255. Google Blogger Stats gone

Update: And...most of the stats are back. (03:19 GMT 15 October 2012)


02:30 GMT 15 October 2012
Did the google stats data just get reset/deleted?

Suddenly my stat counter shows just above 30 visitors -- all-time. That's a bit fewer than the 72k I was expecting. Oh well. I've at least got statcounter too keep me entertained.

It seems to have happened around 0:00 GMT 15 October 2012, although looking at the stats on blogger it may have happened around 9-10 am Eastern Aussie Daylight Savings time.

Update:
The angry posts are already beginning to appear: http://productforums.google.com/forum/#!topic/blogger/eOZyb9ws2IU
which bumps stuff in this direction:
http://productforums.google.com/forum/#!topic/blogger/dSFrwW2SWgE%5B1-25%5D
which has this statement from Blogger:

"We are aware of this issue and working to resolve it. "

And here's the official Blogger blog: http://knownissues.blogspot.com.au/

Not that I've ever had much use for the 'official' google stats much anyway -- although I obviously care enough about it to 1) notice that they're gone and 2) blog about it. But whatever.

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

249. Quick but precise isotopic pattern (isotope envelope) calculator in Octave

UPDATE: Below is an accurate calculator,  but it is impractically slow for large molecules. A practical AND accurate calculator is found here:http://verahill.blogspot.com.au/2012/10/isotopic-pattern-caculator-in-python.html

Use the post below to learn about the fundamental theory, but then look at the other post to understand how to implement it.

Old post:
Getting fast and accurate isotopic patterns can be tricky using tools available online, for download or which form part of commercial packages. A particular problem is that different tools give slightly different values -- so which one to trust?

The answer: the tool for which you know that the algorithm is sound.

The extreme conclusion of that way of thinking is to write your own calculator.
Below is the conceptual process of calculating the isotopic pattern of a molecule using GNU Octave.

You need the linear algebra package:
sudo apt-get install octave octave-linear-algebra

b is the isotopic distribution for an element, and bb are the masses of those isotopes.

Once you've got a computational engine it's not too difficult to expand it for more general cases, account for charge, and instrument resolution.

---

Molecule: Cl₄

b=[0.7578,0.2422];
bb=[34.96885,36.96885];
e=prod(cartprod(b,b,b,b),2);
ee=sum(cartprod(bb,bb,bb,bb),2);
n=4;
g=histc([ee e],linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1)),2);
h=linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1));
distr=e'*g;
plot(h,100.*distr/max(distr))
[h' (100.*distr/max(distr))']

Here's the output for n=1:

   139.87540    78.22048
   140.87540     0.00000
   141.87540   100.00000
   142.87540     0.00000
   143.87540    47.94141
   144.87540     0.00000
   145.87540    10.21502
   146.87540     0.00000
   147.87540     0.81620

And here's the output from Matt Monroe's calculator:

Isotopic Abundances for Cl4
  Mass/Charge Fraction  Intensity
   139.87541 0.3297755   78.22
   140.87541 0.0000000    0.00
   141.87541 0.4215974  100.00
   142.87541 0.0000000    0.00
   143.87541 0.2021197   47.94
   144.87541 0.0000000    0.00
   145.87541 0.0430662   10.22
   146.87541 0.0000000    0.00
   147.87541 0.0034411    0.82

---

Another molecule: Li2Cl2

Here's the code:

a=[0.0759,0.9241];
aa=[6.01512,7.01512];
b=[0.7578,0.2422];
bb=[34.96885,36.96885];
e=prod(cartprod(a,a,b,b),2);
ee=sum(cartprod(aa,aa,bb,bb),2);
n=1;
g=histc([ee e],linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1)),2);
h=linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1));
distr=e'*g;
plot(h,100.*distr/max(distr))
[h' (100.*distr/max(distr))']

ans =

    81.96794     0.67170
    82.96794    16.35626
    83.96794   100.00000
    84.96794    10.45523
    85.96794    63.71604
    86.96794     1.67079
    87.96794    10.17116

vs Matt Monroe's calculator:

