287. Compiling Wine 1.5.5 from source using the carbon-dev deb patches

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

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
. Use the updated build instead of what follows below.

Here's how to build the wine 1.5.5 packages without any errors.

I'm cheating and using the debian rules from dev.carbon-project.org.-- it's a small file and is a better solution than downloading the deb files from there.

Note that you will probably need more packages than the ones listed here.

1. Download the source and debian build patches

sudo apt-get install bzip2
cd ~/tmp
mkdir wine-1.5.5_carbon/
cd wine-1.5.5_carbon/
wget http://sourceforge.net/projects/wine/files/Source/wine-1.5.5.tar.bz2
mv wine-1.5.5.tar.bz2 wine-unstable_1.5.5.orig.tar.bz2
tar xvf wine-unstable_1.5.5.orig.tar.bz2
cd wine-1.5.5/
wget http://dev.carbon-project.org/debian/wine-unstable/wine-unstable_1.5.5-0.1.debian.tar.bz2
tar xvf wine-unstable_1.5.5-0.1.debian.tar.bz2
rm wine-unstable_1.5.5-0.1.debian.tar.bz2 

2.  Edit control, control.in and rules
Allow any version of gcc (this may obviously backfire if your version is no good)
Edit debian/control and control.in

 27  gcc-4.5-multilib [amd64 kfreebsd-amd64], gcc-4.5 [amd64 kfreebsd-amd64]
 28  g++-4.5 [amd64 kfreebsd-amd64],

so that is says

 27  gcc-multilib [amd64 kfreebsd-amd64], gcc [amd64 kfreebsd-amd64],
 28  g++ [amd64 kfreebsd-amd64],

Edit debian/rules

 53 ifeq ($(DEB_HOST_GNU_CPU),x86_64)
 54 CC=gcc-4.5
 55 CXX=g++-4.5
 56 else
 57 CC=gcc
 58 CXX=g++

to say

 53 ifeq ($(DEB_HOST_GNU_CPU),x86_64)
 54 CC=gcc
 55 CXX=g++
 56 else
 57 CC=gcc
 58 CXX=g++

2. Get dependencies
Note that this list is based on a very old post -- some packages may not be needed.

sudo apt-get install ia32-libs ia32-libs-dev 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 lib32v4l-dev lib32ncurses5-dev lib32asound2-dev libtiff4-dev libgphoto2-2-dev
sudo apt-get install libxkbfile-dev libxxf86dga-dev freeglut3-dev unixodbc-dev gcc-multilib dpkg-dev

Note: I used the following list on debian stable/squeeze.

sudo apt-get install ia32-libs ia32-libs-dev 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 oss4-dev gettext lib32v4l-dev lib32ncurses5-dev lib32asound2-dev libtiff4-dev libgphoto2-2-dev libxkbfile-dev libxxf86dga-dev freeglut3-dev unixodbc-dev gcc-multilib dpkg-dev debhelper libxmu-dev dctrl-tools lzma sharutils lib32z1-dev libgstreamer-plugins-base0.10-dev
sudo apt-get install lib32opencl1

Then continue as normal.

If you're on Wheezy/Testing you should be following this post instead anyway.

3. Compile
in wine-1.5.5/:

dpkg-buildpackage -us -uc

If all went well you saw:

dpkg-deb: building package `wine-unstable' in `../wine-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `wine-bin-unstable' in `../wine-bin-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-dbg-unstable' in `../libwine-dbg-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-dev-unstable' in `../libwine-dev-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-unstable' in `../libwine-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-alsa-unstable' in `../libwine-alsa-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-bin-unstable' in `../libwine-bin-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-capi-unstable' in `../libwine-capi-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-cms-unstable' in `../libwine-cms-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-gl-unstable' in `../libwine-gl-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-gphoto2-unstable' in `../libwine-gphoto2-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-ldap-unstable' in `../libwine-ldap-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-openal-unstable' in `../libwine-openal-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-oss-unstable' in `../libwine-oss-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-print-unstable' in `../libwine-print-unstable_1.5.5-0.1_amd64.deb'.
dpkg-deb: building package `libwine-sane-unstable' in `../libwine-sane-unstable_1.5.5-0.1_amd64.deb'.
[..]
dpkg-source: info: using options from wine-1.5.5/debian/source/options: --compression=bzip2 --compression-level=9
dpkg-source: info: unapplying Bug#28201_proposed-fix-modified.patch
dpkg-source: info: unapplying Bug#28898_squashed-proposed-patches.patch
dpkg-source: info: unapplying fix-winegcc-paths.patch
dpkg-source: info: unapplying Bug#29669_proposed-fix.patch
dpkg-source: info: unapplying function_grep.patch
dpkg-source: info: unapplying readd_xpm.patch
dpkg-source: info: unapplying debian-changes-from-1.1.32-1.patch
dpkg-buildpackage: full upload (original source is included)

Your packages will be found in the wine-1.5.5_carbon/ directory.

../libwine-alsa-unstable_1.5.5-0.1_amd64.deb
../libwine-bin-unstable_1.5.5-0.1_amd64.deb
../libwine-capi-unstable_1.5.5-0.1_amd64.deb
../libwine-cms-unstable_1.5.5-0.1_amd64.deb
../libwine-dbg-unstable_1.5.5-0.1_amd64.deb
../libwine-dev-unstable_1.5.5-0.1_amd64.deb
../libwine-gl-unstable_1.5.5-0.1_amd64.deb
../libwine-gphoto2-unstable_1.5.5-0.1_amd64.deb
../libwine-ldap-unstable_1.5.5-0.1_amd64.deb
../libwine-openal-unstable_1.5.5-0.1_amd64.deb
../libwine-oss-unstable_1.5.5-0.1_amd64.deb
../libwine-print-unstable_1.5.5-0.1_amd64.deb
../libwine-sane-unstable_1.5.5-0.1_amd64.deb
../libwine-unstable_1.5.5-0.1_amd64.deb
../wine-bin-unstable_1.5.5-0.1_amd64.deb
../wine-unstable_1.5.5-0.1_amd64.deb

If something went wrong, it's probably because of a missing dependency.

To install just run

sudo dpkg -i *.deb in the wine-1.5.5_carbon/ directory.

286. Briefly: installing the dev.carbon-project.org wine 1.5.5 from debs

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

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

Update: Try this first: http://verahill.blogspot.com.au/2012/11/compiling-wine-155-from-source-using.html
It uses a lot less bandwidth, and involves compiling wine yourself, but using the build instructions from the carbon-project.org

---

Please Note
For bandwidth reasons please don't use this method if you are satisfied with the version you obtain through compiling by following this method: http://verahill.blogspot.com.au/2012/10/wine-1515-on-debian-testingwheezy.html

---

A long time ago (http://verahill.blogspot.com.au/2012/01/debian-testingwheezy-64-bit-installing.html) I posted three methods for installing Wine on Debian Testing:
1. Use the Squeeze version
2. Get the Wine-unstable build from http://dev.carbon-project.org/debian/wine-unstable/
3. Compile your own version

I've never managed to build Wine to successfully include OpenCL, gstreamer, or libgsm. Also, there are occasional issues with libjpeg, and I recently have problems with libOSMesa.

So here's an alternative solution for installing a relatively recent version of wine, and it involves no compiling.

Note that it seems that the Wine project uses the traditional way of numbering releases i.e. odd version are development versions i.e. the 1.4 series is stable, the 1.5 series is under development, and the 1.6 series will be the next stable.

Please note what it says on the carbon-dev page:

The amount of traffic this little sub-page generates is quite respectable. If you think this service helpful and want to help cover some of the attached costs, please donate a few Euros, either through PayPal, by flattring this or by donating through Flattr. Thank you! (You can, of course, also donate something, for totally different reasons.)

So at the very least don't download the same packages over and over and keep bandwidth to a minimum.

Anyway, here we go.

