217. Recently...

Recently I've been busy preparing lectures (phew!), which means I've been kinder to my computer than is normal. Still, I managed to get myself into a few situations. The need to 'get stuff done' overrode the importance of documentation, but here's the low-down in case someone finds themselves in a similar situation:


1. Upgrades keep on getting stuck when restarting nfs/nfsd (nfs-common, nfs-kernel-server).
Normally I don't have any problems with nfs -- it's a tried and tested technology -- but one of my cluster nodes was giving me grief.

The key was to comment out everything in /etc/exports and commenting out nfs mounted partitions in /etc/fstab, then adding nfs and nfsd to /etc/modprobe.d/blacklist.conf (not sure this actually did anything), rebooting, throwing in

sudo rmmod nfs nfsd 


to be on the safe side, then doing

sudo dpkg --configure -a

to get dpkg/apt back in working order. After that I could uncomment everything in /etc/exports and /etc/fstab, and whitelist my drivers again.

Problem solved.

2. Nvidia is still a headache.
Since I was given a rare opportunity to reboot my front node I did a bit of work on it. Mainly, I wanted to allow gdm to start again, and figured I'd return to my nvidia driver managment to dkms-y goodness.

So I fired up smxi, selected 'debian-nvidia' and...everything was messed up. Long story short: I got it working with gdm3 by picking 'current driver' in smxi (always blacklist nouveau if you want to use/install nvidia drivers), making sure that there was no 'vga' (e.g.  vga=0x0318 ) in GRUB_CMDLINE_LINUX in /etc/default/grub and rebooting liberally.

I later got the debian-nvidia (dkms) version working by 1) not using frambuffer and 2) manually removing all nvidia legacy drivers that smxi pulled in. Well, that's working as in no error messages and the desktop looking fine.

3. GNOME 3 not diplaying all letters
e.g. 'guake' was rendered as 'g ak '. This happened on a low-powered system. A 'fix' was to go to advanced settings (gnome-tweak-tool), select font and change scaling from 1.0 to 1.2 and above.

It's not much of a 'fix', so I ended up nuking GNOME from that system and replacing it with KDE to have a reason to get more familiar with it. In the interest of balance I nuked all other DEs from another box and put LXDE on it. To paraphrase the Dos Equis commercial: I don't always use a DE, but when I do, I want to learn something new.

I've used KDE and GNOME on and off over the past 12 years, but you get rusty -- and both KDE and GNOME have changed enough from v 3.x and 2.x, respectively, that they aren't the same environment anymore. I still get an initial feeling of joy when I sit down by an NMR console and discover a red hat system with a 3.x desktop. Which is quickly followed by being annoyed over not having root access, but whatever. As for the usual gnome 2 vs gnome 3 arguments -- I like gnome3 in general. I just hate the idea of settings being hidden or disabled, and functionality being reduced. Enough so that I'm still looking for a potential replacement.

So far :
KDE -- I like it. It's overdoing the desktop effects a bit (out of the box) but, since it's KDE, it's easy to turn things on and off. I'm still a GNOME man, and KDE doesn't have the warm fuzzy feeling of home yet, but I can see how I could get used to it. I just need to get over my outdated idea that KDE is for windows users (I've never used a Mac so I guess I'm a reformed windows -- actually DOS -- user more than anything else).

KDE on one of my other systems seems to be messing up GNOME 3 though -- e.g. the mouse cursor theme gets transferred to gnome, and the pop-up notifications are those of kwin and not gnome-shell.  Not sure whether it's KDE causing it or whether I've messed a bit too much with my system.

LXDE -- it's functional and has long been my choice for virtual installations of linux for windows users. It's minimalistic in the sense that yes, it does provide a desktop, but no, it doesn't try to do anything beyond providing a set of menus and a bit of themeing. And that's a good thing. If you're going to impress a mate -- use gnome or kde. If you just need to get something done and launch a piece of software, lxde's your mate.

4. One of my systems lacked /etc/init.d/vboxdrv
Not all my collaborators use linux, so I keep a virtual copy of XP around for when I'm absolutely forced to use MS Word (OpenOffice sometimes changes the layout and it quickly becomes messy on collaborative documents). When taking a quick break to edit a manuscript in virtualbox I got the usual no driver present, 'run /etc/init.d/vboxdrv setup' message. Well, there was no /etc/init.d/vboxdrv in spite of dkms and vboxdrv-dkms being installed in addition to all the kernel headers. Turns out that the quickest way, assuming that locate vboxdrv doesn't come up empty (i.e. it's somewhere in the kernel tree) is just to mod it.
modprobe vboxdrv


To avoid it in the future, stick
vboxdrv
somewhere in your /etc/modules


5. Mysteriously self-rotating gnuplot images in latex 
Came down to a stupid mistake. I was doing:

set term postscript enhanced colour
set output 'acid.eps'
set border 3
set xtics nomirror
set ytics nomirror

I forgot to add eps -- getting rusty I suppose.

set term postscript enhanced eps colour
set output 'acid.eps'
set border 3
set xtics nomirror
set ytics nomirror

Surprised it hasn't happened before during all these years of latex usage.

6. Setting default line printer
me@beryllium:$ lpq

lpq: Error - no default destination available.

me@beryllium:$ lpstat -a

AdobePDF accepting requests since Mon 06 Aug 2012 08:01:32 EST
AdobePDF7 accepting requests since Mon 06 Aug 2012 08:01:32 EST
AdobePDF8 accepting requests since Mon 06 Aug 2012 10:04:13 EST
AdobePDF8@johnbowmansimac.dbs.monash.edu.au accepting requests since Mon 06 Aug 2012 08:01:32 EST
AdobePDF9 accepting requests since Mon 06 Aug 2012 08:01:32 EST
AdobePDF9@130.194.162.66 accepting requests since Mon 06 Aug 2012 08:01:32 EST
biol08r159p1 accepting requests since Mon 06 Aug 2012 08:01:32 EST
Canon_iP4300 accepting requests since Mon 06 Aug 2012 08:01:32 EST
Canon_MP460 accepting requests since Mon 06 Aug 2012 10:09:36 EST
Colour_109a accepting requests since Mon 06 Aug 2012 08:01:32 EST
global-mfp accepting requests since Mon 28 May 2012 14:27:30 EST
GlobalMFP@s0001203.dbs.monash.edu.au accepting requests since Mon 06 Aug 2012 08:01:32 EST
HP_LaserJet_Professional_P1102w accepting requests since Sat 04 Aug 2012 23:08:16 ESTHPColourLaserCP3505 accepting requests since Mon 06 Aug 2012 08:01:32 EST
HPLaserJetP3005 accepting requests since Mon 06 Aug 2012 08:01:32 EST

 me@beryllium:$ lpoptions -d HP_LaserJet_Professional_P1102w

auth-info-required=none copies=1 device-uri=hp:/usb/HP_LaserJet_Professional_P1102w?serial=000000000Q91K4WVSI1c finishings=3 job-hold-until=no-hold job-priority=50 job-sheets=none,none marker-change-time=0 number-up=1 printer-commands=AutoConfigure,Clean,PrintSelfTestPage printer-info='HPIJS -- drv:///hpijs.drv/hp-laserjet_professional_p1102w-hpijs.ppd' printer-is-accepting-jobs=true printer-is-shared=true printer-location printer-make-and-model='HP LaserJet Professional p1102w, hpcups 3.12.4, requires proprietary plugin' printer-state=5 printer-state-change-time=1344085696 printer-state-reasons=paused printer-type=8425484 printer-uri-supported=ipp://localhost:631/printers/HP_LaserJet_Professional_P1102w

7. The next Debian is codenamed Jessie!
I'm only 6 days late...apparently that's the cowgirl.

367. Some post-install steps on Debian Wheezy/Testing

-- Skip from here -- 
I lasted 9 days with Arch linux on my laptop, and I have now switched it back to Debian. I've still got Arch on my 'household' computer that we use to watch TV on though -- it's a fine distro, just like debian is a fine distro -- but it's not suitable for the particular work I use my laptop for.

The reasons for switching back aren't that dramatic -- I use my laptop for work.

In particular, I use it to do
* (computationally) light work at home (editing papers, generating figures, analyzing data)  and
* I use it to give seminar talks at other universities.

I got a bit frustrated with the number of packages I had to get via AUR, and even more frustrated over the quality of some of the PKGBUILDS. Not frustrated in a terribly bad way -- I appreciate the time and effort that some of the maintainers put it (e.g. gdis and gcc-gcj) -- but frustrated enough that I appreciate the quality and availability of the packages in the debian repos. I needed to sort out a few quick things before sending off a manuscript:
* generate a structure with avogadro, then generate a pov file in gdis, then render it in povray
* I also needed to extract a couple of pages from a pdf using pdftk  and send them to a collaborator

That took all evening. Avogadro installs fine via the repos, as did povray. There's a small issue with upstreams version of povray 3.7 in that it doesn't create any conf file in ~/.povray/3.7/, and there's no actual help when running povray --help, but even worse was that it rendered incredibly slow. I've compiled 3.7 myself before and my experience using the Arch packages were very different in terms of performance.

I had some issues with building gdis using the AUR PKGBUILD (the maintainer was extremely responsive to feedback and kudos to him/her), and that added an extra 20-30 minutes.

There are two AUR pdftk versions -- I first tried pdftk, which relies on gcc-gcj which is another AUR package. gcc-gcj wouldn't build, but someone beat me to submitting feedback. Again, the maintainer of gcc-gcj is extremely responsive and the issue has already been resolved, less than a day after reporting it.

I ended up giving and installing pdftk-bin and it's dependency (a re-tooled debian package!) which went fine.

All this is really in line with the stated nature of Arch - Arch is bleeding edge and will give you the newest, shiniest stuff. Debian is focused on stability and reliability (all your bugs will remain constant) but offers a middle-ground between Arch and Debian Stable in Debian Testing. And while the shiniest, newest stuff is what I'm looking for in a household computer or a desktop box, I need to go for reliability on my work computer.

So that's why I'm going back on my laptop -- I want to make sure that if I need to pull in a package in an emergency it should go fast and without issue. I also don't want to risk doing a -Syu and ending up with a borked system the morning of a talk.

It's pretty similar to some of the reasons one finds in this remarkably civilised thread: http://forums.debian.net/viewtopic.php?f=3&t=61004

Like a lot of the respondents, I have to agree that the Arch wiki is amazing. In contrast, I've taken to never using the debian guides since they feel horribly out of date (probably because I'm on testing), and may not be that well-written.

Interesting observation: Debian Testing starts (from grub menu to log in prompt) in 9-10 s (SSD), while a fresh Arch install with systemd takes 25s.
-- to here -- 

Anyway. I Installed debian again on my laptop hdd (using this post: http://verahill.blogspot.com.au/2013/03/361-installing-debian-on-usb-stick-from.html) and these are some of the first steps I went through:

0. What I installed in the chroot step
The basics:
sudo apt-get install locales sudo vim aide grub-pc linux-base linux-image-3.2.0-4-amd64 wicd-curses mutt mcabber elinks rcconf gnome firmware-atheros firmware-iwlwifi firmware-ralink firmware-realtek locate dkms openssh-server wicd-gtk screen less conky nautilus-open-terminal lm-sensors acpi gawk

I also used adduser to create the new user to get proper .profile and .bashrc generated.

Post-chroot:
1. Disable services
Run rcconf to disable network-manager, bluetooth, speech-dispatcher

Do
sudo service network-manager stop
if it's running or you won't be able to use it to configure wicd-curses

First time you run wicd-curses, make sure to set Preferences and pick the right interfaces. Note that wicd only handles one wired and one wireless interface. For anything a bit more challenging, use /etc/network/interfaces directly.

