Segmentation fault in the script for opening MAT-file

Question

I want to open a MAT-file in fortran and I followed the example file. The compilation and linking happen without any errors or warnings.

This is the makefile:

FC = gfortran
FCFLAGS = -g -fcheck=all -Wall
INCLUDES = -I/usr/local/matlab2008a/extern/include
LFLAGS = -L/usr/local/matlab2008a/bin/glnxa64
LIBS = -lmat -lmx
LDFLAGS = "-Wl,-rpath,/usr/local/matlab2008a/bin/glnxa64"

main: main.o param.o dmotifs.o ssa.o
    $(FC) $(LFLAGS) $(LIBS) $(LDFLAGS) -o main main.o param.o dmotifs.o ssa.o  
param.o: param.f90
    $(FC) $(FCFLAGS) -c $<    
dmotifs.o: dmotifs.f90 param.o
    $(FC) $(FCFLAGS) -c $<    
ssa.o: ssa.f90 dmotifs.o
    $(FC) $(FCFLAGS) -c $<   
main.o: main.f90 param.o dmotifs.o ssa.o
    $(FC) -c -cpp $(FCFLAGS) $(INCLUDES) $<    
clean:
    rm -f *.o *.mod *.MOD

However when I am running the script I am getting segmentation fault error.

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x37B4C19497
#1  0x37B4C19ADE
#2  0x37B1E358EF
#3  0x7F1EA50EA7C1
#4  0x401A69 in MAIN__ at main.f90:75
Segmentation fault

This is the main code:

#include "fintrf.h"

PROGRAM main     
USE ssa
IMPLICIT NONE

CHARACTER(LEN=6) :: argfun
TYPE(fhandle), DIMENSION(13) :: fmotifs
TYPE(funnames), DIMENSION(13) :: fnames
TYPE(PRM) p
REAL, DIMENSION(4) :: y0
REAL tf
REAL, ALLOCATABLE, DIMENSION(:) :: t
REAL, ALLOCATABLE, DIMENSION(:,:) :: y
TYPE(OPTIONS) opt
INTEGER fin
REAL nM2m

! MAT-FILE Declarations !

INTEGER*8 matOpen, matGetDir !, matGetNextVariable
INTEGER matGetVariableInfo
INTEGER mp, dir, adir(100), pa
INTEGER mxGetM, mxGetN, matClose
INTEGER ndir, i, clstat
CHARACTER*32 names(100) !, name

!===========================!


nM2m=1.355178815844751e3;

opt%numsample=2000
tf=1000000

call get_command_argument(1,argfun)

call makemotifs(fnames,fmotifs)
call getparamdef(p)

if(all(fnames(:)%fn .NE. argfun)) then
    write(*,*) "No such motif: ",argfun
    write(*,*) "Input format-> main <motifname>"
    stop
else


    fin=fchton(argfun)  
    y0=nint(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)

    call gillespie(fmotifs(fin),y0,p,tf,opt,t,y)

end if

Line 75 (as pointed out in the error message is): dir = matgetdir(mp, ndir)

I have no clue how to fix the issue. If I comment out the MAT-file opening part then everything works fine. The MAT-file contains a float 3D array (9x5x10000) and two scalars.

EDIT

As it seems that for 64bit systems, the pointers have to be declared as integer*8 instead of integer. When I did this I am again getting a segmentation fault at this line:
      call mxCopyPtrToPtrArray(dir, adir, ndir)

Mathworks documentation on this topic is almost nothing and they make it seem to be quite an easy routine job. Is there anyone on earth who has actually opened a MAT-file on fortran? Can someone please share their scripts?

Answer 1

From the length of the addresses in the error message it looks like you are on a 64 bit system.

You have declared, and are storing, the results of most of the mat* functions in a default integer. This is probably only a 32 bit type. The mat* functions actually return a machine pointer, which will be 64 bits on a 64 bit machine.

The example code you linked to likely assumes a 32 bit platform.

Adjust your declarations for the mat* functions and the variables that get assigned the results of invoking those functions appropriately. Perhaps INTEGER(C_INTPTR_T), where C_INTPTR_T is from ISO_C_BINDING.

The mathworks provides an archaic C preprocessor means of specifying the relevant type (for example, the return type of matOpen is mwPointer), which the preprocessing changes into the appropriate integer kind. Personally I prefer to use my own interfaces, written using the C interoperability features of Fortran 2003.