Difference between revisions of "GDL"

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The [http://gnudatalanguage.sourceforge.net/ Gnu Data Language (GDL)] is a useful open-source alternative to IDL on Linux.  Although for new astronomical scripting applications we prefer Python, 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.
The [https://github.com/gnudatalanguage/gdl 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.




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We assume that the base [http://www.astro.louisville.edu/mediawiki/index.php/OpenSuse 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.
We assume that the base [http://www.astro.louisville.edu/mediawiki/index.php/OpenSuse 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.


We would like to recommend installing the version in the CVS repository since it is likely to have many known issues corrected.  However, the version 0.9.2 released on 2012-02-20 will compile and is largely compatible with IDL and EXOFAST.  These notes are based on this version and a CVS verion of 2012-07-29 which updates that release.
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 Sourceforge website:  
Go to the github website:  


<center>
<center>
[http://sourceforge.net/projects/gnudatalanguage/ http://sourceforge.net/projects/gnudatalanguage/]
[https://github.com/gnudatalanguage/gdl https://github.com/gnudatalanguage/gdl]
</center>
</center>


Click on the "Code" link in the top menubar to access CVS and  the "Download" button to provide the last stable release. At the bottom of the new CVS "gdl" listing there will be an option to download the GNU tar archive of the entire CVS tree.  Once you have it on your system, make a copy in a permanent location, and  
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:
as superuser (su), also  to the /usr/local/src tree on your Linux system:


cp gnudatalanguage-gdl_20120729.tar.gz /usr/local/src
  cp gdl.zip /usr/local/src


You are ready to compile the code.  Compilation is handled similarly for either CVS or stable release versions.
You are ready to compile the code.  .


== Install and compile the source code ==
== Install and compile the source code ==
Line 28: Line 28:




cd /usr/local/src  
  cd /usr/local/src  


tar xvzf gnudatalanguage-gdl_20120729.tar.gz
  unzip gdl.zip




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


cd gdl


./configure  --without-hdf --with-hdf5
*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/ http://pslib.sourceforge.net/]


If the configuration does not successfully complete and create "Makefile" in the top level directory, look at the list of errors generated during configuration for clues about missing packages. There will distinctive names that you will have to find in the distribution's repositories. For OpenSuse, you would use yast or yast2 as indicated to install a suspect missing package (usually a develoment version), then repeat the configure command and the search for rpm's again until there are no errors.
*udunits build and install from source
[https://www.unidata.ucar.edu/software/udunits/ https://www.unidata.ucar.edu/software/udunits/]


Once those issues are resolved, try building the software with
Now try to build and add other packages as needed.


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


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




We find that during the build you may see an error such as this one:
  cmake -DCMAKE_BUILD_TYPE=Release -DGRIB=OFF -DWXWIDGETS=OFF -DGEOTIFF=off -DNETCDF=OFF -DHDF=off -DLIBPROJ4=OFF -DUDUNITS2=OFF -DGLPK=OFF -DSHAPELIB=OFF  ../


will turn off features used by geosciences and less often by physics and astronomy.  Each of these has a library requirement not present by default in Opensuse, and requiring installation of a package or from source.


''libtool: Version mismatch error.''
The default installation directory top level is /usr/local. To specify another one,  add


  -DCMAKE_INSTALL_PREFIX=/path/to/install/dir


which is corrected by running this command
to the cmake installation command.


Once this runs, scan the output to be sure it will build as intended, that the necessary packages and libraries are installed,  and that the functions needed for your  GDL are set ON. 


aclocal; libtoolize --force; autoconf; automake -a
On Opensuse also edit  the CMakeCache.txt in build for these entries


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


in the toplevel of gdl directory, and then repeating the configure and make commands.
and for these libraries


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


The GDL team notes in their CVS version that they will be using cmake instead of autoconf in the future.  The software can be compiled with cmake once you install the package for your distribution. The process would be something like this:
Centos may only require the library addition with -lutil.  


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


mkdir build
  make
  make check
  make install


cd build
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.


