Lindqvist -- a blog about Linux and Science. Mostly.: February 2012

lindqvist · Labels: compile, debian testing, shared_array.hpp, sinfo 0.0.45, wheezy

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/

lindqvist

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.

lindqvist

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.

lindqvist

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.

lindqvist

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

lindqvist

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

lindqvist

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

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

lindqvist

Update 19 Feb. 2013:
Here's an updated post: http://verahill.blogspot.com.au/2013/02/341-upgradinginstalling-bankid-on-64.html -- see that one instead, in particularly if you're upgrading.

Note that you may have to compile your own nspluginwrapper:
http://verahill.blogspot.com.au/2013/03/366-nspluginwrapper-on-debian.html

and you will need to enable multiarch to install ia32-libs:

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

Original post:
Swedish banks and government institutions use bankid/nexus personal for electronic id verification. Sadly, it's a horrible solution -- it seems to be closed source, the bankid website is a POS which prevents me from downloading the 64 bit version claiming that it's not supported (I've used it for a few years now, so it's clearly bunkum).

Note that there's a FOSS alternative in Fribid (http://verahill.blogspot.se/2012/02/debian-testing-wheezy-64-fribid-as.html) which seems to be working perfectly -- and if you can use it, use it. The main limitation is that in practice you'll have to collect your certificate/ID with it, since newer versions of BankID saves the ID in an incompatible format. Like many foreigners, I don't have the opportunity to visit Sweden for the sole sake of picking up a new ID, so I'm stuck with BankID. But you may not be.

* A Swedish how-to is available here: http://ubuntu-se.org/wiki/NexusPersonal#Installation_p.C3.A5_64-bitarssystem

* Another, more recent how-to is here: http://popqvarnstrom.blogspot.com.au/2011/06/bankid-nexus-personal-on-ubuntu-1104-64.html

Note: I have never 'exported' my ID, but have always copied the ~/.personal directory between computers. The problem with exporting is that you are only allowed to do it once. The problem with Nexus allowing your to copy the file itself is that anyone with physical access to your computer can copy the key.

--START HERE --
Here's a summary of how to get it working on debian testing wheezy:

In theory you should install nexus personal from here:
https://install.bankid.com/

I've got v 4.17.0.11 installed on a 64 bit system. The message on this page is a load of bollocks:

Whatever -- the good guys over at Arch supply a link:
wget http://install.bankid.com/Repository/BISP-4.19.0.11351.tar.gz

EDIT: you can use this generic url instead https://install.bankid.com/Download?defaultFileId=Linux

tar -xvf BISP-4.19.0.11351.tar.gz
cd BISP-4.19.0.11351
sudo sh install.4.19.0.11351.sh i

Installing BankID Security Application
ln: failed to create symbolic link `/usr/lib/firefox-addons/plugins': No such file or directory
WARNING: Failed installing plugin for Firefox 3. Manually add symlink to libplugins.so in your Firefox 3 plugin directory if this browser is to be used.
Installation complete.

Since the plugin is 32 bit, you need to link it with nspluginwrapper, and you need 32 bit libs, so

sudo apt-get install nspluginwrapper ia32-libs

Also, as far as I can tell, you need iceweasel/firefox. Chrome/ium won't work.

sudo nspluginwrapper -i /usr/local/lib/personal/libplugins.so

Check to see if it's installed:
nspluginwrapper -l

/usr/lib/mozilla/plugins/npwrapper.libplugins.so
Original plugin: /usr/local/lib/personal/libplugins.so
Plugin viewer: /usr/lib/nspluginwrapper/i386/linux/npviewer
Wrapper version string: 1.3.0

And visit the following page to make sure
https://test.bankid.com/
Or your bank.

Your key -- on a computer where you've used bankid before -- will be in ~/.personal -- don't bother trying to import or export it using the bankid/nexus personal programme (http://popqvarnstrom.blogspot.com.au/2011/06/bankid-nexus-personal-on-ubuntu-1104-64.html) since you're apparently only allowed to do that a certain number of times.

If you just plain copy the files, however, you can do it as many times as you want. I told you the programme is a POS. Anyway,

tree .personal
.personal
|-- backup
|   |-- config
|   |   `-- Personal.cfg
|   `-- store
|-- config
|   `-- Personal.cfg
`-- store
    |-- 1.ngp
    `-- 2.ngp

Nexus Personal/BankID is installed in /usr/local/lib/personal/

Links to this page:
http://popqvarnstrom.blogspot.se/2011/06/bankid-nexus-personal-on-ubuntu-1104-64.html

lindqvist

Anyone who has needs to interact electronically with banks and government agencies in Sweden will become a victim of BankID/Nexus Personal.

