Qsnake 0.9.12 released
Ondrej Certik
I just released Qsnake 0.9.12. Qsnake is a source distribution for
scientific computing, with unified Python interface, available at:
http://qsnake.com/
Changes since last release:
* Mac should be fully supported (thanks to tremendous help and work done by Min)
* little fixes and improvements ("--verbose", "--lab" options added,
matplotlib updated to 1.0, ...)
Here is how to try it:
wget --no-check-certificate
https://github.com/downloads/qsnake/qsnake/qsnake-0.9.12.tar
tar xf qsnake-0.9.12.tar
cd qsnake-0.9.12
./qsnake -b
The only prerequisites to build qsnake are gcc, g++, gfortran and
python. Note to Mac users: if you don't have gfortran, just do
"./qsnake install gfortran-osx" before doing the "qsnake -b".
And then you run it by:
./qsnake
Check that all is ok by running tests:
./qsnake test
You can also try the GUI (ipython htmlnotebook) in the browser by launching the
lab() inside qsnake, or just:
./qsnake --lab
Linux and Mac is supported. Please report any bugs, or if it
fails to build.
Immediate plans are to work closely with ipython to:
* Keep improving the web notebook, to make it "the" graphical
interface to qsnake (and ipython)
* Allow to create rich graphical output from Python, currently sympy's
latex output works, matplotlib works, but in general to return any
kind of GUI, that would work in the web notebook.
* Make the GUI interactive, so that one can create scientific GUIs
easily, in the browser
Other plans:
* Once things become more tested and polished, advertise Qsnake more.
So far I have been using Qsnake every day for the last 3 months (on
Ubuntu only), Mac support was added yesterday. But there might still
be some little problems on other platforms, so more testing is needed.
* One last missing piece is to make it possible to easily create an
interactive GUI (or at least any interactive explorative way) to
scientific codes that one writes (in Fortran, or C/C++, or Python).
Currently my workflow is to write a Fortran/Python code (with Cython
wrappers) using Qsnake and save a png image from matplotlib to disk
(as no mpl guis work for me), and view it from the disk, as an image.
That's very slow. The "qsnake --lab" is already 80% there, but needs
more polish.
Ondrej
Ondrej Certik
On Sun, May 8, 2011 at 2:23 PM, Gökhan Sever <gokha...@gmail.com> wrote:
> Hi Ondrej,
>
> These sound very exciting indeed:
>>
>> * Allow to create rich graphical output from Python, currently sympy's
>> latex output works, matplotlib works, but in general to return any
>> kind of GUI, that would work in the web notebook.
>
> especially the web-based interactive gui plan.
Indeed. Thanks for trying it out and reporting a bug!
>
>>
>> * Make the GUI interactive, so that one can create scientific GUIs
>> easily, in the browser
>
> This is Fedora 14 64-bit.
> Unfortunately, I get a build error:
> gcc -I/home/gsever/Desktop/python-repo/qsnake-0.9.12/local/include -g -O2
> -fvisibility=hidden -Wall -Wpointer-arith -o .libs/ac-data ac-data.o
> ../src/.libs/libgcrypt.so -Wl,--rpath
> -Wl,/home/gsever/Desktop/python-repo/qsnake-0.9.12/local/lib
> /usr/bin/ld: ac-schemes.o: undefined reference to symbol
> 'gpg_err_code_from_errno'
> /usr/bin/ld: note: 'gpg_err_code_from_errno' is defined in DSO
> /home/gsever/Desktop/python-repo/qsnake-0.9.12/local/lib/libgpg-error.so.0
> so try adding it to the linker command line
> /home/gsever/Desktop/python-repo/qsnake-0.9.12/local/lib/libgpg-error.so.0:
> could not read symbols: Invalid operation
> collect2: ld returned 1 exit status
> make[2]: *** [ac-schemes] Error 1
> make[2]: *** Waiting for unfinished jobs....
> creating ac-data
> gcc -I/home/gsever/Desktop/python-repo/qsnake-0.9.12/local/include -g -O2
> -fvisibility=hidden -Wall -Wpointer-arith -o .libs/mpitests mpitests.o
> ../src/.libs/libgcrypt.so -Wl,--rpath
> -Wl,/home/gsever/Desktop/python-repo/qsnake-0.9.12/local/lib
> gcc -I/home/gsever/Desktop/python-repo/qsnake-0.9.12/local/include -g -O2
> -fvisibility=hidden -Wall -Wpointer-arith -o .libs/tsexp tsexp.o
> ../src/.libs/libgcrypt.so -Wl,--rpath
> -Wl,/home/gsever/Desktop/python-repo/qsnake-0.9.12/local/lib
> /usr/bin/ld: tsexp.o: undefined reference to symbol 'gpg_strerror'
> /usr/bin/ld: note: 'gpg_strerror' is defined in DSO
> /home/gsever/Desktop/python-repo/qsnake-0.9.12/local/lib/libgpg-error.so.0
> so try adding it to the linker command line
> /home/gsever/Desktop/python-repo/qsnake-0.9.12/local/lib/libgpg-error.so.0:
> could not read symbols: Invalid operation
> collect2: ld returned 1 exit status
> make[2]: *** [tsexp] Error 1
> creating mpitests
> make[2]: Leaving directory
> `/home/gsever/Desktop/python-repo/qsnake-0.9.12/spkg/build/libgcrypt-1.4.3.p2/src/tests'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory
> `/home/gsever/Desktop/python-repo/qsnake-0.9.12/spkg/build/libgcrypt-1.4.3.p2/src'
> make: *** [all] Error 2
> failed to build libgcrypt
> Qsnake build failed.
>
> Any ideas about fixing this problem?
Not yet, but I have installed Fedora 14 into VirtualBox on my Ubuntu,
and reproduced the problem:
https://gist.github.com/961767
it happens right at the beginning of the build. I'll try to fix it
soon, and ping you back, once it is done.
Ondrej
Ondrej Certik
So I have just fixed it. It turned out that on Fedora 14, a library
was missing when linking, so this patch fixed it:
https://github.com/qsnake/libgcrypt/commit/4cad9fc68c0b1b54d767c20bf2ec7df1b779ad6a
then there was a similar problem in the "curl" package, so this patch fixed it:
https://github.com/qsnake/curl/commit/b8c566c058816137ff4242243c407b03704b80ce
Then it builds nicely, except that Python fails to build the hashlib
module, due to some problems with SELinux:
https://github.com/qsnake/qsnake/issues/11
So this will require some more investigation and work. If anyone knows
how to fix it, that'd be great. Otherwise I'll try to fix it in the
coming days.
Gökhan, to try the updated development version of Qsnake, just do:
git clone https://github.com/qsnake/qsnake.git
cd qsnake
./qsnake -d
./qsnake -b
and it should build all the way to Python.
Ondrej
Ondrej Certik
I managed to fix it, see the issue #11 for a fix. One needs to white
list the libcrypto library for SELinux. I don't know if the problem is
with libcrypto, or the way we compile it, or somewhere else. But in
any case, in the meantime simply compile Qsnake, once it fails, do:
execstack -c local/lib/libcrypto.so.1.0.0
and keep compiling using "qsnake -b".
Another issue I run into is:
https://github.com/qsnake/qsnake/issues/12, in this case, I think I'll
simply put PERL and the required module into prerequisites, as in
Ubuntu/Mac it seems to be installed by default.
Ondrej