Isotopic Abundances for Li2Cl2
  Mass/Charge Fraction  Intensity
    81.96795 0.0033082    0.67
    82.96795 0.0805564   16.36
    83.96795 0.4925109  100.00
    84.96795 0.0514932   10.46
    85.96795 0.3138084   63.72
    86.96795 0.0082288    1.67
    87.96795 0.0500941   10.17

---

We can then expand the code to allow for plotting

a=[0.0759,0.9241];
aa=[6.01512,7.01512];
b=[0.7578,0.2422];
bb=[34.96885,36.96885];
e=prod(cartprod(a,a,b,b),2);
ee=sum(cartprod(aa,aa,bb,bb),2);
n=1;

g=histc([ee e],linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1)),2);
h=linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1));
distr=e'*g;
gauss= @(x,c,r,s) r.*1./(s.*sqrt(2*pi)).*exp(-0.5*((x-c)./s).^2);
k=100.*distr/max(distr);

npts=1000;
resolution=0.25;

x=linspace(min(ee)-1,max(ee)+1,npts);
l=cumsum(gauss(x,h',k',resolution));
l=100*l./max(l(rows(l),:));
plot(x,l(rows(l),:))

which gives:

Compare with Matt Monroe's calculator:

248. Matt Monroe's Molecular Weight Calculator under Wine on Linux

I've downloaded the source code to Matt Monroe's molecular weight calculator in the past, and having replaced wsearch32 (+wine) with OpenChrom I figured I'd go online, download it and see what Mono can do for me. I had a vague recollection that the source code was only freely available online for a short while, and as it turns out I couldn't find it this time.

Anyway, not finding the source code I decided to update my Molecular Weight calculator from version 6.46 to 6.49 which (finally) allows you to set the charge of an ion WITHOUT having the mass of a H+ added for each charge. It's not difficult to compensate for, but it's always confusing to new students.

1. Install Wine and winetricks, add dlls
You can either install wine from the repos (old version)
sudo apt-get install wine-bin

Or you can download a newer, unstable version from dev.carbon-project.org:
http://verahill.blogspot.com.au/2012/01/debian-testingwheezy-64-bit-installing.html

Or you can compile your own:
http://verahill.blogspot.com.au/2013/01/308-compiling-wine-1521-on-debian.html

The mono step was a right headache and would fail unless I nuked everything winetricks and wine knew about each other/

To get winetricks and set everything up:

sudo apt-get install cabextract

wget http://winetricks.org/winetricks
sudo mv winetricks /usr/local/bin/
sudo chmod +x /usr/local/bin/winetricks
wget http://downloads.sourceforge.net/project/wine/Wine%20Mono/0.0.4/wine-mono-0.0.4.msi
wine msiexec /i wine-mono-0.0.4.msi

You're now asked whether to download and install mono...sigh...more often that not this has failed in the past.

winetricks vcrun6sp6

Download the file from the browser window that just opened

cd ~/.cache/winetricks/vcrun6sp6 

mv ~/Downloads/Vs6sp6.exe .
winetricks vcrun6sp6
winetricks corefonts
winetricks riched30
wine uninstaller --remove '{E45D8920-A758-4088-B6C6-31DBB276992E}'
winetricks dotnet20
cd ~/.cache/winetricks/dotnet20/
mv ~/Downloads/dotnetfx.exe .
winetricks dotnet20

Ignore this error. Installation will take a while after that. Have patience. Like 10 minutes kind of patience.

And finally:

winetricks wsh57

2. Download the molecular weight calculator and install
If you go to http://www.alchemistmatt.com/mwtwin.html
you get redirected to here: http://omics.pnl.gov/software/MWCalculator.php

cd ~/tmp
mkdir molw
cd molw/
wget http://omics.pnl.gov/installers/MolecularWeightCalculator_Installer.zip
wget http://omics.pnl.gov/installers/MwtWinDll_SourceAndSupportingDLLs.zip
ls *.zip|xargs -I {} unzip {}
unzip MwtWinDll_Source_v3.4.4518.zip

You'll get some warning about Revisionhistory.txt etc. being overwritten. That's fine.