It's a piece of crap. I've used it for several years, and have managed to get by. Now, however, if you try to download a newer version (I currently have 4.17.0.11) from a 64 bit debian machine you end up on a page that says:

And there's little hope of getting past it.

Luckily, there's apparently an open-source project, fribid, which may be able to replace bankid/nexus personal for those who don't want to get stuck with 32 bit linux (seriously -- why does 4.17 work on 64 bit and future versions won't? And why won't you let me download an older, supported version? And why can't I chose what version I download? 32 bit windows from a 64 bit linux box -- and vice versa -- SHOULD BE POSSIBLE)

Anyway, fribid:

wget http://fribid.se/releases/source/fribid-1.0.0.tar.bz2
tar -xvf fribid-1.0.0.tar.bz2
cd fribid-1.0.0
./configure
make
sudo make install

I didn't have to do anything to 'install' it beyond that. Navigating in iceweasel to a website requiring bankid started fribid as it should and prompted me for the key file.

I can't explore the functionality beyond this, as fribid can only read keys downloaded with bankid/nexus v 4.10 or earlier -- pk12. The clincher here is that you can download the keys using fribid to begin with instead of first downloading them with bankid.

Lock-in, anyone?

Error:

ERROR: Unsatisfied dependencies:
gtk+-2.0 >= 2.12
gdk-2.0
glib-2.0

Solution:
sudo apt-get install libgtk2.0-dev

lindqvist

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

A more exhaustive description of installing wine in general is here: http://verahill.blogspot.com.au/2012/01/debian-testingwheezy-64-bit-installing.html

I'm not a fan of running windows programmes on linux -- there are enough high-quality packages out there for linux to last you a life-time, and no matter how good wine is¸ the experience of running a windows program on linux is likely to be worse (if faster) than running it natively.

But like most people I'm help prisoner by my fellow co-workers who insists on dog+world using MS Office etc. Also, in spite of everything there are a few pieces of specialised software which lack linux equivalents.

UPDATE (10th Jan 2013): See here for Wine 1.5.21 using the multiarch approach: http://verahill.blogspot.com.au/2013/01/308-compiling-wine-1521-on-debian.html

Finally, from the point of view of easing new users off of windows and onto a real OS, wine and virtualbox fill important functions. I was myself a heavy user of both in the beginning, before learning how to use gnuplot, latex etc.

JPEG support is a PITA, but possible -- see below.

opencl -dev and lib32opencl1 require the contrib non-free repos, e.g.

deb ftp://ftp.au.debian.org/debian/ testing main contrib non-free

Updated: I've tried the same guide on wine 1.4-rc5

--- START HERE ---
With that out of the way, here's building wine 1.4-rc4

First, you need a whole lot of packages -- these will be installed if you've previously compiled wine according to this:

sudo apt-get install bison flex gcc libc6-dev libfontconfig-dev libfreetype6-dev libglu-dev libgsm1-dev libice-dev libjpeg-dev libldap-dev libmpg123-dev libncurses5-dev libopenal-dev libpng-dev libsm-dev libssl-dev libusb-dev libx11-dev libxcomposite-dev libxcursor-dev libxext-dev libxi-dev libxinerama-dev libxml2-dev libxrandr-dev libxrender-dev libxslt-dev libxt-dev libxxf86vm-dev make libcapi20-dev liblcms-dev libsane-dev libhal-dev libdbus-1-dev valgrind prelink libcups2-dev opencl-dev lib32opencl1 oss4-dev gettext

sudo apt-get install lib32v4l-dev lib32ncurses5-dev lib32asound2-dev lib32z-dev ia32-libs-dev

To enable jpeg support you are SUPPOSED TO:
First, remove existing symlinks
sudo rm /usr/lib32/libjpeg.so.62 /usr/lib32/libjpeg.so.62.0.0
Then, create new ones
sudo ln -s /usr/lib32/libjpeg.so.8 /usr/lib32/libjpeg.so.62
sudo ln -s /usr/lib32/libjpeg.so.8 /usr/lib32/libjpeg.so.62.0.0

Download the sources and expand:
wget http://prdownloads.sourceforge.net/wine/wine-1.4-rc4.tar.bz2
bzip2 -d wine-1.4-rc4.tar.bz2
tar -xvf wine-1.4-rc4.tar
./configure

If you get errors, see below and here for solutions. Missing libraries are often ok -- it just means certain functionality will be missing. It's up to you what is important. If you followed the instructions above you'll have jpeg support in spite of what configure spits out.

make -j7

as usual 7 is the number of cores +1. If you have a dual core, replace 7 with 3. Parallel building is sometimes much, much faster than just using one core, sometimes not.
If you already have a version of wine installed, this is a good time to uninstall it. Then,

sudo checkinstall

builds a .deb package and installs it. It's useful if you need to uninstall in the future.

