fourcube7.pov +A0.1
takes 9 seconds on an AMD II X3. The standard, serial Debian version takes 21 seconds.

231. Compiling john the ripper: single/serial, parallel/OMP and MPI

Update: updated for v1.7.9-jumbo-7 since hccap2john in 1.7.9-jumbo-6 was broken

For no particular reason at all, here's how to compile John the Ripper on Debian Testing (Wheezy). It's very easy, and this post is probably a bit superfluous. The standard version only supports serial and parallel (OMP). See below for MPI.

---

The regular version: 

mkdir ~/tmp
cd ~/tmp
wget http://www.openwall.com/john/g/john-1.7.9.tar.gz
tar xvf john-1.7.9.tar.gz
cd john-1.7.9/src

If you don't edit the Makefile you build a serial/single-threaded binary.
If you want to build a threaded version for a single node with a multicore processor (OMP) do:
Edit Makefile and uncomment row 19 or 20

 18 # gcc with OpenMP
 19 OMPFLAGS = -fopenmp
 20 OMPFLAGS = -fopenmp -msse2

make clean linux-x86-64

cd ../run

You now have a binary called john in your ../run folder.

---

The Jumbo version:
If you want to build a distributed version with MPI (can split jobs across several nodes) you need the enhanced, community version:

sudo apt-get install openmpi-bin libopenmpi-dev

cd ~/tmp

wget http://www.openwall.com/john/g/john-1.7.9-jumbo-7.tar.gz

tar xvf john-1.7.9-jumbo-7.tar.gz 

cd john-1.7.9-jumbo-7/src

Edit the Makefile

  20 ## Uncomment the TWO lines below for MPI (can be used together with OMP as well)

  21 ## For experimental MPI_Barrier support, add -DJOHN_MPI_BARRIER too.

  22 ## For experimental MPI_Abort support, add -DJOHN_MPI_ABORT too.

  23 CC = mpicc -DHAVE_MPI

  24 MPIOBJ = john-mpi.o

and do

make clean linux-x86-64-native
cd ../run

I had a look at the passwords on one of our lab boxes -- it immediately discovered that someone had used 'password' as the password...

---

These test were run on my old AMD II X3 445. Processes which don't speed up with MP are highlighted in red. LM DES is borderline -- it's faster, but doesn't scale well.

Here's the single thread/serial version:
./john --test

Benchmarking: Traditional DES [128/128 BS SSE2-16]... DONE
Many salts:     2906K c/s real, 2918K c/s virtual
Only one salt:  2796K c/s real, 2807K c/s virtual
Benchmarking: BSDI DES (x725) [128/128 BS SSE2-16]... DONE
Many salts:     95564 c/s real, 95948 c/s virtual
Only one salt:  93593 c/s real, 93781 c/s virtual
Benchmarking: FreeBSD MD5 [32/64 X2]... DONE
Raw:    14094 c/s real, 14122 c/s virtual
Benchmarking: OpenBSD Blowfish (x32) [32/64 X2]... DONE
Raw:    918 c/s real, 919 c/s virtual
Benchmarking: Kerberos AFS DES [48/64 4K]... DONE
Short:  474316 c/s real, 475267 c/s virtual
Long:   1350K c/s real, 1356K c/s virtual
Benchmarking: LM DES [128/128 BS SSE2-16]... DONE
Raw:    39843K c/s real, 39923K c/s virtual
Benchmarking: generic crypt(3) [?/64]... DONE
Many salts:     262867 c/s real, 263393 c/s virtual
Only one salt:  260121 c/s real, 260642 c/s virtual
Benchmarking: Tripcode DES [48/64 4K]... DONE
Raw:    369843 c/s real, 370584 c/s virtual
Benchmarking: dummy [N/A]... DONE
Raw:    99512K c/s real, 99712K c/s virtual

Here's the OMP version:

Benchmarking: Traditional DES [128/128 BS SSE2-16]... DONE
Many salts:     6706K c/s real, 2555K c/s virtual
Only one salt:  5015K c/s real, 2091K c/s virtual
Benchmarking: BSDI DES (x725) [128/128 BS SSE2-16]... DONE
Many salts:     205670 c/s real, 85411 c/s virtual
Only one salt:  238524 c/s real, 86720 c/s virtual
Benchmarking: FreeBSD MD5 [32/64 X2]... DONE
Raw:    38400 c/s real, 13812 c/s virtual
Benchmarking: OpenBSD Blowfish (x32) [32/64 X2]... DONE
Raw:    2306 c/s real, 845 c/s virtual
Benchmarking: Kerberos AFS DES [48/64 4K]... DONE
Short:  474675 c/s real, 476581 c/s virtual
Long:   1332K c/s real, 1335K c/s virtual
Benchmarking: LM DES [128/128 BS SSE2-16]... DONE
Raw:    49046K c/s real, 16785K c/s virtual
Benchmarking: generic crypt(3) [?/64]... DONE
Many salts:     721670 c/s real, 246640 c/s virtual
Only one salt:  699168 c/s real, 239605 c/s virtual
Benchmarking: Tripcode DES [48/64 4K]... DONE
Raw:    367444 c/s real, 369657 c/s virtual
Benchmarking: dummy [N/A]... DONE
Raw:    100351K c/s real, 100552K c/s virtual

