New problems with new install

[juliotux]

I installed the S4 again and the first run of sagui returns:

[julio@bd2093ea ~]$ sagui
/usr/lib64/python2.7/site-packages/gtk-2.0/gtk/__init__.py:122: RuntimeWarning: PyOS_InputHook is not available for interactive use of PyGTK
  set_interactive(1)
ERROR: IOError: Calculated spectrum is not available. Check if syn(spec|plot) ran correctly. [s4.synthesis.synplotwrapper]
Traceback (most recent call last):
  File "/usr/bin/sagui", line 513, in <module>
    main()
  File "/usr/bin/sagui", line 508, in main
    mw = MainWindow()
  File "/usr/bin/sagui", line 41, in __init__
    self.wdg = Widget()
  File "/usr/bin/sagui", line 139, in __init__
    self.synplot()
  File "/usr/bin/sagui", line 172, in synplot
    self.syn.run()
  File "/usr/lib/python2.7/site-packages/s4/synthesis/synplotwrapper.py", line 97, in run
    'syn(spec|plot) ran correctly.')
IOError: Calculated spectrum is not available. Check if syn(spec|plot) ran correctly.

IDL and Intel Fortran are installed and working.

[gabraganca]

Are you running inside a virtualenv?

Are you sure that ifort is working? When you installed S4 could you see that it compiled synspec?

[gabraganca]

I think I had this problem. I lose one day and then decided to use virtualenv.

[gabraganca]

Also, you can try the following: open an ipython and type:

from s4.synthesis import Synplot
Synplot(20000, 4, wstart=4460, wend=4480).plot()

EDIT: Do not need to try this. The problem is not with sagui. Is with the synplot wrapper.

[juliotux]

I tryed it. ifort and idl are running ok. I'm not running it in a virtualenv.

I think the problem is that the folder .s4 in the home is not available.

[gabraganca]

Ok. Try the following:

python setup.py build
pip install . --upgrade > test

Then paste the contents of the test file here.

[juliotux]

Here:

ifort available.
Compiling Synspec49.
Compiling Rotin3
running build
running build_py
creating build
creating build/lib
creating build/lib/s4
copying s4/__init__.py -> build/lib/s4
creating build/lib/s4/spectools
copying s4/spectools/__init__.py -> build/lib/s4/spectools
copying s4/spectools/gen_tools.py -> build/lib/s4/spectools
creating build/lib/s4/plottools
copying s4/plottools/analysis_plot.py -> build/lib/s4/plottools
copying s4/plottools/__init__.py -> build/lib/s4/plottools
copying s4/plottools/windows.py -> build/lib/s4/plottools
creating build/lib/s4/synthesis
copying s4/synthesis/__init__.py -> build/lib/s4/synthesis
copying s4/synthesis/synplotwrapper.py -> build/lib/s4/synthesis
creating build/lib/s4/utils
copying s4/utils/handling.py -> build/lib/s4/utils
copying s4/utils/__init__.py -> build/lib/s4/utils
creating build/lib/s4/io
copying s4/io/wrappers.py -> build/lib/s4/io
copying s4/io/__init__.py -> build/lib/s4/io
copying s4/io/specio.py -> build/lib/s4/io
running build_scripts
creating build/scripts-2.7
copying and adjusting s4/GUI/sagui -> build/scripts-2.7
copying and adjusting scripts/sensi_line -> build/scripts-2.7
changing mode of build/scripts-2.7/sagui from 664 to 775
changing mode of build/scripts-2.7/sensi_line from 664 to 775
Unpacking /home/julio/S4
  Running setup.py egg_info for package from file:///home/julio/S4
    s4/synthesis/synplot/synspec49.f(16669): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
      602 format(14x,4(i4,1x,e9.3))
    --------------------------^
    s4/synthesis/synplot/synspec49.f(16668): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
      601 format(3i4,2x,4(i4,1x,e9.3))
    -----------------------------^
    s4/synthesis/synplot/synspec49.f(17809): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
     511    FORMAT (A8,E11.5,4E12.5,I1,(I2,I3),3(I2,I2))
    --------------------^
    ifort available.
    Compiling Synspec49.
    Compiling Rotin3

Installing collected packages: S4
  Found existing installation: S4 0.0.0
    Uninstalling S4:
Exception:
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/pip/basecommand.py", line 139, in main
    status = self.run(options, args)
  File "/usr/lib/python2.7/site-packages/pip/commands/install.py", line 271, in run
    requirement_set.install(install_options, global_options, root=options.root_path)
  File "/usr/lib/python2.7/site-packages/pip/req.py", line 1181, in install
    requirement.uninstall(auto_confirm=True)
  File "/usr/lib/python2.7/site-packages/pip/req.py", line 495, in uninstall
    paths_to_remove.remove(auto_confirm)
  File "/usr/lib/python2.7/site-packages/pip/req.py", line 1518, in remove
    renames(path, new_path)
  File "/usr/lib/python2.7/site-packages/pip/util.py", line 293, in renames
    shutil.move(old, new)
  File "/usr/lib64/python2.7/shutil.py", line 302, in move
    os.unlink(src)
OSError: [Errno 13] Permission denied: '/usr/bin/sagui'

Storing complete log in /home/julio/.pip/pip.log

[gabraganca]

Sorry, I forgot the sudo!

sudo pip install . --upgrade > test

[gabraganca]

So @juliotux got the following problem:

sudo pip install .
Unpacking /home/julio/S4
Running setup.py egg_info for package from file:///home/julio/S4
g77 and ifort are not available. Synspec and Rotin will not be compiled.

Cleaning up...
[julio@bd2093ea S4]$ sudo ifort
sudo: ifort: command not found
[julio@bd2093ea S4]$ ifort
ifort: command line error: no files specified; for help type "ifort -help"

This means the ifort was not "sourced".

I recommend that you put the following text in your ~/.bashrc

# Intel Fortran Compiler                                                        
MACHINE_TYPE=`uname -m`                                                         
if [ ${MACHINE_TYPE} == 'x86_64' ]; then                                        
      # 64-bit stuff here                                                       
      source /opt/intel/composer_xe_2011_sp1.9.293/bin/compilervars.sh intel64  
else                                                                            
      # 32-bit stuff here                                                       
      source /opt/intel/composer_xe_2011_sp1.9.293/bin/compilervars.sh ia32     

fi    

Now, every time you open a terminal, it will source ifort for you.

[gabraganca]

@juliotux try installing from this new branch. If it works for you I will do a PR.

To install do the following:

git fetch origin
git checkout -b installation origin/installation
sudo pip uninstall s4
git clean -fXd
python setup.py build
sudo pip install .

Synspec will be compile only when you call python setup.py build. We are uninstalling it and cleaning the repository just to be safe.

[gabraganca]

Solved automagically.