The

Copying documentation directory...
./
./VERSION
./AUTHORS
./LICENSE
./README
./ANNOUNCE
./COPYING.LIB

part takes forever. It will finish in about ten minutes or so. If the building of the debian package fails, make sure you set the version number correctly (see errors below).

aptitude show wine-1.4

Package: wine-1.4
New: yes
State: installed
Automatically installed: no
Version: 1.4-rc4-1
Priority: extra
Section: checkinstall
Maintainer: root@beryllium
Uncompressed Size: 129 M
Description: Wine 1.4-rc4

Done.

Updated 02/03/2012:

For Wine1.4-rc5:
wget http://sourceforge.net/projects/wine/files/Source/wine-1.4-rc5.tar.bz2

tar -xvf wine-1.4-rc5.tar.bz2

cd wine-1.4-rc5/

./configure

gstreamer, libgsm, libtiff, libjpeg warnings. You can ignore them.
make
sudo checkinstall

List of errors:

Error:
configure: OpenCL 32-bit development files not found, OpenCL won't be supported.

Solution:
sudo apt-get install lib32opencl1 opencl-dev

Error:
configure: gstreamer-0.10 base plugins 32-bit development files not found, gstreamer support disabled
No solution:
Not the only one with this problem...I don't care enough about video to follow this up any more. Likely, an approach similar to this will work: http://forum.winehq.org/viewtopic.php?t=5797&sid=afde9de83a98b8cb24df2bb3646930b6

Error:
configure: OSS sound system found but too old (OSSv4 needed), OSS won't be supported.

Solution:
sudo apt-get install oss4-dev

Error:
configure: libgsm 32-bit development files not found, gsm 06.10 codec won't be supported.
Solution, maybe:
I don't care too much, but there are solutions if you are desperate enough: http://forum.winehq.org/viewtopic.php?t=5797&sid=afde9de83a98b8cb24df2bb3646930b6

Error:

configure: libtiff 32-bit development files not found, TIFF won't be supported.

No soution:

This comes up on some boxes, but not others. Comparing the installed packages I have no idea why.

aptitude search tiff|grep dev

v libtiff-dev -
i A libtiff4-dev - Tag Image File Format (TIFF) library (old
p libtiff5-dev - Tag Image File Format library (TIFF), deve

ls /usr/lib32/libtiff* -lah

/usr/lib32/libtiff.a

/usr/lib32/libtiff.la

/usr/lib32/libtiff.so -> libtiff.so.4.3.3

/usr/lib32/libtiff.so.4 -> libtiff.so.4.3.3

/usr/lib32/libtiff.so.4.3.3

/usr/lib32/libtiffxx.a

/usr/lib32/libtiffxx.la

/usr/lib32/libtiffxx.so -> libtiffxx.so.0.0.7

Error:

configure: WARNING: gettext tools not found, translations won't be built.
Solution:
sudo apt-get install gettext

Error:
configure: WARNING: libjpeg 32-bit development files not found, JPEG won't be supported.

Solution:
First, install
sudo apt-get install libjpeg8-dev

This pointed me here.

Here's how to check for the bug
locate libjpeg | grep 32

/usr/lib32/libjpeg.a
/usr/lib32/libjpeg.la
/usr/lib32/libjpeg.so
/usr/lib32/libjpeg.so.62
/usr/lib32/libjpeg.so.62.0.0
/usr/lib32/libjpeg.so.8
/usr/lib32/libjpeg.so.8.0.2

ls /usr/lib32/libjpeg.* -lah

/usr/lib32/libjpeg.a

/usr/lib32/libjpeg.la

/usr/lib32/libjpeg.so -> libjpeg.so.62.0.0

/usr/lib32/libjpeg.so.62 -> libjpeg.so.62.0.0

/usr/lib32/libjpeg.so.62.0.0

/usr/lib32/libjpeg.so.8 -> libjpeg.so.8.0.2

/usr/lib32/libjpeg.so.8.0.2

Yup, libjpeg.so points to v 6.2 instead of v 8 which I have installed.