And here's the MPI version:
mpirun -n 3 ./john --test
(note that this includes a great many more tests than the default version)

Benchmarking: Traditional DES [128/128 BS SSE2-16]... (3xMPI) DONE
Many salts:     8533K c/s real, 8707K c/s virtual
Only one salt:  7705K c/s real, 8110K c/s virtual
Benchmarking: BSDI DES (x725) [128/128 BS SSE2-16]... (3xMPI) DONE
Many salts:     279808 c/s real, 282634 c/s virtual
Only one salt:  273362 c/s real, 276096 c/s virtual
Benchmarking: FreeBSD MD5 [128/128 SSE2 intrinsics 12x]... (3xMPI) DONE
Raw:    65124 c/s real, 65781 c/s virtual
Benchmarking: OpenBSD Blowfish (x32) [32/64 X2]... (3xMPI) DONE
Raw:    2722 c/s real, 2749 c/s virtual
Benchmarking: Kerberos AFS DES [48/64 4K]... (3xMPI) DONE
Short:  1387K c/s real, 1415K c/s virtual
Long:   3880K c/s real, 3959K c/s virtual
Benchmarking: LM DES [128/128 BS SSE2-16]... (3xMPI) DONERaw:    114781K c/s real, 115940K c/s virtual

I don't quite understand the Kerberos results.

---

Other targets of interest are:

linux-x86-64-avx         Linux, x86-64 with AVX (2011+ Intel CPUs)
linux-x86-64-xop         Linux, x86-64 with AVX and XOP (2011+ AMD CPUs)
linux-x86-64             Linux, x86-64 with SSE2 (most common)
linux-x86-avx            Linux, x86 32-bit with AVX (2011+ Intel CPUs)
linux-x86-xop            Linux, x86 32-bit with AVX and XOP (2011+ AMD CPUs)
linux-x86-sse2           Linux, x86 32-bit with SSE2 (most common, if 32-bit)
linux-x86-mmx            Linux, x86 32-bit with MMX (for old computers)
linux-x86-any            Linux, x86 32-bit (for truly ancient computers)

The FX 8150 does AVX and XOP, while my 1055T doesn't.

The community version has more options:

linux-x86-64-native      Linux, x86-64 'native' (all CPU features you've got)
linux-x86-64-gpu         Linux, x86-64 'native', CUDA and OpenCL (experimental)
linux-x86-64-opencl      Linux, x86-64 'native', OpenCL (experimental)
linux-x86-64-cuda        Linux, x86-64 'native', CUDA (experimental)
linux-x86-64-avx         Linux, x86-64 with AVX (2011+ Intel CPUs)
linux-x86-64-xop         Linux, x86-64 with AVX and XOP (2011+ AMD CPUs)
linux-x86-64[i]          Linux, x86-64 with SSE2 (most common)
linux-x86-64-icc         Linux, x86-64 compiled with icc
linux-x86-64-clang       Linux, x86-64 compiled with clang
linux-x86-gpu            Linux, x86 32-bit with SSE2, CUDA and OpenCL (experimental)
linux-x86-opencl         Linux, x86 32-bit with SSE2 and OpenCL (experimental)
linux-x86-cuda           Linux, x86 32-bit with SSE2 and CUDA (experimental)
linux-x86-sse2[i]        Linux, x86 32-bit with SSE2 (most common, 32-bit)
linux-x86-native         Linux, x86 32-bit, with all CPU features you've got (not necessarily best)
linux-x86-mmx            Linux, x86 32-bit with MMX (for old computers)
linux-x86-any            Linux, x86 32-bit (for truly ancient computers)
linux-x86-clang          Linux, x86 32-bit with SSE2, compiled with clang
linux-alpha              Linux, Alpha
linux-sparc              Linux, SPARC 32-bit
linux-ppc32-altivec      Linux, PowerPC w/AltiVec (best)
linux-ppc32              Linux, PowerPC 32-bit
linux-ppc64              Linux, PowerPC 64-bit
linux-ia64               Linux, IA-64

229. Compile ATLAS (+ gromacs, nwchem) on AMD FX 8150 on Debian Testing (Wheezy)

Xianyi's openblas doesn't seem to be ready for AMD FX 8150 yet. I've played with ATLAS in the past, but  for some reason didn't see the same performance with NWChem and ATLAS as I saw with NWChem and Openblas, so I never ended up using it.