Launch the install with
wine msiexec /i MolecularWeightCalculator.msi

If you try to launch the mol weight calculator at this point you'll get an error about a missing MwtWinDLL.dll:

So sort that out:

cd ~/tmp/molw/bin
regsvr32 MwtWinDll.dll

Successfully registered DLL MwtWinDll.dll

[If I tried to copy the dll to the wine structure first and register that copy I got:

DllRegisterServer not implemented in DLL C:\windows\system\MwtWinDll.dll]

If it seems weird to install wine-mono and then remove it as is done above, it's to get around a bug which causes dotnet20 installation to fail/

Anyway, you're pretty much done:
 wine ~/.wine/drive_c/Program\ Files/Molecular\ Weight\ Calculator/mwtwin.exe

Yay!

---

Comment:
Getting there was a bit of a trek, passing though a whole lot of different sets of dlls:
winetricks msflxgrd

winetricks vcrun2005
winetricks vb6run
winetricks mdac28
winetricks comctl32ocx

winetricks comctl32

The solution above should suffice though.

I even ended up installing mol weight calc on a windows box and using dependency walker, but not even that sorted it out -- googling for scrrun did it in the end.

In particular this last error was bloody annoying:

"Object doesn't support this action." What, saving?

"Error saving default options file. Use the /X switch at the command line to prevent this error."

But it was solved by doing winetricks wsh57

247. Setting up Openchrom (and using it to open Agilent .D ESI-MS files on Linux)

I've been using Wsearch (http://www.wsearch.com.au/wsearch32/wsearch32.htm) to process agilent chemstation ESI-MS spectra for the past few years. It and Matt Monroe's Molecular Weight calculator (why, oh why is there no comparable molecular weight calculator for linux?) have been the only two reasons why I've bother with Wine under Linux. Openchrom is written in java and so will run on both Good (Linux) and Evil (OS X and Win) operating systems.

Having finally discovered openchrom (v 0.6 so still early days) I can now finally retire wsearch from my own computers (it's still a good piece of software, but it's crippled to encourage the purchasing of a 'full' version, and I've had no luck purchasing a license from the author in spite of having tried several times during the past couple of years). OpenChrom can export an entire agilent experiment as a '3D' csv file which makes processing a lot more fun.

As an aside: I hate proprietary file formats since they prevent me from using my own tools (cat, sed, gawk, gnuplot, octave) when processing -- or at a minimum make it more difficult. Most universities and grant agencies now add a provision regarding data management in their grant acceptance agreements/work conduct policies. In general these provisions state that the data shall be made available publicly and /or managed by a university repository. What is REALLY missing is a clause about using open formats -- and that should be taken into account when acquiring new instrumentation. All else being equal, an instrument which is 'open' will be a lot cheaper to manage in the long run since you won't have to feel locked in in terms of software. That's incidentally a reason why I like Metrohm since they provide details of their RS-232 interface allowing you to write your own software.

Anyway, here's how to get set up:

---

1. Install Java v1.7 (need > 1.6)
You can either use openjdk 7 or (Oracle) Java. See here for a general guide to installing Oracle/Sun Java.

As for openjdk, you can easily install it:
sudo apt-get install openjdk-7-jdk

(the openjdk-7-jre package is enough if you don't want the full developer's kit)

Anyway.

Make sure that you've selected the right version:

 sudo update-alternatives --config java
There are 7 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                            Priority   Status
------------------------------------------------------------
  0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
  1            /usr/bin/gij-4.4                                 1044      manual mode
  2            /usr/bin/gij-4.6                                 1046      manual mode
  3            /usr/bin/gij-4.7                                 1047      manual mode
  4            /usr/lib/jvm/j2re1.6-oracle/bin/java             314       manual mode
  5            /usr/lib/jvm/j2sdk1.6-oracle/jre/bin/java        315       manual mode
  6            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
 *7            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode

---

2. Get openchrom

cd ~/tmp

wget http://sourceforge.net/projects/openchrom/files/REL-0.6.0/openchrom_linux.gtk.x86_64_0.6.0.zip

unzip openchrom_linux.gtk.x86_64_0.6.0.zip

cd linux.gtk.x86_64/OpenChrom/

sudo mkdir /opt/openchrom

sudo chown $USER /opt/openchrom 

cp * -R /opt/openchrom

chmod +x /opt/openchrom/openchrom

Stick

alias openchrom='/opt/openchrom/openchrom'

in your ~/.bashrc and source it.

