327. Installing Octave, Gnuplot, maxima etc on OSX 10.8.2 via macports

Update 7 Feb 2013: Got my hand on a Mac again and sorted out the octave forge packages.

NOTE: while on the surface this has little to do with linux, it IS in our interest to get people on other platforms to use the same tools we do. Or at least compatible ones. So knowing about macports will help even the most die-hard linux user. In fact, it will help especially those.

---

I'm no friend of Apple, Mac or OS X for many reasons (restrictive environment, weird mouse, their typical target audience), but pragmatism will make you happier than zealotry. What doesn't work for me obviously works for other people.

Students (and professors) at Australian universities do use apple laptops in significant number though (yet our ERP system only works properly with Internet Explorer -- try requesting leave using chrome on linux and you may be in for a surprise) so I've recently been faced with the issue of installing my standard linux tools on students' apple laptops. In fact it's gotten so bad that several Australian universities 'give' ipads to all their students for 'free' (nothing is free when you're paying for it through your tuition). As someone working at a uni I resent this since, by using the one platform where you can't install what you want on it, this puts pressure on me to restrict my teaching to what can be had via the almighty app store. (there's a lot of BS about blended learning, and you'd be lucky to find a white board anywhere. Blackboards are completely gone which is idiocy of the first degree)

Anyway. There's plenty of people here using Macbook-thingies and it's in my own interest to get them on the narrow path to justice, liberty and the FOSS way.

Macports is a really cool package manager/repository for linux software for Mac OSX and works by compiling the software from the sources -- pretty much how I imagine that the Gentoo experience may be like. Anyway, it works fine although it takes a fair amount of time to install things.

---

So here's how to do it (no screenshots because I'm typing this from memory):

1. Open the App Store and install XCode (free)
2. Open Xcode, go to Preferences/Download, and install Command Line Tools
3. Download macports via this link for OS X 10.8: https://distfiles.macports.org/MacPorts/MacPorts-2.1.2-10.8-MountainLion.pkg
   Other versions of OS X are also supported, see here: http://www.macports.org/install.php
4. Install the downloaded macports by opening the .pkg file
5. Open a Terminal window  (Applications/Utilities/Terminal) and run

sudo port -v selfupdate

6. Run

sudo port install gnuplot maxima vim nano xterm

which will take a while -- it needs to set up the build environment from scratch in addition to regular dependencies. Set aside an hour or so just in case. If there's an error, try running the command once more.


7. Run

sudo port install octave-devel qtoctave-mac

which will take a long while. If the compile seems to have stopped, checked the titlebar of the terminal window -- the command it's executing will continously change during the compile)


8. Run octave by running the command

   octave

   in the terminal.
9. To install octave packages you can install them in the Octave environment :

   pkg install -forge miscellaneous struct general optim

10. addpath
In case you're having problems actually using the octave-forge packages, you might need to create/edit your ~/.octaverc along the lines of

addpath('/Users/verahill/octave/optim-1.2.2')

Replace verahill with the proper user name, and edit the version number as needed.


11. X11/Xquartz - setting DISPLAY
At this point

echo $DISPLAY

gave nothing, and trying to launch an X11 program (e.g. xterm) complained that DISPLAY was not set. Setting DISPLAY manually (export DISPLAY=:0.0) didn't help either.

'Bad' solution: the first solution was to install xorg-server (sudo port install xorg-server), and then manually

X &
export DISPLAY=:0.0

or

Xquartz &
export DISPLAY=:0.0

Both X and Xquartz come from macports.

Good solution
I then tried to change tack and went to http://xquartz.macosforge.org/landing/ and downloaded XQuartz-2.7.4.dmg (I was originally under the impression that it came as default with "mountain lion" but no.).
Open the file, then run the .pkg file in that archive. Log out of OSX, then log in again. Now try launching e.g. xterm form a terminal and it should work.

---

The entire process will take well over an hour, but at the end of it you'll have Octave, Gnuplot AND a complete build environment!

And there are plenty more things you can install with macports (e.g. qtoctave (qtoctave-mac), gedit (gedit gedit-plugins), kile, maxima, qtiplot).

Not sure why I am so excited over it since all these things are available in most linux repos, but there you go -- compiling stuff is ALWAYS exciting.

326. Compiling Thunderbird 17.0.2 on Debian Testing

I tested this compile in a bare chroot, so the dependencies should be pretty much hammered out. The build is easy but fairly slow.

sudo apt-get install bzip2 build-essential python zip libgtk2.0-dev libdbus-glib-1-dev libasound2-dev libogg-dev libxt-dev yasm libcurl4-openssl-dev mesa-common-dev
mkdir ~/tmp
cd ~/tmp
wget ftp://ftp.mozilla.org/pub/mozilla.org/thunderbird/releases/17.0.2/source/thunderbird-17.0.2.source.tar.bz2
rm -rf comm-release/
tar xvf thunderbird-17.0.2.source.tar.bz2
mkdir bldthunder17
cd bldthunder17/
../comm-release/./configure --disable-necko-wifi
make
sudo make install

That took 122 minutes on a single core.
Checkinstall doesn't work and ends with segfault.

325. Compiling ECCE 6.4 on Debian Testing

!NOTE! If you provide ECCE with 'localhost' as the hostname, be aware that this will block outside access: http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id858/#post_3178

There's a new release of ECCE 6.4 out which fixes the following bug: http://verahill.blogspot.com.au/2012/11/minor-bug-in-ecce.html

---

A note on Java: I've only had luck with the openjdk packages -- not with the Oracle/sun java ones (see here: http://verahill.blogspot.com.au/2012/06/building-ecce-on-debian-testingwheezy.html).

This build was tested in a chrooted Testing/Wheezy i.e. I should've caught most of the necessary packages.

---

Compiling:
Download the source to ecce from http://ecce.emsl.pnl.gov/using/download.shtml, and put it in e.g. ~/tmp

sudo apt-get install bzip2 build-essential autoconf libtool ant pkg-config gtk+-2.0-dev libxt-dev csh gfortran openjdk-7-jdk python-dev libjpeg-dev imagemagick xterm
cd ~/tmp
tar xvf ecce-v6.4-src.tar.bz2
cd ecce-v6.4/
export ECCE_HOME=`pwd`
cd build/
./build_ecce

Hit return if xterm was found... 
The /home/sandbox/tmp/ecce-v6.4/scripts/sysdir script identifies the build
platform directory as: empty
Because this value is empty no platform-specific parent
directory will be created for ECCE executables, libraries, etc.
This works fine unless your site needs support for multiple platforms.
Finished checking prerequisites for building ECCE.
Do you want to skip these checks for future build_ecce invocations (y/n)? Y

./build_ecce

Xerces built
./build_ecce

Mesa OpenGL built

./build_ecce

wxWidgets built

./build_ecce

running build_ext
wxPython built

./build_ecce

Apache HTTP server built

./build_ecce

Making combined tar file ecce.v6.4.tar
Copying NWChem binary distribution nwchem-6.1.1-binary-rhel5-gcc4.1.2-m64.tar.bz2
Copying NWChem common distribution nwchem-6.1.1-binary-common.tar.bz2
Concatenating install script and combined tar file ecce.v6.4.tar
create_ecce_bin finished

ECCE built and distribution created in /home/sandbox/tmp/ecce-v6.4

cd ../
./install_ecce.v6.4.csh

And see the next section for the installation steps.
The compilation steps take progressively longer and longer, so be patient during the build.