---

0. Clean up
Uninstall any newer version of wine if you've compiled e.g. 1.5.15.

sudo apt-get autoremove wine

1. Download
Get the debs for wine 1.5.5:

cd ~/tmp
mkdir wine-1.5.5
cd wine-1.5.5/
wget -r -l1 --no-parent -A amd64.deb http://dev.carbon-project.org/debian/wine-unstable/

FINISHED --2012-11-28 17:05:04--
Total wall clock time: 1m 1s
Downloaded: 18 files, 65M in 54s (1.20 MB/s)

cd dev.carbon-project.org/debian/wine-unstable/

2. Install

sudo dpkg -i *.deb

Processing triggers for man-db ...
Setting up libwine-alsa-unstable (1.5.5-0.1) ...
Setting up libwine-bin-unstable (1.5.5-0.1) ...
Setting up libwine-capi-unstable (1.5.5-0.1) ...
Setting up libwine-cms-unstable (1.5.5-0.1) ...
Setting up libwine-dbg-unstable (1.5.5-0.1) ...
Setting up libwine-dev-unstable (1.5.5-0.1) ...
Setting up libwine-gl-unstable (1.5.5-0.1) ...
Setting up libwine-gphoto2-unstable (1.5.5-0.1) ...
Setting up libwine-ldap-unstable (1.5.5-0.1) ...
Setting up libwine-openal-unstable (1.5.5-0.1) ...
Setting up libwine-oss-unstable (1.5.5-0.1) ...
Setting up libwine-print-unstable (1.5.5-0.1) ...
Setting up libwine-sane-unstable (1.5.5-0.1) ...
Setting up wine-bin-unstable (1.5.5-0.1) ...
Processing triggers for mime-support ...
Processing triggers for gnome-menus ...
Processing triggers for desktop-file-utils ...
Setting up wine-unstable (1.5.5-0.1) ...

3. You're done

285. Minor bug in ECCE

I'll classify this as a bug, since the specificity of it surely must mean that it is an unintended behaviour. Basically you lose your hand-edited changes in your input files if you're not careful.

By Editor I don't mean the vim editor, but rather then Job Editor in Ecce.

 A demonstation: 

1. Create an input in ECCE. In this case I created a single-point energy calculation of dioxygen. Hand-edit the input file by clicking on Final Edit and add e.g. maxiter 99 in the dft block.

 2. Run the job


 3. Open the Editor. With the Editor open, click on Run Mgmt/Reset for restart. (In spite of the figure below, it has nothing to do with whether the vim editor is open or not.)

 4. Your hand-edited changes are now gone.

 In contrast, if the Editor is not open when you click on Run Mgmt/Reset for restart the changes will be kept.

284. Fix for: nautilus-open-terminal opens in $HOME

Update: due to a change in the exec-arg, if you followed the instruction here you now can't open the terminal (using nautilus) at all if you've upgraded to nautilus 3.4.2. Look at this post to fixing it: http://verahill.blogspot.com.au/2012/12/another-nautilus-open-terminal-related.html
Everything should now work perfectly.

Original post:
This has been bothering me for the past week or so: if I use nautilus-open-terminal (i.e. right-click in nautilus and select open in terminal) it now always opens in $HOME instead of in the directory I want it to open in.

 Apparently I'm not the only one: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=692518

Luckily the solution is quick and simple: run this in your terminal, then open a new nautilus window:

gsettings set org.gnome.desktop.default-applications.terminal exec gnome-terminal

283. gnome-shell-extension-common 3.0.2 and gnome-shell-extensions 3.4.0 conflict

Not sure how this came about but I might have downloaded and install an unsupported .deb (from here I think) at some point at the beginning of Gnome 3.
Following this post will get you back to a conflict-free system BUT it will also remove debs that depend on gnome-shell-extension-common (i.e. packages that you have have downloaded from the web as deb packages. It won't affect normal gnome shell extensions).

---

The problem:

Unpacking gnome-shell-extensions (from .../gnome-shell-extensions_3.4.0-2_all.deb) ...
dpkg: error processing /var/cache/apt/archives/gnome-shell-extensions_3.4.0-2_all.deb (--unpack):
 trying to overwrite '/usr/share/locale/fr/LC_MESSAGES/gnome-shell-extensions.mo', which is also in package gnome-shell-extension-common 3.0.2-2
Errors were encountered while processing:
 /var/cache/apt/archives/gnome-shell-extensions_3.4.0-2_all.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

and

sudo apt-get remove gnome-shell-extension-common 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
You might want to run 'apt-get -f install' to correct these:
The following packages have unmet dependencies:
 gnome : Depends: gnome-shell-extensions (>= 3.4) but it is not going to be installed
 gnome-shell-extension-alternate-tab : Depends: gnome-shell-extension-common but it is not going to be installed
 gnome-shell-extension-alternative-status-menu : Depends: gnome-shell-extension-common but it is not going to be installed
 gnome-shell-extension-auto-move-windows : Depends: gnome-shell-extension-common but it is not going to be installed
 gnome-shell-extension-dock : Depends: gnome-shell-extension-common but it is not going to be installed
 gnome-shell-extension-gajim : Depends: gnome-shell-extension-common but it is not going to be installed
 gnome-shell-extension-user-theme : Depends: gnome-shell-extension-common but it is not going to be installed
 gnome-shell-extension-windows-navigator : Depends: gnome-shell-extension-common but it is not going to be installed
 gnome-shell-extension-xrandr-indicator : Depends: gnome-shell-extension-common but it is not going to be installed
E: Unmet dependencies. Try 'apt-get -f install' with no packages (or specify a solution).

---

The solution:

sudo dpkg --force-overwrite -i /var/cache/apt/archives/gnome-shell-extensions_3.4.0-2_all.deb
sudo apt-get install -f
sudo apt-get autoremove gnome-shell-extension-common=3.0.2-1
sudo apt-get update && sudo apt-get upgrade

282. Mesa 9.0.1 (64 bit) on debian wheezy

This post is intended as a step towards building wine with libOSmesa. Apparently any version of libOSmesa lower than 9 is no good, and debian wheezy currently have version 8.

Unfortunately building the 32 bit version turns out to be more complex than just requesting it via --enable-32-bit, so I'll be making a post on a chrooted build of the missing wine libraries later. I've also noticed that libOSMesa is just a small part of Mesa -- this build overlaps a lot with mesa-common-dev as well.

Finally, I don't really have a good grasp over graphics on linux -- which means that I'm still confused by OpenGl, CL, Mesa etc.

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

As usual: I have a lot of packages installed on my standard compile node, so there are probably a lot of packages which are needed which I didn't notice. But here we go:

---

First you need to build e.g. libdrm 2.4.40 since wheezy and sid currently have v2.4.33 and you need 2.4.39 or newer.

sudo apt-get install libpciaccess-dev checkinstall
wget http://cgit.freedesktop.org/mesa/drm/snapshot/libdrm-2.4.40.tar.gz
tar xvf libdrm-2.4.40.tar.gz
cd libdrm-2.4.40/
./autogen 
make
sudo checkinstall

When you're asked for a description, type 'libdrm 2.4.40' and it should get the version number right.
(you could also build with --prefix and install it somewhere else but that makes things trickier later)

Make sure it installed correctly:

aptitude show libdrm
Package: libdrm                          
New: yes
State: installed
Automatically installed: no
Version: 2.4.40-1
Priority: extra
Section: checkinstall
Maintainer: root@beryllium
Architecture: amd64
Uncompressed Size: 733 k
Description: libdrm 2.4.40

---

Build OS mesa v.9.0.1.

sudo apt-get install flex bison libdrm-dev xutils-dev x11proto-gl-dev x11proto-dri2-dev libx11-xcb-dev libxcb-glx0-dev libxcb-dri2-0-dev libxcb-xfixes0-dev llvm automake
cd ~/tmp
wget ftp://ftp.freedesktop.org/pub/mesa/9.0.1/MesaLib-9.0.1.tar.gz
tar xvf MesaLib-9.0.1.tar.gz
cd Mesa-9.0.1/
./autogen.sh --enable-osmesa
make
sudo checkinstall

This package will be built according to these values: 

0 -  Maintainer: [ root@beryllium ]
1 -  Summary: [ Mesa 9.0.1 64 bit]
2 -  Name:    [ mesa ]
3 -  Version: [ 9.0.1 ]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ amd64 ]
8 -  Source location: [ Mesa-9.0.1 ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ mesa ]
12 - Conflicts: [  ]
13 - Replaces: [  ]

Some notes:
xutils-dev contains makedepend; x11proto-gl-dev is GLPROTO, x11proto-dri2-dev is DRI2PROTO
LLVM is needed for one step in the build process (gallium). I'm sure you can get around it, but I'm not too bothered.