2. ssh, .gnupg, BankID, conky
SSH
Copy .ssh/id_[dr]sa and id_[dr]sa.pub from old installation to ~/.ssh on new installation. Make sure to
chmod 700 ~/.ssh

GPG
mkdir ~/.gnupg
chmod  og-rwx ~/.gnupg -R
Copy gpa.conf, gpg.conf, pubring.gpg, pubring.kbx, random_seed, secring.gpg, trustdb.gpg

BankID
mkdir .personal
chmod 700 ~/.personal
copy ~/.personal/config/Personal.cfg and ~/.personal/store/*.npg

Conky
copy /etc/conky/conky.conf

3. apt-file and bash completion
sudo apt-get install apt-file bash-completion
sudo apt-file update

4. Data analysis
sudo apt-get install gnuplot octave maxima

5. Chemistry
sudo apt-get install gdis pymol povray bkchem avogadro

6. TeX
texmake texlive-science texlive-publishers texlive-bibtex-extra texlive-fonts-recommended latex-cjk-common latex-cjk-chinese

7. Internet/Network
sudo apt-get install chromium gajim filezilla flashplugin-nonfree

8. Misc
sudo apt-get install gnucash kate pdftk inkscape gimp keepassx sinfo saidar guake

9.  multiarch
sudo dpkg --add-architecture i386
sudo apt-get update

10. GNOME
sudo apt-get install gnome-tweak-tool

Icons
mkdir ~/tmp/faenza  -p
cd ~/tmp/faenza
wget https://faenza-icon-theme.googlecode.com/files/faenza-icon-theme_1.3.zip
unzip  faenza-sources_1.3.tar.gz
sudo cp Faenza -R /usr/share/icons

frippery extensions
cd ~
wget http://intgat.tigress.co.uk/rmy/extensions/gnome-shell-frippery-0.4.1.tgz
tar xvf gnome-shell-frippery-0.4.1.tgz

Do alt+f2, r
then use gnome-tweak-tool
select e.g. bottom panel, move clock, applications menu.

Change default browser:
System/Details/Default Applications -> Chromium

autostart guake-- create ~/.config/autostart/guake.desktop

[Desktop Entry]
Type=Application
Exec=/usr/bin/guake
Hidden=false
X-GNOME-Autostart-enabled=true
Name=guake
Comment=guake

Start guake in gnome, open preferences, and disable "Enable popup notification on startup"

autostart conky -- create ~/.config/autostart/conky.desktop
[Desktop Entry]
Type=Application
Exec=conky
Hidden=false
X-GNOME-Autostart-enabled=true
Name=conky
Comment=conky

11. Dropbox
cd ~/Downloads
sudo apt-get install python-gpgme
wget https://linux.dropbox.com/packages/debian/dropbox_1.6.0_amd64.deb
sudo dpkg -i dropbox_1.6.0_amd64.deb

11. Truecrypt
cd ~/Downloads
wget http://www.truecrypt.org/download/truecrypt-7.1a-linux-x64.tar.gz
tar xvf truecrypt-7.1a-linux-x64.tar.gz
sudo sh truecrypt-7.1a-setup-x64

12. Keyboard
Go to keyboard in system setttings, click on the shortcuts tab.
Under Launchers, click on Explorer next to Home Folder so that it says New Accelerator...
Do shift+ctrl+left arrow

Do the same for web browser, with ctrl+shift+down arrow

Click on the plus (+), and set
Name: gnome terminal
Command: gnome-terminal

Click on Apply. Click on Disabled and set the shortcut to ctrl+shift+arrow up.

Do the same for gEdit, with ctrl+shift+arrow right.

Go to System settings, Region and Language. Click on the Layout tab, then on the Options button in the bottom right corner. Expand Compose Key Options. Tick Right+Alt.

13. BankID
See http://verahill.blogspot.com.au/2013/02/341-upgradinginstalling-bankid-on-64.html

12. Virtualbox
sudo apt-get install virtualbox virtualbox-dkms virtualbox-guest-dkms

14. Thunderbird
http://verahill.blogspot.com.au/2013/01/326-compiling-thunderbird-1702-on.html
Install the following addons: enigmail, lightning, provider for google calendar
Go to File, new, new calendar, and paste the ICAL string for google calendar
To look up the ical string, go to gmail in a web browser, click on calendar, select your calendar, click on the ICAL button for the private calendar.

15. Firefox
http://verahill.blogspot.com.au/2013/03/365-compile-firefox-19-on-debian.html

16. screenrc and vimrc
Add to /etc/vim/vimrc:
set number
set pastetoggle=<F3>
set spell
set wrap


Add to /etc/screenrc:
termcapinfo xterm|xterms|xs|rxvt ti@:te@
caption always "%{+b rk}%H%{gk} |%c %{yk}%d.%m.%Y | %72=Load: %l %{wk}"
hardstatus alwayslastline "%?%{yk}%-Lw%?%{wb}%n*%f %t%?(%u)%?%?%{yk}%+Lw%"


17. Skype
sudo apt-get install pulseaudio

Edit ~/.asoundrc:
pcm.!default.type pulse
ctl.!default.type pulse


Go to skype.com, download and get skype for debian 7.0 (multiarch)
sudo dpkg -i skype-debian_4.1.0.20-1_i386.deb

It will fail
sudo apt-get install -f

and now everything works.

18. wine
sudo apt-get install wine clamav

19. Tools for chroot
sudo apt-get install debootstrap x11-xserver-utils
http://verahill.blogspot.com.au/2013/01/316-briefly-automated-chrootsandbox.html

20. Tools for Kernel compile

sudo apt-get install kernel-package fakeroot build-essential ncurses-bin

http://verahill.blogspot.com.au/2013/02/342-compiling-kernel-38-on-debian.html

21. Java support in browsers
Install the icedtea-plugin

22. Install apt-listbugs
If you're running testing you'll want to be aware of critical bugs before upgrading each time. Luckily apt-listbugs does that for you if installed -- it's run during each apt-get update if it is installed:
sudo apt-get install apt-listbugs

---

Links to this post:
http://schultkl.blogspot.fr/2013/06/configuring-debian-gnulinux-7-wheezy.html

358. Gentoo in a virtual machine

This post took a LONG time to write, so hopefully someone, somewhere, will find it useful. My enthusiasm was also somewhat tempered during the installation. Gentoo just didn't speak to me. Maybe I'll feel differently in 6-12 months of Arch?

The post...

I'm sure that there are plenty of similar posts out there, and I admit that my main reason for writing this post isn't as much to get anyone else to play with gentoo (although it's certainly an interesting experience -- but probably a bit more fun on native hardware with a bit more oomph) as to provide myself with a written step-by-step instruction set if I should switch my mini-server to gentoo (I use it for testing/educational purposes).

I also realise that given that the most obvious advantage of gentoo is the hardware optimised binaries, running things in a virtual machine isn't going to show off the real strength of gentoo. Hopefully it might give an accurate impression of the complexity (or lack thereof) of gentoo as compared to other distros such as Arch and Debian.

Virtual machine
I'm doing this in a virtual machine. The principal reason is that I don't have any spare metal at the moment. The secondary reason is that because gentoo installation is very interactive, you will most likely not be able to do a complete installation in a single 2-hour sitting the first time (you'll have to look things up, think about modules etc. -- and compiling everything takes time), and doing things in a virtual machine makes it very easy to freeze the system until you have time to continue. Obviously you can also do it the old-fashioned way (simply chroot the system when you are ready to continue), but freezing is easier.

I probably should have switched to KVM by now, but since I'm not really that interested in using virtual machines for work, and since virtualbox is so simple to use, I'll be using Virtualbox here.

I wouldn't recommend trying Gentoo until you first feel somewhat familiar with the basic concepts on Linux (by using e.g. Debian), followed by trying a more hands-on distro like Arch, or one of the BSDs. Obviously, I'm biased since this is the path I've taken, but I still think that you're better off pushing yourself little by little, than suddenly jumping into something unfamiliar which then may turn into something that seems unfriendly and losing all interest as a consequence.

That's not to say that gentoo is difficult. What is or isn't difficult depends on your expectations and frame of reference. What I am saying is that gentoo will make a lot more sense if you have at least a conceptual idea of what is needed for a system to be bootable and useful (if you don't know that you need an X server, you won't enjoy this. If you haven't played with GRUB, you won't enjoy this).

Anyway.

I've followed http://www.gentoo.org/doc/
-- although I've focused on getting a working system quickly rather than spending a lot of time looking into what hardware I really have.

1. Create the virtual machine.
If you need help setting up a virtual machine you are most likely not going to enjoy gentoo (yet -- so come back in a few months), so I won't show that. Suffice to say that I created a machine with 1024 Mb RAM and 15 Gb HDD. The size of the harddisk is due to compilations normally requiring a fair amount of temporary storage space (you can probably get around it with tempfs if  you can spare it).

2. Get a gentoo cd. 
At this point we have an unpartitioned, unbootable harddrive so we need to boot our machine using some form of linux distro that can partition our virtual machine harddrive, as well as chroot gentoo. You don't need the gentoo cds for this, but it does make sense to use them.

You can use a minimal CD,a full DVD, or a stage 3 tarball. I'll use the CD.

Mirrors are found here: http://www.gentoo.org/main/en/mirrors2.xml
You will want to go to /gentoo/releases/amd64/current-iso and pick your architecture, e.g. I did

wget ftp://ftp.swin.edu.au/gentoo/releases/amd64/current-iso/install-amd64-minimal-20130110.iso
wget ftp://ftp.swin.edu.au/gentoo/releases/amd64/current-iso/install-amd64-minimal-20130110.iso.DIGESTS
sha512sum install-amd64-minimal-20130110.iso

77ab0ba00767b6d4668d0f4bf7effbf2af3f38a1bd7cef297a17076478fd46d05b15a80188da473cf7d7f8c220acbe615afd300de4af90011d54185be2697f7d  install-amd64-minimal-20130110.iso

cat install-amd64-minimal-20130110.iso.DIGESTS 

# SHA512 HASH
77ab0ba00767b6d4668d0f4bf7effbf2af3f38a1bd7cef297a17076478fd46d05b15a80188da473cf7d7f8c220acbe615afd300de4af90011d54185be2697f7d  install-amd64-minimal-20130110.iso

3. Boot
Attach the iso to your virtual machine and boot/start.

Hit enter.

The fun begins :)

Note that everything in virtualbox 'just works' since there's a dhcp server etc. Real-world hardware may require a bit more work to get the network etc. up and running. Anyway, the gentoo manual tries to cover most eventualities, which may make it a bit more complicated to follow. We don't have to worry about most options.

4. Partition the drive

ls /dev/sd*

/dev/sda
fdisk /dev/sda

Hit n (for new partition), p (for primary), accept 1, and 2048, set +13G, then n, p, 2, and accept the defaults. Do a, then 1 to make partition 1 bootable. Do t, 2, 82 to set sda2 as swap. Hit w to write. You've now created one bootable root and one swap partition.

mkswap /dev/sda2
mkfs.ext4 /dev/sda1

This isn't the gentoo way -- we're using a single root here instead of making separate partitions for root, usr, home etc. On the other hand, since we're just exploring we might as well keep things simple.

