89. Compiling kernel 3.2.8 on Debian Testing -- example using kernel-packages and kernel.org source

For kernel 3.2.9, see here: http://verahill.blogspot.com.au/2012/03/debian-testing-kernel-329.html

Following: http://www.linuxplanet.com/linuxplanet/tutorials/6853/1 and http://www.sysdesign.ca/guides/linux_kernel.html  and very much http://old-releases.ubuntu.com/ubuntu/dists/hoary/main/installer-ia64/current/doc/manual/en/ch08s04.html

Update: added kernel_headers

I've added very litte to the guides, except proving that yes, the above tutorial works for the current stable kernel version (3.2.8) and the current debian testing (29/12/2012).

Here's what's new in 3.2.8 -- https://lwn.net/Articles/484042/
Here's what will be new in 3.3 -- http://www.h-online.com/open/features/Kernel-Log-Linux-3-3-goes-into-testing-1418516.html

Everything between SAFE START and END are ok -- they won't change anything serious on your system. If you're building on a 32 bit system, have a look at the end of the post before launching the make.

--  SAFE START --
Install tools:
sudo apt-get install kernel-package fakeroot
(if you use apt-bugs you may get a warning about an lguest bug. Ignore it. Look at the bottom of the post for 32 bit issues and a simple solution.)


Get the latest STABLE release from http://kernel.org/
wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.2.8.tar.bz2
It's 75 M and will take a wee while.
tar -xvf linux-3.2.8.tar.bz2
cd linux-3.2.8/

To get a head-start on a configuration file, see if you have one for your current kernel:
ls /boot/config-`uname -r`

If so (I know this is clunky, but the obvious solutions didn't work...)
echo "/boot/config-`uname -r` "|xargs cat > .config

I'm running 3.2.0-1.

Alright. Here's the thing. You shouldn't edit .config unless you know what you're doing. But then how will you ever learn? I don't yet know what I'm doing, so won't lead you into kernel-configuration related temptation.

Instead, we'll just learn how to build.

First
make oldconfig
which uses the .config

But it's not completely automatic -- when it comes to new features you'll have to provide input. Hitting enter i.e. accepting the default option is probably a good idea unless you think otherwise.

Alternatively, you do
make menuconfig
and pick everything you want

Here are the new features in 3.2.8 vs 3.2.0-1: 

  Cirrus Logic (Sound Fusion) New DSP support (SND_CS46XX_NEW_DSP) [Y/n/?] (NEW)
Agere Systems HERMES II Wireless PC Card Model 0110 (WLAGS49_H2) [N/m/?] (NEW)
 Linksys HERMES II.5 WCF54G_Wireless-G_CompactFlash_Card (WLAGS49_H25) [N/m/?] (NEW) 

Y means compile into kernel, m makes a loadable module and no means no.

Now build!
make-kpkg clean
The next step takes forever, in particular if you only use one core (>1 h). It takes ca 50 minutes on an i5 with the -j5 switch. You'll also need around 6.5 Gb of free space for the compilation.
fakeroot make-kpkg -j4 --initrd --revision=3.2.8 kernel_image kernel_headers

where as usual 4 is the number of cores(3)+1. Adjust as necessary.

--SAFE END--

This really isn't dangerous, although you may not want to do it remotely without a back-up plan.

Install with
sudo dpkg -i ../linux-image-3.2.8_3.2.8_amd64.deb
sudo dpkg -i ../linux-headers-3.2.8_3.2.8_amd64.deb

That's it! You don't even have to bother with update-grub.

Reboot at your convenience and admire your handiwork:
uname -a

Linux boron 3.2.8 #2 SMP Wed Feb 29 19:27:04 EST 2012 x86_64 GNU/Lin

The deb built this way is ca 33 M, while the stock debian 3.2.0--1 is a slim 23 M.

Once you're confident that you can compile and install a kernel without mishap you can start to remove kernel modules to make it slimmer -- or start including modules of your own choosing.


Tried and tested on:
AMD Athlon II X3 (64 bit)
2 x AMD Phenom II X6 (64 bit)
Intel i5-2400 (64 bit)
Intel core 2  duo T5870 (laptop, 64 bit)
Intel Celeron 1.6 GHz (32 bit)
-- all running debian testing.

---

Building on 32 bit

I had some issues on an Intel Celeron 1.6 GHz 32 bit due to a bug:

make[1]: Leaving directory `/home/me/tmp/linux-3.2.8'
/usr/bin/make    ARCH=i386 \
    -C Documentation/lguest
make: *** Documentation/lguest: No such file or directory.  Stop.
make: *** [debian/stamp/build/kernel] Error 2

The failure was pretty annoying...

real 157m58.192s
user 132m27.049s
sys 12m5.589s

There's a simple solution in a forum post at http://billy.com.mx/archives/660:

"I solved it by creating a symlink Documentation/lguest to Documentation/virtual/lguest"

that means (on one line)
ln -s /home/me/tmp/linux-3.2.8/Documentation/virtual/lguest  Documentation/lguest


That's all.


Check:
ls Documentation/lguest -lah

Documentation/lguest -> /home/me/tmp/linux-3.2.8/Documentation/virtual/lguest

ls Documentation/lguest/

extract  lguest.c  lguest.txt  Makefile

And once it's installed:
uname -a

Linux kookaburra 3.2.8 #3 SMP Thu Mar 1 14:43:45 EST 2012 i686 GNU/Linu

---

Modules
To get a list over the modules in use on your current system:
lsmod | gawk '{printf("%s ",$1)}'| sed 's/Module//g'

zlib_deflate crc32c libcrc32c ufs qnx4 hfsplus hfs minix ntfs vfat msdos fat jfs xfs reiserfs ext3 jbd ext2 pci_stub vbok8 mperf cpufreq_stats cpufreq_conservative cpufreq_powersave cpufreq_userspace ppdev bnep rfcomm bluetooth binfmt_misc as nfs_acl sunrpc kvm_amd kvm xt_state ipt_REJECT ipt_LOG xt_limit xt_tcpudp xt_conntrack iptable_mangle ipt_MASQUERADE ip
le_filter ip_tables x_tables hwmon_vid lp loop snd_hda_codec_hdmi arc4 rt2800usb rt2800lib crc_ccitt rt2x00usb rt2x00lib xer_oss snd_usb_audio snd_pcm snd_hwdep snd_usbmidi_lib nvidia hid_logitech_dj mac80211 joydev snd_seq_midi cfg80211 rfki5100_tco snd_timer snd_seq_device edac_core edac_mce_amd parport_pc parport snd i2c_piix4 soundcore pcspkr k10temp i2c_combcache jbd2 crc16 usb_storage uas sd_mod crc_t10dif ata_generic pata_atiixp ohci_hcd thermal thermal_sys floppy ahci lib

You can use that as a source of inspiration for what to keep and what to trim.