---

3. Get plugins
On first boot you're asked whether you want to get additional plugins using the 'Openchrom marketplace'. Since I'm mainly processing data from an Agilent ESI-MS, I wanted the plugin for Agilent files. The website says that you need a license key for plugins BUT that it's free to register for one.

This is a 30-days trial version. Afterwards, you need a valid serial key.
You can get a free serial key after registration on http://www.openchrom.net.
You can use the converter for commercial or non-commercial purposes free of charge, but you are not allowed to redistribute this software without my permission.

Note, that clicking on links on the website didn't lead me to a link to download the plugin. Instead, in OpenChrom click on the Plug-ins menu:

As always, make sure you trust your suppliers.

And then you're done installing.

There's nothing odd about registering other than this: you will receive an email with a confirmation of your registration in clear text WITH YOUR PASSWORD. So...be aware of that.

---

4. You can now browse in the tree to the left and select your .D folder:

There's a bit of clever thinking when it comes to the functionality of the program. The upside of this I think will eventually be that it's easy to get a consistent experience for a set of users (not unimportant for a research group). The downside is that it's a bit clunky getting started. Play with it for an hour and you'll get the hang of it, so it's not really that much of a hurdle. Also, too many options seem to be context sensitive -- I am having real trouble finding various options under the 'Accurate' perspective which I can find under the 'default' perspective.

---

5. Some comments:

It's still early days for OpenChrom (v 0.6) , and there are a few minor issues which may or may not affect you:

* Registration keys. They are easy enough to get (register online, log in, click on the plug in online that you want and you'll see the key), but if you have installed a new plug in and open your first spectrum right after that you'll be asked for registration keys. It won't tell you for which plug in the dialogue you're seeing is though, so if you've just installed three different plug ins you'll have to do some trial-and-error. This is fixed in the upcoming version.

* Raw/gaussian plot of mass spectrum. This took a while to figure out, but you have to use perspectives. The default (heavily zoomed in) view looks like this:

This might be good enough for those organic types...us 108 element inorganic types want more detail

If you go to the top right corner, click on 'other' (perspectives)

and select accurate you get

Bingo!

And then there's the obligatory wish list:

* A good quality isotopic pattern calculator would be nice. Anyone who has compared the output from different pieces of software will have discovered that different calculators may yield very different patterns. I think some of it boils down to truncation rather than incorrect isotopic ratios, but that just highlights how difficult it can be to implement a seemingly simple concept. The only calculator which I trust AND find useful is Matt Monroe's calculator -- the predicted patterns look good, and you get proper Gaussian broadening which means that it looks 'right'. This would be perfect as a plug-in. If only I knew how to properly implement it...

* A good quality ion generator -- some pieces of software (Hi Matt) allow you to select a handful of elements or fragments, pick a range of charges, input an m/z value and based on that spits out a list over possible identities for your signal. It's a good thing to have by your side the first time you look at a complex mixture trying to figure out what products may be present. This would be perfect as a plug-in. I've written this type of programmes before, but in python using for-loops...a vectorized version should be faster and maybe even easier to write.

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'

243. My own personal benchmarks for NWChem, gromacs with atlas, openblas, acml on AMD and intel

Update: you can compile against acml on intel as well, and against mkl on amd. Still need to do some performance testing to see how well it works. The artificial penalty of running mkl on AMD is well-publicised and led to a lawsuit, but I don't know how acml performs on mkl.