---

Installing:
Digital ink is cheap, so I'll show the whole process:

./install_ecce.v6.4.csh

Main ECCE installation menu
===========================
1) Help on main menu options
2) Prerequisite software check
3) Full install
4) Full upgrade
5) Application software install
6) Application software upgrade
7) Server install
8) Server upgrade

IMPORTANT: If you are uncertain about any aspect of installing
or running ECCE at your site, please refer to the detailed
ECCE Installation and Administration Guide at 
http://ecce.pnl.gov/docs/installation/2864B-Installation.pdf

Hit  at prompts to accept the default value in brackets.

Selection: [1] 3
Host name: [beryllium] localhost
Application installation directory: [/home/sandbox/tmp/ecce-v6.4/ecce-v6.4/apps] /home/sandbox/.ecce/apps
Server installation directory: [/home/sandbox/.ecce/server]
ECCE v6.4 will be installed using the settings:

  Installation type: [full install]
  Host name: [localhost]
  Application installation directory: [/home/sandbox/.ecce/apps]
  Server installation directory: [/home/sandbox/.ecce/server]

Are these choices correct (yes/no/quit)? [yes] 

Installing ECCE application software in /home/sandbox/.ecce/apps...
  Extracting application distribution...
  Extracting NWChem binary distribution...
  Extracting NWChem common distribution...
  Extracting client WebHelp distribution...
  Configuring application software...
  Configuring NWChem...

Installing ECCE server in /home/sandbox/.ecce/server...
  Extracting data server in /home/sandbox/.ecce/server/httpd...
  Extracting data libraries in /home/sandbox/.ecce/server/data...
  Extracting Java Messaging Server in /home/sandbox/.ecce/server/activemq...
  Configuring ECCE server...

ECCE installation succeeded.

***************************************************************
!! You MUST perform the following steps in order to use ECCE !!
-- Unless only the user 'sandbox' will be running ECCE,
   start the ECCE server as 'sandbox' with:
     /home/sandbox/.ecce/server/ecce-admin/start_ecce_server

-- To register machines to run computational codes, please see
   the installation and compute resource registration manuals
   at http://ecce.pnl.gov/using/installguide.shtml

-- Before running ECCE each user must source an environment
   setup script.  For csh/tcsh users add this to ~/.cshrc:
     if ( -e /home/sandbox/.ecce/apps/scripts/runtime_setup ) then
       source /home/sandbox/.ecce/apps/scripts/runtime_setup
     endif
   For sh/bash users, add this to ~/.profile or ~/.bashrc:
     if [ -e /home/sandbox/.ecce/apps/scripts/runtime_setup.sh ]; then
       . /home/sandbox/.ecce/apps/scripts/runtime_setup.sh
     fi
***************************************************************

Instead of following the instructions above I normally do:

echo 'export ECCE_HOME=/home/sandbox/.ecce/apps' >> ~/.bashrc
echo 'PATH=$PATH:/home/sandbox/.ecce/server/ecce-admin/:/home/sandbox/.ecce/apps/scripts/' >> ~/.bashrc
echo 
source ~/.bashrc

You can now start ecce by either doing

ecce

or if that complains, do

start_ecce_server

then waiting a little while (10 s), followed by

ecce

---

Apppendix:

Selecting Java 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

I've got ECCE running fine with openjdk 7 as well as openjdk 6.

324. Setting up a private git server

Update 11 Feb 2013: fixed a typo that ruined everything.

I've recently moved one of my more mature projects to sourceforge.net, which allowed me to re-discover the joys of using a version management system, in this case git. While I've spent some time playing with SVN in the past, git feels more natural to me. That's it's used widely in the FOSS community certainly doesn't hurt either.

So that got me interested in setting up a local git server for projects that may or may not result in anything tangible i.e. projects that I don't want to put online, but are under so much flux that they may break anytime (and I thus want to be able to roll back).

[A pointer to my students: you can obviously use git to maintain versions of your .tex documents as well...]

In this particular case the development machine and the git host are the same. The project is called shellnmr (an attempt to make a bash-like shell in python for NMR processing)

This is very much inspired by/stolen from: http://tumblr.intranation.com/post/766290565/how-set-up-your-own-private-git-server-linux

---

Getting set up:

On the git host (which has not yet got a copy of the source code)

sudo apt-get install git
mkdir ~/work/programming/var -p
cd ~/work/programming/var
mkdir shellnmr
cd shellnmr/
git init --bare

Initialized empty Git repository in /home/me/work/programming/var/shellnmr

First time:
I''ll use localhost below because in this particular example the git host and the development machine is the same.

On the/a development machine, where we keep the already existing project in ~/work/shellnmr

cd ~/work/shellnmr
git init

Initialized empty Git repository in /home/me/work/shellnmr/.git/

git add .
git commit -m 'initial commit'

[master (root-commit) 5214860] initial commit
 2 files changed, 178967 insertions(+)
 create mode 100644 functions.py
 create mode 100755 main.py

git remote rm origin
git remote add origin me@localhost:/home/me/work/programming/var/shellnmr
git push origin master

Counting objects: 2, done.
Delta compression using up to 3 threads.
Compressing objects: 100% (18/18), done.
Writing objects: 100% (2/2), 339.14 KiB, done.
Total 2 (delta 5), reused 0 (delta 0)
To me@localhost:/home/me/work/programming/var/shellnmr
 * [new branch]      master -> master

---

Everyday usage:

Say you've edited the code on your development machine and want to commit the changes:

git commit -a
git push

Easy.

Let's say you go home and want to continue editing the code there and that this is the first time you're doing so:

git clone user@githost:/home/me/work/programming/var/nmrshell nmrshell-code

When you're done editing, just commit as normal;

git commit -a
git push

Let's say you've edited the code on another computer, committed the code, and then want to get the latest updates on your regular development machine again:

git pull origin master

And that's about it.

---

GUI - gitk:
The debian repos have a git GUI as well. To install do

sudo apt-get install git-gui gitk

Start it by launching gitk from the directory where you keep your files (on the development machine)

323. Wine 1.5.22 on Debian Testing/Wheezy. Compiling using multiarch

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

Another update: It seems like your mileage in terms of how well Wine will work for you will vary using this method. It works fine for me and I suspect it's because I've built earlier Wine versions of my systems and have ia32-libs-dev installed. This package is no longer available in Testing. ia32-libs installs the libs you need, but does not provide symlinks between .so and .so.X files -- you can probably do that by hand if necessary though. It's not for beginners.

An additional thing to remember is that the 1.5 series of Wine is a development series -- 1.4 is the stable series which is meant for end users. Progress made in 1.5 will be included in 1.6.