5. Setting up the chroot
Make sure that the date/time is right.

date -s "18:08 20130307"
mount /dev/sda1 /mnt/gentoo
cd /mnt/gentoo
wget ftp://ftp.swin.edu.au/gentoo/releases/x86/current-stage3/stage3-i686-20121213.tar.bz2
tar xvjpf stage3-i686-20121213.tar.bz2

Extracting the stage3 file creates the standard linux file structure (/var, /boot, /dev, /etc, /proc etc.).
Edit the (/mnt/gentoo)/etc/ports/make.conf

vi etc/ports/make.conf

CFLAGS="-O2 -march=native -pipe"
CXXFLAGS="${CFLAGS}"
MAKEOPTS="-j1"
CHOST="i686-pc-lnux-gnu"
USE="bindist"

If you have multiple cores, change the MAKEOPTS accordingly. The USE flag seems to be 'bindist' on i686, and 'bindist mmx sse sse2' on amd64. Presumably they depend on what gentoo detects on boot, and you will probably want to keep these.

mirrorselect -i -o >> /mnt/gentoo/etc/portage/make.conf
mirrorselect -i -r -o >> /mnt/gentoo/etc/portage/make.conf
cp /etc/resolv.conf etc/resolv.conf
mount -t proc none proc/
mount --rbind /sys sys/
mount --rbind /dev dev/

6. Enter the chroot -- set-up

chroot /mnt/gentoo /bin/bash
source /etc/profile
mkdir /usr/portage
emerge-webrsync

This will take a while, so don't give up if it seems stuck on 'Syncing local tree' and there's no network traffic.
.

emerge --sync
eselect profile list

There are seven different profiles on i686 and 13 on amd64 to choose from. I picked number 4 (default/gnome).

eselect profile set 4

I can't stand nano, so

emerge portage
emerge vim

Vim does take quite a while to install, so if you're happy with nano, stick with it.

Edit /etc/portage/make.conf

USE="bindist gnome gtk -kde -qt4"

Keep the USE flags that were there from the beginning and append gnome, gtk etc. I admit that I can't be bothered reading through /usr/portage/profiles/use.desc just in order to check out gentoo.

cp /usr/share/zoneinfo/Australia/Melbourne /etc/localtime
echo "Australia/Melbourne" > /etc/timezone

7. Compile/Install the kernel

emerge gentoo-sources
cd /usr/src/linux

Time to build a kernel! Do

make help|less

and look at the targets. Be aware that if you do 'emerge pciutils' as recommended by the gentoo guide this will take a long, long time since it pulls in 60 packages...but you need to if you want a working lspci.

My approach here is to first use make localmodconfig to get all the currently loaded modules, and then add more support manually via make menuconfig. Remember that if you screw things up you can always go back and redo it later. Build a minimal configuration, then explore what else you need to add (USB support etc.)

make localmodconfig
make menuconfig

IMPORTANT: 
1. Make sure to change 'Device Drivers/Serial ATA and Parallel ATA drivers' from (M) to (*).
2. Go to the submenu and make sure that AHCI SATA support is starred (i.e. not M) as well as 'Generic ATA support' Otherwise you'll probably find yourself consulting this post: http://wiki.gentoo.org/wiki/Knowledge_Base:Unable_to_mount_root_fs due to

VFS: Cannot open root device "sda1" or unknown-block(0,0)
Please append a correct "root=" boot option; here are the available partions:
...
Kernel panic - not syncing: VFS: Unable to mount root fs on unknown-block(0,0)

Anyway.

make
make modules_install
cp arch/x86_64/boot/bzimage /boot/vmlinuz-3.7.10
cp System.map /boot/System-3.7.10.map
ln -s /boot/System-3.7.10.map /boot/System.map

The first step make took me 16 minutes, which isn't bad for a single-core compile.

While you don't have to (since we have a single / partition), you might as well do

emerge genkernel
genkernel --install initramfs
mv /boot/initramfs-genkernel-x86_64-3.7.10-gentoo /boot/initramfs-3.7.10

You can edit /etc/conf.d/modules and list the modules you want to load. Have a look at the output of lsmod to get an idea. Doing 'lsmod > modules.list' might be a good idea for troubleshooting later.

8. Miscellaneous

Edit /etc/fstab

/dev/sda1    /       ext4    defaults   0  2
/dev/sda2    none    swap    sw         0  0

Set a hostname:

echo 'HOSTNAME="turbotux"' > /etc/conf.d/hostname
echo '127.0.0.1 turbotux localhost' > /etc/hosts

If you don't set a domain name and don't want hostname.unknown_domain to greet you on boot, run

sed -i 's,\\O,,g' /etc/issue

Edit /etc/conf.d/keymap and set keymap.

echo 'en_AU.UTF-8 UTF-8' >> /etc/locale.gen
locale-gen
echo 'LANG="en_AU.UTF-8"'> /etc/env.d/02locale
env-update
source /etc/profile

emerge mlocate vixie-cron sysklogd

rc-update add sshd default
emerge dhcpcd

9. GRUB2
GRUB might be a better, albeit retro, learning experience, but GRUB2 has better auto-configuration features and I'm not interested in hand-configuring grub just yet.

echo 'sys-boot/grub:2' >> /etc/portage/package.accept_keywords
emerge grub:2
mkdir /boot/grub2
grub2-mkconfig -o /boot/grub2/grub.cfg
grub2-install /dev/sda

IMPORTANT: set a root password before restarting or you won't be able to log in:

passwd

exit
shutdown -h now

Remove the CD from the virtual machine. Start the machine again

10. Your first boot
If all went well (i.e. you did exactly what I did above) you'll be greeted with this:

You can now log in as root.

11. Installing Gnome 2

The current version of gnome in gentoo (stable) is 2.32. If you want that, just emerge gnome. If not, the easiest (not safest) way to is switch to testing which might not be the best choice for gentoo novices.
To set up gnome I'm following this post: http://www.gentoo.org/doc/en/gnome-config.xml
If you can't live a single day without gnome 3, then checkout http://en.gentoo-wiki.com/wiki/Gnome_3

Anyway, gnome 2.32:

Then do

emerge --sync
emerge --update --ask world
emerge gentoolkit
equery m gnome

Brace yourself, because this will take a while (549 packages!):

emerge --ask --autounmask-write gnome
dispatch-conf
emerge --ask gnome

Hit Yes when you run the first command (change Use params), u (use new) when you run the second command, and Yes for the third command (emerge new packages). This step took 660 minutes in a virtual machine with a single core assigned.

env-update
source /etc/profile
emerge --sync
rc-update add dbus default
/etc/init.d/dbus start

Create a user:

useradd -m verahill
emerge sudo gksu
echo 'verahill ALL=(ALL) ALL'>>/etc/sudoers
passwd verahill
su verahill
cd ~

Continue setting up gnome:

echo 'export XDG_MENU_PREFIX=-gnome' > ~/.xinitrc
echo 'exec gnome-session' >> ~/.xinitrc
ln -s /etc/xdg/menus/gnome-applications.menu /etc/xdg/menus/applications.menu 
startx

You shouldn't have to do both the XDG_MENU_PREFIX and the symlink, but I had to in order to get a working applications menu.

Without vbox guest additions installed

To install the vbox additions, click on Devices/Install Guest Additions in the virtual machine menu. The CD will fail to mount.

sudo mount -o loop /dev/sr0 /mnt
sh /mnt/autorun.sh

Reboot, then do startx again. If you want gdm to start, then see step three here: http://www.gentoo.org/doc/en/gnome-config.xml

With vbox guest additions installed

Sounds is another story entirely...http://wiki.gentoo.org/wiki/PulseAudio

Anyway, that's enough of Gentoo for me for now.

568. PyMol troubles in Jessie -- no solutions [update]

I and linux are not on speaking terms at the moment. My main issue right now is that the routing that I set up a long time ago (http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-configuring.html) no longer works properly -- yes, I can see the subnets, but the routing table is wrong, and traffic is routed over the wrong physical interface which leads to a significant slowdown.

In addition, pymol is unusable on my laptop which is running debian jessie. I'm not the only one with pymol related issues either -- follow the thread at the end of http://verahill.blogspot.com.au/p/miscellaneous.html and you will see another example of pymol troubles, troubles which I accidentally reproduced in the virtual machine later in this post. Anyway, these are unsolved issues but I post them here in case other people are wondering whether they are the only ones. I might even muster the courage to submit a bug report to debian although the first issue is definitely present in upstreams...and I think that the second one is as well. Unfortunately, pymol isn't quite free software and the online support doesn't appear to be as good as for many traditional FOSS packages.

Either way, here are some observations:

---

On a physical machine (Lenovo Thinkpad SL410 running Jessie:
UPDATE 26/3/2014: this works now after doing a full upgrade/dist-upgrade. Not sure what did it -- no obvious package that would've fixed it. The issue below with gallium remains though.

Version 1.7.0.0 on Linux niobium 3.11-2-amd64 #1 SMP Debian 3.11.10-1 (2013-12-04) x86_64 GNU/Linux.

Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.20.
 OpenGL graphics engine:
  GL_VENDOR:   Intel Open Source Technology Center
  GL_RENDERER: Mesa DRI Mobile Intel GM45 Express Chipset 
  GL_VERSION:  2.1 Mesa 9.2.2
 Adjusting settings to improve performance for Intel cards.
 Detected 2 CPU cores.  Enabled multithreaded rendering.

Building the upstreams version doesn't solve the issue.

inxi -G:

Graphics:  Card: Intel Mobile 4 Series Integrated Graphics Controller 
           X.Org: 1.15.0 drivers: intel (unloaded: fbdev,vesa) Resolution: 1366x768@60.0hz 
           GLX Renderer: Mesa DRI Mobile Intel GM45 Express GLX Version: 2.1 Mesa 9.2.2

---

In a debian testing virtual machine (virtual box) running jessie:
Default DE seems to be Xfce. Before installing gnome i.e. in Xfce:

X Error of failed request:  0
  Major opcode of failed request:  155 (GLX)
  Minor opcode of failed request:  26 (X_GLXMakeContextCurrent)
  Serial number of failed request:  49
  Current serial number in output stream:  49
 PyMOL: abrupt program termination.

After installing gnome:

Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.30.
 OpenGL graphics engine:
  GL_VENDOR:   VMware, Inc.
  GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.3, 128 bits)
  GL_VERSION:  2.1 Mesa 9.2.2
pure virtual method called

and a normal window is opened:

While it says v 1.6.x it is version 1.7.0.0 and it says so in the terminal output -- just not in the fancy figure.

However, on loading any structure (e.g. xyz or pdb -- even as small as methane):

OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.30.
 OpenGL graphics engine:
  GL_VENDOR:   VMware, Inc.
  GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.3, 128 bits)
  GL_VERSION:  2.1 Mesa 9.2.2
 CmdLoad: "/home/me/Downloads/methane.pdb" loaded as "methane".
Segmentation fault

Running catchsegv gives a lot of output -- see bottom of this post.

I next installed the guest additions from the debian repos using

sudo apt-get install virtualbox-guest-*

(the guest additions that are installable via virtualbox itself fail to build on kernel 3.13) and rebooted.

At this point pymol shows

me@debian:~$ pymol ~/Downloads/methane.pdb 
OpenGL Warning: glFlushVertexArrayRangeNV not found in mesa table
OpenGL Warning: glVertexArrayRangeNV not found in mesa table
OpenGL Warning: glCombinerInputNV not found in mesa table
OpenGL Warning: glCombinerOutputNV not found in mesa table
OpenGL Warning: glCombinerParameterfNV not found in mesa table
OpenGL Warning: glCombinerParameterfvNV not found in mesa table
OpenGL Warning: glCombinerParameteriNV not found in mesa table
OpenGL Warning: glCombinerParameterivNV not found in mesa table
OpenGL Warning: glFinalCombinerInputNV not found in mesa table
OpenGL Warning: glGetCombinerInputParameterfvNV not found in mesa table
OpenGL Warning: glGetCombinerInputParameterivNV not found in mesa table
OpenGL Warning: glGetCombinerOutputParameterfvNV not found in mesa table
OpenGL Warning: glGetCombinerOutputParameterivNV not found in mesa table
OpenGL Warning: glGetFinalCombinerInputParameterfvNV not found in mesa table
OpenGL Warning: glGetFinalCombinerInputParameterivNV not found in mesa table
OpenGL Warning: glDeleteFencesNV not found in mesa table
OpenGL Warning: glFinishFenceNV not found in mesa table
OpenGL Warning: glGenFencesNV not found in mesa table
OpenGL Warning: glGetFenceivNV not found in mesa table
OpenGL Warning: glIsFenceNV not found in mesa table
OpenGL Warning: glSetFenceNV not found in mesa table
OpenGL Warning: glTestFenceNV not found in mesa table
 PyMOL(TM) Molecular Graphics System, Version 1.7.0.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
 
    Created by Warren L. DeLano, Ph.D. 
 
