rnt compilation problem (solved)

[mcobas]

Hello,

I've been struggling for some time with a problem regarding the mex compilation of the fortran functions under the rnt directory of the RNT toolbox.

For some reason, matlab can't find the libsvml.so dynamic library, although the LD_LIBRARY_PATH is set correctly, pointing to the directory where the library is. I have always thought that matlab inherits the environment variables of the shell from where it was invoked, but this time it couldn't find the library. Every time I tried to call the rnt_oa2d_mex matlab function, matlab issued the error:

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??? Invalid MEX-file '/home/cesga/mcobas/RNT/matlib/rnt/rnt_oa2d_mex.mexa64':
/home/cesga/mcobas/RNT/matlib/rnt/rnt_oa2d_mex.mexa64: undefined symbol: __svml_exp2.

Error in ==> rnt_oa2d at 80
   [t2,t2err]=rnt_oa2d_mex(lonr,latr,t1,lon,lat,pmap,a,b);

[/color]

I tried workarounds in several webs, like (http://www.linux-forum.de/gel-st-compil ... 14040.html, http://software.intel.com/en-us/forums/ ... hp?t=60482 or [url]ttp://software.intel.com/en-us/forums/showthread.php?t=62218[/url], to mention a few, but no success. Matlab kept giving me the same error.

In the end, I had to compile against the static library, libsvml.a, located on the same directory. You can do this "by hand", copying and pasting the command that matlab uses. If you type

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mex -v rnt_oa2d_mex.f

matlab will produce a lot of output. Among other stuff, you will find

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ifort -c  -I/opt/cesga/matlabR2008b/extern/include -I/opt/cesga/matlabR2008b/simulink/include -fexceptions -fPIC -fno-omit-frame-pointer  -DMX_COMPAT_32 -O3  "rnt_oa2d_mex.f"

to compile, and

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ifort -O3 -pthread -shared -Wl,--version-script,/opt/cesga/matlabR2008b/extern/lib/glnxa64/fexport.map -Wl,--no-undefined -o  "rnt_oa2d_mex.mexa64"  rnt_oa2d_mex.o  "/opt/cesga/matlabR2008b/extern/lib/glnxa64/version4.o"  -Wl,-rpath-link,/opt/cesga/matlabR2008b/bin/glnxa64 -L/opt/cesga/matlabR2008b/bin/glnxa64 -lsvml -lifcoremt -lmx -lmex -lmat -lm

to link.

if you add

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 -static-intel /absolute/path/to/the/library/libsvml.a

to the linking command, and remove the "-lsvml" library, it will link against the static library. Of course, other compilers may use other options instead of "-static-intel".

You can go to the rnt directory and compile and link each "_mex.f" individually, but perhaps it is better to include these options in the file "mexopts.sh", located under the $HOME/.matlab directory. This is how my mexopts.sh file looks like now. I changed the section glnxa64.

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FC='ifort'
            FFLAGS='-fexceptions'
            FFLAGS="$FFLAGS -fPIC -fno-omit-frame-pointer"
            FLIBS="$RPATH $MLIBS -lm"
            FOPTIMFLAGS='-O3'
            FDEBUGFLAGS='-g'
#
            LD="$COMPILER"
            LDEXTENSION='.mexa64'
            LDFLAGS="-pthread -shared -Wl,--version-script,$TMW_ROOT/extern/lib/$Arch/$MAPFILE -Wl,--no-undefined -static-intel /opt/cesga/intel/Compiler/11.0/083/lib/intel64/libsvml.a"
            LDOPTIMFLAGS='-O3'
            LDDEBUGFLAGS='-g'
#
            POSTLINK_CMDS=':'

Also, around line 31, I changed the variable MLIBS, removing the dynamic library ( -lsvml )

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MLIBS="-L$TMW_ROOT/bin/$Arch -lifcoremt -lmx -lmex -lmat"

After doing this, you can execute the script rnt_compile in matlab (under the rnt directory), and it will link all the mex.f files against the static library. You can check this by using

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 ldd rnt_oa2d_mex.mexa64 

and you'll see there is no "libsvml.so".

I know this is not the best solution, but it is the best I could find. I'm just posting it in case someone comes across the same problem, and in case someone can find a better solution.

Kind regards,

Marcos Cobas Garcia

Centro de Supercomputacion de Galicia
A Coruna, Galicia, Spain