88. Building Apache 2.4.1 on Debian Testing

WARNING:
Don't remove your existing installation of apache2 without thinking. gnome-core depends on it.

Updated 1 March 2012. Added missing information which prevented building and now provide information about auto-start using an /etc/init.d/ script. Original post at 2012-02-23

---

Building
 A new version of apache is kind of a big deal. Here's how to build it.

sudo apt-get install libapr1-dev uuid-dev libaprutil1-dev libmysqlclient-dev libpq-dev libsqlite3-dev rcconf
wget http://apache.mirror.aussiehq.net.au//httpd/httpd-2.4.1.tar.gz
tar -xvf httpd-2.4.1.tar.gz
cd httpd-2.4.1/
./configure
make -j5

where 5 is the number of cores+1. Four-core i5 => 4+1=5.

To install run
sudo make install
or
sudo checkinstall
sudo dpkg -i *.deb


Done.


sudo checkinstall won't work unless you first
sudo mkdir -p /usr/local/apache2/modules
(see comment below by Y&S who pointed this out)

If you don't create the directory first, you get

/usr/share/apr-1.0/build/libtool --silent --mode=install install mod_allowmethods.la /usr/local/apache2/modules/
ranlib: could not create temporary file whilst writing archive: No more archived files
make[3]: *** [install-modules-yes] Error 1
make[3]: Leaving directory `/home/me/tmp/httpd-2.4.1/modules/aaa'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/me/tmp/httpd-2.4.1/modules/aaa'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/me/tmp/httpd-2.4.1/modules'
make: *** [install-recursive] Error 1
****  Installation failed. Aborting package creation.

Anyway, your compiled httpd is now in /usr/local/apache2/bin/httpd
In my case /usr/local/apache2/bin is not in my PATH -- whether you want to add it or not is a matter of choice.

In order for you to bind your own httpd to port 80 you need to stop apache2 if it is running
sudo service apache2 stop


Test your build:

me@tantalum:~$ /usr/local/apache2/bin/httpd -v
Server version: Apache/2.4.1 (Unix)
Server built:   Feb 23 2012 11:51:26

So far, very easy.

I've tried it on amd64 and i386 debian testing machines.

---

Replacing old version of apache2
Don't try to remove apache2.2-bin since gnome-core depends on it:
http://www.linuxformat.com/forums/viewtopic.php?p=101538

The easiest way to deal with this is to do
sudo rcconf 
and de-select apache2. This way it's still installed, but won't run as a rc service.

---

Making it boot -- init.d script
I had a look at this: http://www.cyberciti.biz/tips/linux-write-sys-v-init-script-to-start-stop-service.html

And here's my /etc/init.d/httpd script

#!/bin/bash
# description: apache2 httpd 2.4.1 server
# Start the service httpd
start() {
        /usr/local/apache2/bin/httpd &
        echo "Up and running"
}
# Restart the service httpd
stop() {
        killall httpd
        echo "Killing httpd"
}
### main logic ###
case "$1" in
  start)
        start
        ;;
  stop)
        stop
        ;;
  *)
        echo $"Usage: $0 {start|stop}"
        exit 1
esac
exit 0

Don't forget to chmod+x

Finally,
sudo rcconf
and select httpd (it'll be at the bottom of the list)

It's not the prettiest of scripts, and you can probably do better by editing /etc/init.d/apache2

87. Polyoxometalate Molecules - povray images

Here's a bunch of povray generated figures of polyoxometalates. I've spent too much time on them not to share them. You may use them freely in posters, websites or talks.

Leave a comment if you want the original POV files.

alpha-Mo8

alpha-Mo8 -- octamolybdate

alpha Mo8 -- octamolybdate

beta-Mo8 -- octamolybdate

beta-Mo8 -- octamolybdate

Hexamolybdate -- Mo6O19

Decaniobate -- [Nb10O28]6-

Decaniobate -- [Nb10O28]6-

Eicosaniobate -- dodecaniobate --[Nb20O54]

Eicosaniobate -- dodecaniobate --[Nb20O54]

Hexaniobate -- lindqvist ion -- [Nb6O19]8-

Hexaniobate -- lindqvist ion -- [Nb6O19]8-

Peroxo- hexaniobate --[Nb6O13(O2)6]8-

Para-Mo7 -- para hepta molybdate

Para-Mo7 -- para hepta molybdate

Para-W7 -- para hepta tungstate

Para-W7 -- para hepta tungstate

Tetrasiliconiobate -- Si4Nb16

Tetrasiliconiobate -- Si4Nb16

Siliconiobate -- SiNb12 -- keggin ion

Siliconiobate -- SiNb12 -- keggin ion

Hexatantalate - [Ta6O19]8-

Superlindqvist -- [Ti12Nb6O44]10- 

Superlindqvist -- [Ti12Nb6O44]10- 

[Ti2Nb8O28]8- -- dititanoniobate

[Ti2Nb8O28]8- -- dititanoniobate

[TiNb9O28]7- -- monotitanoniobate

[TiNb9O28]7- -- monotitanoniobate

W10 - decatungstate

W10 - decatungstate

W12 -- dodecatungstate

W12 -- dodecatungstate

W12 -- dodecatungstate

Hexamolybdate -- lindqvist ion -- [Mo6O19]8-

86. Building sinfo 0.0.45 on Debian Testing

I use sinfo to keep an eye on my cluster:
http://www.ant.uni-bremen.de/whomes/rinas/sinfo/#down