    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.
 
    If PyMOL is helpful in your work or study, then please volunteer 
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".
 
    Enter "help" for a list of commands.
    Enter "help " for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 4.20.
OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU
 OpenGL graphics engine:
  GL_VENDOR:   Humper
  GL_RENDERER: Chromium
  GL_VERSION:  2.1 Chromium 1.9
 CmdLoad: "/home/me/Downloads/methane.pdb" loaded as "methane".
OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU

and the molecule shows up briefly before the window goes black, which constitutes a bit of progress.

Closing the program gives

PyMOL: normal program termination.
Segmentation fault

---

catchsegv output using the gallium driver

PyMOL(TM) Molecular Graphics System, Version 1.7.0.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
 
    Created by Warren L. DeLano, Ph.D. 
 
    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.
 
    If PyMOL is helpful in your work or study, then please volunteer 
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".
 
    Enter "help" for a list of commands.
    Enter "help " for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.30.
 OpenGL graphics engine:
  GL_VENDOR:   VMware, Inc.
  GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.3, 128 bits)
  GL_VERSION:  2.1 Mesa 9.2.2
 ExecutiveLoad: "methane.xyz" loaded as "methane", through state 1.
Segmentation fault
*** Segmentation fault
Register dump:

 RAX: 0000000002214e08   RBX: 000000000000ffff   RCX: 0000000000000000
 RDX: 00007f1db5b69640   RSI: 00000000ffffffff   RDI: 00007fff4c2e7d60
 RBP: 00007fff4c0e7d80   R8 : 0000000000000000   R9 : 0000000000000000
 R10: 0000000002088a50   R11: 000000000208c940   R12: 000000000248b650
 R13: 00007f1dafad70fc   R14: 00007fff4c0e7c94   R15: 0000000000000000
 RSP: 00007fff4c0e7c10

 RIP: 00007f1daf8f4202   EFLAGS: 00010206

 CS: 0033   FS: 0000   GS: 0000

 Trap: 0000000e   Error: 00000006   OldMask: 00000000   CR2: 4c2eb110

 FPUCW: 0000037f   FPUSW: 00000000   TAG: 00000000
 RIP: 00000000   RDP: 00000000

 ST(0) 0000 0000000000000000   ST(1) 0000 0000000000000000
 ST(2) 0000 0000000000000000   ST(3) 0000 0000000000000000
 ST(4) 0000 0000000000000000   ST(5) 0000 0000000000000000
 ST(6) 0000 0000000000000000   ST(7) 0000 0000000000000000
 mxcsr: 9ffb
 XMM0:  00000000000000000000000000000000 XMM1:  00000000000000000000000000000000
 XMM2:  00000000000000000000000000000000 XMM3:  00000000000000000000000000000000
 XMM4:  00000000000000000000000000000000 XMM5:  00000000000000000000000000000000
 XMM6:  00000000000000000000000000000000 XMM7:  00000000000000000000000000000000
 XMM8:  00000000000000000000000000000000 XMM9:  00000000000000000000000000000000
 XMM10: 00000000000000000000000000000000 XMM11: 00000000000000000000000000000000
 XMM12: 00000000000000000000000000000000 XMM13: 00000000000000000000000000000000
 XMM14: 00000000000000000000000000000000 XMM15: 00000000000000000000000000000000

Backtrace:
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2ed202)[0x7f1daf8f4202]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2e8dfe)[0x7f1daf8efdfe]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2f1a69)[0x7f1daf8f8a69]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x338f6f)[0x7f1daf93ff6f]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x33a059)[0x7f1daf941059]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(llvmpipe_update_fs+0x99d)[0x7f1daf945bbd]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(llvmpipe_update_derived+0x1a0)[0x7f1daf93e9c0]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(lp_setup_update_state+0xe8)[0x7f1daf938d08]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x33726b)[0x7f1daf93e26b]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x208c40)[0x7f1daf80fc40]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x20908e)[0x7f1daf81008e]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x201f94)[0x7f1daf808f94]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2049fa)[0x7f1daf80b9fa]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x200235)[0x7f1daf807235]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2010e4)[0x7f1daf8080e4]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2f7285)[0x7f1daf8fe285]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2f7454)[0x7f1daf8fe454]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x212b21)[0x7f1daf819b21]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x20b916)[0x7f1daf812916]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x20bd96)[0x7f1daf812d96]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x326a72)[0x7f1daf92da72]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x14fb1c)[0x7f1daf756b1c]
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x1294c4)[0x7f1daf7304c4]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0xf3bb9)[0x7f1db4c16bb9]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(CGORenderGL+0x745)[0x7f1db4c359b5]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x1a5b7c)[0x7f1db4cc8b7c]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(CoordSetRender+0x323)[0x7f1db4d56253]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x1e5203)[0x7f1db4d08203]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(SceneRenderAllObject+0xc1)[0x7f1db4beb291]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0xc8898)[0x7f1db4beb898]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(DoRendering+0x204)[0x7f1db4bebe54]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(SceneRender+0x13c7)[0x7f1db4bf2a77]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(OrthoDoDraw+0x104c)[0x7f1db4c918ec]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(ExecutiveDrawNow+0xc1)[0x7f1db4df4ab1]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(PyMOL_DrawWithoutLock+0x16e)[0x7f1db4e5a73e]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x3233a0)[0x7f1db4e463a0]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x3241fc)[0x7f1db4e471fc]
/usr/lib/x86_64-linux-gnu/libglut.so.3(+0x22834)[0x7f1db3cd7834]
/usr/lib/x86_64-linux-gnu/libglut.so.3(fgEnumWindows+0x39)[0x7f1db3cdb279]
/usr/lib/x86_64-linux-gnu/libglut.so.3(glutMainLoopEvent+0x11c)[0x7f1db3cd7d7c]
/usr/lib/x86_64-linux-gnu/libglut.so.3(glutMainLoop+0xa1)[0x7f1db3cd8671]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x324b30)[0x7f1db4e47b30]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(main_shared+0x88)[0x7f1db4e48698]
/usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x3039b4)[0x7f1db4e269b4]
python2.7(PyEval_EvalFrameEx+0x42d)[0x51f18d]
python2.7(PyEval_EvalCodeEx+0x2ac)[0x53bd7c]
python2.7(PyEval_EvalFrameEx+0x7f6)[0x51f556]
python2.7(PyEval_EvalCodeEx+0x2ac)[0x53bd7c]
python2.7(PyEval_EvalCode+0x32)[0x5b0b62]
python2.7(PyEval_EvalFrameEx+0x4f5c)[0x523cbc]
python2.7(PyEval_EvalCodeEx+0x2ac)[0x53bd7c]
python2.7(PyEval_EvalFrameEx+0x7f6)[0x51f556]
python2.7[0x4e738a]
python2.7(PyObject_Call+0x36)[0x55f4c6]
python2.7[0x41e910]
python2.7(Py_Main+0x898)[0x44bfba]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f1db57e7b45]
python2.7[0x57b33e]

Memory map:

00400000-006bc000 r-xp 00000000 08:01 274159 /usr/bin/python2.7
008bc000-008bd000 r--p 002bc000 08:01 274159 /usr/bin/python2.7
008bd000-00932000 rw-p 002bd000 08:01 274159 /usr/bin/python2.7
00932000-00944000 rw-p 00000000 00:00 0
01316000-02a92000 rw-p 00000000 00:00 0 [heap]
7f1da4000000-7f1da465c000 rw-p 00000000 00:00 0
7f1da465c000-7f1da8000000 ---p 00000000 00:00 0
7f1da8e6b000-7f1da8eeb000 rw-p 00000000 00:00 0
7f1da913e000-7f1da917e000 rw-p 00000000 00:00 0
7f1da917e000-7f1da91fe000 rwxp 00000000 00:00 0
7f1da91fe000-7f1da936b000 rw-p 00000000 00:00 0
7f1da936b000-7f1da9373000 r-xp 00000000 08:01 274422 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so
7f1da9373000-7f1da9572000 ---p 00008000 08:01 274422 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so
7f1da9572000-7f1da9573000 r--p 00007000 08:01 274422 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so
7f1da9573000-7f1da9574000 rw-p 00008000 08:01 274422 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so
7f1da9574000-7f1da9580000 r-xp 00000000 08:01 521244 /lib/x86_64-linux-gnu/libnss_files-2.18.so
7f1da9580000-7f1da977f000 ---p 0000c000 08:01 521244 /lib/x86_64-linux-gnu/libnss_files-2.18.so
7f1da977f000-7f1da9780000 r--p 0000b000 08:01 521244 /lib/x86_64-linux-gnu/libnss_files-2.18.so
7f1da9780000-7f1da9781000 rw-p 0000c000 08:01 521244 /lib/x86_64-linux-gnu/libnss_files-2.18.so
7f1da9781000-7f1da978b000 r-xp 00000000 08:01 521253 /lib/x86_64-linux-gnu/libnss_nis-2.18.so
7f1da978b000-7f1da998a000 ---p 0000a000 08:01 521253 /lib/x86_64-linux-gnu/libnss_nis-2.18.so
7f1da998a000-7f1da998b000 r--p 00009000 08:01 521253 /lib/x86_64-linux-gnu/libnss_nis-2.18.so
7f1da998b000-7f1da998c000 rw-p 0000a000 08:01 521253 /lib/x86_64-linux-gnu/libnss_nis-2.18.so
7f1da998c000-7f1da9993000 r-xp 00000000 08:01 521246 /lib/x86_64-linux-gnu/libnss_compat-2.18.so
7f1da9993000-7f1da9b92000 ---p 00007000 08:01 521246 /lib/x86_64-linux-gnu/libnss_compat-2.18.so
7f1da9b92000-7f1da9b93000 r--p 00006000 08:01 521246 /lib/x86_64-linux-gnu/libnss_compat-2.18.so
7f1da9b93000-7f1da9b94000 rw-p 00007000 08:01 521246 /lib/x86_64-linux-gnu/libnss_compat-2.18.so
7f1da9b94000-7f1da9b95000 ---p 00000000 00:00 0
7f1da9b95000-7f1daa415000 rw-p 00000000 00:00 0 [stack:5355]
7f1daa415000-7f1daa595000 rwxp 00000000 00:00 0
7f1daa595000-7f1daa615000 rw-p 00000000 00:00 0
7f1daa615000-7f1daa616000 ---p 00000000 00:00 0
7f1daa616000-7f1daae16000 rw-p 00000000 00:00 0 [stack:5354]
7f1daae16000-7f1daae1f000 r-xp 00000000 08:01 270355 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f1daae1f000-7f1dab01e000 ---p 00009000 08:01 270355 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f1dab01e000-7f1dab01f000 r--p 00008000 08:01 270355 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f1dab01f000-7f1dab020000 rw-p 00009000 08:01 270355 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f1dab020000-7f1dab022000 r-xp 00000000 08:01 277479 /usr/lib/x86_64-linux-gnu/libXss.so.1.0.0
7f1dab022000-7f1dab222000 ---p 00002000 08:01 277479 /usr/lib/x86_64-linux-gnu/libXss.so.1.0.0
7f1dab222000-7f1dab223000 rw-p 00002000 08:01 277479 /usr/lib/x86_64-linux-gnu/libXss.so.1.0.0
7f1dab223000-7f1dab25d000 r-xp 00000000 08:01 270332 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.8.0
7f1dab25d000-7f1dab45c000 ---p 0003a000 08:01 270332 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.8.0
7f1dab45c000-7f1dab45e000 r--p 00039000 08:01 270332 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.8.0
7f1dab45e000-7f1dab45f000 rw-p 0003b000 08:01 270332 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.8.0
7f1dab45f000-7f1dab473000 r-xp 00000000 08:01 275893 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.1
7f1dab473000-7f1dab673000 ---p 00014000 08:01 275893 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.1
7f1dab673000-7f1dab674000 rw-p 00014000 08:01 275893 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.1
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7f1dab889000-7f1dab88a000 rw-p 00015000 08:01 521239 /lib/x86_64-linux-gnu/libnsl-2.18.so
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7f1dabba5000-7f1dabba9000 r--p 00119000 08:01 299562 /usr/lib/x86_64-linux-gnu/libtcl8.5.so
7f1dabba9000-7f1dabbb0000 rw-p 0011d000 08:01 299562 /usr/lib/x86_64-linux-gnu/libtcl8.5.so
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7f1dabbb1000-7f1dabcdd000 r-xp 00000000 08:01 299568 /usr/lib/x86_64-linux-gnu/libtk8.5.so
7f1dabcdd000-7f1dabedc000 ---p 0012c000 08:01 299568 /usr/lib/x86_64-linux-gnu/libtk8.5.so
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7f1dac003000-7f1dac203000 ---p 00107000 08:01 299629 /usr/lib/libBLT.2.4.so.8.5
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7f1dac221000-7f1dac222000 rw-p 00000000 00:00 0
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7f1dad976000-7f1dadb75000 ---p 00037000 08:01 278421 /usr/lib/x86_64-linux-gnu/libtxc_dxtn_s2tc.so.0.0.0
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7f1dadb76000-7f1dadb77000 rw-p 00037000 08:01 278421 /usr/lib/x86_64-linux-gnu/libtxc_dxtn_s2tc.so.0.0.0
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7f1daf0ac000-7f1daf1c3000 rw-p 01535000 08:01 270279 /usr/lib/x86_64-linux-gnu/libLLVM-3.3.so.1
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7f1daf1d5000-7f1daf1dc000 r-xp 00000000 08:01 265205 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.1
7f1daf1dc000-7f1daf3db000 ---p 00007000 08:01 265205 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.1
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7f1daf3dc000-7f1daf3dd000 rw-p 00007000 08:01 265205 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.1
7f1daf3dd000-7f1daf404000 r-xp 00000000 08:01 521410 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f1daf404000-7f1daf604000 ---p 00027000 08:01 521410 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f1daf604000-7f1daf606000 r--p 00027000 08:01 521410 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f1daf606000-7f1daf607000 rw-p 00029000 08:01 521410 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f1daf607000-7f1dafb63000 r-xp 00000000 08:01 401825 /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
7f1dafb63000-7f1dafd63000 ---p 0055c000 08:01 401825 /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
7f1dafd63000-7f1dafd80000 r--p 0055c000 08:01 401825 /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
7f1dafd80000-7f1dafd8a000 rw-p 00579000 08:01 401825 /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
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7f1daffb7000-7f1db03b1000 rw-p 00000000 00:00 0
7f1db03b1000-7f1db0575000 r-xp 00000000 08:01 265863 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7f1db0575000-7f1db0775000 ---p 001c4000 08:01 265863 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7f1db0775000-7f1db0790000 r--p 001c4000 08:01 265863 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7f1db0790000-7f1db079f000 rw-p 001df000 08:01 265863 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7f1db079f000-7f1db07a3000 rw-p 00000000 00:00 0
7f1db07a3000-7f1db07f8000 r-xp 00000000 08:01 265878 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f1db07f8000-7f1db09f8000 ---p 00055000 08:01 265878 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f1db09f8000-7f1db09fb000 r--p 00055000 08:01 265878 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f1db09fb000-7f1db0a02000 rw-p 00058000 08:01 265878 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f1db0a02000-7f1db0a06000 r-xp 00000000 08:01 274397 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7f1db0a06000-7f1db0c05000 ---p 00004000 08:01 274397 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
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7f1db0c06000-7f1db0c07000 rw-p 00004000 08:01 274397 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7f1db0c07000-7f1db0d08000 rw-p 00000000 00:00 0
7f1db0d08000-7f1db0d0c000 r-xp 00000000 08:01 521455 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f1db0d0c000-7f1db0f0b000 ---p 00004000 08:01 521455 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f1db0f0b000-7f1db0f0c000 r--p 00003000 08:01 521455 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f1db0f0c000-7f1db0f0d000 rw-p 00004000 08:01 521455 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f1db0f0d000-7f1db0f24000 r-xp 00000000 08:01 271415 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f1db0f24000-7f1db1123000 ---p 00017000 08:01 271415 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f1db1123000-7f1db1125000 rw-p 00016000 08:01 271415 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f1db1125000-7f1db1128000 rw-p 00000000 00:00 0
7f1db1128000-7f1db112f000 r-xp 00000000 08:01 271417 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f1db112f000-7f1db132e000 ---p 00007000 08:01 271417 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f1db132e000-7f1db132f000 rw-p 00006000 08:01 271417 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f1db132f000-7f1db1334000 r-xp 00000000 08:01 270065 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f1db1334000-7f1db1533000 ---p 00005000 08:01 270065 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f1db1533000-7f1db1534000 rw-p 00004000 08:01 270065 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f1db1534000-7f1db1537000 r-xp 00000000 08:01 270059 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f1db1537000-7f1db1736000 ---p 00003000 08:01 270059 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f1db1736000-7f1db1737000 r--p 00002000 08:01 270059 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f1db1737000-7f1db1738000 rw-p 00003000 08:01 270059 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f1db1738000-7f1db1797000 r-xp 00000000 08:01 271512 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f1db1797000-7f1db1997000 ---p 0005f000 08:01 271512 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f1db1997000-7f1db1998000 r--p 0005f000 08:01 271512 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f1db1998000-7f1db199d000 rw-p 00060000 08:01 271512 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f1db199d000-7f1db199e000 rw-p 00000000 00:00 0
7f1db199e000-7f1db19a5000 r-xp 00000000 08:01 521242 /lib/x86_64-linux-gnu/librt-2.18.so
7f1db19a5000-7f1db1ba4000 ---p 00007000 08:01 521242 /lib/x86_64-linux-gnu/librt-2.18.so
7f1db1ba4000-7f1db1ba5000 r--p 00006000 08:01 521242 /lib/x86_64-linux-gnu/librt-2.18.so
7f1db1ba5000-7f1db1ba6000 rw-p 00007000 08:01 521242 /lib/x86_64-linux-gnu/librt-2.18.so
7f1db1ba6000-7f1db1bb1000 r-xp 00000000 08:01 270264 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f1db1bb1000-7f1db1db0000 ---p 0000b000 08:01 270264 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f1db1db0000-7f1db1db1000 r--p 0000a000 08:01 270264 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f1db1db1000-7f1db1db2000 rw-p 0000b000 08:01 270264 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f1db1db2000-7f1db1db7000 r-xp 00000000 08:01 270342 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f1db1db7000-7f1db1fb6000 ---p 00005000 08:01 270342 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f1db1fb6000-7f1db1fb7000 r--p 00004000 08:01 270342 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f1db1fb7000-7f1db1fb8000 rw-p 00005000 08:01 270342 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f1db1fb8000-7f1db1fd6000 r-xp 00000000 08:01 270070 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f1db1fd6000-7f1db21d5000 ---p 0001e000 08:01 270070 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f1db21d5000-7f1db21d6000 r--p 0001d000 08:01 270070 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f1db21d6000-7f1db21d7000 rw-p 0001e000 08:01 270070 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f1db21d7000-7f1db21da000 r-xp 00000000 08:01 270293 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f1db21da000-7f1db23da000 ---p 00003000 08:01 270293 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f1db23da000-7f1db23db000 r--p 00003000 08:01 270293 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f1db23db000-7f1db23dc000 rw-p 00004000 08:01 270293 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f1db23dc000-7f1db23f1000 r-xp 00000000 08:01 270334 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f1db23f1000-7f1db25f0000 ---p 00015000 08:01 270334 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f1db25f0000-7f1db25f2000 r--p 00014000 08:01 270334 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f1db25f2000-7f1db25f3000 rw-p 00016000 08:01 270334 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f1db25f3000-7f1db25f4000 r-xp 00000000 08:01 270305 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f1db25f4000-7f1db27f3000 ---p 00001000 08:01 270305 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f1db27f3000-7f1db27f4000 r--p 00000000 08:01 270305 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f1db27f4000-7f1db27f5000 rw-p 00001000 08:01 270305 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f1db27f5000-7f1db27fa000 r-xp 00000000 08:01 270336 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f1db27fa000-7f1db29f9000 ---p 00005000 08:01 270336 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f1db29f9000-7f1db29fa000 r--p 00004000 08:01 270336 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f1db29fa000-7f1db29fb000 rw-p 00005000 08:01 270336 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f1db29fb000-7f1db29fd000 r-xp 00000000 08:01 270338 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f1db29fd000-7f1db2bfc000 ---p 00002000 08:01 270338 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f1db2bfc000-7f1db2bfd000 r--p 00001000 08:01 270338 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f1db2bfd000-7f1db2bfe000 rw-p 00002000 08:01 270338 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f1db2bfe000-7f1db2c1f000 r-xp 00000000 08:01 270266 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f1db2c1f000-7f1db2e1f000 ---p 00021000 08:01 270266 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f1db2e1f000-7f1db2e22000 r--p 00021000 08:01 270266 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f1db2e22000-7f1db2e23000 rw-p 00024000 08:01 270266 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f1db2e23000-7f1db2e24000 rw-p 00000000 00:00 0
7f1db2e24000-7f1db2f59000 r-xp 00000000 08:01 270078 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f1db2f59000-7f1db3159000 ---p 00135000 08:01 270078 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f1db3159000-7f1db315a000 r--p 00135000 08:01 270078 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f1db315a000-7f1db315f000 rw-p 00136000 08:01 270078 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f1db315f000-7f1db3170000 r-xp 00000000 08:01 270340 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f1db3170000-7f1db336f000 ---p 00011000 08:01 270340 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f1db336f000-7f1db3370000 r--p 00010000 08:01 270340 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f1db3370000-7f1db3371000 rw-p 00011000 08:01 270340 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f1db3371000-7f1db3380000 r-xp 00000000 08:01 270932 /usr/lib/x86_64-linux-gnu/libXi.so.6.1.0
7f1db3380000-7f1db357f000 ---p 0000f000 08:01 270932 /usr/lib/x86_64-linux-gnu/libXi.so.6.1.0
7f1db357f000-7f1db3580000 r--p 0000e000 08:01 270932 /usr/lib/x86_64-linux-gnu/libXi.so.6.1.0
7f1db3580000-7f1db3581000 rw-p 0000f000 08:01 270932 /usr/lib/x86_64-linux-gnu/libXi.so.6.1.0
7f1db3581000-7f1db3599000 r-xp 00000000 08:01 272833 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f1db3599000-7f1db3799000 ---p 00018000 08:01 272833 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f1db3799000-7f1db379b000 rw-p 00018000 08:01 272833 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f1db379b000-7f1db37b0000 r-xp 00000000 08:01 521230 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1db37b0000-7f1db39b0000 ---p 00015000 08:01 521230 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1db39b0000-7f1db39b1000 rw-p 00015000 08:01 521230 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1db39b1000-7f1db3a96000 r-xp 00000000 08:01 265853 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f1db3a96000-7f1db3c96000 ---p 000e5000 08:01 265853 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f1db3c96000-7f1db3c9e000 r--p 000e5000 08:01 265853 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f1db3c9e000-7f1db3ca0000 rw-p 000ed000 08:01 265853 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f1db3ca0000-7f1db3cb5000 rw-p 00000000 00:00 0
7f1db3cb5000-7f1db3cf7000 r-xp 00000000 08:01 299556 /usr/lib/x86_64-linux-gnu/libglut.so.3.9.0
7f1db3cf7000-7f1db3ef7000 ---p 00042000 08:01 299556 /usr/lib/x86_64-linux-gnu/libglut.so.3.9.0
7f1db3ef7000-7f1db3efb000 r--p 00042000 08:01 299556 /usr/lib/x86_64-linux-gnu/libglut.so.3.9.0
7f1db3efb000-7f1db3f00000 rw-p 00046000 08:01 299556 /usr/lib/x86_64-linux-gnu/libglut.so.3.9.0
7f1db3f00000-7f1db3f6c000 r-xp 00000000 08:01 272794 /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1
7f1db3f6c000-7f1db416c000 ---p 0006c000 08:01 272794 /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1
7f1db416c000-7f1db416d000 r--p 0006c000 08:01 272794 /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1
7f1db416d000-7f1db416e000 rw-p 0006d000 08:01 272794 /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1
7f1db416e000-7f1db41c8000 r-xp 00000000 08:01 270344 /usr/lib/x86_64-linux-gnu/libGL.so.1.2.0
7f1db41c8000-7f1db43c8000 ---p 0005a000 08:01 270344 /usr/lib/x86_64-linux-gnu/libGL.so.1.2.0
7f1db43c8000-7f1db43ca000 r--p 0005a000 08:01 270344 /usr/lib/x86_64-linux-gnu/libGL.so.1.2.0
7f1db43ca000-7f1db43cb000 rw-p 0005c000 08:01 270344 /usr/lib/x86_64-linux-gnu/libGL.so.1.2.0
7f1db43cb000-7f1db43cc000 rw-p 00000000 00:00 0
7f1db43cc000-7f1db444d000 r-xp 00000000 08:01 273938 /usr/lib/x86_64-linux-gnu/libGLEW.so.1.10.0
7f1db444d000-7f1db464d000 ---p 00081000 08:01 273938 /usr/lib/x86_64-linux-gnu/libGLEW.so.1.10.0
7f1db464d000-7f1db4653000 rw-p 00081000 08:01 273938 /usr/lib/x86_64-linux-gnu/libGLEW.so.1.10.0
7f1db4653000-7f1db4658000 rw-p 00000000 00:00 0
7f1db4658000-7f1db46f6000 r-xp 00000000 08:01 270326 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.11.1
7f1db46f6000-7f1db48f5000 ---p 0009e000 08:01 270326 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.11.1
7f1db48f5000-7f1db48fb000 r--p 0009d000 08:01 270326 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.11.1
7f1db48fb000-7f1db48fc000 rw-p 000a3000 08:01 270326 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.11.1
7f1db48fc000-7f1db4922000 r-xp 00000000 08:01 525952 /lib/x86_64-linux-gnu/libpng12.so.0.50.0
7f1db4922000-7f1db4b21000 ---p 00026000 08:01 525952 /lib/x86_64-linux-gnu/libpng12.so.0.50.0
7f1db4b21000-7f1db4b22000 r--p 00025000 08:01 525952 /lib/x86_64-linux-gnu/libpng12.so.0.50.0
7f1db4b22000-7f1db4b23000 rw-p 00026000 08:01 525952 /lib/x86_64-linux-gnu/libpng12.so.0.50.0
7f1db4b23000-7f1db4f84000 r-xp 00000000 08:01 300014 /usr/lib/python2.7/dist-packages/pymol/_cmd.so
7f1db4f84000-7f1db5184000 ---p 00461000 08:01 300014 /usr/lib/python2.7/dist-packages/pymol/_cmd.so
7f1db5184000-7f1db5193000 r--p 00461000 08:01 300014 /usr/lib/python2.7/dist-packages/pymol/_cmd.so
7f1db5193000-7f1db55bd000 rw-p 00470000 08:01 300014 /usr/lib/python2.7/dist-packages/pymol/_cmd.so
7f1db55bd000-7f1db5601000 rw-p 00000000 00:00 0
7f1db5601000-7f1db57c6000 r--p 00000000 08:01 260609 /usr/lib/locale/locale-archive
7f1db57c6000-7f1db5966000 r-xp 00000000 08:01 521248 /lib/x86_64-linux-gnu/libc-2.18.so
7f1db5966000-7f1db5b65000 ---p 001a0000 08:01 521248 /lib/x86_64-linux-gnu/libc-2.18.so
7f1db5b65000-7f1db5b69000 r--p 0019f000 08:01 521248 /lib/x86_64-linux-gnu/libc-2.18.so
7f1db5b69000-7f1db5b6b000 rw-p 001a3000 08:01 521248 /lib/x86_64-linux-gnu/libc-2.18.so
7f1db5b6b000-7f1db5b6f000 rw-p 00000000 00:00 0
7f1db5b6f000-7f1db5c70000 r-xp 00000000 08:01 521245 /lib/x86_64-linux-gnu/libm-2.18.so
7f1db5c70000-7f1db5e70000 ---p 00101000 08:01 521245 /lib/x86_64-linux-gnu/libm-2.18.so
7f1db5e70000-7f1db5e71000 r--p 00101000 08:01 521245 /lib/x86_64-linux-gnu/libm-2.18.so
7f1db5e71000-7f1db5e72000 rw-p 00102000 08:01 521245 /lib/x86_64-linux-gnu/libm-2.18.so
7f1db5e72000-7f1db5e89000 r-xp 00000000 08:01 521435 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f1db5e89000-7f1db6088000 ---p 00017000 08:01 521435 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f1db6088000-7f1db6089000 r--p 00016000 08:01 521435 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f1db6089000-7f1db608a000 rw-p 00017000 08:01 521435 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f1db608a000-7f1db608c000 r-xp 00000000 08:01 521236 /lib/x86_64-linux-gnu/libutil-2.18.so
7f1db608c000-7f1db628b000 ---p 00002000 08:01 521236 /lib/x86_64-linux-gnu/libutil-2.18.so
7f1db628b000-7f1db628c000 r--p 00001000 08:01 521236 /lib/x86_64-linux-gnu/libutil-2.18.so
7f1db628c000-7f1db628d000 rw-p 00002000 08:01 521236 /lib/x86_64-linux-gnu/libutil-2.18.so
7f1db628d000-7f1db6290000 r-xp 00000000 08:01 521240 /lib/x86_64-linux-gnu/libdl-2.18.so
7f1db6290000-7f1db648f000 ---p 00003000 08:01 521240 /lib/x86_64-linux-gnu/libdl-2.18.so
7f1db648f000-7f1db6490000 r--p 00002000 08:01 521240 /lib/x86_64-linux-gnu/libdl-2.18.so
7f1db6490000-7f1db6491000 rw-p 00003000 08:01 521240 /lib/x86_64-linux-gnu/libdl-2.18.so
7f1db6491000-7f1db64a9000 r-xp 00000000 08:01 521234 /lib/x86_64-linux-gnu/libpthread-2.18.so
7f1db64a9000-7f1db66a8000 ---p 00018000 08:01 521234 /lib/x86_64-linux-gnu/libpthread-2.18.so
7f1db66a8000-7f1db66a9000 r--p 00017000 08:01 521234 /lib/x86_64-linux-gnu/libpthread-2.18.so
7f1db66a9000-7f1db66aa000 rw-p 00018000 08:01 521234 /lib/x86_64-linux-gnu/libpthread-2.18.so
7f1db66aa000-7f1db66ae000 rw-p 00000000 00:00 0
7f1db66ae000-7f1db66b2000 r-xp 00000000 08:01 521254 /lib/x86_64-linux-gnu/libSegFault.so
7f1db66b2000-7f1db68b1000 ---p 00004000 08:01 521254 /lib/x86_64-linux-gnu/libSegFault.so
7f1db68b1000-7f1db68b2000 r--p 00003000 08:01 521254 /lib/x86_64-linux-gnu/libSegFault.so
7f1db68b2000-7f1db68b3000 rw-p 00004000 08:01 521254 /lib/x86_64-linux-gnu/libSegFault.so
7f1db68b3000-7f1db68d3000 r-xp 00000000 08:01 521238 /lib/x86_64-linux-gnu/ld-2.18.so
7f1db6902000-7f1db69c2000 rw-p 00000000 00:00 0
7f1db69f3000-7f1db6ab8000 rw-p 00000000 00:00 0
7f1db6acf000-7f1db6ad2000 rw-p 00000000 00:00 0
7f1db6ad2000-7f1db6ad3000 r--p 0001f000 08:01 521238 /lib/x86_64-linux-gnu/ld-2.18.so
7f1db6ad3000-7f1db6ad4000 rw-p 00020000 08:01 521238 /lib/x86_64-linux-gnu/ld-2.18.so
7f1db6ad4000-7f1db6ad5000 rw-p 00000000 00:00 0
7fff4c0d5000-7fff4c0f6000 rw-p 00000000 00:00 0
7fff4c178000-7fff4c17a000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