NOTE: there are a couple of issues, and they will depend on how your system is set up.
* libosmesa6-dev:i386 will require mesa-common-dev:i386 which will remove libosmesa6-dev:amd64 and more, which is bad.
* libglu1-mesa-dev:i386 depends on libgl1-mesa-dev:i386 which will remove libgl1-mesa-dev:amd64 and more, which is bad.
*  libgstreamer-plugins-base0.10-dev:i386 depends on libgstreamer0.10-dev:i386 which depends on gir1.2-gstreamer-0.10:i386 which depends on gir1.2-freedesktop:i386 which depends on gir1.2-glib-2.0:i386 which depends on libgirepository-1.0-1:i386 which will remove a whole lot of packages (132 on one of my systems, including gnome, gdm3 etc.)

I'm working on figuring out what's triggering this on some systems but not others.
In the mean time see http://verahill.blogspot.com.au/2013/01/308-compiling-wine-1521-on-debian.html to see how to build wine in a chroot, which is safe. You can then install that .deb package on your normal system and HOPEFULLY there won't be any broken dependencies. You won't need the -dev:i386 packages on the install target.

ldd `which wine` 

linux-gate.so.1 =>  (0x55573000)
 libwine.so.1 => /usr/local/lib/libwine.so.1 (0x55576000)
 libpthread.so.0 => /lib32/libpthread.so.0 (0x556ec000)
 libc.so.6 => /lib32/libc.so.6 (0x55705000)
 libdl.so.2 => /lib32/libdl.so.2 (0x55867000)

so you really don't seem to need much in the way of shared libs installed.

---

A new incremental version of wine is out.

There's little difference between building 1.5.21 and 1.5.22 but here it is anyway. The build is very easy on an up-to-date installation of Testing/Wheezy. If you are on stable, the list over needed packages can be found in this post.

See here for recent changes between different Wine versions: http://linux.softpedia.com/progChangelog/Wine-Changelog-148.html

Compiling

sudo dpkg --add-architecture i386
sudo apt-get update

sudo apt-get install libx11-dev:i386 libfreetype6-dev:i386 libxcursor-dev:i386 libxi-dev:i386 libxxf86vm-dev:i386 libxrandr-dev:i386 libxinerama-dev:i386 libxcomposite-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libdbus-1-dev:i386 libgnutls-dev:i386 libncurses-dev:i386 libsane-dev:i386 libv4l-dev:i386 libgphoto2-2-dev:i386 liblcms-dev:i386 libgstreamer-plugins-base0.10-dev:i386 libcapi20-dev:i386 libcups2-dev:i386 libfontconfig-dev:i386 libgsm1-dev:i386 libtiff-dev:i386 libpng-dev:i386 libjpeg-dev:i386 libmpg123-dev:i386 libopenal-dev:i386 libldap-dev:i386 libxrender-dev:i386 libxml2-dev:i386 libxslt-dev:i386 libhal-dev:i386 libcurl4-openssl-dev:i386 gettext prelink bzip2 bison flex oss4-dev checkinstall ocl-icd-libopencl1:i386 opencl-headers gcc-multilib

mkdir ~/tmp
cd ~/tmp
wget http://prdownloads.sourceforge.net/wine/wine-1.5.22.tar.bz2
tar xvf wine-1.5.22.tar.bz2
cd wine-1.5.22/
./configure

config.status: executing include/wine commands
config.status: executing Makefile commands


configure: Finished.  Do 'make' to compile Wine.

time make -j4
sudo checkinstall --install=no

*****************************************
**** Debian package creation selected ***
*****************************************

This package will be built according to these values: 

0 -  Maintainer: [ root@lithium ]
1 -  Summary: [ wine 1.5.22 ]
2 -  Name:    [ wine ]
3 -  Version: [ 1.5.22 ]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ amd64 ]
8 -  Source location: [ wine-1.5.22 ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ wine ]
12 - Conflicts: [  ]
13 - Replaces: [  ]
[..]
Copying files to the temporary directory...

sudo dpkg -i wine_1.5.22-1_amd64.deb

where 4 is the number of cores on your build machine (see here and here for -jN). The build took 13 minutes on a three-core AMD Athlon II X3 445 (3.1 GHz) with -j4. The 'Copying files to...' can take quite a while, so let it run to completion.

Anyway, that's it. An easy build.

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.

---

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

---

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

---

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.

---

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.

---

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

---

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.

---

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

---

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.

319. Collection of errors when compiling kernel 3.7.x on AMD FX 8150

Update 20th Feb 2013:  Kernel 3.8 compiles fine on AMD FX 8150. Just ignore kernel 3.7.

Original post:

This is a collection of errors
(although you can obviously compile the kernel this way -- just not on AMD FX 8150...)

It does not hold any solutions

See here for how to compile kernel 3.7.0 to 3.7.1:
http://verahill.blogspot.com.au/2012/12/compiling-kernel-37-on-debian.html
and here for how to patch 3.7.1
http://verahill.blogspot.com.au/2012/12/patching-kernel-371-to-fix.html

See here for how to compile 3.7.2 and 3.7.3:
http://verahill.blogspot.com.au/2013/01/321-compiling-kernel-372-on-debian.html

Post continues:
Normally this wouldn't merit its own post, but because I've been annoyed over the inability to compile
kernels on my AMD FX 8150 I decided to collect as much data on the errors as possible.

Basically, kernel 3.7.x fails to build on AMD FX 8150, while kernels 3.6.3 and 3.5 build just fine.
Here's the lspci -n hardware profile for my system, although I'm fairly certain it's due to AMD FX 8150:

00:00.0 0600: 1002:5a14 (rev 02)
00:04.0 0604: 1002:5a18
00:09.0 0604: 1002:5a1c
00:11.0 0106: 1002:4390 (rev 40)
00:12.0 0c03: 1002:4397
00:12.2 0c03: 1002:4396
00:13.0 0c03: 1002:4397
00:13.2 0c03: 1002:4396
00:14.0 0c05: 1002:4385 (rev 42)
00:14.1 0101: 1002:439c (rev 40)
00:14.2 0403: 1002:4383 (rev 40)
00:14.3 0601: 1002:439d (rev 40)
00:14.4 0604: 1002:4384 (rev 40)
00:14.5 0c03: 1002:4399
00:15.0 0604: 1002:43a0
00:15.1 0604: 1002:43a1
00:15.2 0604: 1002:43a2
00:15.3 0604: 1002:43a3
00:16.0 0c03: 1002:4397
00:16.2 0c03: 1002:4396
00:18.0 0600: 1022:1600
00:18.1 0600: 1022:1601
00:18.2 0600: 1022:1602
00:18.3 0600: 1022:1603
00:18.4 0600: 1022:1604
00:18.5 0600: 1022:1605
01:00.0 0300: 10de:0a65 (rev a2)
01:00.1 0403: 10de:0be3 (rev a1)
02:00.0 0c03: 1b6f:7023 (rev 01)
03:06.0 0200: 10ec:8169 (rev 10)
04:00.0 0200: 10ec:8168 (rev 06)

The lower number of errors for kernel 3.7 below is because I did -j1 (so fewer threads to finish), not because it's any better.