The debian repo version is 0.0.42-1
The latest version is sinfo 0.0.45

Here's the changelog since 0.0.42

sinfo 0.0.45- Tue, 13 Mar 2012 07:07:27 +0100corrected README compile hint for FreeBSDadded configure flag --disable-IPv6 to disable IPv6 supportsinfo 0.0.44 - Tue, 13 Dec 2011 18:32:33 +0100added reconnect for TCP connectionsadded LIBADD to make it --as-needed linkable tnx to T.Hardersinfo 0.0.43 - Thu, 01 Sep 2011 09:00:13 +0200fixed printing bug (integer underflow) when using sinfo -L or -W tnx to J.Erkkilae

There's little reason for compiling it yourself, but there's really no reason not to try either. I like debian and I like using apt-get to manage my system. Learning to be a bit more independent won't hurt though.
So here we go:

--START HERE --
wget http://www.ant.uni-bremen.de/whomes/rinas/sinfo/download/sinfo-0.0.45.tar.gz

tar -xvf sinfo-0.0.45.tar.gz 

cd sinfo-0.0.45/

sudo apt-get install libboost-dev libasio-dev libboost-signals-dev

./configure
(If your interface configuration has disabled IPv6 you must use ../configure --disable-IPv6 or sinfod will silently exit)
make 
sudo checkinstall


Done.

Start the sinfo daemon by
sudo sinfod --quiet --bcastaddress=192.168.1.255


Use
sinfo
to monitor

If you had sinfo installed before, autoremove it, then edit the left-behind /etc/init.d/sinfo script and change

/usr/sbin/sinfod

 to

 /usr/sbin/local/sinfod

Otherwise see http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-building_23.html for an example of writing your own init.d script.


To see all the cluster nodes running sinfo, just start
sinfo

If you don't see anything, then you've most likely not opened up your firewall -- you need to be able to listen to bcast.

---

Build errors:

---

Error:

In file included from message.cc:2:0:

message.h:5:34: fatal error: boost/shared_array.hpp: No such file or directory

compilation terminated.

make[2]: *** [message.lo] Error 1

make[2]: Leaving directory `/home/me/tmp/sinfo-0.0.45/libmessage'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/home/me/tmp/sinfo-0.0.45/libmessage'

make: *** [all-recursive] Error 1

Solution:

sudo apt-get install libboost-dev

---

Error:
In file included from udpmessagereceiver.cc:2:0:
udpmessagereceiver.h:4:20: fatal error: asio.hpp: No such file or directory
compilation terminated.
make[1]: *** [udpmessagereceiver.lo] Error 1
make[1]: Leaving directory `/home/me/tmp/sinfo-0.0.45/libmessageio'
make: *** [all-recursive] Error 1

Solution:
sudo apt-get install libasio-dev

which provides

/usr/include/asio.hpp
which is different from the asio.hpp included in libboost

---

Error:

/usr/bin/ld: cannot find -lboost_signals-mt

collect2: ld returned 1 exit status

make[2]: *** [sinfod] Error 1

make[2]: Leaving directory `/home/me/tmp/sinfo-0.0.45/sinfod'

make[1]: *** [all] Error 2

make[1]: Leaving directory `/home/me/tmp/sinfo-0.0.45/sinfod'

make: *** [all-recursive] Error 1

Solution:

sudo apt-get install libboost-signals-dev

---

Links to this post:
http://ant.uni-bremen.de/whomes/rinas/sinfo/

85. Nvidia bug causes evolution to crash/segmentation fault. Temporary and permanent fixes on Debian Testing

The nvidia-tls bug is affecting evolution too...
(and it's not just GNOME - http://www.linuxmintusers.de/index.php?topic=6859.0)


UPDATE: I have two nvidia boxes running debian testing. Only the one with GT 430 is exhibiting problems. My GT 520 box is unaffected.


UPDATE: Here's how to downgrade your drivers:
http://verahill.blogspot.com.au/2012/03/debian-testing-downgrading-nvidia.html

If you don't want to read the entire post, here's the summary:
1. I think the only semi-permanent solution is to downgrade from 295.20 to nvidia driver version 290.10
2. you can run evolution with
strace -o evolution.log evolution
and IT WILL NOT CRASH
3. It doesn't matter whether you use the nvidia binary straight from nvidia, using sgfxi, or use the nvidia-kernel-dkms/glx debian way. Evolution still dies.

PS strace is normally used to track system calls for the purpose trouble shooting. That it prevents evolution from crashing is completely unintended. But it works as a quick-fix.

PPS  What it does:

"The nvidia-tls libraries (/usr/lib/libnvidia-tls.so.x.y.z and /usr/lib/tls/libnvidia-tls.so.x.y.z); these files provide thread local storage support for the NVIDIA OpenGL libraries (libGL, libGLcore, and libglx). Each nvidia-tls library provides support for a particular thread local storage model (such as ELF TLS), and the one appropriate for your system will be loaded at run time."