According to the bug report, the cause of the error is that the header file jpeglib.h states one version, and the /usr/lib32/libjpeg.so points to another:

cat /usr/include/jpeglib.h|grep "LIB_VERSION"| grep define

#define JPEG_LIB_VERSION 80 /* Compatibility version 8.0 */
#define JPEG_LIB_VERSION_MAJOR 8
#define JPEG_LIB_VERSION_MINOR 4

FIX:

Remove existing symlinks

sudo rm /usr/lib32/libjpeg.so.62 /usr/lib32/libjpeg.so.62.0.0

Create new ones

sudo ln -s /usr/lib32/libjpeg.so.8 /usr/lib32/libjpeg.so.62

sudo ln -s /usr/lib32/libjpeg.so.8 /usr/lib32/libjpeg.so.62.0.0

ls /usr/lib32/libjpeg.* -lah now gives

/usr/lib32/libjpeg.a

/usr/lib32/libjpeg.la

/usr/lib32/libjpeg.so -> libjpeg.so.62.0.0

/usr/lib32/libjpeg.so.62 -> /usr/lib32/libjpeg.so.8

/usr/lib32/libjpeg.so.62.0.0 -> /usr/lib32/libjpeg.so.8

/usr/lib32/libjpeg.so.8 -> libjpeg.so.8.0.2

/usr/lib32/libjpeg.so.8.0.2

The error message remains on ./configure, but jpeg support is /supposed/ to work in spite of this.

Error:

Building Debian package... FAILED!
*** Failed to build the package
Do you want to see the log file? [y]:
dpkg-deb: error: parsing file '/var/tmp/tmp.Y50XUaisW0/package/DEBIAN/control' near line 7 package 'wine-1.4': error in Version string 'rc4-1': version number does not start with digit

Solution:

sudo checkinstall

This package will be built according to these values:
0 - Maintainer: [ root@beryllium ]
1 - Summary: [ Wine 1.4-rc4 ]
2 - Name: [ wine-1.4 ]
3 - Version: [ rc4 ]
4 - Release: [ 1 ]
5 - License: [ GPL ]
6 - Group: [ checkinstall ]
7 - Architecture: [ amd64 ]
8 - Source location: [ wine-1.4-rc4 ]
9 - Alternate source location: [ ]
10 - Requires: [ ]
11 - Provides: [ wine-1.4 ]
12 - Conflicts: [ ]
13 - Replaces: [ ]
Enter a number to change any of them or press ENTER to continue: 3
Enter new version:
>> 1.4-rc4

lindqvist

The situation:
you have a DSL service with a dynamic IP. Your IP typically changes once per month or so, perhaps a bit more often. It would be nice to connect a domain name to your IP address and have it automatically point in the right direction.

The solution:
The easiest way to do this is probably by using the tomato router firmware for linksys routers. Presuming that you've got it installed and running:

1. Register for a free dns account at freedns.afraid.org
2. Create a subdomain e.g. jibberjabber.mooo.com. Link it to an IP address.

3. Generate a URL for dynamic update

4. Log on to your router and add the URL (the irrelevant parts will probably be excised automatically)

5. Wait. It will take a couple of hours for the domain name to point in the right direction. In the beginning my domain name pointed at 127.0.0.2.

lindqvist

EDIT 18 May 2012:
It's now been solved
Compiling nwchem 6.1 with internal libs on debian:
http://verahill.blogspot.com.au/2012/05/compiling-nwchem-61-with-internal-libs.html
Compiling nwchem 6.1 with openblas on debian:
http://verahill.blogspot.com.au/2012/05/building-nwchem-61-on-debian.html

UPDATE April 2012: Someone else is having the same problem: http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id435/ . Binaries built on ROCKS 5.4.3 work, but binaries built on debian testing don't: the gfortran version is GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50). On debian, which yields a segfaulting binary, the version is GNU Fortran (Debian 4.6.3-1) 4.6.3

Nwchem 6.1 was released in February this year. The build instructions are ALMOST the same as for Nwchem 6.0 -- the difference is the use of export USE_MPIF4=y. Well, that and me not having much success in actually USING nwchem as opposed to building it.

There is now an nwchem version with mpi support in the debian unstable repos. I have not used or tested it.