537. Building ECCE 7.0 on CentOS 6.4

Following a report that there were issues building ECCE 7 on Centos 6.4 I decided to investigate.

1. Download 
Download the centos 6.4 iso: At ftp://mirror.stanford.edu/pub/mirrors/centos/6.4/isos/x86_64/ I downloaded ftp://mirror.stanford.edu/pub/mirrors/centos/6.4/isos/x86_64/CentOS-6.4-x86_64-minimal.iso

wget ftp://mirror.stanford.edu/pub/mirrors/centos/6.4/isos/x86_64/CentOS-6.4-x86_64-minimal.iso

2. Install centos in virtualbox
Not much to say other than that I gave the VM 12 gb disk and 1024 mb ram.
During installation I selected Install or Upgrade an existing system (option 1).  I went with all the defaults during installation.

3. Basic setup
Following the installation I rebooted.

First I activated eth by editing /etc/sysconfig/network-scripts/ifcfg-eth0 and changing onboot from no to yes. I rebooted and installed Gnome

Then install X and gnome.

yum groupinstall -y 'X Window System'
yum groupinstall -y 'Desktop'
useradd verahill
passwd verahill

Edit /etc/inittab and change

id:3:initdefault:

to

id:5:initdefault:

Reboot.

Install openGL libraries. The way to do that depends on what graphics chip your have, e.g. libgl1-nvidia-glx for nvidia. In my virtualbox example I didn't have to do anything.  

4. ECCE
Launch gnome-terminal
Become root and install packages, then exit:

su
yum install vim csh gcc gcc-c++ gcc-gfortran java-1.7.0-openjdk-devel python-devel ant gtk2-devel libjpeg-turbo-devel libtool ImageMagick libXt-devel xterm mesa-libGLU-devel kernel-devel perl-Digest-Perl-MD5 perl-Digest-MD5
yum install 
exit

mkdir ~/tmp
cd ~/tmp

Download ecce from http://ecce.pnl.gov/using/download.shtml into ~/tmp

tar xvf ecce-v7.0-src.tar.bz2
cd ecce-v7.0/
export ECCE_HOME=`pwd`
cd build/
./build_ecce
./build_ecce
./build_ecce
./build_ecce
./build_ecce
./build_ecce
./build_ecce

Everything builds just fine.

You can then install the ecce_install.v7.0.csh file created in the parent directory by following e.g. this post: http://verahill.blogspot.com.au/2013/08/487-version-70-of-ecce-out-now.html

57. Making life in linux easier -- Small fixes and tasks

Here's a list over simple fixes and tasks in Debian that I've been running into the past few weeks. I'll be adding to it over time.

---

Index of the ever-growing list
1. INIT: Id "co" respawning too fast: disabled for 5 minutes
2. Boot into terminal instead of gdm (kdm/xdm etc.)
3. Change the logical name of an ethernet card -- why do I have eth1 and rename2 and how to get eth0 and eth1 instead?

