Mex problems on 64bit machine

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Adrianna
Adrianna 2011-8-10
编辑： Walter Roberson 2018-2-14
I have a code which creates a mex file fine on a 32 bit machine but it does not work correctly for a 64 bit machine. The code compiles without errors or warnings however when I run the code I get a segmentation fault.
Does anyone have a suggestion of how to fix this?
Here is the output from the crash.
------------------------------------------------------------------------
Segmentation violation detected at Wed Aug 10 15:12:08 2011
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : 0x21 (class 4, depth 24)
Default Encoding: UTF-8
GNU C Library : 2.13 stable
MATLAB License : 207107
MATLAB Root : /usr/local/MATLAB/R2011a
MATLAB Version : 7.12.0.635 (R2011a)
Operating System: Linux 2.6.38-10-generic #46-Ubuntu SMP Tue Jun 28 15:07:17 UTC 2011 x86_64
Processor ID : x86 Family 6 Model 10 Stepping 7, GenuineIntel
Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : The X.Org Foundation (11001000), display :0.0
Fault Count: 1
Abnormal termination:
Segmentation violation
Register State (from fault):
RAX = 30a3d42800007fd6 RBX = 0000000000000000
RCX = 00007fd630a456c0 RDX = 0000000000000000
RSP = 00007fd653276760 RBP = 00007fd653276760
RSI = 00007fd653276f40 RDI = 00007fd653277004
R8 = 00007fd62e970440 R9 = 00007fd663749400
R10 = 00007fd6532765d0 R11 = 00007fd65c61df50
R12 = 0000000000000002 R13 = 00007fd653277000
R14 = 00007fd62c0d4b40 R15 = 00007fd653276990
RIP = 00007fd663795847 EFL = 0000000000010246
CS = 0033 FS = 0000 GS = 0000
Stack Trace (from fault):
[ 0] 0x00007fd663a48f49 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00474953 fl::sysdep::linux::unwind_stack(void const**, unsigned long, unsigned long, fl::diag::thread_context const&)+000009
[ 1] 0x00007fd6639fedc1 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00171457 fl::diag::stacktrace_base::capture(fl::diag::thread_context const&, unsigned long)+000161
[ 2] 0x00007fd663a080dd /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00209117
[ 3] 0x00007fd663a08364 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00209764 fl::diag::terminate_log(char const*, fl::diag::thread_context const&, bool)+000100
[ 4] 0x00007fd662a74be5 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00420837 fl::diag::terminate_log(char const*, ucontext const*, bool)+000085
[ 5] 0x00007fd662a71b54 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00408404
[ 6] 0x00007fd662a7303d /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00413757
[ 7] 0x00007fd662a73197 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00414103
[ 8] 0x00007fd662a73b1d /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00416541
[ 9] 0x00007fd662a74435 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00418869
[ 10] 0x00007fd6615cac60 /lib/x86_64-linux-gnu/libpthread.so.0+00064608
[ 11] 0x00007fd663795847 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmx.so+00292935 mxgetpr_+000007
[ 12] 0x00007fd625c1f9ea /home/adrianna/Research/mex_lowrank/id_decomp.mexa64+00002538 mexfunction_+000182
[ 13] 0x00007fd65c61dfbc /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmex.so+00049084 mexRunMexFile+000108
[ 14] 0x00007fd65c61af19 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmex.so+00036633
[ 15] 0x00007fd65c61bbbe /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmex.so+00039870
[ 16] 0x00007fd6627e97ef /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_dispatcher.so+00391151 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)+000511
[ 17] 0x00007fd6620f01f0 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01532400
[ 18] 0x00007fd662091975 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01145205
[ 19] 0x00007fd6620ab96e /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01251694
[ 20] 0x00007fd6620b00ec /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01269996
[ 21] 0x00007fd6620adc7a /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01260666
[ 22] 0x00007fd6620ae741 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01263425
[ 23] 0x00007fd6621077d9 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01628121
