322. Libreoffice and zotero for reference management

I'm happy using latex and bibtex whenever possible, and I'm forced to use Microsoft Office and Endnote in most of my collaborations, so I;m not that interested in libreoffice/openoffice.

However, having heard of a reference manager called Zotero has made me curious to learn more.

You can either get it as a plug-in for firefox, or as a stand-alone program which plugs into any browser of your choice.

While I haven't used Endnote seriously for about half a decade and thus may not know about any fancy recently added functionality, I just can't see any reason whatsoever to use Endnote anymore if you have a choice. Obviously, given the inertia of the 'common user' and the tendency for people to equal costly with good and cheap with rubbish, it will probably take a generation or two for change to happen, no matter how good zotero gets.

And here's another thing: when I went to Google Scholar using Chrome, zotero was recognised, and a list of 'updates' was suggested. I wasn't really interested, until I had a look at them -- Scholar had generated a pretty impressive list of articles that it thought might interest me. The match was surprisingly good. If nothing else I'll certainly make sure to keep my zotero database synced with my bibtex one.

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Get it:

sudo apt-get install bzip2
wget http://download.zotero.org/standalone/3.0.11.1/Zotero-3.0.11.1_linux-x86_64.tar.bz2
tar xvf Zotero-3.0.11.1_linux-x86_64.tar.bz2
cd Zotero_linux-x86_64/
./run-zotero.sh

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First time:

First time you run it it opens a browser window as well as an installation process

For some reason I keep getting errors about DBus even though the dbus-daemon is running. It hasn't caused any other problems beyond the error message in the screenshot.

Even the openoffice I installed for testing purposes got detected

And you're done

To make it work in Chrome, install the extension

The main Zotero window, without any references

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Testing:

Importing a bibtex library

Everything looks ok

If you click on the icon by the arrow you can insert a citation. You need to have zotero running in the background though.

Determine what format to use

Generate the bibliography and you're done

Google Scholar, Chrome and Zotero play nicely together

321. Compiling Kernel 3.7.3 (and 3.7.2) on Debian Testing/Wheezy. More data on make -jN.

Updated for 3.7.3

Since post '319. Collection of errors when compiling kernel 3.7.x on AMD FX 8150' is getting traffic from people wanting to compile kernel 3.7.2, and because I didn't know whether the azx_runtime_suspend bug had been fixed, I had to try it out. So here's how to compile kernel 3.7.2 and 3.7.3 -- for 3.7.2 simply replace all instances of 3.7.3..

Looking at the code changes here: http://lists-archives.com/linux-kernel/27763782-alsa-hda-move-runtime-pm-check-to-runtime_idle-callback.html and comparing with what I'm actually seeing in sound/pci/hda/hda_intel.c it seems that 3.7.2 and 3.7.3 have been fixed and no patches need to be applied.

Testing the kernel bears that out.

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Compiling the kernel

sudo apt-get install kernel-package fakeroot build-essential ncurses-bin ncurses-dev
mkdir ~/tmp
cd ~/tmp
wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.7.3.tar.bz2
tar xvf linux-3.7.3.tar.bz2
cd linux-3.7.3/
cat /boot/config-`uname -r`>.config
make oldconfig
make-kpkg clean

If you want to add specific drivers etc to the kernel, run

make menuconfig

Note that if you're transitioning from kernel 3.5 to 3.7 you will needto specifically and explicitly include a lot of the graphics (pci tv cards, usb web cams) drivers that used to be automatically included before. Then continue:

time fakeroot make-kpkg -j6 --initrd kernel_image kernel_headers
sudo dpkg -i ../linux-image-3.7.3_3.7.3-10.00.Custom_amd64.deb ../linux-headers-3.7.3_3.7.3-10.00.Custom_amd64.deb

And you're done. Keep reading to learn more about -j6.

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Optimal -jN
See here for another post on -jN: http://verahill.blogspot.com.au/2013/01/305-make-jn-should-n-equal-number-of.html. In short, it's not always clear whether N should equal the number of cores, or be larger than the number of cores. In that post, N+1 was the optimal configuration, but that was a very short compilation where i/o likely played a large role.

More data is needed, so here it is. Seems like N=number of cores is the best option for long builds (as was pointed out to me in a comment). This was done with kernel 3.7.2.

