482. kernel 3.10.2 with CK patch

NOTE: the 304.88 nvidia kernel modules DO NOT BUILD on this kernel. I've also tried 3.10.5 and it also does not work.

NOTE II: I'm getting random slowdowns on my SL410 laptop with intel graphics. Not sure if it's the same issue as this: http://verahill.blogspot.com.au/2013/03/368-slow-mouse-and-keyboard-triggered.html
Once kworker shows up in top everything grinds to a slow crawl.

Nothing odd here. For a list of what questions to expect when going from 3.9 to 3.10, see e.g. http://verahill.blogspot.com.au/2013/07/468-kernel-310-on-debian.html

The CK patch set supposedly improves desktop performance of the kernel. As it seems like Con doesn't update that page anymore, go directly to the patches: http://ck.kolivas.org/patches/3.0/

sudo apt-get install xz-utils kernel-package fakeroot ncurses-dev
mkdir ~/tmp
cd ~/tmp
wget https://www.kernel.org/pub/linux/kernel/v3.x/linux-3.10.2.tar.xz
tar xvf linux-3.10.2.tar.xz
cd linux-3.10.2/
wget http://ck.kolivas.org/patches/3.0/3.10/3.10-ck1/patch-3.10-ck1.bz2
bunzip2 patch-3.10-ck1.bz2
patch -p1 < patch-3.10-ck1

patching file arch/powerpc/platforms/cell/spufs/sched.c
patching file Documentation/scheduler/sched-BFS.txt
patching file Documentation/sysctl/kernel.txt
patching file fs/proc/base.c
patching file include/linux/init_task.h
patching file include/linux/ioprio.h
patching file include/linux/sched.h
patching file init/Kconfig
patching file init/main.c
patching file kernel/delayacct.c
patching file kernel/exit.c
patching file kernel/posix-cpu-timers.c
patching file kernel/sysctl.c
patching file lib/Kconfig.debug
patching file include/linux/jiffies.h
patching file drivers/cpufreq/cpufreq.c
patching file drivers/cpufreq/cpufreq_ondemand.c
patching file kernel/sched/bfs.c
patching file include/uapi/linux/sched.h
patching file include/linux/sched/rt.h
patching file kernel/stop_machine.c
patching file drivers/cpufreq/cpufreq_conservative.c
patching file kernel/sched/Makefile
patching file kernel/time/Kconfig
patching file kernel/Kconfig.preempt
patching file kernel/Kconfig.hz
patching file arch/x86/Kconfig
patching file Makefile

make-kpkg clean
cat /boot/config-`uname -r`>.config
make oldconfig
time fakeroot make-kpkg -j3 --initrd kernel_image kernel_headers
sudo dpkg -i ../*3.10.2-ck*.deb
sudo rm /lib/modules/3.10.2-ck1/build
sudo ln -s /usr/src/linux-headers-3.10.2-ck1/ /lib/modules/3.10.2-ck1/build
sudo dkms autoinstall -k 3.10.2-ck1

481. A little bit of samba on the command line

I have a bit of a problem with samba currently.

My problem is that my computers are sitting behind a router (on a 192.168.2.0/24 subnet) and the computers that I want to access sit on the university network, to which the router is connected. The address range is, say, 131.172.x.x.

In other words, I (think I) want to use samba across two subnets.

I've opened up ports 13-139,445 to tcp and udp on both the router and in iptables on my desktop.

My problem:
1. I can't see the network shares of the other computers using
   a) nautilus (Network/Windows Network)
   b) nmblookup
   c) sambascanner

2. I can't connect to network shares using their netbios names. For example, I'd like to connect to e.g. smb://avance400/data, but I have to use the IP address instead. For some curious reason not even that works using nautilus.

Workaround:
So here's not a solution, but a workaround.

I can connect to other computers from the command line as long as I know the IP address, and here's how

smbclient //131.172.123.30/data -U myuni/me

If you actually want to mount the share, which is password protected, and you do, then do

sudo mount -t cifs -o user=me //131.172.123.30/data /media/smbmounts/

where /media/smbmounts belong to you (e.g. sudo mkdir /media/smbmounts && sudo chown $USER /media/smbmounts).

And that's more or less it.

