Some experiences in working with Madagascar: installa7on & development Tengfei Wang, Peng Zou Tongji university
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Reproducible research in Madagascar How to conduct a successful installation Programming & writing Some suggestions
Madagascar Madagascar: A very powerful open- source software package for multidimensional data analysis and reproducible computational experiments. It provides: ü A convenient and powerful environment ü A convenient technology transfer tool ü Intellectual property from the contributors ü A active community for researchers (including students) in geophysics and related @ields.
The attached codes contain the up-to-date work. Programming in Madagascar is easy (standing on the shoulders of previous authors). Writing paper/abstract with LaTeX in Madagascar is amazing, strongly recommended!
Reproducible research in Madagascar How to conduct a successful installation Programming & writing Some suggestions
Step 1:./con@igure - - pre@ix=/directory/madagascar/installed Step 2: Make & make install Step 3 Set the environment varibles source $RSFROOT/share/madagascar/etc/env.sh
After many times of installation and update, I find it s always not so easy! (7.1) (6.5) (5.5)
Python Scons Packages Necessary Necessary Necessary Additional Successful Complete Installation
Very dif@icult to @ix if there are problems. Luckily, these problems are rare. Set RSFROOT in the.bashrc is ok
If internet is ok, then it is easy. Otherwise, cumbersome Ø You can download the *.rpm that is needed, e.g. libx11-1.6.0-2.2.el6.x86_64.rpm Ø The rpm must be suitable for your system version!
configure configure à search for the PATH of a certain package or support and create the config.py Ø con@ig.py Log of configure Ø con@ig.log
configure framework/configure.py Ø Python script to check the packages
In framework/con3igure.py In con3ig.log In con3ig.py
Latest released CentOS version Everything is ok, except the BLAS and LAPACK. And they are important math libraries for me. (7.1) We use the ATLAS package for the BLAS and LAPACK.
In con3ig.log For blas For lapack In this new version of ATLAS package, there are no libf77blas and libcblas at all!! And the name for libatlas is not the same as previous one!!
The original version The @ixed version
Reproducible research in Madagascar How to conduct a successful installation Programming & writing Some suggestions
No especially restricts Start with the codes in the directory of user/ and choose a simple one. Tip: add comments with /*< >*/ in your subfunctions, otherwise it will fail when compiling. Attention: please respect others work if you want use them. Add proper citation and acknowledgement!
Put the libraries in the default include path and export C_INCLUDE_PATH Compiling & linking Ø Add the libraries into the SConstruct Tip: when testing your program, you don t need make install. Just add the full- path before the executable 3ile in the work3low, e.g.
My way: modify the config.py directly, and compile only in your own source code directory Caution: do not make & make install in the RSFSRC directory after you modify the con@ig.py
Tailor-made tool for researchers More efficient than Word if there is template Work Ef@iciently
Reproducible research in Madagascar How to conduct a successful installation Programming & writing Some suggestions
It is challenging to let the information which are originally shown on the screen to save in a log file ü Installing : make (error info) ü Programming: some intermediate output for check ü Run a program in the background How to debug the code easily
About the manual of this software - Thanks to the developers, there are many useful manuals - But a single and integrated manual may be more helpful, so that we can learn to solve some problems according to the outline of the manual About the templates for publication - Not easy to use the templates for Geophysical Journal International - More templates, e.g., Geophysical Prospecting