I can build the 32 bit version of nwchem 6.1 just fine.Building the 64 bit version works absolutely fine too. However, once you attempt to run, it crashes. Ergo, this is NOT A SOLUTION. It's a bunch of error messages so that more seasoned and skilled operators than I may offer a solution. If you have an option, build and use version 6.0 instead.

Update:
I built a version with openmpi support as well, which also segfaults:
Here are the build instructions:

sudo apt-get install openmpi-bin openmpi-dev
export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=/home/me/tmp/nwchem-6.1
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export MPI_LOC=/usr/lib/openmpi
export MPI_INCLUDE=/usr/lib/openmpi/include
export USE_MPIF4=y
export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran

and here's what happens on execution

[beryllium:24650] *** Process received signal ***
[beryllium:24650] Signal: Segmentation fault (11)
[beryllium:24650] Signal code: Address not mapped (1)
[beryllium:24650] Failing at address: 0x44000098
[beryllium:24650] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x324f0) [0x7f08deeb84f0]
[beryllium:24650] [ 1] /usr/lib/libmpi.so.0(PMPI_Comm_set_errhandler+0x60) [0x7f08e0526c30]
[beryllium:24650] [ 2] ./nwchem() [0x292d504]
[beryllium:24650] [ 3] ./nwchem() [0x292d596]
[beryllium:24650] [ 4] ./nwchem() [0x40657a]
[beryllium:24650] [ 5] ./nwchem() [0x406f7d]
[beryllium:24650] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [0x7f08deea4ead]
[beryllium:24650] [ 7] ./nwchem() [0x405189]
[beryllium:24650] *** End of error message ***

This only happens on 64 bit debian -- 32 bit deb and 64 bit centos are both fine

OLD POST:

--start here --

Here's what I've done so far

Put a hold on your mpich2 and mpich2-dev packages (see e.g. here for more details)
1. edit your /etc/apt/sources.list to allow packages from stable e.g.

deb ftp://ftp.au.debian.org/debian/ testing main contrib non-fre
deb ftp://ftp.au.debian.org/debian/ stable main contrib non-free

2. create an /etc/apt/preferences file e.g.

Package: *
Pin: release a=testing
Pin-Priority: 990
Package: *
Pin: release a=stable
Pin-Priority: -10

2. install v 1.2 explicitly

sudo apt-get update && sudo apt-get install mpich2=1.2.1.1-5 libmpich2-dev=1.2.1.1-5

3. put a hold on the packages

sudo su
echo "mpich2 hold"|dpkg --set-selections
echo "libmpich2-dev hold"|dpkg --set-selections

exit

Download the nwchem source
cd ~
wget http://www.nwchem-sw.org/images/Nwchem-6.1-2012-Feb-10.tar.gz
tar -xvf Nwchem-6.1-2012-Feb-10.tar.gz
cd nwchem-6.1

create buildconf.sh in ~/nwchem-6.1
Put the following in it (for 64 bit system):

export LARGE_FILES=TRUE
export TCGRSH=/usr/local/bin/ssh
export NWCHEM_TOP=/home/me/nwchem-6.1
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=$MPI_LOC/include/mpich2
export LIBMPI="-lmpich -lfmpich"
export NWCHEM_MODULES="all"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran

Build
Start the build
sh buildconf.sh

Building takes about half an hour. Everything builds fine. However, running -- with or without mpdrun -- causes the error below.

It doesn't matter how much memory I allocated. The error seems to have something to do with "Invalid write of size 8" which I understand to mean that pointers are 8 bytes long but don't have 8 bytes allocated to them. But then I'm not an expert.

Would it have something to do with
USE_MPIF4=y?

Without USE_MPIF4 I end up with the stupid_* error messages (stupid_sum, stupid_task etc.)