Links to this post:
http://forums.linuxmint.com/viewtopic.php?f=190&p=696973

281. Visualising NWChem output with GabEdit

Update: please read Karol's comment below. I will put a link here once I've written up a post on how to modify nwchem.

Update 2: Here's the post: http://verahill.blogspot.com.au/2013/02/3xx-modifying-nwchem-611-to-work-with.html .The conclusion is that you MUST edit nwchem. Luckily, it's easy.

Original post:
I've never liked Gabedit much (looks a bit dated, tries to do 'too much') -- until today. Suddenly I have a newfound respect for the developer(s) behind it. It actually doesn't try to do 'too much' -- it simply does A LOT, and actually does it in a pretty transparent way.

Long story short -- you can do things with gabedit which you can't do (easily) with ECCE, and as such it has become an important ally. Besides, it's always nice to have alternatives.

GabEdit is in the Debian repos.

Running your calculations
There are some restrictions"
1. NOTE: you must run your nwchem job with explicit basis sets (i.e. entered as text) -- to do that in ECCE tick the box as shown in the figure below. If you're running 'pure' nwchem, you (probably) have to cut and paste from the basis set directory -- see e.g. section 7.2 here. It's a minor convenience for gaining access to what GabEdit has to offer.

2. You can only open Single point/Energy calculations i.e. Optimizations won't work. So do a single point calculation on your optimized structure.

3. Also, you need to rename/copy your output file so that it ends with .out.

gabedit won't read it otherwise

GabEdit
It's fairly straightforward -- just point and click. One thing which you will want to play with are the iso-surface settings. The defaults are rarely good.

Anyway, I'll let the screenshots do the talking:

Go straight to the Output viewer -- Geometry/Orbital/Density

Click on the M, or right-click anywhere in the window, and load your renamed nwchem output file.

Here's triplet oxygen. The alpha, beta orbitals are listed in the right window

You can do electron localisation

Look at spin density (the unpaired electrons are in the anti-bonding  pi orbitals)

Contour plots are neat -- here showing spin density

Electrostatic potential. 

There's a lot to explore. GabEdit can obviously also prepare and submit jobs, but I'm happy with ECCE in this respect, and content with using GabEdit for post-processing.

280. gOpenMol on Debian Wheezy

This is a quick description of how to install gOpenMol (software for visualising output from various comp. chem. packages) on debian:

wget http://www.csc.fi/english/pages/g0penMol/Downloads/gopenmol-3.00-linux.tar.gz
gopenmol-3.00-linux.tar.gz
tar xvf gopenmol-3.00-linux.tar.gz
sudo mv gOpenMol-3.00 /opt/
/opt/gOpenMol-3.00/./install
echo 'export PATH=$PATH:/opt/gOpenMol-3.00/bin' >> ~/.bashrc
source ~/.bashrc
rungOpenMol

I'm having issues with a transparent background in the main window on my nvidia box. Not sure what it's like  on other machines.

279. Formatting and adding a disk with fdisk

I've got a box with two harddrives -- sda (160 gb) has debian and sdb has CentOS (500 gb). I never use CentOS and I need the space for debian.

sudo fdisk -l

WARNING: GPT (GUID Partition Table) detected on '/dev/sda'! The util fdisk doesn't support GPT. Use GNU Parted.
Disk /dev/sda: 160.0 GB, 160041885696 bytes
255 heads, 63 sectors/track, 19457 cylinders, total 312581808 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00000000

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1               1   312581807   156290903+  ee  GPT

Disk /dev/sdb: 500.1 GB, 500107862016 bytes
255 heads, 63 sectors/track, 60801 cylinders, total 976773168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x0007e385

   Device Boot      Start         End      Blocks   Id  System
/dev/sdb1   *          63    32772599    16386268+  83  Linux
/dev/sdb2        32772600    40965749     4096575   83  Linux
/dev/sdb3        40965750    43006004     1020127+  82  Linux swap / Solaris
/dev/sdb4        43006005   976768064   466881030    5  Extended
/dev/sdb5        43006068   976768064   466880998+  83  Linux

We're in 'luck' since we're only interested in killing sdb, and gparted wants a Display (this is done remotely).
So

sudo fdisk /dev/sdb

Command (m for help): d
Partition number (1-5): 1

Command (m for help): d 
Partition number (1-5): 2

Command (m for help): d
Partition number (1-5): 3

Command (m for help): d
Partition number (1-5): 4

Command (m for help): w
The partition table has been altered!

Calling ioctl() to re-read partition table.
Syncing disks.

So did it work?

 sudo fdisk -l

WARNING: GPT (GUID Partition Table) detected on '/dev/sda'! The util fdisk doesn't support GPT. Use GNU Parted.


Disk /dev/sda: 160.0 GB, 160041885696 bytes
255 heads, 63 sectors/track, 19457 cylinders, total 312581808 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00000000

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1               1   312581807   156290903+  ee  GPT

Disk /dev/sdb: 500.1 GB, 500107862016 bytes
255 heads, 63 sectors/track, 60801 cylinders, total 976773168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x0007e385

   Device Boot      Start         End      Blocks   Id  System

Time to create a new partition

sudo fdisk /dev/sdb

Command (m for help): n
Partition type:
   p   primary (0 primary, 0 extended, 4 free)
   e   extended
Select (default p): p
Partition number (1-4, default 1): 
Using default value 1
First sector (2048-976773167, default 2048): 
Using default value 2048
Last sector, +sectors or +size{K,M,G} (2048-976773167, default 976773167): 
Using default value 976773167

Command (m for help): w
The partition table has been altered!

Calling ioctl() to re-read partition table.
Syncing disks.

Did it work?

sudo fdisk -l /dev/sdb

Disk /dev/sdb: 500.1 GB, 500107862016 bytes
81 heads, 63 sectors/track, 191411 cylinders, total 976773168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x0007e385

   Device Boot      Start         End      Blocks   Id  System
/dev/sdb1            2048   976773167   488385560   83  Linux

Create a file system:

sudo mkfs.ext4 /dev/sdb1

mke2fs 1.42.5 (29-Jul-2012)
Filesystem label=
OS type: Linux
Block size=4096 (log=2)
Fragment size=4096 (log=2)
Stride=0 blocks, Stripe width=0 blocks
30531584 inodes, 122096390 blocks
6104819 blocks (5.00%) reserved for the super user
First data block=0
Maximum filesystem blocks=4294967296
3727 block groups
32768 blocks per group, 32768 fragments per group
8192 inodes per group
Superblock backups stored on blocks: 
        32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208, 
        4096000, 7962624, 11239424, 20480000, 23887872, 71663616, 78675968, 
        102400000

Allocating group tables: done                            
Writing inode tables: done                            
Creating journal (32768 blocks): done
Writing superblocks and filesystem accounting information: done     

Let's automount it:

mkdir /home/me/scratch

and edit /etc/fstab

/dev/sdb1  /home/me/scratch    ext4    defaults        0       2

You're done.

278. Monitoring your office with a webcam and zoneminder on debian

Update: so this worked fine with my thinkpad sl410 camera, but I'm having a lot of trouble getting an image off of my usb Pixio cam (Z-Star Microelectronics Corp. USB 1.1 Webcam) with "Got signal 11 (Segmentation fault), crashing" and "'zmc -d /dev/video0' exited abnormally, exit status 11". Zoneminder feels annoyingly temperamental at times. Anyway, I ended up hacking together a poor but functional solution by using a shell script and streamer to save stills every few seconds, then letting zoneminder analyse and capture. Setting up two Airlink 101 AIC250W was remarkably easy though (although I remember having a lot of trouble in the past). I've also experimented with motion,  and although I'm having issues with the image colours it's working very well.

