Difference between revisions of "GDL"

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To run gdl you simply issue on the command line "gdl" and you will be in a command line environment for the Gnu Data Language.  To exit and return  to the shell, "exit".  GDL commands are identical to IDL, and most are supported in the recent code.   
To run gdl you simply issue on the command line "gdl" and you will be in a command line environment for the Gnu Data Language.  To exit and return  to the shell, "exit".  GDL commands are identical to IDL, and most are supported in the recent code.  If the EXOFAST library is in the search path the compiling will be automatic.  One way to do this is to have a named directory "exofast" which is a softlink to the version you want to run, and add that to your .profile as noted above.  This allows some flexibility in testing or using different versions without changing the environment.




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There are modifications to the exofast procedures and additions to GDL  needed to run  within the GDL framework.  A list of known ones is provided below but it may be obsolete.  For help with finding solutions, a [http://aramis.obspm.fr/~coulais/IDL_et_GDL/Matrice_IDLvsGDL_intrinsic.html list of routines supported in GDL] is available, but it too is not current.
For help with finding procedures and their status in development, a [http://aramis.obspm.fr/~coulais/IDL_et_GDL/Matrice_IDLvsGDL_intrinsic.html list of routines supported in GDL] is available, but it too is not current.




== EXOFAST under GDL: problems and solutions ==
== EXOFASTv2 under GDL ==


As of July 2020, the github release of EXOFASTv2 will run under GDL.  Download it from [https://github.com/jdeast/EXOFASTv2 https://github.com/jdeast/EXOFASTv2] and unzip the contents into EXOFASTv2-master.  That directory has to be in the GDL search path, which as noted above, could be with a soft link from the .profile for the user.  To test it, go to examples and try hat3.


With he version 1.0rc3 of GDL available on github in July 2020, EXOFAST will run the fitting with the libraries given above, addition of a few missing procedures,  and changes edited into specific exofast procedure files which we will note here.  It mail fail because of missing intrinsics in the plotting.  The workarounds are to edit the original exofast procedures to avoid these calls.  This is a soluble problem since the plotting can be rewritten to use the minimum set of features currently available in gdl, or to export the plotting to external programs. It may in part have been solved recently with improvements to gdl since the version 0.9 for much of our testing was done.
  gdl -e fithat3.pro


The output of EXOFAST for these examples will be in a fitresults directory with  files of text tables, LaTeX tex,  and PostScript graphics.  For viewing on Linux, try "gv", or convert to pdf with ps2pdf and use evince or okular.


'''Missing procedures'''
There were no errors generated in a test run on our system with the latest GDL and EXOFASTv2 at this time.
 
 
*chisqr_cvf.pro -- is not in the libraries noted above
 
It is available on a web search.  It appears to be an ITT Visual Information Solutions contributed routine, though it derives from code published elsewhere.  It could be recoded into a gdl procedure if needed.  We add it to /usr/local/gdl/extra/.
 
 
*chisqr_pdf.pro -- is not in the librarires noted above
 
It is available on a web search.  While it appears to be an ITT Visual Information Solutions procedure, it simply calls IGAMMA which is
a GDL routine.  We add it to /usr/local/gdl/extra/.
 
 
*bisect_pdf.pro -- is not in the librarires noted above
 
It is available on a web search.  It appears to be an ITT Visual Information Solutions procedure.  We add it to /usr/local/gdl/extra/.
 
 
*oploterr.pro -- is not included in gdl. 
 
It is an ITT Visual Information Solutions procedure that is available for download from the NASA IDL support [http://idlastro.gsfc.nasa.gov/idllibsrch.html search site].  We add it to /usr/local/gdl/extra.
 
The code lines
 
oploterr, time, rv.rv - (rv.bjd - t0)*slope-gamma, rv.err, 8
 
oploterr, time, rv.rv-modelrv, rv.err, 8
 
could be replaced by oplot with different parameters, or a perhaps a simple ploterr procedure could be defined. There is a note in the GDL urgent needs file that oploterr should be easily derived from ploterr.  When these lines are not commented out and the oploterr is allowed to run, there is a warning from EXOFAST
 
''Warning: multi-page PostScript not supported yet (FIXME!)''
 
generated immediately following the OPLOTERR call.  The (FIXME!) comes from GDL.
 