Error:
running e.g. mpdrun -n 2 nwchem nwchem.nw gives:

Screening Tolerance Information
-------------------------------
Density screening/tol_rho: 1.00D-10
AO Gaussian exp screening on grid/accAOfunc: 14
CD Gaussian exp screening on grid/accCDfunc: 20
XC Gaussian exp screening on grid/accXCfunc: 20
Schwarz screening/accCoul: 1.00D-08

0:Segmentation Violation error, status=: 11
(rank:0 hostname:tantalum pid:19944):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0

More detail:
Running just nwchem nwchem.nw gives a bit more detail:

Screening Tolerance Information
-------------------------------
Density screening/tol_rho: 1.00D-10
AO Gaussian exp screening on grid/accAOfunc: 14
CD Gaussian exp screening on grid/accCDfunc: 20
XC Gaussian exp screening on grid/accXCfunc: 20
Schwarz screening/accCoul: 1.00D-08

0:Segmentation Violation error, status=: 11
(rank:0 hostname:tantalum pid:19676):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
application called MPI_Abort(comm=0x84000001, 11) - process 0
*** glibc detected *** nwchem: corrupted double-linked list: 0x000000010ac34880 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x75ab6)[0x7f597b129ab6]
/lib/x86_64-linux-gnu/libc.so.6(+0x7754c)[0x7f597b12b54c]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f597b12e7ec]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xcc811)[0x7f597bbd5811]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xdba7f)[0x7f597bbe4a7f]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xdbbaa)[0x7f597bbe4baa]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0x1ab09)[0x7f597bb23b09]
/lib64/ld-linux-x86-64.so.2(+0xe21c)[0x7f597c42421c]
/lib/x86_64-linux-gnu/libc.so.6(+0x36df2)[0x7f597b0eadf2]
/lib/x86_64-linux-gnu/libc.so.6(+0x36e45)[0x7f597b0eae45]
/usr/lib/libmpich.so.1.2(+0xbedc9)[0x7f597c101dc9]
/usr/lib/libmpich.so.1.2(MPID_Abort+0x6d)[0x7f597c122d0d]
/usr/lib/libmpich.so.1.2(PMPI_Abort+0x2f5)[0x7f597c090805]
nwchem[0x2896591]
nwchem[0x2883883]
/lib/x86_64-linux-gnu/libc.so.6(+0x324f0)[0x7f597b0e64f0]
nwchem[0x29b6043]
nwchem[0x27a04a0]
nwchem[0x27a3955]
nwchem[0x271492b]
nwchem[0x5cf410]
nwchem[0x5b3d18]
nwchem[0x5a9735]
nwchem[0x5a99b6]
nwchem[0x418ee8]
nwchemAborted

And more detail:

valgrind nwchem nwchem.nw

==19910== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==19910== by 0x5A9734: nwdft_ (nwdft.F:274)
==19910== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==19910== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==19910== by 0x41A57B: task_energy_ (task_energy.F:95)
==19910== by 0x40DAD2: task_ (task.F:337)
==19910== by 0x4068F5: MAIN__ (nwchem.F:251)
==19910== Address 0x199750a0 is not stack'd, malloc'd or (recently) free'd
==19910==
==19910== Invalid write of size 8
==19910== at 0x29B6043: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==19910== by 0x5A9734: nwdft_ (nwdft.F:274)
==19910== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==19910== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==19910== by 0x41A57B: task_energy_ (task_energy.F:95)
==19910== by 0x40DAD2: task_ (task.F:337)
==19910== by 0x4068F5: MAIN__ (nwchem.F:251)
==19910== Address 0x199750b0 is not stack'd, malloc'd or (recently) free'd
==19910==
0:Segmentation Violation error, status=: 11
(rank:0 hostname:tantalum pid:19910):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
application called MPI_Abort(comm=0x84000001, 11) - process 0
==19910==
==19910== HEAP SUMMARY:
==19910== in use at exit: 4,303,284,335 bytes in 695 blocks
==19910== total heap usage: 2,132 allocs, 1,437 frees, 4,305,897,103 bytes allocated
==19910==
==19910== LEAK SUMMARY:
==19910== definitely lost: 24 bytes in 1 blocks
==19910== indirectly lost: 512 bytes in 1 blocks
==19910== possibly lost: 0 bytes in 0 blocks
==19910== still reachable: 4,303,283,799 bytes in 693 blocks
==19910== suppressed: 0 bytes in 0 blocks
==19910== Rerun with --leak-check=full to see details of leaked memory
==19910==
==19910== For counts of detected and suppressed errors, rerun with: -v
==19910== Use --track-origins=yes to see where uninitialised values come from
==19910== ERROR SUMMARY: 662 errors from 9 contexts (suppressed: 4 from 4)

And way too much detail:
valgrind --leak-check=full --track-origins=yes --log-file=valgrind.log nwchem nwchem.nw
==20005== Memcheck, a memory error detector