The title says it all, really. Since I'm back to exploring ways of improving performance for my little cluster I figured I'd break this out as a separate post. Most of this data was found here before: http://verahill.blogspot.com.au/2012/09/new-compute-node-using-amd-fx-8150.html

All units are running up-to-date debian testing (wheezy).

Configuration:
Boron (B): Phenom II X6 2.8 GHz, 8Gb RAM (2.8*6=16.8 GFLOPS predicted)
Neon (Ne): FX-8150 X8 3.6 GHz, 16 Gb RAM (3.6*8=28.8 GFLOPS predicted (int), 3.6*4=14.4 GFLOPS (fpu))
Tantalum (Ta): Quadcore i5-2400 3.1 GHz, 8 Gb RAM (3.1*4=12.4 GFLOPS predicted)
Vanadium (V):  Dual socket 2x Quadcore Xeon X3480 3.06 GHz, 8Gb. CentOS (ROCKS 5.4.3)/openblas.

---

Results

Gromacs --double (1 ns 6x6x6 nm tip4p water box; dynamic load balancing, double precision, 500k steps)
B  :  10.662 ns/day (11.8  GFLOPS, runtime 8104 seconds)***
B  :    9.921 ns/day ( 10.9 GFLOPS, runtime 8709 seconds)**
Ne:  10.606 ns/day (11.7  GFLOPS, runtime 8146 seconds) *
Ne:  12.375 ns/day (13.7  GFLOPS, runtime 6982 seconds)**
Ne:  12.385 ns/day (13.7  GFLOPS, runtime 6976 seconds)****
Ta:  10.825 ns/day (11.9  GFLOPS, runtime 7981 seconds)***
V :   10.560 ns/dat (11.7  GFLOPS, runtime 8182 seconds)***
*no external blas/lapack.
**using ACML libs
*** using openblas
**** using ATLAS

Gromacs --single (1 ns 6x6x6 nm tip4p water box; dynamic load balancing, single precision, 500 k steps)
B  :   17.251 ns/day (19.0 GFLOPS, runtime 5008 seconds)***
Ne:   21.874 ns/day (24.2 GFLOPS, runtime  3950 seconds)**
Ne:   21.804 ns/day (24.1 GFLOPS, runtime 3963  seconds)****
Ta:   17.345 ns/day (19.2 GFLOPS, runtime  4982 seconds)***
V :   17.297 ns/day (19.1 GFLOPS, runtime 4995 seconds)***
*no external blas/lapack.
**using ACML libs
*** using openblas
**** using ATLAS

NWChem (opt biphenyl cation, cp-md/pspw):
B  :   5951 seconds**
B  :   4084 seconds ***
B  :   5782 seconds ***xy
Ne:    3689 seconds**
Ta :   4102 seconds***
Ta :   4230 seconds***xy
V :    5396 seconds***

*no external blas/lapack.
**using ACML libs
*** using openblas
x Reconfigured using getmem.nwchem

NWChem (opt biphenyl cation, geovib, 6-31G**/ub3lyp):
B  :  2841 seconds **
B  :  2410 seconds***
B  :  2101 seconds ***x
B  :  2196 seconds ***xy
Ne: 1665 seconds **
Ta : 1785 seconds***
Ta : 1789 seconds***xy

V  : 2600 seconds***

*no external blas/lapack.
**using ACML libs
*** using openblas
x Reconfigured using getmem.nwchem
y NWChem 6.1.1

A Certain Commercial Ab Initio Package (Freq calc of pre-optimised H₁₄C₁₉O₃ at 6-31+G*/rb3lyp):
B  :    2h 00 min (CPU time 10h 37 min)
Ne:   1h 37 min (CPU time: 11h 13 min)
Ta:   1h 26 min (CPU time: 5h 27 min)
V  :   2h 15 min (CPU time 15h 50 min)
Using precompiled binaries.


Gamess:
(I'm still working on learning how to run gamess efficiently, so take these values with a huge saucer of salt for now). bn.inp does a geometry optimisation of a biphenyl cation (mult 2) at ub3lyp/6-31G**. bn.inp has no $STATPT card while bn3.inp does and it makes a huge difference -- but is this because it does 20 steps (nsteps=20), then kills the run? The default is 50 steps and it does seem like all the runs do the maximum number of steps, then exit.

