I have to import a MAT-file in a fortran program. I followed the example file but I am facing some problems while linking. The compilation happens fine.
Minimal code:
#include "fintrf.h"
PROGRAM main
USE ssa
USE dmotifs
USE param
IMPLICIT NONE
! MAT-FILE Declarations !
INTEGER matOpen, matGetDir
INTEGER matGetVariableInfo
INTEGER mp, dir, adir(100), pa
INTEGER mxGetM, mxGetN, matClose
INTEGER ndir, i, clstat
CHARACTER*32 names(100)
!===========================!
if(all(fnames(:)%fn .NE. argfun)) then
write(*,*) "No such motif: ",argfun
write(*,*) "Input format-> main <motifname>"
stop
else
fin=fchton(argfun)
y0=nM2m*analys(p,argfun)
! ==> OPEN MAT-file <== !
mp=matOpen('./PRMS_lxr_29Apr15.mat','r')
if (mp .eq. 0) then
write(6,*) "Can't open MAT-file"
stop
end if
dir = matgetdir(mp, ndir)
if (dir .eq. 0) then
write(6,*) "Can't read MAT-file-directory."
stop
endif
call mxCopyPtrToPtrArray(dir, adir, ndir)
do 20 i=1,ndir
call mxCopyPtrToCharacter(adir(i), names(i), 32)
20 continue
write(6,*) 'Directory of Mat-file:'
do 30 i=1,ndir
write(6,*) names(i)
30 continue
write(6,*) 'Getting Header info from first array.'
pa = matGetVariableInfo(mp, names(1))
write(6,*) 'Retrieved ', names(1)
write(6,*) ' With size ', mxGetM(pa), '-by-', mxGetN(pa)
call mxDestroyArray(pa)
clstat=matClose(mp)
end if
END PROGRAM main
I am using gfortran 4.8.3 for compiling+linking using the default command:
gfortran main.f90 dmotifs.o param.o ssa.o -o main
This code compiles fine (without linking) when I do not include: #include "finitrf.h", otherwise the compiler says
Warning: main.f90:1: Illegal preprocessor directive
I tried renaming finitrf.h to finitrf.f90 but it did not make any difference. Nonetheless during linking I am getting these errors:
main.f90:(.text+0x3ea): undefined reference to `matopen_'
main.f90:(.text+0x487): undefined reference to `matgetdir_'
main.f90:(.text+0x52b): undefined reference to `mxcopyptrtoptrarray_'
main.f90:(.text+0x583): undefined reference to `mxcopyptrtocharacter_'
main.f90:(.text+0x71b): undefined reference to `matgetvariableinfo_'
main.f90:(.text+0x804): undefined reference to `mxgetm_'
main.f90:(.text+0x855): undefined reference to `mxgetn_'
main.f90:(.text+0x89c): undefined reference to `mxdestroyarray_'
main.f90:(.text+0x8b0): undefined reference to `matclose_'
collect2: error: ld returned 1 exit status
Do I need a makefile or add additional arguments in the compile command?
EDIT:
I added the -cpp option and that eliminates the problem of Illegal preprocessor directive
Now when I am compiling with paths to matlab external components (where finitf.h) is, I am still getting the same error.
gfortran main.f90 dmotifs.o param.o ssa.o -I/usr/local/matlab2008a/extern/include -L/usr/local/matlab2008a/extern/lib -cpp -o main
If I provide library path to /usr/local/matlab2008a/bin/glnxa64 that contains other matlab libraries including libmat.so, I still get the same errors.
As pointed out by Alexander Vogt, the compiler requires -cpp option for the pre-processor to recognize the header file and not to treat it as illegal.
Linking requires finitrf.h which is usually located in the <matlabroot>/extern/include and the essential libraries are present in <matlabroot>/bin/<arch>/.
But just specifying this does not work and specification of the exact matlab library seems essential; these are libmat.so and libmx.so.
These libraries are in turn dependent on other libraries so another flag is required to set the rpath.
Finally it works with following command:
gfortran main.f90 dmotifs.o param.o ssa.o -I/usr/local/matlab2008a/extern/include -L/usr/local/matlab2008a/bin/glnxa64 -cpp -o main -lmat -lmx -Wl,-rpath /usr/local/matlab2008a/bin/glnxa64/
or in general
gfortran program.f90 -I<matlabroot>/extern/include -L<matlabroot>/bin/<arch> -cpp -lmat -lmx -Wl, -rpath <matlabroot>/bin/<arch> -o program.out
Also see this post that is about the same problem in C.