11 June 2012

185. Troubleshooting: ECCE


10 June 2012

184. Fixing Gnome screenshot (3.4.1) in Debian Wheezy by patching and compiling

Approach
Putting a hold on gnome-screenshot forever will likely prevent gnome from upgrading properly since I'd suspect it's a required dependency.

Clarification: this fix restores the original behaviour. gnome-screenshot --interactive is NOT an acceptable solution. This guide restores gnome-screenshot to it's good old functional state.

So, time to build our own gnome-screenshot -- but one which actually works in a reasonable way. The gnome-screenshot cockup is just another sign that something is clearly amiss with the way gnome is being developed. And this, if true, is another truly idiotic 'feature' -- turn gnome into windows? Most of us left for a reason...

Anyway, linux is still sane though -- if we don't like something we're not entirely up a creek, which will buy us a bit more time while we're getting ready to move to xmonad  -- or for debian to move away from not making downstreams changes to gnome.

We have two options:
Either look here: http://git.gnome.org/browse/gnome-screenshot/commit/?id=3bbc1e158fd58ec7f4f984f6d3c15ec95e65a035&ignorews=1 and try to come up with your own way of reverting the crippling.

Or use the ubuntu patches as a guide: http://packages.ubuntu.com/precise/gnome-screenshot

Normally you shouldn't mix ubuntu and debian packages, and we won't: we'll be compiling our own package, but using the work done by the ubuntu maintainers.

In particular, look at this: http://archive.ubuntu.com/ubuntu/pool/main/g/gnome-screenshot/gnome-screenshot_3.4.1-0ubuntu1.debian.tar.gz

Look in the debian/patches directory and you'll find the ubuntu_interative_screenshots.patch

Building:
sudo apt-get install libgtk-3-dev libcanberra-gtk3-dev intltool
wget http://ftp.de.debian.org/debian/pool/main/g/gnome-screenshot/gnome-screenshot_3.4.1.orig.tar.xz
tar xvf gnome-screenshot_3.4.1.orig.tar.xz
cd gnome-screenshot-3.4.1/src

You can wget http://archive.ubuntu.com/ubuntu/pool/main/g/gnome-screenshot/gnome-screenshot_3.4.1-0ubuntu1.debian.tar.gz and untar it to look at the debian/patches/ubuntu_interactive_screenshots.patch, which what we do below is based on:

In the ubuntu patch there's a test to see whether unity is used. We'll do it a bit cruder -- we'll just make sure the condition is always true by testing for 0<1.


Edit src/screenshot-application.c and change the part in red

130 static void
131 save_pixbuf_handle_error (ScreenshotApplication *self,
132                           GError *error)
133 {
134   if (screenshot_config->interactive)
135     {
136       ScreenshotDialog *dialog = self->priv->dialog;
137       GtkWidget *toplevel = screenshot_dialog_get_toplevel (dialog);
138 
139       screenshot_dialog_set_busy (dialog, FALSE);
to

134   if (0 < 1)

Also, change

348   screenshot_play_sound_effect ("screen-capture", _("Screenshot taken"));
349 
350   if (screenshot_config->interactive)
351     {
352       self->priv->dialog = screenshot_dialog_new (self->priv->screenshot, self->priv->save_uri);
353       toplevel = screenshot_dialog_get_toplevel (self->priv->dialog);
354       gtk_widget_show (toplevel);
to


350   if (0 < 1 )

Time to build!
./configure --prefix=${HOME}/.gsc --program-suffix=.debugged
make
make install

Note: the install prefix here works fine for a single-user desktop. If you want everyone to be able to use our shiny new gnome-screenshot, put everything in /usr/bin instead.

We now have a working gnome screenshot in ~/.gsc that behaves as intended.
tree -L 2 -d
.
|-- bin
`-- share
    |-- applications
    |-- GConf
    |-- glib-2.0
    |-- gnome-screenshot
    |-- locale
    `-- man


 However, we need to make sure our fixed gnome-screenshot gets invoked.

In Gnome Shell 3.2.X
sudo apt-get install gconf-editor
Start gconf-editor
go to /apps/metacity/keybinding_commands/command_screenshot
change to e.g.  /home/verahill/.gsc/bin/gnome-screenshot.debugged
Also, change command_window_screenshot to
/home/verahill/.gsc/bin/gnome-screenshot.debugged --window

Note: defining Print/Alt+print keyboard shortcuts the 'gnome-shell' way (i.e. via system-settings) doesn't seem to work in gnome 3.2. Conversely, doing it the gconf-editor way in gnome 3.4 doesn't work.


In Gnome Shell 3.4.X
Go to System Settings, Keyboard, Shortcuts
Disable the automatically defined shortcuts for gnome-screenshot

And add your own under custom shortcuts:




Done! 
Unless you want to add to PATH in which case you can put this in your ~/.bashrc:
export PATH=$PATH:${HOME}/.gsc/bin




Note: If it's still not working, try to launch from the terminal. If you get
(gnome-screenshot.debugged:7493): GLib-GIO-ERROR **: Settings schema 'org.gnome.gnome-screenshot' does not contain a key named 'auto-save-directory'
Trace/breakpoint trap
it's because you had the old, good gnome-screenshot. 
sudo su
echo "gnome-screenshot install"|dpkg --set-selections
exit
sudo apt-get install gnome-screenshot

Now try
gsettings get org.gnome.gnome-screenshot auto-save-directory
which should be empty.

gsettings set org.gnome.gnome-screenshot auto-save-directory '/home/verahill/Pictures'

Finally, make sure to re-set your keybindings.