Compilation (-O1 example)

mkdir ~/tmp
cd ~/tmp
wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.7.2.tar.bz2
tar xvf linux-3.7.2.tar.bz2
cd linux-3.7.2/
cat /boot/config-`uname -r`>.config
make oldconfig
make-kpkg clean

find -name Makefile|xargs -I {} sed -i 's/\-O2/\-O1/g' {}
time fakeroot make-kpkg -j9 --initrd kernel_image kernel_headers

Errors:

---

-O2 on kernel 3.7.2 with AMD FX 8150:

net/mac80211/mesh_hwmp.c:1224:1: internal compiler error: in dwarf2out_finish, at dwarf2out.c:22603
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[3]: *** [net/mac80211/mesh_hwmp.o] Error 1
make[2]: *** [net/mac80211] Error 2
make[2]: *** Waiting for unfinished jobs....
net/netfilter/xt_esp.c:94:1: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[3]: *** [net/netfilter/xt_esp.o] Error 1
make[2]: *** [net/netfilter] Error 2
make[1]: *** [net] Error 2
make[1]: *** Waiting for unfinished jobs....
/home/me/tmp/linux-3.7.2/arch/x86/include/asm/msr-index.h:1:0: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[6]: *** [drivers/net/wireless/ath/ath9k/ar5008_phy.o] Error 1
make[6]: *** Waiting for unfinished jobs....
make[5]: *** [drivers/net/wireless/ath/ath9k] Error 2
make[4]: *** [drivers/net/wireless/ath] Error 2
make[3]: *** [drivers/net/wireless] Error 2
make[3]: *** Waiting for unfinished jobs....
/home/me/tmp/linux-3.7.2/arch/x86/include/asm/elf.h:78:1: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[4]: *** [drivers/tty/ipwireless/main.o] Error 1
make[3]: *** [drivers/tty/ipwireless] Error 2
make[3]: *** Waiting for unfinished jobs....
drivers/tty/serial/jsm/jsm_neo.c: In function 'neo_intr':
drivers/tty/serial/jsm/jsm_neo.c:1244:1: internal compiler error: Aborted
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[5]: *** [drivers/tty/serial/jsm/jsm_neo.o] Error 1
make[4]: *** [drivers/tty/serial/jsm] Error 2
make[3]: *** [drivers/tty/serial] Error 2
make[2]: *** [drivers/tty] Error 2
make[2]: *** Waiting for unfinished jobs....
drivers/staging/silicom/bp_proc.c:74:31: warning: 'bp_procfs_dir' defined but not used [-Wunused-variable]
drivers/staging/silicom/bp_proc.c:76:31: warning: 'proc_getdir' defined but not used [-Wunused-function]
{standard input}: Assembler messages:
{standard input}:37643: Error: can't resolve `.LVL231' {*UND* section} - `.Ltext0' {.text section}
{standard input}:37739: Error: can't resolve `.LVL231' {*UND* section} - `.Ltext0' {.text section}
{standard input}:37743: Error: can't resolve `.LVL231' {*UND* section} - `.Ltext0' {.text section}
{standard input}:37783: Error: can't resolve `.LVL231' {*UND* section} - `.Ltext0' {.text section}
make[4]: *** [drivers/staging/speakup/kobjects.o] Error 1
make[3]: *** [drivers/staging/speakup] Error 2
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [drivers/staging] Error 2
make[2]: *** [drivers/net] Error 2
In file included from include/linux/genhd.h:65:0,
                 from include/linux/blkdev.h:9,
                 from include/scsi/scsi_cmnd.h:5,
                 from drivers/scsi/sym53c8xx_2/sym_glue.h:58,
                 from drivers/scsi/sym53c8xx_2/sym_hipd.c:44:
include/linux/fs.h:1550:49: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[4]: *** [drivers/scsi/sym53c8xx_2/sym_hipd.o] Error 1
make[3]: *** [drivers/scsi/sym53c8xx_2] Error 2
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [drivers/scsi] Error 2
make[1]: *** [drivers] Error 2
make: *** [debian/stamp/build/kernel] Error 2

and finally

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)[0x2b377411eead]
/usr/lib/gcc/x86_64-linux-gnu/4.7/cc1[0x4d2f51]
======= Memory map: ========
00400000-00fd3000 r-xp 00000000 08:01 1312897                            /usr/lib/gcc/x86_64-linux-gnu/4.7/cc1
011d2000-011dd000 rw-p 00bd2000 08:01 1312897                            /usr/lib/gcc/x86_64-linux-gnu/4.7/cc1
011dd000-0133c000 rw-p 00000000 00:00 0
01df7000-020b7000 rw-p 00000000 00:00 0                                  [heap]
2b3772f20000-2b3772f40000 r-xp 00000000 08:01 11800025                   /lib/x86_64-linux-gnu/ld-2.13.so
2b3772f40000-2b3772f42000 rw-p 00000000 00:00 0
2b377313f000-2b3773140000 r--p 0001f000 08:01 11800025                   /lib/x86_64-linux-gnu/ld-2.13.so
2b3773140000-2b3773141000 rw-p 00020000 08:01 11800025                   /lib/x86_64-linux-gnu/ld-2.13.so
2b3773141000-2b3773142000 rw-p 00000000 00:00 0
2b3773148000-2b3773151000 r-xp 00000000 08:01 2233201                    /usr/lib/x86_64-linux-gnu/libfakeroot/libfakeroot-sysv.so
2b3773151000-2b3773351000 ---p 00009000 08:01 2233201                    /usr/lib/x86_64-linux-gnu/libfakeroot/libfakeroot-sysv.so
2b3773351000-2b3773352000 rw-p 00009000 08:01 2233201                    /usr/lib/x86_64-linux-gnu/libfakeroot/libfakeroot-sysv.so
2b377336b000-2b377336c000 rw-p 00000000 00:00 0
2b3773370000-2b3773384000 r-xp 00000000 08:01 1321607                    /usr/lib/x86_64-linux-gnu/libmpc.so.2.0.0
2b3773384000-2b3773584000 ---p 00014000 08:01 1321607                    /usr/lib/x86_64-linux-gnu/libmpc.so.2.0.0
2b3773584000-2b3773585000 rw-p 00014000 08:01 1321607                    /usr/lib/x86_64-linux-gnu/libmpc.so.2.0.0
2b3773588000-2b37735e3000 r-xp 00000000 08:01 1321605                    /usr/lib/x86_64-linux-gnu/libmpfr.so.4.1.0
2b37735e3000-2b37737e3000 ---p 0005b000 08:01 1321605                    /usr/lib/x86_64-linux-gnu/libmpfr.so.4.1.0
2b37737e3000-2b37737e5000 rw-p 0005b000 08:01 1321605                    /usr/lib/x86_64-linux-gnu/libmpfr.so.4.1.0
2b37737e8000-2b377384f000 r-xp 00000000 08:01 1321603                    /usr/lib/x86_64-linux-gnu/libgmp.so.10.0.5
2b377384f000-2b3773a4f000 ---p 00067000 08:01 1321603                    /usr/lib/x86_64-linux-gnu/libgmp.so.10.0.5
2b3773a4f000-2b3773a57000 rw-p 00067000 08:01 1321603                    /usr/lib/x86_64-linux-gnu/libgmp.so.10.0.5
2b3773a57000-2b3773a58000 rw-p 00000000 00:00 0
2b3773a58000-2b3773a5a000 r-xp 00000000 08:01 11800014                   /lib/x86_64-linux-gnu/libdl-2.13.so
2b3773a5a000-2b3773c5a000 ---p 00002000 08:01 11800014                   /lib/x86_64-linux-gnu/libdl-2.13.so
2b3773c5a000-2b3773c5b000 r--p 00002000 08:01 11800014                   /lib/x86_64-linux-gnu/libdl-2.13.so
2b3773c5b000-2b3773c5c000 rw-p 00003000 08:01 11800014                   /lib/x86_64-linux-gnu/libdl-2.13.so
2b3773c60000-2b3773c76000 r-xp 00000000 08:01 11796562                   /lib/x86_64-linux-gnu/libz.so.1.2.7
2b3773c76000-2b3773e75000 ---p 00016000 08:01 11796562                   /lib/x86_64-linux-gnu/libz.so.1.2.7
2b3773e75000-2b3773e76000 r--p 00015000 08:01 11796562                   /lib/x86_64-linux-gnu/libz.so.1.2.7
2b3773e76000-2b3773e77000 rw-p 00016000 08:01 11796562                   /lib/x86_64-linux-gnu/libz.so.1.2.7
2b3773e78000-2b3773ef9000 r-xp 00000000 08:01 11800003                   /lib/x86_64-linux-gnu/libm-2.13.so
2b3773ef9000-2b37740f8000 ---p 00081000 08:01 11800003                   /lib/x86_64-linux-gnu/libm-2.13.so
2b37740f8000-2b37740f9000 r--p 00080000 08:01 11800003                   /lib/x86_64-linux-gnu/libm-2.13.so
2b37740f9000-2b37740fa000 rw-p 00081000 08:01 11800003                   /lib/x86_64-linux-gnu/libm-2.13.so
2b37740fa000-2b37740fb000 rw-p 00000000 00:00 0
2b3774100000-2b3774280000 r-xp 00000000 08:01 11796538                   /lib/x86_64-linux-gnu/libc-2.13.so
2b3774280000-2b3774480000 ---p 00180000 08:01 11796538                   /lib/x86_64-linux-gnu/libc-2.13.so
2b3774480000-2b3774484000 r--p 00180000 08:01 11796538                   /lib/x86_64-linux-gnu/libc-2.13.so
2b3774484000-2b3774485000 rw-p 00184000 08:01 11796538                   /lib/x86_64-linux-gnu/libc-2.13.so
2b3774485000-2b377448d000 rw-p 00000000 00:00 0
2b3774490000-2b3774681000 r--p 00000000 08:01 1310939                    /usr/lib/locale/locale-archive
2b3774681000-2b377469e000 rw-p 00000000 00:00 0
2b37746a3000-2b37750d8000 rw-p 00000000 00:00 0
2b3775119000-2b3776444000 rw-p 00000000 00:00 0
2b3776460000-2b3776475000 r-xp 00000000 08:01 11796737                   /lib/x86_64-linux-gnu/libgcc_s.so.1
2b3776475000-2b3776675000 ---p 00015000 08:01 11796737                   /lib/x86_64-linux-gnu/libgcc_s.so.1
2b3776675000-2b3776676000 rw-p 00015000 08:01 11796737                   /lib/x86_64-linux-gnu/libgcc_s.so.1
2b3778000000-2b3778021000 rw-p 00000000 00:00 0
2b3778021000-2b377c000000 ---p 00000000 00:00 0
7ffffd08f000-7ffffd0b2000 rw-p 00000000 00:00 0                          [stack]
7ffffd200000-7ffffd201000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