../cmake
modified to allow for variations in your installation requirements.  Instructions are in the gdl INSTALL.cmake file.
After a successful make operation, install the binaries and library with
make install
Prepare a location for the procedures that you will add:
cd /usr/local/
mkdir gdl
cd gdl
cp -p -r /usr/local/src/gdl/src/pro ./


== Add new procedures ==
== Add new procedures ==
Line 108: Line 112:




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


mkdir astro
  mkdir astro


mkdir tmp
  mkdir tmp


cd tmp
  cd tmp


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


tar xvzf astron.tar.gz
  tar xvzf astron.tar.gz


cd pro
  cd pro


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


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


rm -r tmp
  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 gdl/astro, or if you anticipate updating them individually, into a separate directory for each one.
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:
When you are done, assign the ownership of the gdl directory to root, or to a trusted user:


cd /usr/local
  cd /usr/local/share/
 
  chown -R root.root gnudatalanguage


chown -R root.root gdl
to assure accessibility of all files and assure read access to the library:
 
  cd /usr/local/share/gnudatalanguage
  chmod a+r -R lib


to assure accessibility of all files and limit access for writing.


== Set environment variables ==
== Set environment variables ==
Line 148: Line 156:




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


GDL_PATH=$GDL_PATH:/usr/local/gdl/textoidl


GDL_PATH=$GDL_PATH:/usr/local/gdl/extra
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.
 
export EXOFAST_PATH=/home/john/gdl/exofast
 
GDL_PATH=$GDL_PATH:$EXOFAST_PATH
 
export GDL_STARTUP=/home/john/gdl/gdlstartup
 
 
We include here access to Jason Eastman's EXOFAST, assuming it may be installed in an indivdual user directory.  In that case, these changes would be in that user's "hidden" .profile  file.


== Run EXOFAST under gdl ==
== 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.   
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
To run a process


gdl -e 'myprocess'
  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.
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.
Line 184: Line 180:
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
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 /home/user/gdl/exofast
  cd /fullpathto/exofast
 
Test it with this command:
 
gdl -e "exofast, rvpath='hat3.rv',tranpath='hat3.flux',pname='HAT-P-3b',band='Sloani',/circular,/noslope,/specpriors,minp=2.85,maxp=2.95"
 
There may be small modifications to the exofast procedures needed to make this work.  A list of known ones as of 2012-07-30 is provided below.  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.
 
 
== Running EXOFAST under GDL: problems and solutions ==
 
 
With stable version 0.9.2 of GDL, 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 will fail when trying to create a plot because of a missing routine (that is documented in GDL as present in the core code).  The missing routine is said to have been added back in the CVS version as of 30 July 2012.  However, the CVS version generated errors when EXOFAST reads its basic data files.  This section documents our efforts to resolve this problem.
 
 
'''Missing procedures'''
 
 
*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.
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


*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.
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.




'''Missing intrinsics'''
== 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.


*USERSYM -- called by the astro library routine plotsym is not present in 0.9.2
  gdl -e fithat3.pro


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.
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.


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

Latest revision as of 22:08, 27 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.


 cmake -DCMAKE_BUILD_TYPE=Release -DGRIB=OFF -DWXWIDGETS=OFF -DGEOTIFF=off -DNETCDF=OFF -DHDF=off -DLIBPROJ4=OFF -DUDUNITS2=OFF -DGLPK=OFF -DSHAPELIB=OFF   ../ 

will turn off features used by geosciences and less often by physics and astronomy. Each of these has a library requirement not present by default in Opensuse, and requiring installation of a package or from source.

The default installation directory top level is /usr/local. To specify another one, add

 -DCMAKE_INSTALL_PREFIX=/path/to/install/dir

to the cmake installation command.

Once this runs, scan the output to be sure it will build as intended, that the necessary packages and libraries are installed, and that the functions needed for your GDL are set ON.

On Opensuse also edit the CMakeCache.txt in build for these entries

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

and for these libraries

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

Centos may only require the library addition with -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.