---

The symptoms:
Start  evolution, and it will crash with a segmentation fault within the first ten seconds or so

dmesg points to the nvidia bug:

[19690.606196] evolution[13032]: segfault at 10 ip 00007f5a0f53ac0f sp 00007f59ddde6508 error 6 in libnvidia-tls.so.295.20[7f5a0f53a000+3000]
[21476.236668] evolution[18197]: segfault at 10 ip 00007fd4389c2c0f sp 00007fd418d56508 error 6 in libnvidia-tls.so.295.20[7fd4389c2000+3000]
[21513.224145] evolution[18387]: segfault at 10 ip 00007f2cd3e85c0f sp 00007f2cb3a44508 error 6 in libnvidia-tls.so.295.20[7f2cd3e85000+3000]
[21954.867694] evolution[19803]: segfault at 10 ip 00007f1680aa9c0f sp 00007f165bffe508 error 6 in libnvidia-tls.so.295.20[7f1680aa9000+3000]
[22129.426444] evolution[20435]: segfault at 10 ip 00007f2a05bf8c0f sp 00007f29e5725508 error 6 in libnvidia-tls.so.295.20[7f2a05bf8000+3000]

Running
CAMEL_DEBUG=all evolution >& evolution.log
three times had it crash with

First time:

DB SQL operation [BEGIN] started
Camel SQL Exec:
BEGIN
Camel SQL Exec:
COMMIT
DB Operation ended. Time Taken : 0.000060
###########
received: * LSUB (\HasNoChildren) "/" "INBOX"
received: B00005 OK Success
sending : B00006 LIST "" "*"

--> Segmentation fault

Second time:

===========

DB SQL operation [ATTACH DATABASE ':memory:' AS mem] started

Camel SQL Exec:

ATTACH DATABASE ':memory:' AS mem

POP3_STREAM_LINE (25): '-ERR unrecognized command'

DB Operation ended. Time Taken : 0.011516

###########

Database succesfully opened  

===========

DB SQL operation [ATTACH DATABASE ':memory:' AS mem] started

Camel SQL Exec:

ATTACH DATABASE ':memory:' AS mem

DB Operation ended. Time Taken : 0.010961

###########

**

GLib-GIO:ERROR:/tmp/buildd/glib2.0-2.30.2/./gio/gdbusmessage.c:1986:append_value_to_blob: assertion failed: (g_utf8_validate (v, -1, &end) && (end == v + len))

--> Segmentation fault

Third time:

===========

DB SQL operation [BEGIN] started

Camel SQL Exec:

BEGIN

Camel SQL Exec:

COMMIT

DB Operation ended. Time Taken : 0.000070

###########

sending : A00004 SELECT INBOX

--> Segmentation fault

strace:

I can't crash evolution with either strace or valgrind running. Now why is that?

---

Solution:

Downgrading. Which turns out to be more difficult than one would imagine.

UPDATE: Here's how to downgrade your drivers:
http://verahill.blogspot.com.au/2012/03/debian-testing-downgrading-nvidia.html

If you don't want to downgrade the nvidia drivers:
A temporary solution is, odd as it may seem, to use
strace -o evolution.log evolution
because it just refuses to crash. I don't know why, but it works. 

84. Downloading Debian installation ISOs using jigdo

Jigdo is the preferred way of downloading and maintaining debian ISOs for those who can't use torrents (e.g. company policies etc.). The advantage is that you only need to download what has changed since you last used jigdo, thus saving on traffic.

What I'm showing here is also described on the debian website -- my contribution is just to provide another, perhaps more detailed, example.

Anyway, it's fairly easy to use jigdo:
sudo apt-get install jigdo-file

mkdir ~/debiso
cd ~/debiso
jigdo-lite

Pick a url from here: http://www.debian.org/CD/jigdo-cd/#which
I'll use a jigdo file for amd64 testing by clicking here http://cdimage.debian.org/cdimage/weekly-builds/amd64/jigdo-cd/ and picking the following url:
http://cdimage.debian.org/cdimage/weekly-builds/amd64/jigdo-cd/debian-testing-amd64-CD-1.jigdo

You also need to pick a mirror -- your country mirror or a nearby university are good choices. I picked ftp://ftp.au.debian.org/debian.

Here's how it works:

me@beryllium:~/jigdo$ jigdo-lite


Jigsaw Download "lite"
Copyright (C) 2001-2005  |  jigdo@
Richard Atterer          |  atterer.net
Loading settings from `/home/me/.jigdo-lite'


-----------------------------------------------------------------
To resume a half-finished download, enter name of .jigdo file.
To start a new download, enter URL of .jigdo file.
You can also enter several URLs/filenames, separated with spaces,
or enumerate in {}, e.g. `http://server/cd-{1_NONUS,2,3}.jigdo'
jigdo [http://cdimage.debian.org/cdimage/weekly-builds/amd64/jigdo-cd/debian-testing-amd64-CD-1.jigdo]: http://cdimage.debian.org/cdimage/weekly-builds/amd64/jigdo-cd/debian-testing-amd64-CD-1.jigdo


Not downloading .jigdo file - `debian-testing-amd64-CD-1.jigdo' already present


-----------------------------------------------------------------
Images offered by `http://cdimage.debian.org/cdimage/weekly-builds/amd64/jigdo-cd/debian-testing-amd64-CD-1.jigdo':
  1: 'Debian GNU/Linux testing "Wheezy" - Official Snapshot amd64 CD Binary-1 20120220-05:20 (20120220)' (debian-testing-amd64-CD-1.iso)


Further information about `debian-testing-amd64-CD-1.iso':
Generated on Mon, 20 Feb 2012 05:33:08 +0000


-----------------------------------------------------------------
If you already have a previous version of the CD you are
downloading, jigdo can re-use files on the old CD that are also
present in the new image, and you do not need to download them
again. Mount the old CD ROM and enter the path it is mounted under
(e.g. `/mnt/cdrom').
Alternatively, just press enter if you want to start downloading
the remaining files.
Files to scan: 


-----------------------------------------------------------------
The jigdo file refers to files stored on Debian mirrors. Please
choose a Debian mirror as follows: Either enter a complete URL
pointing to a mirror (in the form
`ftp://ftp.debian.org/debian/'), or enter any regular expression
for searching through the list of mirrors: Try a two-letter
country code such as `de', or a country name like `United
States', or a server name like `sunsite'.
Debian mirror [http://sluglug.ucsc.edu/debian/]: ftp://ftp.au.debian.org/debian


Downloading .template file
--2012-02-28 10:22:04--  http://cdimage.debian.org/cdimage/weekly-builds/amd64/jigdo-cd/debian-testing-amd64-CD-1.template
Resolving cdimage.debian.org (cdimage.debian.org)... 2001:6b0:e:2018::138, 2001:6b0:e:2018::163, 130.239.18.163, ...
Connecting to cdimage.debian.org (cdimage.debian.org)|2001:6b0:e:2018::138|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 48901055 (47M) [text/plain]


Saving to: `debian-testing-amd64-CD-1.template'


100%[===================================================================================================================================================>] 48,901,055  4.92M/s   in 15s     


2012-02-28 10:22:19 (3.16 MB/s) - `debian-testing-amd64-CD-1.template' saved [48901055/48901055]

[....]