On a four-core Intel i5-2400 with 16 Gb memory

N    Time
-------------
2    30m 58s
3    22m 36s
4    19m 49s
5    22m  2s
6    23m 13s

Acquired using sar/sysstat

Here's what's happening with -j4:

Basically, the first 15 minutes things are running in parallel, with t i/o slowing things down during the last 5 minutes.

On a six-core AMD Phenom II 1055T with 8 Gb memory

N    Time (s)
-------------
4    34m 16s
5    27m 19s
6    24m 60s
7    30m 18s
8    31m 47s

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Hardware profiles:
Intel machine:

00:00.0 0600: 8086:0100 (rev 09)
00:02.0 0300: 8086:0102 (rev 09)
00:16.0 0780: 8086:1c3a (rev 04)
00:16.3 0700: 8086:1c3d (rev 04)
00:19.0 0200: 8086:1502 (rev 04)
00:1a.0 0c03: 8086:1c2d (rev 04)
00:1b.0 0403: 8086:1c20 (rev 04)
00:1c.0 0604: 8086:1c10 (rev b4)
00:1c.2 0604: 8086:1c14 (rev b4)
00:1d.0 0c03: 8086:1c26 (rev 04)
00:1e.0 0604: 8086:244e (rev a4)
00:1f.0 0601: 8086:1c4e (rev 04)
00:1f.2 0104: 8086:2822 (rev 04)
00:1f.3 0c05: 8086:1c22 (rev 04)

AMD machine:

00:00.0 0600: 1022:9601
00:01.0 0604: 1022:9602
00:07.0 0604: 1022:9607
00:11.0 0106: 1002:4390
00:12.0 0c03: 1002:4397
00:12.1 0c03: 1002:4398
00:12.2 0c03: 1002:4396
00:13.0 0c03: 1002:4397
00:13.1 0c03: 1002:4398
00:13.2 0c03: 1002:4396
00:14.0 0c05: 1002:4385 (rev 3c)
00:14.1 0101: 1002:439c
00:14.2 0403: 1002:4383
00:14.3 0601: 1002:439d
00:14.4 0604: 1002:4384
00:14.5 0c03: 1002:4399
00:18.0 0600: 1022:1200
00:18.1 0600: 1022:1201
00:18.2 0600: 1022:1202
00:18.3 0600: 1022:1203
00:18.4 0600: 1022:1204
01:05.0 0300: 1002:9715
01:05.1 0403: 1002:970f
02:00.0 0200: 10ec:8168 (rev 03)
03:05.0 0200: 10ec:8169 (rev 10

320. Wsearch32 in Wine

Wsearch32 is a windows program that does what it's supposed to -- open mass spectrometer data files. Because our students use it quite a lot and to save me time in training them, here's how to install wsearch32 and how to get started with it. It runs almost perfectly in Wine.

One notable thing about Wsearch is that it opens HP Agilent Chemstation .D files without any problems. It's notable because different versions of HP Agilent Chemstation can't even open files written by other versions (yup, it's true...) of the same damned program.

Another obvious advantage of Wsearch is that it makes it very easy to export data, although it only exports one spectrum at a time (i.e. you can't get the full time-dependent data set).

WSearch was written by Frank Antolasic at the RMIT in Melbourne, Australia.


What doesn't work under Wine: It will freeze if you try to open several files at the same time. This does not happen on native Windows.

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Installation
Download it from here: http://www.wsearch.com.au/

wget http://www.wsearch.com.au/wsearch32/wsearch32.zip
unzip wsearch32.zip

and follow the instructions:

There's nothing odd about the installation process

It works as well as under windows

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Screenshots

This is the default view

Click on the import icon (the red one in the left corner), and select your file. There are plenty of supported formats.

This is the TIC view. Click anywhere on the TIC to get the corresponding spectrum

TIC and spectrum view.

Click on the M/I icon on the right to get a list of all the data in the spectrum plot..

You can then save the spectrum in a range of ascii based formats.

You can get the acquisition headers under Chromatogram/List header info. You can also make ion plots  in the same menu.

Wsearch also comes with a simple isotopic pattern calculator.

The Help works fine under linux/wine

This is the free version of wsearch -- there is some functionality missing.