Links to this post:
http://qfox.nl/notes/153

08 June 2012

183. Compiling OpenMM 4.1 on debian testing

OpenMM 4.0 is still somewhat of a traumatic memory. However, having gotten a question about the compilation of v4.1 I can't really resist giving the new version a go.

Having said that, I never ended up using the GPU-enabled gromacs for which I built openmm, so it was all an enormous waste of time -- for those of you thinking about GPU/Gromacs know this:
* not all graphics cards are supported or worth supporting
* there's no speed-up for explicit solvent molecules, and what else would you use gromacs or MD for?
* consumer-grade graphics cards get very hot

I make no attempt at ferreting out what packages are needed other than what I'm explicitly prompted for. Look at http://verahill.blogspot.com.au/2012/01/debian-testing-64-wheezy_20.html for an indication of what you might need.

Also, I already have openmm 4.0 installed, so e.g. paths and other things defined in the post above are still active.


Start here
Register with simtk.org and download the source file.
sudo apt-get install cmake-curses-gui libgccxml-dev gccxml nvidia-cuda-toolkit
unzip -x OpenMM4.1-Source.zipe
mkdir openmm_build
cd openmm_build/
ccmake -i ../OpenMM4.1-Source/

It'll say Empty Cache. Hit c which will populate the list.

I think we can ignore the EMU libs since they do device emulation. I never figured out what the CUT program was and it's not mentioned in the manual from what I can see.


These are the settings I chose -- I had problems before setting the OPENCL parts (in red) to off.

BUILD_TESTING:BOOL=ON
CMAKE_BUILD_TYPE:STRING=Release
CMAKE_INSTALL_PREFIX:PATH=/home/verahill/.openmm
CUDA_BUILD_TYPE:STRING=Device
CUDA_INSTALL_PREFIX:PATH=/usr/bin
CUDA_NVCC:FILEPATH=/usr/bin/nvcc
DL_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libdl.so
FOUND_CUBLAS:FILEPATH=/usr/lib/x86_64-linux-gnu/libcublas.so
FOUND_CUBLASEMU:FILEPATH=FOUND_CUBLASEMU-NOTFOUND
FOUND_CUFFT:FILEPATH=/usr/lib/x86_64-linux-gnu/libcufft.so
FOUND_CUFFTEMU:FILEPATH=FOUND_CUFFTEMU-NOTFOUND
FOUND_CUT:FILEPATH=FOUND_CUT-NOTFOUND
FOUND_CUT_INCLUDE:PATH=FOUND_CUT_INCLUDE-NOTFOUND

GCCXML_EXTRA_ARGS:STRING=
GCCXML_PATH:FILEPATH=/usr/bin/gccxml
OPENMM_BUILD_AMOEBA_CUDA_LIB:BOOL=ON
OPENMM_BUILD_AMOEBA_PLUGIN:BOOL=ON
OPENMM_BUILD_CUDA_LIB:BOOL=ON
OPENMM_BUILD_CUDA_TESTS:BOOL=TRUE
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS:BOOL=ON
OPENMM_BUILD_FREE_ENERGY_CUDA_LIB:BOOL=ON
OPENMM_BUILD_FREE_ENERGY_PLUGIN:BOOL=ON
OPENMM_BUILD_OPENCL_LIB:BOOL=OFF
OPENMM_BUILD_OPENCL_TESTS:BOOL=OFF
OPENMM_BUILD_PYTHON_WRAPPERS:BOOL=ON
OPENMM_BUILD_RPMD_OPENCL_LIB:BOOL=OFF
OPENMM_BUILD_RPMD_PLUGIN:BOOL=ON
OPENMM_BUILD_SERIALIZATION_SUPPORT:BOOL=ON
OPENMM_BUILD_STATIC_LIB:BOOL=ON
OPENMM_GENERATE_API_DOCS:BOOL=OFF
OPENMM_SVN_REVISION:STRING=exported
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python
SVNVERSION_PROGRAM:FILEPATH=/usr/bin/svnversion
SWIG_EXECUTABLE:FILEPATH=/usr/bin/swig
SWIG_VERSION:STRING=2.0.7

Make your changes and hit c again, then hit g which brings you back to the terminal.



make -d|tee make.log
make test


If all goes well you'll see
126/126 Test #126: TestParser ......................................   Passed    0.02 sec
100% tests passed, 0 tests failed out of 126
Total Test time (real) = 345.83 sec
make install


[..]
-- Installing: /home/verahill/.openmm/examples/Makefile
-- Installing: /home/verahill/.openmm/examples/NMakefile
-- Installing: /home/verahill/.openmm/examples/MakefileNotes.txt
-- Installing: /home/verahill/.openmm/examples/Empty.cpp

And you are done!

tree ~/.openmm/ -L 4 -d
.openmm/
|-- bin
|-- docs
|   |-- api-c++
|   `-- api-python
|-- examples
|   `-- VisualStudio
|-- include
|   `-- openmm
|       |-- internal
|       `-- serialization
|-- lib
|   `-- plugins
`-- licenses