---

-O1; kernel 3.7.2; AMD FX 8150

fs/ecryptfs/keystore.c:1168:28: warning: 'payload_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
sound/pci/hda/patch_cmedia.c:777:1: internal compiler error: in size_of_die, at dwarf2out.c:7795
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[4]: *** [sound/pci/hda/patch_cmedia.o] Error 1
make[3]: *** [sound/pci/hda] Error 2
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [sound/pci] Error 2
make[1]: *** [sound] Error 2
make[1]: *** Waiting for unfinished jobs....
In file included from drivers/mtd/chips/cfi_cmdset_0001.c:35:0:
drivers/mtd/chips/cfi_cmdset_0001.c: In function 'cfi_intelext_write_words':
include/linux/mtd/map.h:331:11: warning: 'r.x[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
drivers/media/usb/gspca/topro.c:4968:1: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[5]: *** [drivers/media/usb/gspca/topro.o] Error 1
make[4]: *** [drivers/media/usb/gspca] Error 2
make[3]: *** [drivers/media/usb] Error 2
make[3]: *** Waiting for unfinished jobs....
drivers/net/ethernet/amd/nmclan_cs.c: In function 'nmclan_config':
drivers/net/ethernet/amd/nmclan_cs.c:625:3: warning: 'pcmcia_request_exclusive_irq' is deprecated (declared at include/pcmcia/ds.h:201) [-Wdeprecated-declarations]
make[2]: *** [drivers/media] Error 2
make[2]: *** Waiting for unfinished jobs....
drivers/net/ethernet/intel/ixgb/ixgb_ee.c:604:1: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[6]: *** [drivers/net/ethernet/intel/ixgb/ixgb_ee.o] Error 1
make[6]: *** Waiting for unfinished jobs....
make[5]: *** [drivers/net/ethernet/intel/ixgb] Error 2
make[4]: *** [drivers/net/ethernet/intel] Error 2
make[3]: *** [drivers/net/ethernet] Error 2
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [drivers/net] Error 2
make[1]: *** [drivers] Error 2
make: *** [debian/stamp/build/kernel] Error 2

-O0, kernel 3.7.2, AMD FX 8150

exec make kpkg_version=12.036+nmu3 -f /usr/share/kernel-package/ruleset/minimal.mk debian INITRD=YES 
exec debian/rules  INITRD=YES  kernel_image kernel_headers 
Setup is 16988 bytes (padded to 17408 bytes).
System is 2884 kB
CRC f8376713
drivers/isdn/hardware/eicon/divasi.c:577:1: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[5]: *** [drivers/isdn/hardware/eicon/divasi.o] Error 1
make[4]: *** [drivers/isdn/hardware/eicon] Error 2
make[4]: *** Waiting for unfinished jobs....
make[3]: *** [drivers/isdn/hardware] Error 2
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [drivers/isdn] Error 2
make[2]: *** Waiting for unfinished jobs....
fs/reiserfs/bitmap.c: In function 'scan_bitmap_block.constprop.9':
fs/reiserfs/bitmap.c:236:9: warning: 'next' may be used uninitialized in this function [-Wmaybe-uninitialized]
make[1]: *** [drivers] Error 2
make[1]: *** Waiting for unfinished jobs....
make: *** [debian/stamp/build/kernel] Error 2

---

Error messages when compiling kernel 3.7 on AMD FX 8150 with -O2 or -O1

exec make kpkg_version=12.036+nmu3 -f /usr/share/kernel-package/ruleset/minimal.mk debian INITRD=YES 
exec debian/rules  INITRD=YES  kernel_image kernel_headers 
net/xfrm/xfrm_sysctl.c:75:1: internal compiler error: in pop_scope, at c-decl.c:1244
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[3]: *** [net/xfrm/xfrm_sysctl.o] Error 1
make[2]: *** [net/xfrm] Error 2
make[1]: *** [net] Error 2
make: *** [debian/stamp/build/kernel] Error 2