 Again, still learning. See below for input files. Will fix this post as I learn what the heck I'm doing. The relative run times on each node are still comparable though, but just don't use the numbers to compare the run speed of e.g. nwchem vs gamess.

Gamess using bn.inp with atlas
B:    9079 seconds
Ne: 7252 seconds
Ta:  9283 seconds

Gamess using bn.inp with openblas
B:   9071 seconds
Ta: 9297 seconds

Gamess using bn.inp with acml

Ne: 7062 seconds

Gamess using bn3.inp with atlas. 

B: 4016 seconds

Ne: 3162 seconds

Ta: 4114 seconds

MPQC:
Here I've used the version in the debian repos. I've created a hostfile

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

and then just looked at changing the order and slots assignment as well as total number of cores assigned using mpirun.

Simple test case looking at number of cores/distribution:
n cores:  Seconds: Configuration(cores,exec nodes)
4    :   11   : 4(Ta)
4    :   17   : 4(Ne)
4    :   17   : 4(B)
4    :   42   : 2(Ta)+2(B)
6    :   12   : 6(B)
6    :   13   : 6(Ne)
6    :   74   : 2(Ta)+2(B)+2(Ne)
8    :   12   : 8(Ne)
10  :   43   : 4(Ta)+6(B)
12  :   47   : 4(Ta)+8(Ne)
14  :   55   : 6(B)+8(Ne)
18  :   170 :  4(Ta)+6(B)+8(Ne)

My beowulf cluster doesn't seem to be much of a super computer. All in all, this looks like a pretty good argument in favour of upgrading to infiniband...

bn.inp:

 $CONTRL 
COORD=CART UNITS=ANGS scftyp=uhf dfttyp=b3lyp runtyp=optimize 
ICHARG=1 MULT=2 maxit=100
$END
 $system mwords=2000 $end
 $BASIS gbasis=n31 ngauss=6 ndfunc=1 npfunc=1 $END
 $guess guess=huckel $end

 $DATA
biphenyl
C1
C      6.0      0.0000000000   -3.5630100000    0.0000000000 
C      6.0     -1.1392700000   -2.8592800000   -0.3938400000 
C      6.0     -1.1387900000   -1.4654500000   -0.3941500000 
C      6.0      0.0000000000   -0.7428100000    0.0000000000 
C      6.0      1.1387900000   -1.4654500000    0.3941500000 
C      6.0      1.1392700000   -2.8592800000    0.3938400000 
C      6.0      0.0000000000    0.7428100000    0.0000000000 
C      6.0      1.1387900000    1.4654500000   -0.3941500000 
C      6.0      1.1392700000    2.8592800000   -0.3938400000 
C      6.0     -1.1387900000    1.4654500000    0.3941500000 
C      6.0      0.0000000000    3.5630100000    0.0000000000 
C      6.0     -1.1392700000    2.8592800000    0.3938400000 
H      1.0      0.0000000000   -4.6489600000    0.0000000000 
H      1.0     -2.0282700000   -3.3966200000   -0.7116100000 
H      1.0     -2.0214800000   -0.9282700000   -0.7279300000 
H      1.0      2.0282700000   -3.3966200000    0.7116100000 
H      1.0      2.0282700000    3.3966200000   -0.7116100000 
H      1.0     -2.0214800000    0.9282700000    0.7279300000 
H      1.0      0.0000000000    4.6489600000    0.0000000000 
H      1.0     -2.0282700000    3.3966200000    0.7116100000 
H      1.0      2.0214800000    0.9282700000   -0.7279300000 
H      1.0      2.0214800000   -0.9282700000    0.7279300000 
 $END

bn3.inp:

$CONTRL 
COORD=CART UNITS=ANGS scftyp=uhf dfttyp=b3lyp runtyp=optimize 
ICHARG=1 MULT=2 maxit=100
$END
 $system mwords=2000 $end
 $BASIS gbasis=n31 ngauss=6 ndfunc=1 npfunc=1 $END
 $STATPT OPTTOL=0.0001 NSTEP=20 HSSEND=.TRUE. $END
 $guess guess=huckel $end