Original post
While I figured that the head of school might have a universal key allowing access to all the offices in the department (the cleaners do), finding out that he had used it to open my office for a trivial purpose has ticked me off.

While you may not have an expectation of privacy at your company office, I certainly do when it comes to my department office.

So I'm not too happy about that, and while monitoring my office will not prevent future breaches of privacy, it will at least ease some of the paranoia if it turns out that my office doesn't routinely get entered.

This post only deals with a locally attached webcam -- I struggled with remote wifi-connected webcams a few years ago with little luck.

sudo apt-get install zoneminder

sudo apt-get install v4l-conf v4l2ucp
sudo cp /etc/zm/apache.conf /etc/apache2/sites-enabled/zm.conf
sudo service apache2 restart

Figure out what video devices you have:

ls /dev/video* 

/dev/video0

and make sure www-data can access them

sudo adduser www-data video

You can now navigate to http://localhost/zm

Click on 'add monitor'

These settings are fine.

Note: these settings did NOT work. Keep reading the post...

Setting up the camera seemed deceptively easy -- everything went fine, except actually getting an image.

note the red colour for the video device. No good.

Looking at the log I was getting

Failed to set video format: Invalid argument
'zmc -d /dev/video0' exited abnormally, exit status 255

which is when I googled and found this post: http://rainbow.chard.org/2012/04/24/using-zoneminder-with-a-cheap-cctv-camera/

Basically, getting the settings absolutely right matters!

v4l-info

which told me

video capture
    VIDIOC_ENUM_FMT(0,VIDEO_CAPTURE)
 index                   : 0
 type                    : VIDEO_CAPTURE
 flags                   : 0
 description             : "YUV 4:2:2 (YUYV)"
 pixelformat             : 0x56595559 [YUYV]
    VIDIOC_ENUM_FMT(1,VIDEO_CAPTURE)
 index                   : 1
 type                    : VIDEO_CAPTURE
 flags                   : 1
 description             : "MJPEG"
 pixelformat             : 0x47504a4d [MJPG]
    VIDIOC_G_FMT(VIDEO_CAPTURE)
 type                    : VIDEO_CAPTURE
 fmt.pix.width           : 1600
 fmt.pix.height          : 1200
 fmt.pix.pixelformat     : 0x47504a4d [MJPG]
 fmt.pix.field           : NONE
 fmt.pix.bytesperline    : 0
 fmt.pix.sizeimage       : 5760000
 fmt.pix.colorspace      : unknown
 fmt.pix.priv            : 0

so changed my settings to

It took a bit of trial and error

Next, I was receiving

Got unexpected memory map file size 49153524, expected 230401524

and this post helped me:
http://jared-oberhaus-tech-notes.blogspot.com.au/2011/12/im-trying-to-capture-video-from-device.html

Our old friend shmmax eh? Apparently I had about 32 mb set up (!) on my laptop, so I changed it to 671088640 (640 mb)

sudo sysctl -w kernel.shmmax=671088640

See this post for how to make it permanent.

Anyway, once all is well you will hopefully see something like this (note the colours -- the /dev/ is a nice orange, although the log is still an unhappy red)

Now we can actually do things. Click on the name of your device (here: laptop) and you should get something like

You can now click on Zones in the main menu and add one (takes a little bit of trial and error, but you'll get there). To get motion detection, and thus get ZM to save things, change the mode from Monitor to e.g. modec

Your files will  be found under /usr/share/zoneminder/events but you can change that using the setting menu which you can access in the top right corner in the main window.

So that's pretty much it. There are a couple of settings you might want to fiddle with:

You might want to set up ffmpeg to allow for generation of video fles

---

So I got fed up with one of my cameras not working together with zoneminder. As a temporary fix I set zoneminder to use 'file' instead of 'local' or 'remote'. So now zoneminder looks at ~/webcam/current.jpg.
In that directory, a script is running (you need to install streamer):

#!/bin/bash
while true
do streamer -c /dev/video0 -b 24 -s 640x480 -o current.jpeg -q 2> /dev/null
        sleep 1
done

Also, I created a directory and symmlinked it to /usr/share/events to prevent my root partition from filling up:

mkdir zm/
chown www-data zm/
sudo rm /usr/share/zoneminder/events -rf
sudo ln -s /home/me/webcam/zm /usr/share/zoneminder/events

277. Compiling LSDALTON on debian testing/wheezy

I'm writing this as a separate post even though it's really an integral part of the compilation of Dalton 2011 which I described here: http://verahill.blogspot.com.au/2012/11/compiling-dalton-2011-on-debian.html

LSDALTON supports Open MP which is neat -- it means you can't run across nodes, but it'll automatically take advantage of the resources on the node it's run on.

Anyway.

Assuming you've followed that post, you're now ready to compile LSDALTON.

cd ~/tmp/Dalton2011_release/LSDALTON/
./configure

There are fewer questions this time so I won't list them -- basically, use gfortran and gcc, and compile with OpenMP support.

This gives you a Makefile.config -- edit it as shown. Note that I have the debian libblas3 and libgomp1 packages installed.

ARCH        = linux
FMMDIR      = mm
#
#
CPPFLAGS      = -DSYS_LINUX -D_FILE_OFFSET_BITS=64 -D'INSTALL_BASDIR="/opt/dalton/basis"' -DGFORTRAN=471 -DVAR_LINSCA -DIMPLICIT_NONE
F77            = gfortran
F90            = gfortran
FLNK           = gfortran
CC             = gcc
RM             = rm -f
FFLAGS         = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -ffloat-store -fno-whole-file
F90OPTFLAGS    = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -ffloat-store -I. -x f95-cpp-input -ffloat-store -fopenmp -fno-whole-file
SAFEFFLAGS     = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -ffloat-store -fno-whole-file
CFLAGS         = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -std=c99 -DRESTRICT=restrict -DFUNDERSCORE=1 -ffloat-store -DUSE_UNDERSCORES
INCLUDES       =  
LIBS           = -lblas -lgomp 
INSTALLDIR     = /opt/dalton/bin
PDPACK_EXTRAS  = linpack.o eispack.o gp_dlapack.o gp_zlapack.o
AR             = ar
ARFLAGS        =  rvs
#
default : linux.x
#
# Suffix rules C
#
.SUFFIXES : .F90 .f90 .F .o .c

.F90.o:
        $(F90) $(INCLUDES) $(CPPFLAGS) $(F90OPTFLAGS) -c $*.F90

.f90.o:
        $(F90) $(INCLUDES) $(CPPFLAGS) $(F90OPTFLAGS) -c $*.f90

.F.o:
        $(F77) $(INCLUDES) $(CPPFLAGS) $(FFLAGS) -c $*.F

.c.o:
        $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -c $*.c

Now compile!

make

Test your installation:

cd test/
 ./TEST all
[..]
-----------------------------------------------------------
TEST ENDED PROPERLY

#####################################################################
                              Summary
#####################################################################

ALL TESTS ENDED PROPERLY!
date and time         : Wed Nov  7 14:57:29 EST 2012

276. Compiling Dalton 2011 on Debian Testing/Wheezy

UPDATE: To deal with basis sets and 'GPOPEN' errors, see bottom of this post
UPDATE2: Because of the basis set issue the code doesn't run in parallel!
UPDATE 3: All issues are solved by -O0 or -O1. The code now works in parallel and you can define basis sets the usual way. Performance-wise? No idea. So you can compile with -O3 or -O2 but the code doesn't read basis sets the intended way, or you use -O1 or -O0 and it works.