4. Configuring ethernet cards in gnome3/gnome-shell -- can't save changes in network-manager
5. Gnome3/gnome-shell -- Alt+f2 yields "command not found"
6. /etc/hosts keep on being overwritten
7. Getting Leadtek DTV1000s to work in Linux
8. Turning off terminal beep
9. Trouble with apt-get  -- can't do apt-get update
10. Adding and removing pages in a pdf using pdftk
11. Updating the locate database
12. My gateway doesn't play well with sinfo
13. Basic proxy via ssh
14. Using a Compose key to type non-standard characters like å, ä, ö
15. Command not found, did you mean ..? Installing command-not-found
16. apt-listbugs
17. Thunar is the default file manager in spite of me running Gnome!
18. Nautilus recognises compressed files, but doesn't know how to open them
19. Finding out when a package was installed
20. Showing your kernel and debian version
21. Screen dump in the terminal
22. Enable java in chrome
23. Changing element colour in gdis
24. CCSD mercury /lib/libc6.so
25. Daemons...rcconf, sysv-rc-conf and update-rc.d
26. Adjusting your webcam
27. Command line burning of iso
29. USB support in virtualbox
30. Start-up applications in Gnome 3.4
31. Changing pulseaudio volume from the command line

---

1. INIT: Id "co" respawning too fast: disabled for 5 minutes
References: http://www.linuxquestions.org/questions/fedora-35/init-id-co-respawning-too-fast-disabled-for-5-minutes-736393/ and http://www.linuxquestions.org/questions/linux-newbie-8/reload-inittab-without-reboot-366505/

Instructions: 
Edit /etc/inittab
Find a line saying
co:2345:respawn:/sbin/getty hvc0 9600 linux
and comment it out by prefixing it with a #;

#co:2345:respawn:/sbin/getty hvc0 9600 linux

Run 

sudo init q

to make the changes take effect.

2. Boot into terminal instead of gdm (kdm/xdm etc.)

References: http://ubuntuforums.org/showthread.php?t=1322949

Instructions:

Method 1:
Edit /etc/default/grub

Change

GRUB_CMDLINE_DEFAULT="quiet splash nomodeset nouveau.modeset=0"

to

GRUB_CMDLINE_DEFAULT="quiet splash text nomodeset nouveau.modeset=0"

(You may obviously not have nomodset etc. in that line. )

IMPORTANT: run

sudo update-grub

to make the changes take effect.

To start up a desktop type startx

3. Change the logical name of an ethernet card -- why do I have eth1 and rename2 and how to get eth0 and eth1 instead?  

Edit /etc/udev/rules.d/70-persistent-net.rules

You'll find lines like this one:

SUBSYSTEM=="net", ACTION=="add", DRIVERS=="?*", ATTR{address}=="08:00:27:e9:90:00", ATTR{dev_id}=="0x0", ATTR{type}=="1", KERNEL=="eth*", NAME="eth0"

You can bind a logical name (NAME="eth0") to a mac address (ATTR{address}=="") here.

NOTE that interfaces handled by network-manager won't show up here. Unless you initialise a network interface in /etc/network/interfaces they will be handled by network-manager.

4. Configuring ethernet cards in gnome3/gnome-shell -- can't save changes in network-manager

If you click on the network icon in gnome3/gnome-shell, then network settings, wired, configure and edit the connection, then hit save, you may find that it won't save the changes. You may even see a black box asking for admin password flash by and disappearing.

There's no real fix -- make sure to start the Network Connections application the 'normal' way instead (top left corner, type in networ... and pick network connections. You'll be able to save your changes now.

5. Gnome3/gnome-shell -- Alt+f2 yields "command not found"

Edit /usr/share/gnome-shell/js/misc/util.js 

Delete all instances of argc e.g. if it say success, argc, argv -- change to success, argv

6. /etc/hosts keep on being overwritten
The culprit is -- no surprise --- network-manager. You can either fight it, or use network-manager to manage your configuration.

My particular case was this: my computer is called tantalum. I don't want tantalum to be associated with 127.0.1.1 or 127.0.0.1 though (mpich2 reasons), but want to associate the host name with the external ip address (192.168.1.102). This is a typical case where you'd edit /etc/hosts and you'd be done. Apart from the fact that the file gets overwritten on each boot.

To force it using network manager, start network-admin in the terminal or using alt+f2, go to Hosts, and remove your hostname from 127.0.1.1 and add it using the desired ip address.

Reading this it seems like it's possible making changes in the configuration files directly. In particular, the option to define unmanaged devices looks interesting.

Network Manager is one of those programs which are great when you need basic functionality from your system, but an absolute pain in the arse when you need to do something non-standard.

7. Getting Leadtek DTV1000s to work in Linux

This is a bit of a non-fix...the card should work out of the box, so to speak.

However, it didn't for me. 

If lspci gives Philips something or other and rev ff rather than e.g. rev 01 as well as MMIO errors, check your BIOS! I kept on getting very little information about my card when doing lspci -vn and it turned out that I had disabled PnP in the BIOS. Once the bios was set to allow the OS to configure PCI devices (Plug-and-play OS), everything worked like a charm.

I put
options saa7134 tuner=48 card=175

in my /etc/modules, but I'm not sure this matters.

Long before discovering that I built and installed the v4l-dvb media build from the git repos,
(Easily done like this:
git clone git://linuxtv.org/media_build.git
cd media_build
./build
)
 and downloaded the firmware packages by Mike Krufky (http://tw1965.myweb.hinet.net/), and spent time reading forum posts (starting with http://forums.whirlpool.net.au/archive/942269). What I'm saying is that I don't THINK you will need to install or compile anything, but you MAY have to. Make sure your BIOS settings are right first though.

Here's lcpci -vvnn for a working leadtek dtv1000s:

01:06.0 Multimedia controller [0480]: Philips Semiconductors SAA7130 Video Broadcast Decoder [1131:7130] (rev 01)
Subsystem: LeadTek Research Inc. WinFast DTV1000S [107d:6655]
Control: I/O- Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx-
Status: Cap+ 66MHz- UDF- FastB2B+ ParErr- DEVSEL=medium >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
Latency: 64 (21000ns min, 8000ns max)
Interrupt: pin A routed to IRQ 19
Region 0: Memory at deeffc00 (32-bit, non-prefetchable) [size=1K]
Capabilities: <access denied>l
Kernel driver in use: saa7134

Here's dmesg|grep saa

    7.213108] saa7130/34: v4l2 driver version 0, 2, 17 loaded

[    7.213383] saa7134 0000:01:06.0: PCI INT A -> Link[LNKC] -> GSI 19 (level, low) -> IRQ 19

[    7.213387] saa7130[0]: found at 0000:01:06.0, rev: 1, irq: 19, latency: 64, mmio: 0xdeeffc00

[    7.213392] saa7130[0]: subsystem: 107d:6655, board: Leadtek Winfast DTV1000S [card=175,autodetected]

[    7.213407] saa7130[0]: board init: gpio is 2020000

[    7.260128] input: saa7134 IR (Leadtek Winfast DTV as /devices/pci0000:00/0000:00:04.0/0000:01:06.0/rc/rc0/input6

[    7.260181] rc0: saa7134 IR (Leadtek Winfast DTV as /devices/pci0000:00/0000:00:04.0/0000:01:06.0/rc/rc0

[    7.412048] saa7130[0]: i2c eeprom 00: 7d 10 55 66 54 20 1c 00 43 43 a9 1c 55 d2 b2 92

[    7.412055] saa7130[0]: i2c eeprom 10: 00 ff 82 0e ff 20 ff ff ff ff ff ff ff ff ff ff

[    7.412060] saa7130[0]: i2c eeprom 20: 01 40 01 01 01 ff 01 03 08 ff 00 8a ff ff ff ff

[    7.412065] saa7130[0]: i2c eeprom 30: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412070] saa7130[0]: i2c eeprom 40: ff 35 00 c0 00 10 03 02 ff 04 ff ff ff ff ff ff

[    7.412074] saa7130[0]: i2c eeprom 50: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412079] saa7130[0]: i2c eeprom 60: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412084] saa7130[0]: i2c eeprom 70: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412089] saa7130[0]: i2c eeprom 80: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412093] saa7130[0]: i2c eeprom 90: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412098] saa7130[0]: i2c eeprom a0: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412103] saa7130[0]: i2c eeprom b0: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412108] saa7130[0]: i2c eeprom c0: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412113] saa7130[0]: i2c eeprom d0: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412117] saa7130[0]: i2c eeprom e0: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.412122] saa7130[0]: i2c eeprom f0: ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff

[    7.608255] saa7130[0]: registered device video0 [v4l2]

[    7.608280] saa7130[0]: registered device vbi0


8. Turning off terminal beep
To remove immediately:
sudo modprobe -r pcspkr snd_pcsp

To turn off permanently:
create a file called blacklist.conf in /etc/modprobe.d
Put the following in it:

blacklist pcspkr
blacklist snd_pcsp

9. Trouble with apt-get  -- can't do apt-get update
The issue:
On running

sudo apt-get update

you get

Reading package lists... Error!
E: Encountered a section with no Package: header
E: Problem with MergeList /var/lib/apt/lists/192.168.1.1:3142_ftp.au.debian.org_debian_dists_testing_contrib_i18n_Translation-en
E: The package lists or status file could not be parsed or opened.

The solution:

First, look in /var/lib/apt/lists

ls /var/lib/apt/lists/ -lah | grep contrib |grep i18n| grep testing

which gives

-rw-r--r-- 1 root root  34K Feb  3 07:01 192.168.1.1:3142_ftp.au.debian.org_debian_dists_testing_contrib_i18n_Translation-en

-rw-r--r-- 1 root root 121K Feb  3 07:01 192.168.1.1:3142_ftp.au.debian.org_debian_dists_testing_contrib_i18n_Translation-en%5fAU

Then remove the offending file:

sudo rm /var/lib/apt/lists/192.168.1.1:3142_ftp.au.debian.org_debian_dists_testing_contrib_i18n_Translation-en

And do sudo apt-get update again -- it should now work.

If it doesn't then you're lacking bzip2 and should look at this post.

10. Adding and removing pages in a pdf using pdftk
Scenario:
I have a pdf document which I need to sign on the last page. Instead of printing the entire document and scanning it, I print the last page, scan it and replace the last page of the original pdf with it.

How to do:
In my case I have a 27 page document and want to replace pages 25, 26 and 27..

Remove pages 25-27 from original document i.e.keep 1-24:
pdftk original.pdf cat 1-24 output new.pdf

Add new pages 25,26 and 27 which make up signatures.pdf
pdftk cat new.pdf signatures.pdf output final_document

11. Updating the locate database
locate is a good command for finding certain types of files. It seems to be continously, but not immediately, updated.

To force the locate database to update:
sudo updatedb

12. My gateway doesn't play well with sinfo
My gateway is a computer with two eth cards -- one connected to the internet and one to a switch making up a local subnet. All the boxes on the local subnet can see each other's sinfod instances, but not the gateway machine.

Turns out the fix is simple -- change /etc/default/sinfo:
from

#OPTS="${OPTS} --bcastaddress=127.0.0.1"

to

OPTS="${OPTS} --bcastaddress=192.168.1.255"

which is the appropriate broadcast for my subnet.

Sinfo is cool and a 'must' for anyone running a small LAN for computational reasons:

/ 3 nodes, 11 CPUs   total CPU utilization:   2.7% ( 0.351 GHz / 12.800 GHz )
beryllium                     uuuuuusssiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii-------------------------( 4) mem: 55.6% swap:  0.0%   us:  4.8%    id: 92.7%        me S   8.9   0 chrome     
me S   6.6   0 vmd_LINUXAMD64     
me S   5.5   0 chrome     
me S   4.5   0 gnome-shell     
root R   4.0   0 Xorg
kookaburra                    iiii---------------------------------------------------------------------------------------------------------------------------------------------------------( 1) mem: 22.9% swap:  0.0%   us:  0.0%                            sy:  0.0%                            ni:  0.0%    wa:  0.0%                            id:100.0%     
me S   0.2   0 sinfo   
daemon R   0.1  10 sinfod       
ntp S   0.0   0 ntpd     
root S   0.0   0 rsyslogd       
root S   0.0   0 /usr/sbin/apachtantalum                      iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii( 1) mem: 20.9% swap:  0.0%   us:  0.0%                            sy:  0.0%                            ni:  0.0%                            wa:  0.0%    ;id:100.0%     
me S   0.3   0 conky       
root S   0.2   0 Xorg     
me S   0.1   0 gnome-shell     
me  S   0.1   0 dropbox     
me S   0.0   0 linphone-3

If you can't see all the boxes on your gateway, change all the LAN boxes to broadcast on 192.168.1.255 (or the appropriate replacement).