FINISHED --2012-02-28 10:37:02--
Total wall clock time: 4.1s
Downloaded: 3 files, 311K in 2.4s (128 KB/s)
Found 3 of the 3 files required by the template                                                                                                                                  
Successfully created `debian-testing-amd64-CD-1.iso'


-----------------------------------------------------------------
Finished!
The fact that you got this far is a strong indication that `debian-testing-amd64-CD-1.iso'
was generated correctly. I will perform an additional, final check,
which you can interrupt safely with Ctrl-C if you do not want to wait.


OK: Checksums match, image is good!  



All the necessary packages are downloaded so it takes a while. Once it's done, the iso is automatically built.

If you want to update your iso - delete it and run jigdo-lite again.

83. Configuring route for multiple network interfaces on Debian Testing

In my previous post I got rid of network-manager.

On my main desktop, which serves as a gateway for two subnets and serves them with access to the internet and has three ifs (eth0 goes to outside world, eth1 serves 192.168.0-127 and provides inet passthrough, eth2 serves 192.168.128-255), I had issues getting the internet connection to work once network-manager was gone -- the issue was the routing table.

Here's what I did to diagnose and solve it:

When I got rid of network manager I set up my /etc/network/interfaces like this:

auto lo
iface lo inet loopback
auto eth0

iface eth0 inet dhcp
auto eth1
iface eth1 inet static
address 192.168.1.1
netmask 255.255.255.0
gateway 192.168.1.1

auto eth2
iface eth2 inet static
address 192.168.1.129
netmask 255.255.255.128
gateway 192.168.1.129

But it gives
sudo route -n

Kernel IP routing table

Destination     Gateway         Genmask         Flags Metric Ref    Use Iface
0.0.0.0         192.168.1.129   0.0.0.0         UG    0      0        0 eth2
0.0.0.0         192.168.1.1     0.0.0.0         UG    0      0        0 eth1
0.0.0.0         XXX.XXX.XXX.254 0.0.0.0         UG    0      0        0 eth0
XXX.XXX.XXX.0   0.0.0.0         255.255.248.0   U     0      0        0 eth0
169.254.0.0     0.0.0.0         255.255.0.0     U     1000   0        0 eth0
192.168.1.0     0.0.0.0         255.255.255.0   U     0      0        0 eth1
192.168.1.128   0.0.0.0         255.255.255.128 U     0      0        0 eth2

The problem is that I DON'T want all traffic via eth2 and eth1. I want the default gateway to be my eth0. Inverting the order of the ifs in /etc/network/interfaces doesn't fix it either.

A quick fix is to do
 sudo route add default dev eth0
 which adds this as the first line:

Destination     Gateway         Genmask         Flags Metric Ref    Use Iface

0.0.0.0         0.0.0.0         0.0.0.0         U     0      0        0 eth0

It looks like we might want to manually configure route.

Turns out you can just add the route options to your /etc/network/interfaces file

auto lo
iface lo inet loopback

auto eth0
iface eth0 inet dhcp

auto eth1
iface eth1 inet static
address 192.168.1.1
netmask 255.255.255.0
gateway 192.168.1.1

auto eth2
iface eth2 inet static
address 192.168.1.129
netmask 255.255.255.128
gateway 192.168.1.129

auto wlan0
iface wlan0 inet static
address 192.168.2.1
netmask 255.255.255.0
gateway 192.168.2.1

post-up ip route flush all
post-up route add default dev eth0
post-up route add -net 169.254.0.0 netmask 255.255.0.0 dev eth0 metric 1000
post-up route add -net 192.168.1.0 netmask 255.255.255.0 gw 192.168.1.1 eth1
post-up route add -net 192.168.1.128 netmask 255.255.255.128 gw 192.168.1.129 eth2
post-up route add -net 192.168.2.0 netmask 255.255.255.0 gw 192.168.2.1 wlan0

The script gives us a nice, compact routing table on doing
sudo service networking restart

sudo route -n

Kernel IP routing table
Destination     Gateway         Genmask         Flags Metric Ref    Use Iface
0.0.0.0         0.0.0.0         0.0.0.0         U     0      0        0 eth0
169.254.0.0     0.0.0.0         255.255.0.0     U     1000   0        0 eth0
192.168.1.0     192.168.1.1     255.255.255.0   UG    0      0        0 eth1
192.168.1.128   192.168.1.129   255.255.255.128 UG    0      0        0 eth2

---

Edit::
An earlier version of this post used a separate script (see below). This works fine on boot. However, sudo service networking restart
does not invoke it -- so you may end up with a faulty route table. Thus, it is preferable to use the method above in which the route options are added to the end of /etc/network/interfaces

The following (below) is kept for posterity only:

We put the commands below into /etc/routing_table.sh:

#!/bin/sh

sudo ip route flush all

sudo route add default dev eth0

sudo route add -net 169.254.0.0 netmask 255.255.0.0 dev eth0 metric 1000

sudo route add -net 192.168.1.0 netmask 255.255.255.0 gw 192.168.1.1 eth1

sudo route add -net 192.168.1.128 netmask 255.255.255.128 gw 192.168.1.129 eth2

exit 0

We change the atttributes:

sudo chmod o-rwx /etc/routing_table.sh

sudo chmod g-rwx /etc/routing_table.sh

sudo chmod u+rwx /etc/routing_table.sh



Here user is root. This way only root can execute and edit the table. I guess the 'sudo' is a bit superfluous in our script.

To make it start on boot, add a line to your /etc/rc.local

My rc.local now looks like this:

#!/bin/sh -e
echo "1" > /proc/sys/net/ipv4/ip_forward
sh /etc/firewall-rules.sh
sh /etc/routing_table.sh
exit 0

The firewall-rules.sh script is described in another post on ip tables.