==20005== Memcheck, a memory error detector
==20005== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==20005== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright info
==20005== Command: nwchem nwchem.nw
==20005== Parent PID: 19563
==20005==
==20005== Warning: set address range perms: large range [0x3952b040, 0x13352b110) (undefined)
==20005== Syscall param write(buf) points to uninitialised byte(s)
==20005== at 0x12803980: __write_nocancel (syscall-template.S:82)
==20005== by 0x127A8B92: _IO_file_write@@GLIBC_2.2.5 (fileops.c:1276)
==20005== by 0x127A8809: new_do_write (fileops.c:530)
==20005== by 0x127A8B34: _IO_do_write@@GLIBC_2.2.5 (fileops.c:503)
==20005== by 0x127A9347: _IO_file_sync@@GLIBC_2.2.5 (fileops.c:905)
==20005== by 0x1279DE19: fflush (iofflush.c:43)
==20005== by 0xA3CF1F: hdbm_file_flush (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x8C84AA: rtdb_seq_put (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x8C55BD: rtdb_put (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x8C48B2: rtdb_put_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x9EAFAC: util_set_rtdb_state_ (util_rtdb_state.F:40)
==20005== by 0x4067FD: MAIN__ (nwchem.F:222)
==20005== Address 0x10950022 is not stack'd, malloc'd or (recently) free'd
==20005== Uninitialised value was created by a stack allocation
==20005== at 0x8C6130: rtdb_seq_put_info (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6048: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975040 is 0 bytes after a block of size 42,008,576 alloc'd
==20005== at 0x1155679D: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==20005== by 0x291F69B: morecore (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x291F793: kr_malloc (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A492B: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B604D: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975050 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6052: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975060 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6057: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975070 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6035: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975080 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6039: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975090 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B603E: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x199750a0 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6043: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x199750b0 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005==
==20005== HEAP SUMMARY:
==20005== in use at exit: 4,303,284,355 bytes in 697 blocks
==20005== total heap usage: 2,135 allocs, 1,438 frees, 4,305,900,787 bytes allocated
==20005==
==20005== 536 (24 direct, 512 indirect) bytes in 1 blocks are definitely lost in loss record 662 of 679
==20005== at 0x1155679D: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==20005== by 0x11D6E128: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==20005== by 0x11E332F8: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==20005== by 0x11E2C573: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==20005== by 0x11D6BB47: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==20005== by 0x1093CCCF: call_init (dl-init.c:85)
==20005== by 0x1093CDC6: _dl_init (dl-init.c:134)
==20005== by 0x1092FB29: ??? (in /lib/x86_64-linux-gnu/ld-2.13.so)
==20005== by 0x1: ???
==20005== by 0x7FF00033A: ???
==20005== by 0x7FF000341: ???
==20005==
==20005== LEAK SUMMARY:
==20005== definitely lost: 24 bytes in 1 blocks
==20005== indirectly lost: 512 bytes in 1 blocks
==20005== possibly lost: 0 bytes in 0 blocks
==20005== still reachable: 4,303,283,819 bytes in 695 blocks
==20005== suppressed: 0 bytes in 0 blocks
==20005== Reachable blocks (those to which a pointer was found) are not shown.
==20005== To see them, rerun with: --leak-check=full --show-reachable=yes
==20005==
==20005== For counts of detected and suppressed errors, rerun with: -v
==20005== ERROR SUMMARY: 663 errors from 10 contexts (suppressed: 4 from 4)

For comparison, here's using nwchem 6.0:
NOTE that this version works just fine and runs to completion without error messages normally.
valgrind --leak-check=full --track-origins=yes --log-file=valgrind.log nwchem nwchem.nw