THIS WORKS NOW  :)

Original post:
I've been wanting to use dalton for a long time, but it's been difficult to compile dalton 2.0, and I didn't realise until a few days ago that there's a newer version.
See here for a description of how to compile on ROCKS 5.4.3 (i.e. Centos 5.6) which uses gfortran v 4.1. The main difference between compiling on CentOS 5.6 and Debian Wheezy is in how you edit the Makefile.config. More specifically, compile works a whole lot better with -fno-whole-file and -march=native..

Other than that the steps are the same.

In terms of running, there's an issue with the discoverability of the basis sets which I don't really understand. There's a solution to that at the end of the file.

---

Before you get started you may want to compile ATLAS as shown here: http://verahill.blogspot.com.au/2012/05/compile-atlas-blas-on-debian-testing.html

Alternatively, you should get the ACML libraries.

NOTE: The compile went without a hitch on my AMD II X3, AMD Phenom II X6 and Intel i5-2400.
My AMF FX 8150 is a trickier story though: it failed to compile with acml libs (gfortran64_fma4_int64) for -O3 and -O2, but compiled with -O1 and -O0. The -O1 binary segfaults though. Never tried the -O0 binary.

WARNING: If you run dalton in parallel it will -- for some reason -- delete your scratch folder when the run is over. The scratch directory is defined in the  /opt/dalton/bin/dalton script (TMPDIR)

License:
First go to http://daltonprogram.org/licence/ and fill out the license agreement. Once that's done you'll get an automated email with a license form, which you should print, sign, scan and email to the email address you're given. Once your form has been processed you'll be sent another email with a user name and password. I received my user name and password the next business day.

Go online and download the source file, Dalton2011_release_v0.tgz, and put it in ~/tmp. Sort out where you want your program to end up

sudo mkdir /share/apps/dalton
sudo chown $USER /share/apps/dalton
mkdir /share/apps/dalton/bin /share/apps/dalton/basis /share/apps/dalton/lsdalton

Next,

cd ~/tmp
tar xvf Dalton2011_release_v0.tgz
cd Dalton2011_release/DALTON
./configure 

and answer all the questions:

./configure

------------------------------------------------------------------
   Configuring the DALTON Makefile.config and "dalton" run script
------------------------------------------------------------------

INFO: Operating system from 'uname -s' : Linux
INFO: Processor type   from 'uname -m' : x86_64
No architecture specified, attempting auto-configuration:
This appears to be a -linux architecture. Is this correct? [Y/n] 
--> Installing DALTON on a -linux computer


Note that 64-bit integers are desirable for Cholesky and very large
scale CI, otherwise the most important effect is that some files will be bigger.

If you choose 64-bit integers, be careful that any system library
routines (incl. MPI) also use 64-bit integers!

Do you want 64-bit integers? [y/N] Do you want to install the program in a parallel MPI version? [Y/n] 
-->WARNING: Makefiles for MPI architecture are difficult to guess
   Please compare the generated Makefile.config with local documentation.

   Checking for Fortran compiler ...
   from this list: mpif90 mpiifort ifort pgf95 pgf90 gfortran g95 

Compiler /usr/bin/mpif90 found, use this compiler? [Y/n] 
-->Compiler mpif90 found and accepted.
Is backend compiler gfortran ? [Y/n] 
   Checking for C compiler ...
   from this list: mpicc  mpiicc   icc ecc pgcc gcc 

Compiler /usr/bin/mpicc found, use this compiler? [Y/n] 
-->Compiler mpicc found and accepted.

Testing existence of libraries in this order:
 libacml.a libmkl.so libmkl_p3.a libatlas.a libblas.a
Directory search list for libraries:
  /opt/ATLAS/lib /home/me/tmp/ATLAS/build/lib /lib /usr/local/lib /usr/lib /usr/local/lib/ATLAS /lib64 /usr/lib64 /usr/local/lib64 

Do you want to replace this with your own directory search list? [y/N] Found /opt/ATLAS/lib/libatlas.a, use it? [Y/n] 
-->The following mathematical library(ies) will be used:
   -L/opt/ATLAS/lib -llapack -llapack -lf77blas -latlas


DALTON uses almost 100 Megabytes of static
allocations, in addition to the dynamic allocation.

DALTON has the possibility to reserve an amount of static memory
for storing two-electron integrals in direct and parallel calculations
Storing some or all of the 2-el. integrals in memory will speed up
direct and parallel calculations (and in particular the latter).
NOTE: This will increase the static memory allocation used by DALTON

Would you like to activate the possibility of storing 2-el.int. in memory? [y/N] How many MB to use for storing 2-el. integrals? 
-->Program will be installed with 300 MB (39000000 words) used for storing 2-el. integrals

Maximum amount of work memory for dynamic allocations can be changed
at run time with the environment variable WRKMEM (in REAL*8 words = megabytes/8)
or by using the -M option to the run script: "dalton -M mb ..." (in megabytes).
We recommend at least 200 MB work memory,
larger for correlated calculations, but it should for maximum
efficiency NOT exceed available physical memory per CPU in parallel calculations.

How many MB to use as default for work memory (hit return for default of 1000 MB)? 
-->Program will be installed with a default work memory of 3900 MB (511000000 words)

-->Current directory is /home/me/tmp/Dalton2011_release/DALTON

Use default ../bin as installation directory for DALTON binaries and scripts? [Y/n] Please enter another installation directory: 
-->DALTON executable and script will be placed in /opt/dalton/bin directory


-->Default basis set directory will be /home/me/tmp/Dalton2011_release/DALTON/../basis/

Use this directory as default basis set directory? [Y/n] 
Please choose another default basis set directory (must end with /) 
-->Default basis set directory will be /opt/dalton/basis/


-->Job specific directories under $SCRATCH/$USER
-->will be used for temporary files when running DALTON

Use SCRATCH=/work as default root scratch space in "dalton" run script? [Y/n] Please enter default root scratch directory: 
-->Creating Makefile.config ...
gfortran version 471 prc=x86_64
INFO: Compiling with 32-bit integers.
INFO: Make sure pre-compiled BLAS, MPI etc. libraries are also with 32-bit integers!!!

Proper 64-bit file access detected.

-->Creating the DALTON run-script in /opt/dalton/bin

   The configuration of DALTON has finished succesfully.
   Check compiler flags etc. in Makefile.config and run "make" to get executable.

which generates Makefile.config. Edit it and

• change the -march to native. 
• add -fno-whole-file to avoid internal compiler errors
• change optimisation level to -O1 (O0 is ok, O2 and O3 give GPOPEN problems)

Like this:

ARCH        = linux
#
#
CPPFLAGS      = -DVAR_GFORTRAN -DSYS_LINUX -DVAR_MFDS -D'INSTALL_WRKMEM=131000000' -D'INSTALL_MMWORK=65000000' -D_FILE_OFFSET_BITS=64 -DVAR_MPI -DGFORTRAN=471 -DIMPLICIT_NONE
F90           = mpif90
CC            = mpicc
LOADER        = mpif90
RM            = rm -f
FFLAGS        = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -fbacktrace -fno-whole-file
SAFEFFLAGS    = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -fbacktrace -fno-whole-file
CFLAGS        = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -std=c99 -DRESTRICT=restrict -DFUNDERSCORE=1
INCLUDES      = -I../include 
MODULES       = -J../modules
LIBS          = -L/opt/ATLAS/lib -llapack -llapack -lf77blas -latlas 
INSTALLDIR    = /opt/dalton/bin
PDPACK_EXTRAS = linpack.o eispack.o gp_zlapack.o gp_dlapack.o
GP_EXTRAS     = 
AR            = ar
ARFLAGS       = rvs
# flags for ftnchek on Dalton /hjaaj
CHEKFLAGS  = -nopure -nopretty -nocommon -nousage -noarray -notruncation -quiet  -noargumants -arguments=number  -usage=var-unitialized
# -usage=var-unitialized:arg-const-modified:arg-alias
# -usage=var-unitialized:var-set-unused:arg-unused:arg-const-modified:arg-alias
#
default : dalton linuxparallel.x
SAFE_FFLAGS_for_ifort = $(FFLAGS)
#
# Parallel initialization
#
MPI_INCLUDE_DIR = 
MPI_LIB_PATH    = -L/usr/lib
MPI_LIB         = -lmpi
#
#
# Suffix rules
# hjaaj Oct 04: .g is a "cheat" suffix, for debugging.
#               'make x.g' will create x.o from x.F or x.c with -g debug flag set.
#
.SUFFIXES : .F .F90 .c .o .i .g .s

.F.o:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -c $*.F 

.F.i:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) -E $*.F > $*.i

.F.g:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(SAFEFFLAGS) -g -c $*.F 

.F.s:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -S -g -c $*.F 

.F90.o:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -c $*.F90 

.F90.i:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) -E $*.F90 > $*.i

make
make install

Now just copy the basis sets and ecp data to the proper location:

cd ../
cp basis/* -R /opt/dalton/basis

and edit your ~/.bashrc;

export PATH=$PATH:/opt/dalton/bin

And you should be good to go.