13. Basic proxy via ssh
If you have an ssh account on another server you can use it as a proxy

ssh -C -D 9889 me@remote.server.org

-C turns on compression
-D redirects traffic sent to port 9889 to the remote.server.org

Chrome/Chromium use the system settings for the network connection:
To use the proxy for web browsing on gnome 3/gnome-shell, left-click on the connection icon in the top right corner of your desktop (or just go to System Settings), select Network Settings, Click on the tab called Network Proxy, Method: Manual, and set SOCKS host to localhost and port to 9889. You can also change it in Chrome/Chromium -- preferences/proxy which opens the system-wide network settings.

Iceweasel/Firefox by default uses it's own settings:
Edit/Preferences/Network tab/Connections - Settings... -- Select Manual Proxy Configuration, SOCKS hosts: localhost, port 9889.

14. Using a Compose key to type non-standard characters like å, ä, ö
In gnome 3/gnome-shell, open Region and Languages in the System Settings; select the Layout tab. Pick your usual language (e.g. English (US)) and click on options. Expand the Compose Key Position and pick a key to use as the Compose Key, e.g. right alt or the windows symbol key.

Now you can type fancy European characters with a lot more ease -- for a list over key sequences, look here.

Two example -- to type É first touch the compose key (don't hold it down), then ', then shift+E. For å do compose, o, a. For € do compose, =, c. For ö, do compose, ", o.

15. Command not found, did you mean ..? Installing command-not-found
On a basic install of debian, typing nfs gets you

me@lithium:~$ nfs
-bash: nfs: command not found

Linux can do better than that:

Install command-not-found

sudo apt-get install command-not-found

sudo update-command-not-found

Restart the shell (or log in and out)

Now, when typing nfs you get:

me@lithium:~$ nfs
No command 'nfs' found, did you mean:
 Command 'lfs' from package 'lustre-utils' (main)
 Command 'xfs' from package 'xfs' (main)
 Command 'knfs' from package 'openafs-client' (main)
 Command 'nns' from package 'tcllib' (main)
 Command 'ns' from package 'ns2' (main)
 Command 'fs' from package 'openafs-client' (main)
 Command 'zfs' from package 'zfs-fuse' (main)
 Command 'hfs' from package 'hfsutils-tcltk' (main)
nfs: command not found

16. apt-listbugs

A useful tool for catching problematic packages when you upgrade/dist-upgrade is to use apt-listbugs. It gets invoked automatically when you run sudo apt-get...

Install by

sudo apt-get install apt-listbugs

For an example of it in action, see http://www.worksinmymind.com/blog/?p=1125

17. Thunar is the default file manager in spite of me running Gnome!
You can either remove thunar -- which you probably got through install xfce4 -- or you can edit .config/xfc4/helpers.rc

me@niobium:~$ cat .config/xfce4/helpers.rc
MailReader=evolution
#FileManager=Thunar
FileManager=nautilus
WebBrowser=google-chrome

18. Nautilus recognises compressed files, but doesn't know how to open them

Install file-roller. You may want to install additional packages as per aptitude show file-roller:

Suggests: arj, binutils, cpio, lha, lzip, lzma, lzop, ncompress, rpm2cpio, rzip, sharutils, unace, unalz, unrar |
          p7zip-rar, unzip, xz-utils, zip, zoo

19. Finding out when a package was installed
Look here.

Listing all packages according to time, most recent last.

ls /var/lib/dpkg/info/*.list -lrth| grep "info/lib"

Looking for a specific subset of packages

ls /var/lib/dpkg/info/*.list -lrth| grep "info/lib"

20. Showing your kernel and debian version
Someone searched for www.google.co.kr — linux debian version check and ended up on this blog. Well, here are the answers:

me@beryllium:~$ uname -a
Linux beryllium 3.2.0-1-amd64 #1 SMP Sun Feb 5 15:17:15 UTC 2012 x86_64 GNU/Linux
me@beryllium:~$ cat /etc/debian_version
wheezy/sid

21. Screen dump in the terminal
Method 1. Works in the 'true' terminals i.e. ttyX:
If you want to save what is already on the screen into a text file, do
sudo cat /dev/vcsX > screendump.txt
where X is the number of your terminal (e.g. tty1, tty2 etc.)

This method does not seem to add linebreaks -- instead it presumes that you're using a standard 80 char terminal.


Method 2. Using framebuffer
First check if you are using the framebuffer
ls /dev/fb0
If so, install fbcat
sudo apt-get install fbcat

Get a screen dump by running
fbgrab screendump.png

22. Enable java in chrome
Java has always been tricky. Sometimes icedtea-plugin has worked, sometimes it hasn't. At the moment it works:
sudo apt-get install icedtea-plugin

update-alternatives: using /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/javaws to provide /usr/bin/javaws (javaws) in auto mode.update-alternatives: using /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/itweb-settings to provide /usr/bin/itweb-settings (itweb-settings) in auto mode.

Not sure about the java-6-openjdk-amd64 since I actually have openjdk-7 installed and not 6. Try installing openjdk7-7-jdk first.

i A openjdk-6-jre                   - OpenJDK Java runtime, using Hotspot JIT   
i A openjdk-6-jre-headless          - OpenJDK Java runtime, using Hotspot JIT (h
i A openjdk-6-jre-lib               - OpenJDK Java runtime (architecture indepen
i   openjdk-7-jdk                   - OpenJDK Development Kit (JDK)             
i   openjdk-7-jre                   - OpenJDK Java runtime, using Hotspot JIT   
i A openjdk-7-jre-headless          - OpenJDK Java runtime, using Hotspot JIT (h
i A openjdk-7-jre-lib               - OpenJDK Java runtime (architecture indepent

23. Changing element colour in gdis
GDIS is, in my opinion, the best linux program for generating povray files from crystallographic data. Mainly this is due to the number of different representations which can be selected: from ball-and-stick to polyhedral to surface -- and it allows mixing different representations in  the same molecule, which is what sets it apart.

Long story short, in order to change the default element colours you have to manually edit /usr/share/gdis/gdis.elements

Each element is contained between a %gdis_elemen and and a %gdis_end tag. The colour is given in RGB code ranging from 0 to 65k. To look up RGB codes, look e.g. here http://www.tayloredmktg.com/rgb/.

%gdis_elem
symbol: Na
  name: Sodium
number: 11
weight: 22.989799
  cova: 0.970000
   vdw: 1.450000
charge: 1.000000
colour: 30000 52600 60600
%gdis_end

You can also change the covalent and van der Waal radii here -- these are used to determine bonding  so if you have too many or not enough bonds in the molecule, you can fiddle with this.

As an aside, I'm having problems in general with converting .tga and .png to good-looking eps. This is the best I've got so far and uses inkscape. Convert and GIMP don't yield results which are as good.

povray +W400 +H400 $1.pov +A
inkscape --verb FileSave --verb FileClose --export-eps=$1.eps $1.png 

Odd though that povray can't directly output vector-based image formats.
Edit: Here are the technical reasons why we're stuck with bitmap formats: http://news.povray.org/povray.pov4.discussion.general/message/%3C4a79fd58%241%40news.povray.org%3E/#%3C4a79fd58%241%40news.povray.org%3E

24. CCSD mercury /lib/libc.so.6

Mercury is a program for displaying crystal structures from the CCSD.
./mercury 

Using native OpenGL
Warning: mercury requires /lib/libc.so.6 but not found

sudo ln -s /lib/x86_64-linux-gnu/libc.so.6 /lib/libc.so.6

ls /lib/libc.so.6 -lah

/lib/libc.so.6 -> /lib/x86_64-linux-gnu/libc.so.6

./mercury 

Using native OpenGL
INFO: The environment variable CSDHOME is not set.

You can set CSDHOME by including

export CSDHOME=/home/me/mercury

(use the correct path)

in your ~/.bashrc

25. Daemons...rcconf and update-rc.d
You can easily enable and disable services to load on boot by using rcconf, which is an curses type tool.

Or use sysv-rc-conf:

Alternative, use update-rc.d which doesn't faff around with any gui.
Usage is described here.
To remove a daemon:
update-rc.d -f apt-cacher-ng remove
To add a daemon:
update-rc.d apt-cacher-ng defaults

If you're more adventurous:
update-rc.d apt-cacher-ng start 20 2 3 4 5 . stop 20 0 1 6 .

where 20 is a two-digit seq code used by init to decide which order to run the script in, and numbers between 1 and 9 and S are the run levels. More information in /etc/inittab

Here: "Default Debian installation does not make any difference between runlevels 2-5. You may customize them to your liking. Runlevels S (single) and 1 are used for maintenance. They start services minimally to avoid possible problems." 0 is halt and 6 is reboot.

26. Adjusting your webcam
I've had problems with webcam images being overly dark -- trying to adjust the image with cheese leads to nothing.

v4l2ucp, which is in the debian repos, however, is a good GUI-based configuration tool which allows you to adjust most things, including, importantly, light sensitivity rather than just brightness.

v4l2ucp on a much-too-small screen

27. Command line burning of iso
sudo apt-get install burn
sudo burn -I -n debian.iso
Simple as that.

For burning audio cds from mp3 files I use a slightly different approach:

sudo apt-get install brasero-cdrkit mpg123
for i in *.mp3; do mpg123 --rate 44100 --stereo --buffer 3072 --resync -w "`basename "$i" .mp3`".wav "$i"; done
Then name the files in a way that they are listed in desired play order.

ls /dev/cdr

cdrom1  cdrw1

 wodim -v -pad speed=1 dev=/dev/cdrw1 -dao -swab *.wav

burns.

28. Finding a file in a package
Two methods:
dpkg --search libglib
apt-file search libglib
(apt-file update before first use)

29. USB support in virtualbox
If you keep getting errors along the lines of:

Failed to access the USB subsystem

and

NS_ERROR_FAILURE

in virtualbox when trying to enable USB devices, make sure that you've added yourself to the vboxusers group in /etc/group. You'll need to reinit before it takes effect (e.g. by rebooting)

30. Startup applications in gnome 3.4
In the past I've always used gnome-session-properties, but it's a hit and miss affair at the moment. So it would be nice with an alternative approach.

According to this: http://ubuntuforums.org/showthread.php?t=1992296
anything which is found in /etc/xdg/autostart will be automatically executed, e.g.

cat /etc/xdg/autostart/guake.desktop 

[Desktop Entry]
Name=Guake Terminal
Name[pt]=Guake Terminal
Name[pt_BR]=Guake Terminal
Comment=Use the command line in a Quake-like terminal
Comment[pt]=Utilizar a linha de comando em um terminal estilo Quake
Comment[pt_BR]=Utilizar a linha de comando em um terminal estilo Quake
TryExec=guake
Exec=guake
Icon=/usr/share/pixmaps/guake/guake.png
Type=Application
Categories=GNOME;GTK;Utility;TerminalEmulator;
StartupNotify=true
X-GNOME-Autostart-enabled=false

Also, it's been suggested that there's a bug in guake: http://motorscript.com/guake-patch-to-fix-focus-on-gnome/
Guake starts well for me on my laptop, but not on my nvidia boxes.

31. Changing pulseaudio volume from the command line
Copy this script (https://gist.github.com/814634) and make executable. Requires ruby.
Invoke using the arguments up, down, toggle.