---

Kernel 3.7 with -O0 on AMD FX 8150

exec make kpkg_version=12.036+nmu3 -f /usr/share/kernel-package/ruleset/minimal.mk debian INITRD=YES 
exec debian/rules  INITRD=YES  kernel_image kernel_headers 
In file included from include/acpi/platform/aclinux.h:59:0,
                 from include/acpi/platform/acenv.h:141,
                 from include/acpi/acpi.h:56,
                 from drivers/acpi/acpica/exmisc.c:45:
include/linux/sched.h:1352:9: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
The bug is not reproducible, so it is likely a hardware or OS problem.
make[4]: *** [drivers/acpi/acpica/exmisc.o] Error 1
make[3]: *** [drivers/acpi/acpica] Error 2
make[2]: *** [drivers/acpi] Error 2
make[1]: *** [drivers] Error 2
make: *** [debian/stamp/build/kernel] Error 2

318. qmol 0.3.2: A molecular weight calculator for Linux

Over a year ago I complained about the lack of a decent molecular weight calculator in linux in general, and in Debian Testing in particular.  I eventually managed to hack together a molecular weight calculator in Python as part of an isotopic pattern calculator in Python.

However, interpreted languages like python tend to be a bit slower than compiled languages (generally not critical for a molecular weight calculator, but could be for an isotopic pattern calculator), and, perhaps more importantly, my scripts don't feature a GUI.

I vaguely remember trying to compile Kmol by Tomislav Gountchev over a year ago, and as far as I can recall it wasn't working out since it depended on packages (kde-3) that were too old.

But things are changing.

Thomas Mitterfellner has revived Kmol in the form of qmol. Since it's very recent (version 0.1 was created in November 2012, and we're now at version 0.3.2) it's not found in the Debian repos, and maybe won't for some time given that Debian Testing/Wheezy is frozen.

There are, however, a pre-built .deb file for debian squeeze/stable (and Suse, Ubuntu, Fedora etc.) -- so if you're on stable you do not have to compile. Instead go here: http://download.opensuse.org/repositories/home:/lineinthesand/

qmol is a fairly complete solution, and importantly is highly configurable while at the same time being straightforward to use. In particular I like the ability to define your own chemical groups AND the ability to run it from the command line. It's basically what I've been waiting for with the exception of the lack of an isotopic pattern calculator -- but that may come by version 1.0.

Also, the documentation -- or qmol handbook -- is quite extensive and is available under help.

---

Enough talking -- time for compiling.

sudo apt-get install bzip2 build-essential cmake libqtcore4 libqtgui4 qt4-qmake libqt4-dev
mkdir ~/tmp 
cd ~/tmp
wget http://downloads.sourceforge.net/project/qmol/qmol-0.3.2/qmol-0.3.2.tar.bz2
tar xvf qmol-0.3.2.tar.bz2
mkdir buildqmol
cd buildqmol/
cmake ../qmol-0.3.2
make
sudo make install

Don't worry if you get

-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found.
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found.
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found.

during the cmake stage.

---

Usage: Either run qmol from the command line:

qmol 'N(CH3)4'

N(CH3)4 = C4H12N: 74.146 g/mol
C 64.80
H 16.31
N 18.89

The output format can be configured when qmol is in gui mode (Edit/Options).

or launch it by typing

qmol

A virgin window

Previous formulae aggregate at the bottom of the  window

It doesn't handle 0, but then neither does my calculator (yet)

It's very easy to define your own group -- but  only the first letter can be  upper case

Options menu -- you can format the command line output here

It works!

There are only two small things to watch out for: the inability to handle 0 (but you get an error message -- my calculator just give you an erroneous result which is arguably worse...) and the requirement that only the first letter in an abbreviation can be upper case (for reasons of ambiguity -- c.f. e.g. CHO vs C, H, O)

317. Compiling samba 4.0.0 on Debian Testing/Wheezy

Not much to say about this one -- samba/SMB is only one among several linux solutions for sharing files, and probably the easiest one for sharing directories with windows computers. Samba has also been around for about as long as linux, so it has a long and interesting history.

New major versions are always exciting though. Information about Samba 4 can be found here: http://wiki.samba.org/index.php/Samba4

I won't cover configuration here -- partly because I don't know much about it -- so see the link above. To get started you might want to look at this post though: http://verahill.blogspot.com.au/2012/12/300-briefly-sharing-folder-using-samba.html

I also wrote this a long time ago, but haven't checked it for accuracy:
http://verahill.blogspot.com.au/2012/03/building-and-installing-samba-from.html

These instructions will build Samba 4.0.0 with LDAP and Cluster support.
Compilation:

sudo apt-get install build-essential libacl1-dev libattr1-dev libaio-dev libpam0g-dev kfreebsd-headers-9.0-2 libtalloc-dev python-talloc-dev libtevent-dev valgrind libsasl2-dev python2.7-dev libgnutls-dev xsltproc libctdb-dev libldap2-dev libcups2-dev python-ldb-dev ldb-tools libldb-dev checkinstall
mkdir ~/tmp 
cd ~/tmp
wget http://www.samba.org/samba/ftp/stable/samba-4.0.0.tar.gz
tar xvf samba-4.0.0.tar.gz
cd samba-4.0.0/
./configure --prefix=$HOME/.smb4
time make
sudo checkinstall
dpkg -i samba_4.0.0-1_amd64.deb

And you're done. 

Takes about 14 minutes to compile. When you run checkinstall and you're asked

Some of the files created by the installation are inside the home directory: /home

You probably don't want them to be included in the package.
Do you want me to list them?  [n]: n
Should I exclude them from the package? (Saying yes is a good idea)  [n]: n

Answer no, you DO want to include them. You're getting this warning because we set a --prefix and the files aren't going to the / structure like normal programs.

The samba daemon, smbd, is in ~/.smb4/sbin/ and the configuration files are in /etc/samba/.

---

Here's the structure of ~/.smb4:

~/.smb4/
|-- bin
|   |-- cifsdd
|   |-- dbwrap_tool
|   |-- eventlogadm
|   |-- gentest
|   |-- ldbadd
|   |-- ldbdel
|   |-- ldbedit
|   |-- ldbmodify
|   |-- ldbrename
|   |-- ldbsearch
|   |-- locktest
|   |-- masktest
|   |-- ndrdump
|   |-- net
|   |-- nmblookup
|   |-- nmblookup4
|   |-- ntlm_auth
|   |-- oLschema2ldif
|   |-- pdbedit
|   |-- pidl
|   |-- profiles
|   |-- regdiff
|   |-- regpatch
|   |-- regshell
|   |-- regtree
|   |-- rpcclient
|   |-- samba-tool
|   |-- sharesec
|   |-- smbcacls
|   |-- smbclient
|   |-- smbclient4
|   |-- smbcontrol
|   |-- smbcquotas
|   |-- smbget
|   |-- smbpasswd
|   |-- smbspool
|   |-- smbstatus
|   |-- smbta-util
|   |-- smbtorture
|   |-- smbtree
|   |-- testparm
|   `-- wbinfo
|-- etc
|-- include
|   |-- charset.h
|   |-- core
|   |-- credentials.h
|   |-- dcerpc.h
|   |-- dcerpc_server.h
|   |-- dlinklist.h
|   |-- domain_credentials.h
|   |-- gen_ndr
|   |-- gensec.h
|   |-- ldap-util.h
|   |-- ldap_errors.h
|   |-- ldap_message.h
|   |-- ldap_ndr.h
|   |-- ldb_wrap.h
|   |-- libsmbclient.h
|   |-- lookup_sid.h
|   |-- machine_sid.h
|   |-- ndr
|   |-- ndr.h
|   |-- netapi.h
|   |-- param.h
|   |-- passdb.h
|   |-- policy.h
|   |-- read_smb.h
|   |-- registry.h
|   |-- roles.h
|   |-- rpc_common.h
|   |-- samba
|   |-- samba_util.h
|   |-- share.h
|   |-- smb2.h
|   |-- smb2_constants.h
|   |-- smb2_create_blob.h
|   |-- smb2_signing.h
|   |-- smb_cli.h
|   |-- smb_cliraw.h
|   |-- smb_common.h
|   |-- smb_composite.h
|   |-- smb_constants.h
|   |-- smb_ldap.h
|   |-- smb_raw.h
|   |-- smb_raw_interfaces.h
|   |-- smb_raw_signing.h
|   |-- smb_raw_trans2.h
|   |-- smb_request.h
|   |-- smb_seal.h
|   |-- smb_share_modes.h
|   |-- smb_signing.h
|   |-- smb_unix_ext.h
|   |-- smb_util.h
|   |-- smbconf.h
|   |-- smbldap.h
|   |-- tdr.h
|   |-- torture.h
|   |-- tsocket.h
|   |-- tsocket_internal.h
|   |-- util
|   |-- util_ldb.h
|   `-- wbclient.h
|-- lib
|   |-- auth
|   |-- bind9
|   |-- gensec
|   |-- idmap
|   |-- ldb
|   |-- libdcerpc-atsvc.so -> libdcerpc-atsvc.so.0.0.1
|   |-- libdcerpc-atsvc.so.0 -> libdcerpc-atsvc.so.0.0.1
|   |-- libdcerpc-atsvc.so.0.0.1
|   |-- libdcerpc-binding.so -> libdcerpc-binding.so.0.0.1
|   |-- libdcerpc-binding.so.0 -> libdcerpc-binding.so.0.0.1
|   |-- libdcerpc-binding.so.0.0.1
|   |-- libdcerpc-samr.so -> libdcerpc-samr.so.0.0.1
|   |-- libdcerpc-samr.so.0 -> libdcerpc-samr.so.0.0.1
|   |-- libdcerpc-samr.so.0.0.1
|   |-- libdcerpc-server.so -> libdcerpc-server.so.0.0.1
|   |-- libdcerpc-server.so.0 -> libdcerpc-server.so.0.0.1
|   |-- libdcerpc-server.so.0.0.1
|   |-- libdcerpc.so -> libdcerpc.so.0.0.1
|   |-- libdcerpc.so.0 -> libdcerpc.so.0.0.1
|   |-- libdcerpc.so.0.0.1
|   |-- libgensec.so -> libgensec.so.0.0.1
|   |-- libgensec.so.0 -> libgensec.so.0.0.1
|   |-- libgensec.so.0.0.1
|   |-- libndr-krb5pac.so -> libndr-krb5pac.so.0.0.1
|   |-- libndr-krb5pac.so.0 -> libndr-krb5pac.so.0.0.1
|   |-- libndr-krb5pac.so.0.0.1
|   |-- libndr-nbt.so -> libndr-nbt.so.0.0.1
|   |-- libndr-nbt.so.0 -> libndr-nbt.so.0.0.1
|   |-- libndr-nbt.so.0.0.1
|   |-- libndr-standard.so -> libndr-standard.so.0.0.1
|   |-- libndr-standard.so.0 -> libndr-standard.so.0.0.1
|   |-- libndr-standard.so.0.0.1
|   |-- libndr.so -> libndr.so.0.0.1
|   |-- libndr.so.0 -> libndr.so.0.0.1
|   |-- libndr.so.0.0.1
|   |-- libnetapi.so -> libnetapi.so.0
|   |-- libnetapi.so.0
|   |-- libnss_winbind.so -> libnss_winbind.so.2
|   |-- libnss_winbind.so.2
|   |-- libnss_wins.so -> libnss_wins.so.2
|   |-- libnss_wins.so.2
|   |-- libpdb.so -> libpdb.so.0
|   |-- libpdb.so.0
|   |-- libregistry.so -> libregistry.so.0.0.1
|   |-- libregistry.so.0 -> libregistry.so.0.0.1
|   |-- libregistry.so.0.0.1
|   |-- libsamba-credentials.so -> libsamba-credentials.so.0.0.1
|   |-- libsamba-credentials.so.0 -> libsamba-credentials.so.0.0.1
|   |-- libsamba-credentials.so.0.0.1
|   |-- libsamba-hostconfig.so -> libsamba-hostconfig.so.0.0.1
|   |-- libsamba-hostconfig.so.0 -> libsamba-hostconfig.so.0.0.1
|   |-- libsamba-hostconfig.so.0.0.1
|   |-- libsamba-policy.so -> libsamba-policy.so.0.0.1
|   |-- libsamba-policy.so.0 -> libsamba-policy.so.0.0.1
|   |-- libsamba-policy.so.0.0.1
|   |-- libsamba-util.so -> libsamba-util.so.0.0.1
|   |-- libsamba-util.so.0 -> libsamba-util.so.0.0.1
|   |-- libsamba-util.so.0.0.1
|   |-- libsamdb.so -> libsamdb.so.0.0.1
|   |-- libsamdb.so.0 -> libsamdb.so.0.0.1
|   |-- libsamdb.so.0.0.1
|   |-- libsmbclient-raw.so -> libsmbclient-raw.so.0.0.1
|   |-- libsmbclient-raw.so.0 -> libsmbclient-raw.so.0.0.1
|   |-- libsmbclient-raw.so.0.0.1
|   |-- libsmbclient.so -> libsmbclient.so.0.2.0
|   |-- libsmbclient.so.0 -> libsmbclient.so.0.2.0
|   |-- libsmbclient.so.0.2.0
|   |-- libsmbconf.so -> libsmbconf.so.0
|   |-- libsmbconf.so.0
|   |-- libsmbldap.so -> libsmbldap.so.0
|   |-- libsmbldap.so.0
|   |-- libsmbsharemodes.so -> libsmbsharemodes.so.0
|   |-- libsmbsharemodes.so.0
|   |-- libtevent-util.so -> libtevent-util.so.0.0.1
|   |-- libtevent-util.so.0 -> libtevent-util.so.0.0.1
|   |-- libtevent-util.so.0.0.1
|   |-- libtorture.so -> libtorture.so.0.0.1
|   |-- libtorture.so.0 -> libtorture.so.0.0.1
|   |-- libtorture.so.0.0.1
|   |-- libwbclient.so -> libwbclient.so.0.11
|   |-- libwbclient.so.0 -> libwbclient.so.0.11
|   |-- libwbclient.so.0.11
|   |-- mit_samba.so
|   |-- nss_info
|   |-- pkgconfig
|   |-- private
|   |-- process_model
|   |-- python2.7
|   |-- security
|   |-- service
|   |-- vfs
|   `-- winbind_krb5_locator.so
|-- private
|-- sbin
|   |-- nmbd
|   |-- samba
|   |-- samba_dnsupdate
|   |-- samba_kcc
|   |-- samba_spnupdate
|   |-- samba_upgradedns
|   |-- samba_upgradeprovision
|   |-- smbd
|   |-- swat
|   `-- winbindd
|-- share
|   |-- codepages
|   |-- man
|   |-- perl5
|   |-- setup
|   `-- swat
`-- var
    |-- cache
    |-- lib
    |-- lock
    |-- locks
    `-- run

316. Briefly: Automated chroot/sandbox creation

EDIT:
There are plenty of reasons to use chroots, but security is not one of them.