[ 24] 0x00007fd6627e97ef /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_dispatcher.so+00391151 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)+000511
[ 25] 0x00007fd6620e39b2 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01481138
[ 26] 0x00007fd6620a5e13 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01228307
[ 27] 0x00007fd6620a4eb7 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01224375
[ 28] 0x00007fd6620a5397 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01225623
[ 29] 0x00007fd662cb38fe /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwbridge.so+00108798
[ 30] 0x00007fd662cb44ae /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwbridge.so+00111790 mnParser+000622
[ 31] 0x00007fd662a5cd39 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00322873 mcrInstance::mnParser_on_interpreter_thread()+000041
[ 32] 0x00007fd662a3fdb2 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00204210
[ 33] 0x00007fd662a3fec0 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00204480
[ 34] 0x00007fd6593e1db6 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmwuix.so+00437686
[ 35] 0x00007fd6593eb13d /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmwuix.so+00475453
[ 36] 0x00007fd659e370bd /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libuij.so+00217277 sysq::during_F<boost::weak_ptr<sysq::ws_ppeHook>, boost::shared_ptr<sysq::ws_ppeHook> > std::for_each<__gnu_cxx::__normal_iterator<boost::weak_ptr<sysq::ws_ppeHook>*, std::vector<boost::weak_ptr<sysq::ws_ppeHook>, std::allocator<boost::weak_ptr<sysq::ws_ppeHook> > > >, sysq::during_F<boost::weak_ptr<sysq::ws_ppeHook>, boost::shared_ptr<sysq::ws_ppeHook> > >(__gnu_cxx::__normal_iterator<boost::weak_ptr<sysq::ws_ppeHook>*, std::vector<boost::weak_ptr<sysq::ws_ppeHook>, std::allocator<boost::weak_ptr<sysq::ws_ppeHook> > > >, __gnu_cxx::__normal_iterator<boost::weak_ptr<sysq::ws_ppeHook>*, std::vector<boost::weak_ptr<sysq::ws_ppeHook>, std::allocator<boost::weak_ptr<sysq::ws_ppeHook> > > >, sysq::during_F<boost::weak_ptr<sysq::ws_ppeHook>, boost::shared_ptr<sysq::ws_ppeHook> >)+000077
[ 37] 0x00007fd659e38989 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libuij.so+00223625
[ 38] 0x00007fd659e354ae /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libuij.so+00210094 svWS_ProcessPendingEvents(int, int, bool)+000494
[ 39] 0x00007fd662a3e1c7 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00197063
[ 40] 0x00007fd662a3e60a /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00198154
[ 41] 0x00007fd662a3ed6f /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00200047
[ 42] 0x00007fd6615c1d8c /lib/x86_64-linux-gnu/libpthread.so.0+00028044
[ 43] 0x00007fd66130d04d /lib/x86_64-linux-gnu/libc.so.6+00942157 clone+000109
  1 个评论
Adrianna
Adrianna 2011-8-10
编辑：Walter Roberson 2018-2-14
Here is the code for the wrapper.
c#include "fintrf.h"
c [T,J,rnorms] = id_decomp(A,INPUT2)
c
c if 0 < INPUT2 < 1
c
c compute to a given accuracy
c
c acc = INPUT2
c
c else
c
c compute a fixed number of columns
c
c k = INPUT2
c
SUBROUTINE MEXFUNCTION(NLHS, PLHS, NRHS, PRHS)
IMPLICIT NONE
INTEGER PLHS(*), PRHS(*)
INTEGER NLHS, NRHS
INTEGER mxCreateDoubleMatrix,mxMalloc
INTEGER mxGetPr,mxGetM,mxGetN,mxIsComplex
INTEGER A_p, INPUT2_p, T_p, rnorms_p, indvec_p, indveci_p
INTEGER m, n, k, flag_fixed_k, flag_complex
REAL*8 INPUT2(1), acc
c Check that we have two inputs and two or three outputs
IF (NRHS .NE. 2) THEN
CALL mexErrMsgTxt('id_decomp requires two input arguments')
ELSEIF (NLHS .LT. 2) THEN
CALL mexErrMsgTxt('id_decomp requires 2 or 3 output arguments')
ELSEIF (NLHS .GT. 3) THEN
CALL mexErrMsgTxt('id_decomp requires 2 or 3 output arguments')
ENDIF
c Extract the problem dimensions from the first input argument.
m = MXGETM(PRHS(1))
n = MXGETN(PRHS(1))
c Assign a pointer to the second input argument.
INPUT2_p = MXGETPR(PRHS(2))
CALL mxCopyPtrToReal8(INPUT2_p,INPUT2,1)
c Check the nature of INPUT2:
c If INPUT2 < 1, then set acc = INPUT2 and use the "specified accuracy" version of id_idd.
c If INPUT2 >= 1, then set k = INPUT2 and use the "specified rank" version of id_idd.