 $DATA
biphenyl
C1
C      6.0      0.0000000000   -3.5630100000    0.0000000000 
C      6.0     -1.1392700000   -2.8592800000   -0.3938400000 
C      6.0     -1.1387900000   -1.4654500000   -0.3941500000 
C      6.0      0.0000000000   -0.7428100000    0.0000000000 
C      6.0      1.1387900000   -1.4654500000    0.3941500000 
C      6.0      1.1392700000   -2.8592800000    0.3938400000 
C      6.0      0.0000000000    0.7428100000    0.0000000000 
C      6.0      1.1387900000    1.4654500000   -0.3941500000 
C      6.0      1.1392700000    2.8592800000   -0.3938400000 
C      6.0     -1.1387900000    1.4654500000    0.3941500000 
C      6.0      0.0000000000    3.5630100000    0.0000000000 
C      6.0     -1.1392700000    2.8592800000    0.3938400000 
H      1.0      0.0000000000   -4.6489600000    0.0000000000 
H      1.0     -2.0282700000   -3.3966200000   -0.7116100000 
H      1.0     -2.0214800000   -0.9282700000   -0.7279300000 
H      1.0      2.0282700000   -3.3966200000    0.7116100000 
H      1.0      2.0282700000    3.3966200000   -0.7116100000 
H      1.0     -2.0214800000    0.9282700000    0.7279300000 
H      1.0      0.0000000000    4.6489600000    0.0000000000 
H      1.0     -2.0282700000    3.3966200000    0.7116100000 
H      1.0      2.0214800000    0.9282700000   -0.7279300000 
H      1.0      2.0214800000   -0.9282700000    0.7279300000 
 $END

242. Briefly: Compiling NWChem 6.1.1 with Python on Debian Testing (Wheezy)

Back at the end of June a minor version of NWChem (bug fixes) was released.

There isn't much difference between compiling 6.1.1 and 6.1. Mainly, the difference is in what line to edit for python compatibility (NWChem 6.1 here:http://verahill.blogspot.com.au/2012/05/building-nwchem-61-on-debian.html )

---

1. Install dev packages
sudo apt-get install libopenmpi-dev openmpi-bin python2.7-dev zlib1g-dev libssl-dev

2. Compile openblas  or download e.g. acml.
(compiles fine, but doesn't run, with atlas)

3. NWchem goodness:

sudo mkdir /opt/nwchem
sudo chown $USER /opt/nwchem
cd /opt/nwchem
wget http://www.nwchem-sw.org/images/Nwchem-6.1.1-src.2012-06-27.tar.gz
(or go here http://www.nwchem-sw.org/index.php/Download)

tar xvf Nwchem-6.1.1-src.2012-06-27.tar.gz
cd nwchem-6.1.1-src/src/config/

Edit makefile.h and hange (line numbers are just for convenience -- don't add them)

1956 #   EXTRA_LIBS += -ltk -ltcl -L/usr/X11R6/lib -lX11 -ldl
1957      EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl
1958   LDOPTIONS = -Wl,--export-dynamic

to

1956 #   EXTRA_LIBS += -ltk -ltcl -L/usr/X11R6/lib -lX11 -ldl
1957      EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl -lssl -lz
1958   LDOPTIONS = -Wl,--export-dynamic

cd to /opt/nwchem/nwchem-6.1.1-src/ Create a file called buildconf.sh with the following content:

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export BLASOPT="-L/opt/openblas/lib -lopenblas"

#export BLASOPT="-L/opt/acml/acml5.2.0/gfortran64_int64/lib -lacml"

#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/openblas/lib

#export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/acml/acml5.2.0/gfortran64_int64/lib

#export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/ATLAS/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran 1> make.log 2>make.err
export FC=gfortran
cd ../contrib
./getmem.nwchem

Start the compilation:
time sh buildconf.sh 

 On a quadcore i5-2400 it took 18 minutes.