For a practical how-to see e.g
http://pen-testing.sans.org/blog/2012/06/06/escaping-restricted-linux-shells

For a bit of yelling, see
http://yarchive.net/comp/linux/chroot.html

chroot will improve your security by creating an obstacle which may filter out some would-be crackers, but it will not make it secure by any standard. (in spite of what I may have written elsewhere on this blog).

Original post:
I've been using chroot to compile and test stuff so much lately that I figure it was time to automate the process.

Before creating your chroot you'll need a few packages:

sudo apt-get install debootstrap coreutils x11-xserver-utils

The scripts

makechroot.sh

mkdir $HOME/tmp/jail/$1 -p
sudo debootstrap --arch amd64 testing $HOME/tmp/jail/$1 http://ftp.au.debian.org/debian/
sudo cp setupchroot.sh $HOME/tmp/jail/$1/

setupchroot.sh

rm /etc/apt/sources.list
echo 'deb  http://ftp.au.debian.org/debian/ wheezy main contrib non-free' >> /etc/apt/sources.list
apt-get update
apt-get install locales sudo vim
echo 'export LC_ALL="C"'>>/etc/bash.bashrc
echo 'export LANG="C"'>>/etc/bash.bashrc
echo 'export DISPLAY=:0.0' >> /etc/bash.bashrc
echo '127.0.0.1 beryllium >> /etc/hosts'
source /etc/bash.bashrc
adduser sandbox
usermod -g sudo sandbox
echo 'Defaults !tty_tickets' >> /etc/sudoers

launchchroot.sh

xhost +
sudo mount -o bind /proc $1/proc
sudo cp /etc/resolv.conf $1/etc/resolv.conf
sudo chroot $HOME/tmp/jail/$1

How to use
To set up the chroot:

sh makechroot.sh mynewchroot
sudo chroot mynewchroot
root@beryllium:/# sh setupchroot.sh

To use the chroot:

sh launchchroot.sh mynewchroot

Once you're done with the chroot and logged out, do

sudo umount $HOME/tmp/jail/mynewchroot/proc

to unmount the /proc -- you can now delete, copy etc. the directory structure of you chroot.

315. Briefly: Compile firefox 18 on debian testing/wheezy

For no better reason than pure curiosity, here's how to build firefox 18. My regular build environment has so many packages installed these days that it's useless for working out dependencies for other people, so I tried it in a fresh chroot to hammer out the current dependencies beyond a doubt. In other words: it will work for you.

In retrospect I'm not sure if you really need the dev package for libgtk2.0.

sudo apt-get install bzip2 build-essential python zip unzip pkg-config libgtk2.0-dev gconf2 libdbus-1-dev libdbus-glib-1-dev yasm libasound2-dev libcurl4-gnutls-dev libxt-dev mesa-common-dev
mkdir ~/tmp/firefox -p
cd ~/tmp/firefox
wget ftp://ftp.mozilla.org/pub/firefox/releases/18.0/source/firefox-18.0.source.tar.bz2
tar xvf firefox-18.0.source.tar.bz2
mkdir build/
cd build/
../mozilla-release/./configure --prefix=$HOME/.firefox18
make
make install
echo "alias firefox18='$HOME/.firefox18/bin/firefox'" >> $HOME/.bashrc
source $HOME/.bashrc

Launch by typing

firefox18

314. Briefly: Installing talkd on ROCKS 5.4.3

I was asked to set up talkd on our Rocks 5.4.3 cluster (Centos 5.4) . There's no talkd or talk-server packages in the repos on that server.

Note: The general consensus seems to be that talk is
1. insecure and
2. outdated.

To install:

wget http://mirror.centos.org/centos/5/os/x86_64/CentOS/talk-server-0.17-31.el5.x86_64.rpm
yum localinstall talk-server-0.17-31.el5.x86_64.rpm
sudo iptables -A INPUT -p udp --dport 517 -s 127.0.0.1 -j ACCEPT
sudo iptables -A INPUT -p udp --dport 518 -s 127.0.0.1 -j ACCEPT

Above I've added, but haven't yet tried, -s 127.0.0.1 to limit connections from the local computer (localhost). If it doesn't work with -s 127.0.0.1, then try without -- but then be aware of the security implications. These rules also aren't permanent and will be lost on reboot. To make them permanent, edit /etc/sysconfig/iptables.

I couldn't get talk to work before opening the ports and would get

Error on read from talk daemon : Connection refused

Note that talkd uses Xinet and not init -- it will not run as  memory resident daemon, but instead be launched by xinet only when talkd is needed (traffic is detected to the ports associated with talkd). Xinet.d is a bit like a concierge, waking up whomever seems to be the adressee.

Edit both /etc/xinetd.d/talk and /etc/xinetd.d/ntalk. Change to:

# default: off
# description: The talk server accepts talk requests for chatting with users \
#       on other systems.
service talk
{
        flags                   = IPv4
        disable                 = no
        socket_type             = dgram
        wait                    = yes
        user                    = nobody
        group                   = tty
        server                  = /usr/sbin/in.talkd
}

Finally, restart xinet.d (doing chkconfig talk on wasn't enough):

sudo /etc/init.d/xinet.d restart

---

Note: If you or the other user have several terminals open you should figure out which terminal to use. If you're user2, do

ps

PID TTY          TIME CMD
 5455 pts/23   00:00:00 bash
 9321 pts/23   00:00:00 ps

user1 can then do

[user1@host ~]$ talk user2@localhost pts/23

and user2 will see the following in that terminal:

Message from Talk_Daemon@host at 14:49 ...   
talk: connection requested by user1@localhost.localdomain.  
talk: respond with:  talk user1@localhost.localdomain 

If you are user1 and have no idea on what terminal user2 is logged on, you can try

w|grep user2

user2     pts/8    remote:S.0    04Nov12 59:00   0.04s  0.04s /bin/bash
user2     pts/9    remote:S.1    04Nov12 17:28   0.03s  0.03s /bin/bash
user2     pts/10   remote Mon12  2days  0.03s  0.00s ssh -X -v volde
user2     pts/11   local  Mon12  2days  0.29s  0.26s perl eccejobmon
user2     pts/23   remote 14:30  7.00s  0.00s  0.00s -bash