82. Getting rid of network-manager (and trying wicd) on Debian Testing

Network-manager is a fine program, but it interferes with the 'linux' way of doing things by using text files for configuration.

While network-manager makes it easy to do easy things,  /etc/network/interfaces makes it easy to do everything since it makes every setting transparent.

The main problem with remove network-manager is that gnome-core depends on it. Remove network-manager, everything in gnome goes. No good, and completely unnecessary.

I'm still a bit hesitant about configuring WPA on the command line, so I want to have wicd as a backup once network manager is gone.

--START HERE --
So
sudo apt-get install wicd-cli wicd-curses wicd-gtk wpasupplicant

Turn off network-manager (temporarily) and restart your network
sudo service networking restart && sudo service network-manager stop

Start wicd-gtk and configure your wireless network (if that's what you need) to make sure that everything is in working order and you can live without network-manager.

sudo apt-get install rcconf

sudo rcconf

Uncheck network-manager and exit.

update-rc.d: using dependency based boot sequencing
update-rc.d: warning: network-manager start runlevel arguments (none) do not match LSB Default-Start values (2 3 4 5)
update-rc.d: warning: network-manager stop runlevel arguments (0 1 2 3 4 5 6) do not match LSB Default-Stop values (0 1 6)

You can use sysv-rc-conf instead.  Don't worry about the warning about the LSB default -start values -- (2 3 4 5) just means that by default network-manager should be running at runlevels 2-5 (i.e. normal operation). 0 would be halt, 1 would effectively be rescue mode ('single-user mode') and 6 is system reboot. Anyway, here's sysv-rc-conf:

After your next reboot you can check whether network-manager has started:

sudo service network-manager status

[sudo] password for me:
NetworkManager is not running ... failed!

You can make wicd-gtk autostart on starting gnome:
start gnome-sessions-manager and add wicd-gtk if it isn't /already/ there.

The wicd network manager icon will show up in the notification area in gnome (lower right) instead of top right (see picture above). You can supposedly use this to move it: http://blog.norida.me/blog/2011/12/05/move-wicds-icon-to-gnome-shells-status-bar-top-bar/

Given that I use Faenza I also use this: http://gnome-look.org/content/show.php/Faenza+Wicd+Iconset?content=133821
(unzip it, go to the directory and do sh install )


Anyway, the real advantage of wicd is hat there are cli and curses versions available e.g. wicd-curses:

---

Links to this post:
http://eulez.blogspot.com.es/2013/07/de-ubuntu-debian.html

81. nvidia 295.20 bug causing gnome-shell to crash on Debian Testing

UPDATE: Here's how to downgrade your drivers:
http://verahill.blogspot.com.au/2012/03/debian-testing-downgrading-nvidia.html

Update: 
A bigger issue is what this bug does to evolution:
http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-no-real.html


The symptoms:
I've tried to use the correct gnome-shell terminology.

1. Go to the top left corner (Hot Corner) of the desktop to get the Overview and Search Entry field
2. Start typing in the name of an application
3. The window will flicker as if gnome-shell is being restarted (similar to alt+f2++r)
4. Do it again and you get a full-on crash with an unhappy looking computer

dmesg based on repeatedly crashing gnome-shell says:

[ 7011.967820] gnome-shell[32742]: segfault at 10 ip 00007fa1b6d98c0f sp 00007fa1914a1638 error 6 in libnvidia-tls.so.295.20[7fa1b6d98000+3000]
[ 7111.276979] gnome-shell[748]: segfault at 10 ip 00007ff7eb598c0f sp 00007ff7beffc638 error 6 in libnvidia-tls.so.295.20[7ff7eb598000+3000]
[ 7620.952276] gnome-shell[2933]: segfault at 10 ip 00007f0a9fdd9c0f sp 00007f0a710fe638 error 6 in libnvidia-tls.so.295.20[7f0a9fdd9000+3000]
[ 7628.106656] gnome-shell[2986]: segfault at 10 ip 00007f26423f3c0f sp 00007f2612ffd638 error 6 in libnvidia-tls.so.295.20[7f26423f3000+3000]
[ 7658.755466] gnome-shell[3818]: segfault at 10 ip 00007f76bbf2cc0f sp 00007f7691a77638 error 6 in libnvidia-tls.so.295.20[7f76bbf2c000+3000]
[ 7666.310714] gnome-shell[3905]: segfault at 10 ip 00007f3279e64c0f sp 00007f325469d638 error 6 in libnvidia-tls.so.295.20[7f3279e64000+3000]
[ 7717.061483] gnome-shell[4829]: segfault at 10 ip 00007f245ad26c0f sp 00007f243469c638 error 6 in libnvidia-tls.so.295.20[7f245ad26000+3000]

The libnvidia-tls files are found here:

/usr/lib/x86_64-linux-gnu/libnvidia-tls.so.295.20
/usr/lib/x86_64-linux-gnu/tls/libnvidia-tls.so.295.20

and
 dpkg --search libnvidia-tls.so.295.20 
gives

libgl1-nvidia-glx: /usr/lib/x86_64-linux-gnu/tls/libnvidia-tls.so.295.20
libgl1-nvidia-glx: /usr/lib/x86_64-linux-gnu/libnvidia-tls.so.295.20

Ergo, that's where the bug is.

---

Cause:
Bad nvidia drivers -- in package libgl1-nvidia-glx

This is not unique to debian.

"Confirmed, I'm seeing the same on Gentoo ~amd64. gnome-shell 3.2.2.1 crashes while doing a search with nvidia-drivers 295.20 installed (backtrace is in libnvidia-tls.so). Downgrading to nvidia-drivers 290.10 resolves the issue, so it is a problem with the drivers."