Some additional information:
If you don't get prompted for the password, and get

mount: block device //131.172.123.30/data is write-protected, mounting read-only
mount: cannot mount block device //131.172.123.30/data read-only

but supplying the password as part of the command line works, then you are missing cifs-utils, so install them.

Note that mount.cifs can handle credentials from a special file, e.g. like this , which you chmod to 600. My chief issue with that is that ~/.bash_history has exactly the same permissions (u+rw, go-rwx) and so I don't see how it's that's any safer than exposing everything by supplying your password as part of the mount command. Both should be avoided if possible.

On the other hand you could argue that since the password is transmitted over the network in cleartext you're inviting trouble either way...

480. MS data, part II. Plotting and comparing with predicted isotopic enveloped

NOTE: I've heard rumours about problems with Matt Monroe's calculator on Windows 7 Home, and on Windows 8. I've heard reports of it working on Windows 7 Professional. Given that wsearch also has issues,  this may be linked to VB.

This post is, like this one, is written with two particular students in mind.

MS here stands for Mass Spectrometry.

I'll be presuming that you have exported your data as a csv file as shown in http://verahill.blogspot.com.au/2013/07/474-exporting-data-from-wsearch32-and.html

Our scenario:
So you've exported your data as e.g. data.csv, and you have assigned a signal in your spectrum to a species, and you'd now like to plot the predicted and observed isotopic envelopes in a way that will help you compare them.

The signal we have identified is at 211.90 m/z and we think it belongs to [Ga(CH₃OH)₂(OH)(NO₃)]⁺.

---

The Linux way:
You'll need: sed, gawk, gnuplot, pyisocalc or Matt Monroe's Molecular Weight calculator

1. Generating the isotopic envelope:

A. Using pyisocalc:
Set the charge to 1 and output the data to 1.dat, with a gaussian broadening factor of 0.3:

isocalc -f 'Ga(CH3OH)2(OH)(NO3)' -c 1 -o 1.dat -g 0.3

B. Using Matt Monroe's molecular weight calculator
Go to Tools/Isotopic Distribution Modelling

In the spectrum window, go to Edit, Copy Data Points, and paste into e.g. a Gedit window. Save as 1.dat

2. Formatting the data.csv for gnuplot (can skip for spreadsheet programs):
In a single line we remove the first eight lines, replace all commans (,) with tabs, only keep the m/z and relative isotopic abundance columns (2 an 4) and save the output to data.dat

tail -n +8 data.csv |sed 's/\,/\t/g'|gawk '{print $2,$4}' > data.dat

3. Plotting:

A. Using gnuplot:
Create a file called 1.gplt which contains the gnuplot commands:

set term postscript eps enhanced color
set output '1.eps'
set xrange [206:220]
plot '1.dat' u ($1-0.05):($2*0.092) w lines ti 'Calculated' lc -1 lw 2,\
 'data.dat' u 1:2 w lines ti 'Observed' lc 1 lw 2

($1-0.05) means we're offsetting the calculated data by 0.05 m/z. ($2*0.092) means that we're scaling the calculated data intensity to match that of the observed. lc sets line colour and lw sets the width


If you want the output as png instead of eps, just change the first two lines to

set term png size 1000,667
set output '1.png'

Using pyisocalc

Using Matthew Monroe's calculator

B. Using QtiPlot
Qtiplot is in the debian repos and is 'origin'-like (as in Microcal Origin).

You'll need to rescaled your calculated data first, which is a major drawback:

cat 1.dat|gawk '{print $1-0.05,$2*0.095}'> 1_scaled.dat

Start QtiPlot and select Open. Make sure you select 'all files' as the file type. Open 1_scaled.dat.

Next, make sure that the spreadsheet is active, and go to File, Import, Import Ascii

Change the type of column 3

Select all columns and go to Plot, Line. Change the axes (double click on the axes and set the new ranges), set the top and right axes no to show, edit the titles etc.

---

The Windows way: 
You'll probably need: excel or open/libreoffice, origin, pyisocalc or Matt Monroe's Molecular Weight calculator

Doing this on windows is a PITA compared to Linux, and I don't have the time to go through it. If you do have Origin, it should be straightforward to translate the instructions above into an MS Win-like environment.

Any scaling will have to be done in Excel or a similar spreadsheet program. Not difficult, but it'll add a few extra steps.