==21014== Memcheck, a memory error detector
==21014== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==21014== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright info
==21014== Command: nwchem nwchem.nw
==21014== Parent PID: 20854
==21014==
==21014== Warning: set address range perms: large range [0x3952b040, 0x13352b110) (undefined)
==21014== Syscall param write(buf) points to uninitialised byte(s)
==21014== at 0x11673980: __write_nocancel (syscall-template.S:82)
==21014== by 0x11618B92: _IO_file_write@@GLIBC_2.2.5 (fileops.c:1276)
==21014== by 0x11618809: new_do_write (fileops.c:530)
==21014== by 0x11618B34: _IO_do_write@@GLIBC_2.2.5 (fileops.c:503)
==21014== by 0x11619347: _IO_file_sync@@GLIBC_2.2.5 (fileops.c:905)
==21014== by 0x1160DE19: fflush (iofflush.c:43)
==21014== by 0x8A16D7: hdbm_file_flush (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x83C973: rtdb_seq_put (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x83ADA6: rtdb_put (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x83A13F: rtdb_put_ (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x85C72C: util_set_rtdb_state_ (util_rtdb_state.F:40)
==21014== by 0x40636B: MAIN__ (nwchem.F:223)
==21014== Address 0xf7c0022 is not stack'd, malloc'd or (recently) free'd
==21014== Uninitialised value was created by a stack allocation
==21014== at 0x83B7D0: rtdb_seq_put_info (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014==
==21014== Conditional jump or move depends on uninitialised value(s)
==21014== at 0x8A5E1F: sym_op_class_name_ (sym_op_cname.F:26)
==21014== by 0x83FB41: sym_op_classify_ (sym_op_clsfy.F:49)
==21014== by 0x845AE9: sym_movecs_adapt_ (sym_mo_adapt.F:77)
==21014== by 0x719A4A: scf_movecs_sym_adapt_ (scf_sym_adap.F:70)
==21014== by 0x731028: scf_vectors_guess_ (scf_vec_guess.F:403)
==21014== by 0x58D4E6: dft_scf_ (dft_scf.F:526)
==21014== by 0x58B67B: dft_main0d_ (dft_main0d.F:537)
==21014== by 0x5818B3: nwdft_ (nwdft.F:309)
==21014== by 0x581B24: dft_energy_ (nwdft.F:18)
==21014== by 0x4174D7: task_energy_doit_ (task_energy.F:229)
==21014== by 0x418AEB: task_energy_ (task_energy.F:74)
==21014== by 0x40C646: task_ (task.F:301)
==21014== Uninitialised value was created by a stack allocation
==21014== at 0x83F9BD: sym_op_classify_ (sym_op_clsfy.F:32)
==21014==
==21014==
==21014== HEAP SUMMARY:
==21014== in use at exit: 4,254,665,672 bytes in 20 blocks
==21014== total heap usage: 10,491 allocs, 10,471 frees, 4,275,242,731 bytes allocated
==21014==
==21014== 17 bytes in 2 blocks are definitely lost in loss record 9 of 19
==21014== at 0x103C679D: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==21014== by 0x11626881: strdup (strdup.c:43)
==21014== by 0x24D33F7: pbeginf_ (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x405F53: MAIN__ (nwchem.F:66)
==21014== by 0x406964: main (nwchem.F:336)
==21014==
==21014== 536 (24 direct, 512 indirect) bytes in 1 blocks are definitely lost in loss record 13 of 19
==21014== at 0x103C679D: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==21014== by 0x10BDE128: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==21014== by 0x10CA32F8: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==21014== by 0x10C9C573: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==21014== by 0x10BDBB47: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==21014== by 0xF7ACCCF: call_init (dl-init.c:85)
==21014== by 0xF7ACDC6: _dl_init (dl-init.c:134)
==21014== by 0xF79FB29: ??? (in /lib/x86_64-linux-gnu/ld-2.13.so)
==21014== by 0x1: ???
==21014== by 0x7FF00032A: ???
==21014== by 0x7FF000331: ???
==21014==
==21014== LEAK SUMMARY:
==21014== definitely lost: 41 bytes in 3 blocks
==21014== indirectly lost: 512 bytes in 1 blocks
==21014== possibly lost: 0 bytes in 0 blocks
==21014== still reachable: 4,254,665,119 bytes in 16 blocks
==21014== suppressed: 0 bytes in 0 blocks
==21014== Reachable blocks (those to which a pointer was found) are not shown.
==21014== To see them, rerun with: --leak-check=full --show-reachable=yes
==21014==
==21014== For counts of detected and suppressed errors, rerun with: -v
==21014== ERROR SUMMARY: 178 errors from 4 contexts (suppressed: 4 from 4)

Pages

28 February 2012

86. Building sinfo 0.0.45 on Debian Testing

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

84. Downloading Debian installation ISOs using jigdo

83. Configuring route for multiple network interfaces on Debian Testing

27 February 2012

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

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

26 February 2012

80. Compiling octave 3.6.1 on Debian Testing

79. Bankid/nexus personal and iceweasel on Debian Testing

78. Fribid as an alternative to nexus personal on debian

77. Compiling Wine 1.4-rc4 and wine 1.4-rc5 on debian testing

24 February 2012

76. Tomato router and free dns

75. [solved] Problems with homebuilt nwchem 6.1 on Debian Testing

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