And plenty of people are having the same problem, regardless of distro:
https://bbs.archlinux.org/viewtopic.php?id=135826 (15 Feb 2012)
https://bugs.launchpad.net/ubuntu/+source/nvidia-graphics-drivers/+bug/936132 (19 Feb 2012)
https://bugs.launchpad.net/ubuntu/+source/gnome-shell/+bug/941200 

http://www.nvnews.net/vbulletin/showthread.php?t=174049 (14 Feb 2012)

UPDATE: Here's how to downgrade your drivers:
http://verahill.blogspot.com.au/2012/03/debian-testing-downgrading-nvidia.html


There are no bugs listed for libgl1-nvidia-glx
http://bugs.debian.org/cgi-bin/pkgreport.cgi?pkg=libgl1-nvidia-glx

But nvidia-glx has it's fair share of bugs filed against it:
http://bugs.debian.org/cgi-bin/pkgreport.cgi?package=nvidia-glx

From what I can tell this is the relevant bug report (17 February 2012):
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=660189
which points to
http://www.nvnews.net/vbulletin/showthread.php?t=174049&page=3

---

Solution:

1. The 'proper way':
Downgrade your drivers.

UPDATE: Here's how to downgrade your drivers:
http://verahill.blogspot.com.au/2012/03/debian-testing-downgrading-nvidia.html


2. The easy, interesting way:
"For me deleting recently-used.xbel and recreating it with no content solved the problem just temporary. But instead of creating a equally named directory one could also sudo chattr +i recently-used.xbel to keep the file empty.  Keeping the file empty also significantly speeds up the application launcher for me. so it would be nice to have a way to configure this instead of fixing it that rude way, for folks that dont want or need recently used files."


In practical terms, this means:

echo ""> ~/.local/share/recently-used.xbel

sudo chattr +i ~/.local/share/recently-used.xbel

And you are done!

Once the bug has been fixed, you can do
 chattr -i ~/.local/share/recently-used.xbel 

to restore normal functionality

This solution worked for me on an up-to-date debian testing.

Oh well. At least the folks at nvidia are aware of the bug:

---

Thoughts:
The nvidia binaries only entered the debian testing repos around the 25-26 of February from what I can tell. The bug was known for ten days by then, so why did the binaries get promoted to testing?

Here's what I've got installed:

i A glx-alternative-nvidia          - allows the selection of NVIDIA as GLX prov
i A libgl1-nvidia-alternatives      - transition libGL.so* diversions to glx-alt
i A libgl1-nvidia-glx               - NVIDIA binary OpenGL libraries          
i A libglx-nvidia-alternatives      - transition libgl.so diversions to glx-alte
pi  libnvidia-compiler-ia32         - NVIDIA runtime compiler library (32-bit)
i A libnvidia-ml1                   - NVIDIA management library (NVML) runtime l
i A nvidia-alternative              - allows the selection of NVIDIA as GLX prov
i A nvidia-compute-profiler         - NVIDIA Compute Visual Profiler          
i   nvidia-cuda-dev                 - NVIDIA CUDA development files          
i A nvidia-cuda-doc                 - NVIDIA CUDA and OpenCL documentation    
i A nvidia-cuda-gdb                 - NVIDIA CUDA GDB                        
i A nvidia-cuda-toolkit             - NVIDIA CUDA toolkit                    
i   nvidia-glx                      - NVIDIA metapackage                      
i A nvidia-installer-cleanup        - Cleanup after driver installation with the
i   nvidia-kernel-3.1.0-1-amd64     - NVIDIA binary kernel module for Linux 3.1.
i   nvidia-kernel-common            - NVIDIA binary kernel module support files
i A nvidia-kernel-dkms              - NVIDIA binary kernel module DKMS source
i   nvidia-kernel-source            - NVIDIA binary kernel module source      
i A nvidia-libopencl1               - NVIDIA OpenCL library                  
i   nvidia-libopencl1-ia32          - NVIDIA OpenCL 32-bit library            
pi  nvidia-opencl-common            - NVIDIA OpenCL driver                    
i   nvidia-opencl-dev               - NVIDIA OpenCL development files        
pi  nvidia-opencl-icd-ia32          - NVIDIA OpenCL ICD (32-bit)              
i   nvidia-settings                 - Tool for configuring the NVIDIA graphics d
i A nvidia-smi                      - NVIDIA System Management Interface      
i A nvidia-support                  - NVIDIA binary graphics driver support file
i A nvidia-vdpau-driver             - NVIDIA vdpau driver                    
pi  nvidia-xconfig                  - X configuration tool for non-free NVIDIA d
i A xserver-xorg-video-nvidia       - NVIDIA binary Xorg driver

80. Compiling octave 3.6.1 on Debian Testing

I originally was hesitant towards building my own packages, not so much because it is difficult (well-maintained packages are easy to build using configure/make), but because you can end up with a system where dependencies break and you constantly have to manually track new releases of packages you want.

Having had to struggle with outdated or bug-ridden debian packages during the past year has made me change my mind. It obviously depends on what you use you computer for -- the debian packages are supposed to be of high quality and they do unarguably go through a lot of stability testing before being released down the chain from SID to Stable. But I also get the impression that some debian maintainers aren't...well...maintaining their packages sufficiently.

Take the alt+f2 gnome bug for example -- in an ideal world a fix should've been rolled out within 24 hours, rather than just waiting for future version increments to take care of it. The gnuplot bug is another example. There's no solution in sight, even though it has been solved in upstream. Maybe there are reasons to which I'm oblivious for this, but the end result is that I'm a lot more cautious with trusting the debian vs upstreams maintainers now.

So, as part of the  series of science packages that you should compile yourself, here's Octave 3.6.1
At the moment of writing the versions in the deb repos are 3.4.2-8, 3.4.2-12 and 3.4.2-12+b1.

As an aside, if you know what you'll be doing with each software package, create a couple of test scripts so you can track regressions. That way you can be just a little bit more confident in the results you obtain -- if you publish incorrect data you will have to go through the humiliating experience of a retraction or correction.

In addition to everything listed below you need to have a working build environment  with a good fortran compiler.
sudo apt-get install gfortran build-essential 
at a minimum thus.