 
*poly_fit.pro -- is not included ingdl.
 
It is an ITT Visual Information Solutions procedure that is available for download from the NASA IDL support [http://idlastro.gsfc.nasa.gov/idllibsrch.html search site].  We add it to /usr/local/gdl/extra.
 
 
 
 
 
 
'''Missing intrinsics'''
 
 
*USERSYM -- called by the astro library routine plotsym is not present in 0.9.2
 
This routine is internally coded and should be in the distribution. In this version it is annotated in plotting.ccp with the note "//for now usersym is a circle".  It was introduced into the CVS source code in response to a bug report. However, the CVS version now generates errors in reading the data files used with EXOFAST, making it unusable in its current form.
 
USERSYM is called by plotsym.pro, an astro library routine.  It is used to create distinctive point plotting in  routines exofast_chi2.pro and exofast_plotdist.pro.  A workaround could be to comment out the call to plotsym and edit the symbol choice to a standard symbol for the following plot so that usersym (a user-defined symbol) is not requested.
 
 
*HISTOGRAM -- keyword parameter NAN not allowed in 0.9.2 . 
 
There is a note in a development discussion group that it has been added to the CVS version but not fully tested.
 
The problem shows up in exofast_plotdist.pro with calls to histogram using the /nan keyword.  We tried editing it out from the code lines:
 
  hist = histogram(pars[angular[i],*],nbins=100,locations=x,/nan)
 
  hist = histogram(pars[i,sorted],nbins=100,locations=x,min=xmin,max=xmax,/nan)
 
 
*CONTOUR --keyword parameter PATH_INFO, PATH_XY and PATH_DATA_COORDS are not allowed in 0.9.2
 
The function is called in exofast_errell.pro and fails for the first time at this line:
 
  contour, hist2d, xtitle=xtitle,ytitle=ytitle, levels=levels,
  path_info=info,path_xy=xy,/path_data_coords,/overplot,/path_double
 
with the error messages
 
 
*CONTOUR: Keyword parameter PATH_INFO not allowed in call to: CONTOUR
 
*CONTOUR: Keyword parameter PATH_XY not allowed in call to: CONTOUR
 
*CONTOUR: Keyword parameter PATH_DATA_COORDS not allowed in call to: CONTOUR
 
*CONTOUR: Keyword parameter PATH_DOUBLE not allowed in call to: CONTOUR

Revision as of 19:07, 21 July 2020

The Gnu Data Language (GDL) is a useful open-source alternative to IDL on Linux. Although for new astronomical scripting applications we prefer Python and Julia, the proprietary IDL system is widely used and there are many astronomical routines written for it that are freely available. This page is a guide to the installation of GDL on an OpenSuse Linux platform in order to use the community resources available.


Download the recent source code

We assume that the base OpenSuse system has been installed with the packages that are often used to support scientific computing. There are some unusual dependencies to build a complete GDL. Additional procedures may be added after the fact since they are compiled as needed by GDL itself.

These notes are based on latest github version as of July 2020. It is an improved version over the last Sourceforge release and should be largely compatible with IDL routines.

Go to the github website:

https://github.com/gnudatalanguage/gdl

Click on the "Code" link in the top menubar the "Download" button to provide the last stable release as a zip file. Once you have it on your system, make a copy in a permanent location, and as superuser (su), also to the /usr/local/src tree on your Linux system: 

 cp gdl.zip /usr/local/src

You are ready to compile the code. .

Install and compile the source code

The source tree will be in /usr/local/src/ where you made a copy of the downloaded tarfile: 


 cd /usr/local/src 

 unzip gdl.zip


This will create a "gdl-master" directory in /usr/local/src containing the files you will compile.

These are some of the required packages on a new installation of Gnu Data Language:


  • cmake
  • graphicsmagick development
  • pyplot and subpackages
  • libgraphicsmagick++-devel
  • libgeotiff2
  • geotiff-devel
  • netcdf-devel
  • eigen3-devel
  • tirpc
  • pslib build and install from source

http://pslib.sourceforge.net/

  • udunits build and install from source

https://www.unidata.ucar.edu/software/udunits/

Now try to build and add other packages as needed. 

 cd gdl-master
 mkdir build
 cd build
 cmake -DCMAKE_BUILD_TYPE=Release -DGRIB=OFF  ../

We turn off GRIB because the functionality is not needed in astrophysics and it requires external code that does not compile readily.