I'm also having issues using openblas with CPMD and quantum espresso, and ATLAS is a well-established, respectable project, so it's time to give it another shot. As in most cases in these situations, it's probably a matter of PEBKAC.

Building ATLAS
Anyway. On we go...

mkdir /opt/ATLAS
chown ${USER} /opt/ATLAS
mkdir ~/tmp
cd ~/tmp
wget http://www.netlib.org/lapack/lapack-3.4.1.tgz
 wget http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%29/3.9.72/atlas3.9.72.tar.bz2
tar xvf atlas3.9.72.tar.bz2
cd ATLAS/

Edit ATLAS/Make.top
change the V on line 6 to lowercase i.e. from
- $(ICC) -V 2>&1 >> bin/INSTALL_LOG/ERROR.LOGto
- $(ICC) -v 2>&1 >> bin/INSTALL_LOG/ERROR.LOG
mkdir build/
cd build/

sudo apt-get install cpufreq-utils

cat /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor

ondemand

sudo cpufreq-set -g performance

Unfortunately that only takes care of cpu0:

cat /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor

performance

but

cat /sys/devices/system/cpu/cpu1/cpufreq/scaling_governor

ondemand

So...since we have 8 cores (cpu0-cpu7):

sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu1/cpufreq/scaling_governor
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu2/cpufreq/scaling_governor
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu3/cpufreq/scaling_governor
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu4/cpufreq/scaling_governor
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu5/cpufreq/scaling_governor
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu6/cpufreq/scaling_governor
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu7/cpufreq/scaling_governor

OK, we're ready to compile:
.././configure --prefix=/opt/ATLAS -Fa alg '-fPIC' --with-netlib-lapack-tarfile=$HOME/tmp/lapack-3.4.1.tgz --shared

Some of the info that's important is:

OS configured as Linux (1)
Assembly configured as GAS_x8664 (2)
Vector ISA Extension configured as  AVXFMA4 (4,496)
Architecture configured as  AMDDOZER (34)
Clock rate configured as 3600Mhz

If that checks out you don't need to manually set your architecture. To get a list over options, do
 make xprint_enums ; ./xprint_enums

If all is well,

make
make install

You should now be done.

Linking Gromacs against ATLAS

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/ATLAS/lib
#single precision
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/single/lib -L/opt/ATLAS/lib -lsatlas -ltatlas -lgfortran"
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/single/include -I/opt/ATLAS/include"
./configure --disable-mpi --enable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_spatlas --prefix=/opt/gromacs/gromacs-4.5.5
make -j6 2>make.err 1>make.log
make install

#double precision
make distclean
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/double/lib -L/opt/ATLAS/lib -lsatlas -ltatlas -lgfortran" 
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/double/include -I/opt/ATLAS/include"
./configure --disable-mpi --disable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_dpatlas --prefix=/opt/gromacs/gromacs-4.5.5
make -j6 2>make2.err 1>make2.log
make install

#single + mpi
make distclean
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/single/lib -L/opt/ATLAS/lib -lsatlas -ltatlas -lgfortran"
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/single/include -I/opt/ATLAS/include"
./configure --enable-mpi --enable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_spmpiatlas --prefix=/opt/gromacs/gromacs-4.5.5
make -j6 2>make3.err 1>make3.log
make install

#double + mpi
make distclean
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/double/lib -L/opt/ATLAS/lib -lsatlas  -ltatlas  -lgfortran" 
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/double/include -I/opt/ATLAS/include"
./configure --enable-mpi --disable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_dpmpiatlas --prefix=/opt/gromacs/gromacs-4.5.5
make -j6 2>make4.err 1>make4.log
make install

Linking NWChem against ATLAS

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all"
export BLASOPT="-L/opt/ATLAS/lib -lsatlas -ltatlas"
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/lib/openmpi/lib
export MPI_INCLUDE=/usr/lib/openmpi/include
export LIBRARY_PATH="$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/ATLAS/lib"
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
export LDFLAGS="-I/opt/ATLAS/include"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran 2> make.err 1>make.log
export FC=gfortran
cd $NWCHEM_TOP/contrib
./getmem.nwchem