-- START HERE ---
sudo apt-get install libqhull-dev libpcre++-dev libblas-dev liblapack-dev libreadline-dev
sudo apt-get install libcurl4-openssl-dev libfltk1.3-dev libgraphicsmagick++-dev libhdf5-serial-dev libqrupdate-dev libsuitesparse-metis-dev glpk gperf flex bison libfontconfig1-dev
 wget ftp://ftp.gnu.org/gnu/octave/octave-3.6.1.tar.gz

tar -xvf octave-3.6.1.tar.gz
cd octave-3.6.1/
./configure

make -j4

where 4 is the number of cores +1 (for me 3 cores)

To validate your  compiled version, run
make check

Summary:
  PASS  10008
  FAIL      0
There were 2 expected failures (see fntests.log for details).
Expected failures are known bugs.  Please help improve Octave
by contributing fixes for them.

To install
either
sudo checkinstall
or
sudo make install
Done.

---

---

Error:

checking for qhull.h... no

configure: WARNING: Qhull library not found -- this will result in loss of functionality of some geometry functions.

Solution:

sudo apt-get libqhull-dev

---

Error:

checking pcre.h usability... no

checking pcre.h presence... no

checking for pcre.h... no

checking pcre/pcre.h usability... no

checking pcre/pcre.h presence... no

checking for pcre/pcre.h... no

checking whether pcre.h defines the macros we need... no

configure: error: to build Octave, you must have the PCRE library and header files installed

Solution:

sudo apt-get install libpcre++-dev

---

Error:

checking if sgemm_ is being linked in already... no

checking for ATL_xerbla in -latlas... no

checking for sgemm_ in -lblas... no

checking for sgemm_ in -lmkl... no

checking for sgemm_ in -framework vecLib... no

checking for sgemm_ in -lcxml... no

checking for sgemm_ in -ldxml... no

checking for sgemm_ in -lscs... no

checking for sgemm_ in -lcomplib.sgimath... no

checking for sgemm_ in -lblas... (cached) no

checking for sgemm_ in -lblas... (cached) no

configure: error: You are required to have BLAS and LAPACK libraries

Solution:

sudo apt-get install libblas-dev

(libopenblas-dev is still only in the unstable repo)

---

Error:

checking for cheev_... no
checking for cheev_ in -llapack... no
checking for cheev_ in -llapack_rs6k... no
configure: error: You are required to have BLAS and LAPACK libraries
Solution:
sudo apt-get install liblapack-dev

---

Error:

configure: WARNING: I need GNU Readline 4.2 or later

configure: error: this is fatal unless you specify --disable-readline

Solution:

sudo apt-get install libreadline-dev

---

Error:

configure: WARNING: I didn't find gperf, but it's only a problem if you need to reconstruct oct-gperf.h
configure: WARNING: UMFPACK not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: qrupdate not found.  The QR & Cholesky updating functions will be slow.
configure: WARNING: AMD library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: COLAMD library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: CCOLAMD library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: CHOLMOD library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: CXSparse library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: cURL library not found.  The ftp objects, urlread and urlwrite functions will be disabled.
configure: WARNING: GLPK library not found.  The glpk function for solving linear programs will be disabled.
configure: WARNING: GraphicsMagick++ library not found.  The imread function for reading image files will not be fully functional.
configure: WARNING: HDF5 library not found.  Octave will not be able to save or load HDF5 data files.
configure: WARNING: FLTK config script not found.  Native graphics will be disabled.
configure: WARNING: 
configure: WARNING: I didn't find the necessary libraries to compile native
configure: WARNING: graphics.  It isn't necessary to have native graphics,
configure: WARNING: but you will need to have gnuplot installed or you won't
configure: WARNING: be able to use any of Octave's plotting commands
configure: WARNING: 
configure: 
configure: NOTE: libraries may be skipped if a library is not found OR
configure: NOTE: if the library on your system is missing required features.

Solution:

First, make a few decisions:

Package libhdf5-dev is a virtual package provided by:
  libhdf5-serial-dev 1.8.4-patch1-3
  libhdf5-openmpi-dev 1.8.4-patch1-3
  libhdf5-mpich-dev 1.8.4-patch1-3
  libhdf5-lam-dev 1.8.4-patch1-3
You should explicitly select one to install.

Package libcurl-dev is a virtual package provided by:
  libcurl4-openssl-dev 7.24.0-1
  libcurl4-nss-dev 7.24.0-1
  libcurl4-gnutls-dev 7.24.0-1
You should explicitly select one to install.

Package libfltk-dev is a virtual package provided by:
  libfltk1.3-dev 1.3.0-5
  libfltk1.1-dev 1.1.10-10
You should explicitly select one to install.

Package libumfpack4-dev is a virtual package provided by:
  libsuitesparse-metis-dev 3.1.0-2
  libsuitesparse-dev 1:3.4.0-2
You should explicitly select one to install.

I chose thusly:

sudo apt-get install libcurl4-openssl-dev libfltk1.3-dev libgraphicsmagick++-dev libhdf5-serial-dev libqrupdate-dev libsuitesparse-metis-dev

The following errors/mesages remain:

  Do internal array bounds checking:  false
  Use octave_allocator:               false
  Build static libraries:             false
  Build shared libraries:             true
  Dynamic Linking:                    true (dlopen)
  Include support for GNU readline:   true
  64-bit array dims and indexing:     false

configure: WARNING: I didn't find gperf, but it's only a problem if you need to reconstruct oct-gperf.h
configure: WARNING: GLPK library not found.  The glpk function for solving linear programs will be disabled.
configure: 
configure: NOTE: libraries may be skipped if a library is not found OR
configure: NOTE: if the library on your system is missing required features.

The 64 bit issue can probably  be solved using ./configure --enable-64 BUT requires BLAS that is compatible with 64 bit integers.

---

Links to this page:
http://tata-box-blog.blogspot.nl/2012/04/install-octave-361-in-debian-squeeze.html
http://askubuntu.com/questions/124731/when-will-octave-3-6-1-be-available-to-be-installed