---

So far I haven't run all the tests, but

./TEST -dalton /opt/dalton/bin/dalton short

gave

#####################################################################
                              Summary
#####################################################################

ALL TESTS ENDED PROPERLY!

date and time         : Wed Nov  7 11:57:02 EST 2012

---

GPOPEN errors and how to get around them.

To make the story short: if you use -O3 or -O2 for some reason Dalton can't find the basis sets if you declare them the normal way (-O0 and -O1 take care of the problem). However, using ATOMBASIS it works.

Here's an example. Typically you'd specify the basis set for a whole molecule in your .mol file:

BASIS
STO-3G
DFT PROPERTIES TEST 
This doesn't work with O3
AtomTypes=2 Angstrom
        8.    1     
O -0.141254 0.0998816 0.00000
        1.    2     
H 0.589315 0.718039 0.00000
H -0.922641 0.652406 0.00000

but that leads to errors on the debian (but not centos) builds:

   0: Directories for basis set searches:
     /jobs/dalton:/opt/dalton/basis

 MPI node no.:     0
 Reason: ERROR (GPOPEN) UPON OPENING A FILE


 Node      0:  --- SEVERE ERROR, PROGRAM WILL BE ABORTED ---
 ERROR (GPOPEN) UPON OPENING A FILE

and

  Atomic type no.    1
  --------------------
  Nuclear charge:   8.00000
  Number of symmetry independent centers:    1
  Number of basis sets to read;    2
  Basis set file used for this atomic type with Z =   8 :
     "/opt/dalton/basis/                                                                                "


--> ERROR (GPOPEN) UPON TRYING TO OPEN FILE ON UNIT 11
--> with filename /opt/dalton/basis/
--> IOSTAT ERROR CODE RETURNED      21


 QTRACE dump of internal trace stack

 ========================
      level    module
 ========================
          7    GPOPEN      
          6    BASLIB      
          5    READ_MOL    
          4    READIN      
          3    HERMIT      
          2    DALTON      
          1    DALTON main 

whereas

ATOMBASIS
DFT PROPERTIES TEST 
This works with O3
AtomTypes=2 Angstrom
        8.    1    basis=STO-3G 
O -0.141254 0.0998816 0.00000
        1.    2     basis=STO-3G
H 0.589315 0.718039 0.00000
H -0.922641 0.652406 0.00000

works and gives

   0: Directories for basis set searches:
     /opt/dalton/basis:/opt/dalton/basis

 NOTE:    1 informational messages have been issued.
 Check output, result, and error files for "INFO".

and a normal exit:

 CPU time statistics for ABACUS
 ------------------------------

 LINRES     00:00:02      77 %

 TOTAL      00:00:03     100 %


 >>>> Total CPU  time used in ABACUS:   3.21 seconds
 >>>> Total wall time used in ABACUS:   3.22 seconds


                   .-------------------------------------------.
                   | End of Static Property Section (ABACUS) - |
                   `-------------------------------------------'

 >>>> Total CPU  time used in DALTON:   6.04 seconds
 >>>> Total wall time used in DALTON:   6.06 seconds

 
     Date and time (Linux)  : Tue Nov  6 14:54:24 2012
     Host name              : beryllium   

275. Compiling Dalton 2011 on ROCKS 5.4.3/CentOS

I've previously struggled with Dalton 2.0-cam and given up. I somehow didn't know about Dalton 2011 at that point, but it turns out it's much easier to build. Well, I managed to build it on ROCKS/CentOS (gcc 4.1). I'm still working on the debian version which has a much newer gcc (4.7)

Before you get started you may want to compile ATLAS as shown here: http://verahill.blogspot.com.au/2012/09/rocks-543-atlas-and-gromacs-on-xeon.html

License:
First go to http://daltonprogram.org/licence/ and fill out the license agreement. Once that's done you'll get an automated email with a license form, which you should print, sign, scan and email to the email address you're given. Once your form has been processed you'll be sent another email with a user name and password. I received my user name and password the next business day.

Go online and download the source file, Dalton2011_release_v0.tgz, and put it in ~/tmp. Sort out where you want your program to end up

sudo mkdir /share/apps/dalton
sudo chown $USER /share/apps/dalton
mkdir /share/apps/dalton/bin /share/apps/dalton/basis /share/apps/dalton/lsdalton

Next,

cd ~/tmp
tar xvf Dalton2011_release_v0.tgz
cd Dalton2011_release/DALTON
./configure 

and answer all the questions:

------------------------------------------------------------------
   Configuring the DALTON Makefile.config and "dalton" run script
------------------------------------------------------------------

INFO: Operating system from 'uname -s' : Linux
INFO: Processor type   from 'uname -m' : x86_64
No architecture specified, attempting auto-configuration:
This appears to be a -linux architecture. Is this correct? [Y/n] 
--> Installing DALTON on a -linux computer


Note that 64-bit integers are desirable for Cholesky and very large
scale CI, otherwise the most important effect is that some files will be bigger.

If you choose 64-bit integers, be careful that any system library
routines (incl. MPI) also use 64-bit integers!

Do you want 64-bit integers? [y/N] Do you want to install the program in a parallel MPI version? [Y/n] 
-->WARNING: Makefiles for MPI architecture are difficult to guess
   Please compare the generated Makefile.config with local documentation.

   Checking for Fortran compiler ...
   from this list: mpif90 mpiifort ifort pgf95 pgf90 gfortran g95 

Compiler /opt/openmpi/bin/mpif90 found, use this compiler? [Y/n] 
-->Compiler mpif90 found and accepted.
Is backend compiler gfortran ? [Y/n] 
   Checking for C compiler ...
   from this list: mpicc  mpiicc   icc ecc pgcc gcc 

Compiler /opt/openmpi/bin/mpicc found, use this compiler? [Y/n] 
-->Compiler mpicc found and accepted.

Testing existence of libraries in this order:
 libacml.a libmkl.so libmkl_p3.a libatlas.a libblas.a
Directory search list for libraries:
  /state/partition1/home/me/tmp/ATLAS/build/lib /state/partition1/apps/ATLAS/lib /lib /usr/local/lib /usr/lib /usr/local/lib/ATLAS /lib64 /usr/lib64 /usr/local/lib64 

Do you want to replace this with your own directory search list? [y/N] Found /state/partition1/home/me/tmp/ATLAS/build/lib/libatlas.a, use it? [Y/n] Found /state/partition1/apps/ATLAS/lib/libatlas.a, use it? [Y/n] 
-->The following mathematical library(ies) will be used:
   -L/state/partition1/apps/ATLAS/lib -llapack -llapack -lf77blas -latlas


DALTON uses almost 100 Megabytes of static
allocations, in addition to the dynamic allocation.

