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!

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---

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) #

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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