185. Troubleshooting: ECCE

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

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