DALTON has the possibility to reserve an amount of static memory
for storing two-electron integrals in direct and parallel calculations
Storing some or all of the 2-el. integrals in memory will speed up
direct and parallel calculations (and in particular the latter).
NOTE: This will increase the static memory allocation used by DALTON

Would you like to activate the possibility of storing 2-el.int. in memory? [y/N] How many MB to use for storing 2-el. integrals? 
-->Program will be installed with 500 MB (65000000 words) used for storing 2-el. integrals

Maximum amount of work memory for dynamic allocations can be changed
at run time with the environment variable WRKMEM (in REAL*8 words = megabytes/8)
or by using the -M option to the run script: "dalton -M mb ..." (in megabytes).
We recommend at least 200 MB work memory,
larger for correlated calculations, but it should for maximum
efficiency NOT exceed available physical memory per CPU in parallel calculations.

How many MB to use as default for work memory (hit return for default of 1000 MB)? 
-->Program will be installed with a default work memory of 900 MB (117000000 words)

-->Current directory is /home/me/tmp/Dalton2011_release/DALTON

Use default ../bin as installation directory for DALTON binaries and scripts? [Y/n] Please enter another installation directory: 
-->DALTON executable and script will be placed in /share/apps/dalton/test directory


-->Default basis set directory will be /home/me/tmp/Dalton2011_release/DALTON/../basis/

Use this directory as default basis set directory? [Y/n] 
Please choose another default basis set directory (must end with /) 
-->Default basis set directory will be /share/apps/dalton/basis/


I did not find /work, /scratch, /scr, or /temp. I will use /tmp

-->Job specific directories under $SCRATCH/$USER
-->will be used for temporary files when running DALTON

Use SCRATCH=/tmp as default root scratch space in "dalton" run script? [Y/n] 
-->Creating Makefile.config ...
gfortran version 412 prc=x86_64
INFO: Compiling with 32-bit integers.
INFO: Make sure pre-compiled BLAS, MPI etc. libraries are also with 32-bit integers!!!

Proper 64-bit file access detected.

-->Creating the DALTON run-script in /share/apps/dalton/test

   The configuration of DALTON has finished succesfully.
   Check compiler flags etc. in Makefile.config and run "make" to get executable.

Regardless of what you'll answer, here's an example of a Makefile.config that I used. The key is to add -I../modules to INCLUDES, and delete -fbacktrace.

ARCH        = linux
#
#
CPPFLAGS      = -DVAR_GFORTRAN -DSYS_LINUX -DVAR_MFDS -D'INSTALL_WRKMEM=117000000' -D'INSTALL_MMWORK=65000000' -D_FILE_OFFSET_BITS=64 -DVAR_MPI -DGFORTRAN=412 -DIMPLICIT_NONE
F90           = mpif90
CC            = mpicc
LOADER        = mpif90
RM            = rm -f
FFLAGS        = -march=x86-64 -O3 -ffast-math -funroll-loops -ftree-vectorize 
SAFEFFLAGS    = -march=x86-64 -O3 -ffast-math -funroll-loops -ftree-vectorize 
CFLAGS        = -march=x86-64 -O3 -ffast-math -funroll-loops -ftree-vectorize -std=c99 -DRESTRICT=restrict -DFUNDERSCORE=1
INCLUDES      = -I../include -I../modules
MODULES       = -J../modules
LIBS          = -L/state/partition1/apps/ATLAS/lib -llapack -llapack -lf77blas -latlas -L/opt/openmpi/lib -lmpi
INSTALLDIR    = /share/apps/dalton/test
PDPACK_EXTRAS = linpack.o eispack.o gp_zlapack.o gp_dlapack.o
GP_EXTRAS     = 
AR            = ar
ARFLAGS       = rvs
# flags for ftnchek on Dalton /hjaaj
CHEKFLAGS  = -nopure -nopretty -nocommon -nousage -noarray -notruncation -quiet  -noargumants -arguments=number  -usage=var-unitialized
# -usage=var-unitialized:arg-const-modified:arg-alias
# -usage=var-unitialized:var-set-unused:arg-unused:arg-const-modified:arg-alias
#
default : dalton linuxparallel.x
SAFE_FFLAGS_for_ifort = $(FFLAGS)
#
# Parallel initialization
#
MPI_INCLUDE_DIR = 
MPI_LIB_PATH    = 
MPI_LIB         = 
#
#
# Suffix rules
# hjaaj Oct 04: .g is a "cheat" suffix, for debugging.
#               'make x.g' will create x.o from x.F or x.c with -g debug flag set.
#
.SUFFIXES : .F .F90 .c .o .i .g .s

.F.o:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -c $*.F 

.F.i:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) -E $*.F > $*.i

.F.g:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(SAFEFFLAGS) -g -c $*.F 

.F.s:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -S -g -c $*.F 

.F90.o:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -c $*.F90 

.F90.i:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) -E $*.F90 > $*.i

.F90.g:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(SAFEFFLAGS) -g -c $*.F90 

.F90.s:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -S -g -c $*.F90 

.c.o:
        $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -c $*.c 

.c.i:
        $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -E $*.c > $*.i

.c.g:
        $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -g -c $*.c 

.c.s:
        $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -S -g -c $*.c 

 

If all is looking well, make.

make
cd ../
cp basis/* /share/apps/dalton/basis

DO NOT RUN MAKE IN PARALLEL i.e. no make -j3 or anything like that.
Add /share/apps/dalton/bin to your PATH i.e. add a line saying

export PATH=$PATH:/share/apps/dalton/bin

to your ~/.bashrc and source it.
So far I haven't had much time to look at it, but here's the result of the 'short' test series:

./TEST -dalton /share/apps/dalton/bin/dalton short 
[..]
#####################################################################
                              Summary
#####################################################################

THERE IS A PROBLEM IN TEST CASE(S)
 prop_exci prop_vibg2 walk_vibave2 dftmm_1
date and time         : Sun Nov  4 18:41:59 PST 2012

Here's what I found for each of the troublesome ones above:

prop_exci:

126:  INFO from READIN: Threshold for discarding integrals was    1.00D-16
127:  INFO from READIN: Threshold is reset to minimum value       1.00D-15

But otherwise it finished ok.

prop_vibg2:

 SIROUT stat info, IST and IEND =                   0                  -1
 IST or IEND out of bounds - probably no optimization in this run.

But otherwise it finished ok.

walk_vibave2:

3 informational messages have been issued by Dalton,
output from 'grep -n INFO'  (max 10 lines):
549: *** SETSIR-INFO, time in NSETUP:       0.00 seconds.
2346: *** SETSIR-INFO, time in NSETUP:       0.00 seconds.
3691: *** SETSIR-INFO, time in NSETUP:       0.00 seconds

But otherwise it finished ok.

dftmm_1:

 NOTE:    1 warnings have been issued.
 Check output, result, and error files for "WARNING".
dftmm_1.tar.gz has been copied to /home/me/tmp/Dalton2011_release/DALTON/test
----------------------------------------------------------
2 WARNINGS have been issued by Dalton,
output from 'grep -n -i WARNING'  (max 10 warnings):
711: NOTE:    1 warnings have been issued.
712: Check output, result, and error files for "WARNING".

I can't find the warning in the output, which looks like it finished ok.

All in all, it looks very promising.

---

Note on running in parallel
I had to do

mkdir /tmp/$USER

first.

In addition, when running I have to explicitly define my scratch directory:

dalton -t /tmp/$USER -N 4 myinput.dal myinput.mol

Other than that it's OK. I just get the overall impression that things aren't very stable (some jobs crash, some don't)

274. Kernel 3.7-rc3

There's a specific driver (Silicom devices) included in the new kernel (3.7) that interests a friend. I do not suggest people in general run an -rc kernel, so I'm not going to put any effort into making this post user-friendly.

Having said that, in general you should be fine. In general.

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

mkdir ~/tmp
cd ~/tmp
wget http://www.kernel.org/pub/linux/kernel/v3.0/testing/linux-3.7-rc3.tar.bz2
tar xvf linux-3.7-rc3.tar.bz2 
cd linux-3.7-rc3/
cat /boot/config-`uname -r`>.config
make oldconfig

At this stage you'll be asked questions about all the shiny new things that are found in the kernel. See bottom of the post for a list of the questions.