IF (INPUT2(1) .LT. 1) THEN
flag_fixed_k = 0
k = min(m,n)
acc = INPUT2(1)
ELSE
flag_fixed_k = 1
k = min(int(INPUT2(1)), min(m,n))
END IF
c Check whether the input matrix A is complex.
flag_complex = mxIsComplex(PRHS(1))
IF (flag_complex .EQ. 1) THEN
CALL mexErrMsgTxt('id_decomp cannot yet handle complex input')
END IF
c Create the output matrix T and copy A onto T.
IF (flag_complex .EQ. 0) THEN
A_p = mxGetPr(PRHS(1))
PLHS(1) = mxCreateDoubleMatrix(m,n,0)
T_p = mxGetPr(PLHS(1))
CALL mxCopyPtrToReal8(A_p,%VAL(T_p),m*n)
END IF
c Create the vector "rnorms".
c If there are only 2 output arguments, then it is
c created simply as a temporary array, otherwise it
c is created as an output.
IF (NLHS .EQ. 2) THEN
rnorms_p = mxMalloc(8*n)
ELSE
PLHS(3) = mxCreateDoubleMatrix(1,n,0)
rnorms_p = mxGetPr(PLHS(3))
ENDIF
c Create an array for the index vector. This is only
c a temporary work array since the actual output has
c to consist of reals to follow matlab standards.
indveci_p = mxMalloc(4*n)
c Do the actual computations.
IF (flag_fixed_k .EQ. 0) THEN
CALL iddp_id(acc,m,n,%VAL(T_p),k,%VAL(indveci_p),%VAL(rnorms_p))
CALL mxSetM(PLHS(1),k)
CALL mxSetN(PLHS(1),n-k)
ELSE
CALL iddr_id(m,n,%VAL(T_p),k,%VAL(indveci_p),%VAL(rnorms_p))
CALL mxSetM(PLHS(1),k)
CALL mxSetN(PLHS(1),n-k)
ENDIF
c Create the REAL VALUED output index vector indvec.
c Then copy the integer vector indveci to the real valued output indvec.
PLHS(2) = mxCreateDoubleMatrix(1,n,0)
indvec_p = mxGetPr(PLHS(2))
CALL COPY_IND2REAL(%VAL(indveci_p), %VAL(indvec_p), n)
c Free the temporary work arrays.
CALL mxFree(indveci_p)
IF (NLHS .EQ. 2) THEN
CALL mxFree(rnorms_p)
ENDIF
RETURN
END

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回答（1 个）

James Tursa
James Tursa 2011-8-10
You need to strictly follow the API types. You don't get automatic argument type conversion in Fortran like you do in C. Change these lines:
INTEGER PLHS(*), PRHS(*)
INTEGER NLHS, NRHS
INTEGER mxCreateDoubleMatrix,mxMalloc
INTEGER mxGetPr,mxGetM,mxGetN,mxIsComplex
INTEGER A_p, INPUT2_p, T_p, rnorms_p, indvec_p, indveci_p
INTEGER m, n, k, flag_fixed_k, flag_complex
To these:
mwPointer PLHS(*), PRHS(*)
INTEGER*4 NLHS, NRHS
mwPointer, external :: mxCreateDoubleMatrix,mxMalloc
mwPointer, external :: mxGetPr
mwSize, external :: mxGetM,mxGetN
INTEGER*4, external :: mxIsComplex
mwPointer A_p, INPUT2_p, T_p, rnorms_p, indvec_p, indveci_p
mwSize m, n, k, p
INTEGER*4 flag_fixed_k, flag_complex
And change this line:
k = min(int(INPUT2(1)), min(m,n))
To these:
p = INPUT2(1)
k = min(p, min(m,n))
And change this line:
CALL mxCopyPtrToReal8(INPUT2_p,INPUT2,1)
To these:
p = 1
CALL mxCopyPtrToReal8(INPUT2_p,INPUT2,p)
And change this line:
PLHS(3) = mxCreateDoubleMatrix(1,n,0)
To these:
p = 1
PLHS(3) = mxCreateDoubleMatrix(p,n,0)
And change this line:
PLHS(2) = mxCreateDoubleMatrix(1,n,0)
To these:
p = 1
PLHS(2) = mxCreateDoubleMatrix(p,n,0)
As a side comment, you have some pretty strange code in there for copying mxArray variables and for changing the sizes of pre-existing mxArray variables.
  3 个评论
显示 1更早的评论
Adrianna
Adrianna 2011-8-11
I figured out what was wrong. Thank you again for your help.
Urankhai
Urankhai 2018-2-14
Hi Adrianna, what was your problem? I have similar one

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