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GenericMappingTools / gmtmex

GMT API for MATLAB
https://github.com/GenericMappingTools/gmtmex/wiki
GNU Lesser General Public License v2.1
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Building gmtmex on Linux #8

Open ahankak opened 5 years ago

ahankak commented 5 years ago

While searching for documentation regarding building gmtmex on Linux, I noticed that the readme was looking for volunteers. With the steps outlined below, I am able to get GMT to work with my MATLAB project on Ubuntu 18.04. I am sure there is a more elegant way of achieving this, however, I thought it best to share this solution, since it does appear to work well.

With both MATLAB R2019a and GMT Version 6.1.0_3ede8d1_2019.08.04 installed in /home, in the gmtmex directory cloned from GitHub:

  1. Built gmtmex object file as gcc -I$GMT_dir/include/gmt -I$MATLAB_dir/extern/include -O2 -Wall -m64 -fPIC -fno-strict-aliasing -std=c99 -DGMT_MATLAB -I$GMT_dir/include/gmt -c gmtmex.c

  2. Built gmtmex_parser object file as gcc -I$GMT_dir/include/gmt -I$MATLAB_dir/extern/include -O2 -Wall -m64 -fPIC -fno-strict-aliasing -std=c99 -DGMT_MATLAB -I$GMT_dir/include/gmt -c gmtmex_parser.c

  3. Compiled mex file as $MATLAB_dir/bin/mex -DGMT_MATLAB -I$GMT_dir/include/gmt -I/$GMT_dir/include/gmt/lib -I$MATLAB_dir/extern/include gmtmex.o gmtmex_parser.o -L$GMT_dir/lib -lgmt -L$MATLAB_dir/bin/glnxa64 -lmx -lmex -output gmtmex.mexa64

Copied over the gmt.m and generated gmtmex.mexa64 files to $GMT_dir/bin, added $GMT_dir along with subfolders to MATLAB path.

In order to prevent runtime errors associated with MATLAB not being able to find shared libraries, launch MATLAB as: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GMT_dir/lib export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libtiff.so.5:/usr/lib/x86_64-linux-gnu/libstdc++.so.6 $MATLAB_dir/bin/matlab

I hope this proves to be helpful. Please let me know in case further tests are required.

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thomasAmorrow commented 5 years ago

I have had success building gmtmex following ahankak's instructions above, using MATLAB R2019a and GMT 6.1.0_58a5b88_2019.09. In my case, MATLAB and GMT are in the standard installation locations. The following commands worked for me, hopefully they may help others:

  1. Build gmtmex in gmtmex src directory gcc -I/usr/local/include/gmt -I/usr/local/MATLAB/R2019a/extern/include -O2 -Wall -m64 -fPIC -fno-strict-aliasing -std=c99 -DGMT_MATLAB -I/usr/local/include/gmt -c gmtmex.c

  2. Build parser gcc -I/usr/local/include/gmt -I/usr/local/MATLAB/R2019a/extern/include -O2 -Wall -m64 -fPIC -fno-strict-aliasing -std=c99 -DGMT_MATLAB -I/usr/local/include/gmt -c gmtmex_parser.c

  3. Compile /usr/local/MATLAB/R2019a/bin/mex -DGMT_MATLAB -I/usr/local/include/gmt -I/usr/local/include/gmt/lib -I/usr/local/MATLAB/R2019a/extern/include gmtmex.o gmtmex_parser.o -L$GMT_dir/lib -lgmt -L/usr/local/MATLAB/R2019a/bin/glnxa64 -lmx -lmex -output gmtmex.mexa64

To run MATLAB with gmtmex capabilities, I have to perform the same library modifications export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GMT_dir/lib export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libtiff.so.5:/usr/lib/x86_64-linux-gnu/libstdc++.so.6 matlab &

I tried for some time to use MATLAB's setenv functions to get these libraries working, but with no luck. I also tried putting the export commands in my .profile, but that also did not seem to work. The only way I can get MATLAB to start in an automated sense is to make a shell script:

#!/bin/bash ` export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GMT_dir/lib export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libtiff.so.5:/usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/local/MATLAB/R2019a/bin/matlab -desktop &`

Hopefully someone with a little more MATLAB experience can figure out a way to include these library modifications in the startup.m file, I tried a bit but had no luck.

In the past, I have been using GMT through MATLAB by invoking the following setenv LD_LIBRARY_PATH usr/lib/x86_64-linux-gnu/ before calling GMT functions using the system function. Here's an example of how I used to do this, passing MATLAB variables in to GMT system(['grdmath ' num2str(rho_c) ' ' num2str(rho_w) ' SUB ' num2str(rho_m) ' ' ... num2str(rho_c) ' SUB DIV ED.grd MUL NEG = ' grdfile '_airy_compensation.grd']);

The new gmtmex functionality seems like a great improvement over this type of tedious coding, I hope we can smooth out the Linux compatibility with a little effort from the community.