If you regret the answer to a question you can change your mind later by doing

make menuconfig

Once you're done answering questions, compile!

make-kpkg clean
time fakeroot make-kpkg -j3 --initrd --revision=3.7.0 --append-to-version=-rc3 kernel_image kernel_headers

It takes 43 minutes on my old AMD X3.



To install the kernel:

mv ../linux-*-3.7.0-rc3*.deb .
sudo dpkg -i *.deb

And you're done!

---

New stuff (compared to kernel 3.6.3):

* CPU/Task time and stats accounting
*
Cputime accounting
> 1. Simple tick based cputime accounting (TICK_CPU_ACCOUNTING) (NEW)
  2. Fine granularity task level IRQ time accounting (IRQ_TIME_ACCOUNTING)
choice[1-2]: 1

Consider userspace as in RCU extended quiescent state (RCU_USER_QS) [N/y/?] (NEW) 
Module signature verification (MODULE_SIG) [N/y/?] (NEW)  
Legacy cpb sysfs knob support for AMD CPUs (X86_ACPI_CPUFREQ_CPB) [Y/n/?] (NEW) 
Packet: sockets monitoring interface (PACKET_DIAG) [N/m/y/?] (NEW)
IPv6: GRE tunnel (IPV6_GRE) [N/m/y/?] (NEW) 
IPv4 NAT (NF_NAT_IPV4) [N/m/?] (NEW) 
IPv6 NAT (NF_NAT_IPV6) [N/m/?] (NEW) 
OMAP OCP2SCP DRIVER (OMAP_OCP2SCP) [N/m/y/?] (NEW) 
Maximum expected bad eraseblock count per 1024 eraseblocks (MTD_UBI_BEB_LIMIT) [20] (NEW)
UBI Fastmap (Experimental feature) (MTD_UBI_FASTMAP) [N/y/?] (NEW)
Calxeda Highbank SATA support (SATA_HIGHBANK) [N/m/?] (NEW) 
Virtual eXtensible Local Area Network (VXLAN) (VXLAN) [N/m/y/?] (NEW) Y
PCH PTP clock support (PCH_PTP) [N/y/?] (NEW)
Solarflare SFC9000-family PTP support (SFC_PTP) [Y/n/?] (NEW)
Drivers for Atheros AT803X PHYs (AT803X_PHY) [N/m/?] (NEW)
MAX310X support (SERIAL_MAX310X) [N/y/?] (NEW)
SCCNXP serial port support (SERIAL_SCCNXP) [N/m/y/?] (NEW)
TPM HW Random Number Generator support (HW_RANDOM_TPM) [M/n/?] (NEW) 
TPM Interface Specification 1.2 Interface (I2C - Infineon) (TCG_TIS_I2C_INFINEON) [N/m/?] (NEW) 
NXP SC18IS602/602B/603 I2C to SPI bridge (SPI_SC18IS602) [N/m/?] (NEW)
OMAP HDQ driver (HDQ_MASTER_OMAP) [N/m/?] (NEW)
Analog Devices ADT7410 (SENSORS_ADT7410) [N/m/?] (NEW)
Maxim MAX197 and compatibles (SENSORS_MAX197) [N/m/y/?] (NEW)
generic cpu cooling support (CPU_THERMAL) [N/y/?] (NEW) Y
Fairchild FAN53555 Regulator (REGULATOR_FAN53555) [N/m/?] (NEW)
Media USB Adapters (MEDIA_USB_SUPPORT) [N/y/?] (NEW)
Media PCI Adapters (MEDIA_PCI_SUPPORT) [N/y/?] (NEW) 
Media test drivers (V4L_TEST_DRIVERS) [N/y] (NEW) 
ISA and parallel port devices (MEDIA_PARPORT_SUPPORT) [N/y/?] (NEW) 
Autoselect tuners and i2c modules to build (MEDIA_SUBDRV_AUTOSELECT) [Y/n/?] (NEW) 
Maximum debug level (NOUVEAU_DEBUG) [5] (NEW)
Default debug level (NOUVEAU_DEBUG_DEFAULT) [3] (NEW)
Backlight Driver for LM3630 (BACKLIGHT_LM3630) [N/m/?] (NEW)
Backlight Driver for LM3639 (BACKLIGHT_LM3639) [N/m/?] (NEW)
Sony PS3 BD Remote Control (HID_PS3REMOTE) [N/m/?] (NEW)
HID Sensors framework support (HID_SENSOR_HUB) [N/m/?] (NEW)
ZTE USB serial driver (USB_SERIAL_ZTE) [N/m/?] (NEW)
Functions for loading firmware on EZUSB chips (USB_EZUSB_FX2) [M/y/?] (NEW) 
OMAP USB2 PHY Driver (OMAP_USB2) [N/m/y/?] (NEW)
LED support for LM3642 Chip (LEDS_LM3642) [N/m/?] (NEW)
LED support for LM355x Chips, LM3554 and LM3556 (LEDS_LM355x) [N/m/?] (NEW)
LED CPU Trigger (LEDS_TRIGGER_CPU) [N/y/?] (NEW)
Dallas DS2404 (RTC_DRV_DS2404) [N/m/y/?] (NEW) 
Silicom devices (NET_VENDOR_SILICOM) [Y/n/?] (NEW) Y
Silicom BypassCTL library support (SBYPASS) [N/m/?] (NEW)m
Silicom BypassCTL net support (BPCTL) [N/m/?] (NEW) m
Cambridge Electronic Design 1401 USB support (CED1401) [N/m/?] (NEW)
Digi Realport driver (DGRP) [N/m/y/?] (NEW)
STE-Modem remoteproc support (STE_MODEM_RPROC) [N/m/y/?] (NEW)
SMB2 network file system support (EXPERIMENTAL) (CIFS_SMB2) [N/y/?] (NEW)
Red-Black tree test (RBTREE_TEST) [N/m/?] (NEW)
Interval tree test (INTERVAL_TREE_TEST) [N/m/?] (NEW)
CAST5 (CAST-128) cipher algorithm (x86_64/AVX) (CRYPTO_CAST5_AVX_X86_64) [N/m/y/?] (NEW)
CAST6 (CAST-256) cipher algorithm (x86_64/AVX) (CRYPTO_CAST6_AVX_X86_64) [N/m/y/?] (NEW)
Asymmetric (public-key cryptographic) key type (ASYMMETRIC_KEY_TYPE) [N/m/y/?] (NEW)

As for Intel devices the pre-existing settings were:

Intel devices (NET_VENDOR_INTEL) [Y/n/?] y
      Intel(R) PRO/100+ support (E100) [M/n/y/?] m
      Intel(R) PRO/1000 Gigabit Ethernet support (E1000) [M/n/y/?] m
      Intel(R) PRO/1000 PCI-Express Gigabit Ethernet support (E1000E) [M/n/y/?] m
      Intel(R) 82575/82576 PCI-Express Gigabit Ethernet support (IGB) [M/n/y/?] m
        Direct Cache Access (DCA) Support (IGB_DCA) [Y/n/?] y
        PTP Hardware Clock (PHC) (IGB_PTP) [N/y/?] n
      Intel(R) 82576 Virtual Function Ethernet support (IGBVF) [M/n/y/?] m
      Intel(R) PRO/10GbE support (IXGB) [M/n/y/?] m
      Intel(R) 10GbE PCI Express adapters support (IXGBE) [M/n/y/?] m
        Intel(R) 10GbE PCI Express adapters HWMON support (IXGBE_HWMON) [Y/n/?] y
        Direct Cache Access (DCA) Support (IXGBE_DCA) [Y/n/?] y
        Data Center Bridging (DCB) Support (IXGBE_DCB) [Y/n/?] y
        PTP Clock Support (IXGBE_PTP) [N/y/?] n
      Intel(R) 82599 Virtual Function Ethernet support (IXGBEVF) [M/n/y/?] m
      Intel (82586/82593/82596) devices (NET_VENDOR_I825XX) [Y/n/?] y
        Zenith Z-Note support (EXPERIMENTAL) (ZNET) [N/m/y/?] n