Once this runs, the necessary packages and libraries are installed, and the all the functions needed in GDL are set ON, make this change so that it will compile on Opensuse.

edit CMakeCache.txt for these entries

//CXX compiler CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++


//Flags used by the CXX compiler during all build types. CMAKE_CXX_FLAGS:STRING=-ltirpc -lutil

Compile, check, and install by default in /usr/local/share 

 make
 make check
 make install

The gdl source code is complex and has many dependencies. There may be missing libraries to contend with that that will not be apparent until the make process is tried. They can be added as needed using YAST.


Add new procedures

For astronomical use, there are additional procedures to install system-wide. Download and save in your long term archive the code from these sites:



Copy the .pro files from these sources into one or more separate directories under /usr/local/share/gnudatalanguage/lib/ For example, we would use something like this: 


 cd /usr/local/share/gnudatalanguage/lib/

 mkdir astro

 mkdir tmp

 cd tmp

 cp /home/john/gdl/archive/astron.tar.gz ./

 tar xvzf astron.tar.gz

 cd pro

 cp *.pro /usr/local/share/gnudatalanguage/lib/astro/

 cd /usr/local/share/gnudatalanguage/lib/

 rm -r tmp


and repeat this for each of the libraries you want to add, copying only the *.pro files into gdl. They can all go into astro, or if you anticipate updating them individually, into a separate directory for each one.

When you are done, assign the ownership of the gdl directory to root, or to a trusted user: 

 cd /usr/local/share/

 chown -R root.root gnudatalanguage

to assure accessibility of all files and assure read access to the library: 

 cd /usr/local/share/gnudatalanguage
 chmod a+r -R lib


Set environment variables

In the bash shell edit the .profile directory for each user who would access gdl, or add to /etc/profile.local for everyone, to make these changes (written assuming separated directories for each added library): 


 export GDL_PATH=$GDL_PATH:/usr/local/share/gnudatalanguage/lib/cmsvlib/
 export GDL_PATH=$GDL_PATH:/usr/local/share/gnudatalanguage/lib/astro/
 export GDL_PATH=$GDL_PATH:/fullpathto/gdl/programs/
 export GDL_PATH=$GDL_PATH:/fullpathto/exofast/
 export EXOFAST_PATH=/fullpathto/exofast/


We include here access to Jason Eastman's EXOFAST, assuming it may be installed in an indivdual user directory rather than the full gdl library location. In that case, these changes would be in that user's "hidden" .profile file.

Run EXOFAST under gdl

To run gdl you simply issue on the command line "gdl" and you will be in a command line environment for the Gnu Data Language. To exit and return to the shell, "exit". GDL commands are identical to IDL, and most are supported in the recent code. If the EXOFAST library is in the search path the compiling will be automatic. One way to do this is to have a named directory "exofast" which is a softlink to the version you want to run, and add that to your .profile as noted above. This allows some flexibility in testing or using different versions without changing the environment.


To run a process 

 gdl -e 'myprocess'

is all that's needed. The myprocess.pro file must be in the current working directory or the path. Note that ".pro" is not on the command line.


To run and test EXOFAST, install it in your user home directory under your own "gdl" with the appropriate addition to your .profile as noted above. Then 

 cd /fullpathto/exofast

Exofast currently provides examples to test and under the examples directory there are specfic test procedures, such as 

 cd /fullpathto/exofast/examples/hat3/
 gdl -e fithat3


For help with finding procedures and their status in development, a list of routines supported in GDL is available, but it too is not current.


EXOFASTv2 under GDL

As of July 2020, the github release of EXOFASTv2 will run under GDL. Download it from https://github.com/jdeast/EXOFASTv2 and unzip the contents into EXOFASTv2-master. That directory has to be in the GDL search path, which as noted above, could be with a soft link from the .profile for the user. To test it, go to examples and try hat3. 

 gdl -e fithat3.pro

The output of EXOFAST for these examples will be in a fitresults directory with files of text tables, LaTeX tex, and PostScript graphics. For viewing on Linux, try "gv", or convert to pdf with ps2pdf and use evince or okular.

There were no errors generated in a test run on our system with the latest GDL and EXOFASTv2 at this time.

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