Dear Arvind,
I don't remember clearly but I think that that the use of mwSize and
mwIndex has been added for the compatibility with 64bit machines. It
it possible that using an old version of gfm_common.c (namely revision
2722) this solves the problem. I attached the revision 2722. I hope it
is still compatible but I am not sure.
Yves.
Arvind Ajoy <[email protected]> a écrit :
Dear Yves,
Thank you for your input. Unfortunately, the problem remains
unresolved. Specifically, the problem seems to be a linker error with
mex, corresponding to largeArrayDims. Additionally,
http://www.mathworks.com/support/solutions/en/data/1-5C27B9/?solution=1-5C27B9
seems to mention that largeArrayDims is included only from Matlab7.3
upwards. Couls this be the source of the problem I am facing? If so,
is there a workaround?
Details are as below ....
Including in gfm_common.c,
typedef size_t mwSize;
typedef size_t mwIndex;
mex -largeArrayDims -output gf_matlab -g CDEBUGFLAGS="-O3" LD="g++" \
-I. -I./.. -DMATLAB_RELEASE=14 \
./gfm_mex.c ./gfm_common.c ./../gfi_array.c \
../.libs/libgetfemint.a ../../../src/.libs/libgetfem.a -lblas
-llapack || (rm gf_matlab.mexa64; false)
./gfm_common.c: In function ?mxarray_to_gfi_array?:
./gfm_common.c:144: warning: assignment from incompatible pointer type
./gfm_common.c:157: warning: assignment from incompatible pointer type
./gfm_common.c: In function ?gfi_array_to_mxarray?:
./gfm_common.c:260: warning: passing argument 2 of
?mxCreateNumericArray? from incompatible pointer type
./gfm_common.c:271: warning: passing argument 2 of
?mxCreateNumericArray? from incompatible pointer type
./gfm_common.c:279: warning: passing argument 2 of
?mxCreateNumericArray? from incompatible pointer type
./gfm_common.c:294: warning: passing argument 2 of ?mxCreateCellArray?
from incompatible pointer type
./gfm_common.c:304: warning: passing argument 2 of
?mxCreateStructArray? from incompatible pointer type
./gfm_common.c:310: warning: passing argument 2 of
?mxCreateNumericArray? from incompatible pointer type
./gfm_common.c:315: warning: passing argument 2 of
?mxCreateNumericArray? from incompatible pointer type
./gfm_common.c:333: warning: assignment from incompatible pointer type
./gfm_common.c:341: warning: assignment from incompatible pointer type
/usr/bin/ld: cannot find -largeArrayDims
collect2: ld returned 1 exit status
mex: link of 'gf_matlab.mexa64' failed.
----------------------------------------------------------------------------------------------------------------------------------------------------
Including
typedef int mwSize;
typedef int mwIndex;
yields the same error. Tehre are however no warning messages as above.
==========================================================================
Regards
Arvind
On Tue, Sep 21, 2010 at 1:10 PM, Yves Renard
<[email protected]> wrote:
Dear Arvind,
In mex.h, mwSize and mwIndex are defined by
typedef int mwSize;
typedef int mwIndex;
for 32-bits machines and
typedef size_t mwSize;
typedef size_t mwIndex;
for 64-bits ones.
You can add one of the two pairs of definitions at the begining of
gfm_common.c
and see if it fixes the problem.
Yves.
On lundi 20 septembre 2010, Arvind Ajoy wrote:
Dear Users,
I have been using getfem happily for the last year and a half on my
PC. I run Debian 5.0 + Matlab 7.4 on this system.
I intend to use getfem on a computer with better resources.
Unfortunately, this machine has only Matlab7.1 installed on it. I do
not have permission to change the version of Matlab on this system.
Using gcc-4.1.2 and Matlab 7.1.0.183 (R14), with the following
./configure --prefix=/sfs1/phd/ee06d006/tools/getfem-4.0.0
--enable-matlab --enable-shared --with-pic
I get the following error when compiling getfem-matlab on this system ...
mex -largeArrayDims -output gf_matlab -g CDEBUGFLAGS="-O3" LD="g++" \
-I. -I./.. -DMATLAB_RELEASE=14 \
./gfm_mex.c ./gfm_common.c ./../gfi_array.c \
../.libs/libgetfemint.a ../../../src/.libs/libgetfem.a -lblas
-llapack || (rm gf_matlab.mexa64; false)
./gfm_common.c: In function ?mxarray_to_gfi_array?:
./gfm_common.c:66: error: ?mwSize? undeclared (first use in this function)
./gfm_common.c:66: error: (Each undeclared identifier is reported only once
./gfm_common.c:66: error: for each function it appears in.)
./gfm_common.c:66: error: expected ?;? before ?n2?
./gfm_common.c:67: error: ?n2? undeclared (first use in this function)
./gfm_common.c:72: error: expected ?;? before ?i?
./gfm_common.c:76: error: ?i? undeclared (first use in this function)
./gfm_common.c:134: error: ?mwIndex? undeclared (first use in this
function) ./gfm_common.c:134: error: ?ptr2? undeclared (first use in this
function) ./gfm_common.c:213: error: ?pm? undeclared (first use in this
function) ./gfm_common.c:217: error: expected expression before ?)? token
./gfm_common.c: In function ?gfi_array_to_mxarray?:
./gfm_common.c:238: error: ?mwSize? undeclared (first use in this function)
./gfm_common.c:238: error: expected ?;? before ?ndim2?
./gfm_common.c:243: error: ?ndim2? undeclared (first use in this function)
./gfm_common.c:244: error: ?dim2? undeclared (first use in this function)
./gfm_common.c:297: error: expected ?;? before ?j?
./gfm_common.c:300: error: ?j? undeclared (first use in this function)
./gfm_common.c:301: error: expected ?)? before ?mwSize?
./gfm_common.c:307: error: expected ?)? before ?mwSize?
./gfm_common.c:309: error: ?i2? undeclared (first use in this function)
./gfm_common.c:312: error: expected ?)? before ?mwSize?
./gfm_common.c:322: error: ?mwIndex? undeclared (first use in this
function) ./gfm_common.c:322: error: expected ?;? before ?d1?
./gfm_common.c:323: error: ?pr2? undeclared (first use in this function)
./gfm_common.c:325: error: ?d1? undeclared (first use in this function)
./gfm_common.c:326: error: ?d2? undeclared (first use in this function)
./gfm_common.c:327: error: ?nnz? undeclared (first use in this function)
mex: compile of './gfm_common.c' failed.
rm: cannot remove `gf_matlab.mexa64': No such file or directory
make[5]: *** [gf_matlab.mexa64] Error 1
make[5]: Leaving directory
`/sfs1/phd/ee06d006/tools/getfem-4.0.0/interface/src/matlab'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory
`/sfs1/phd/ee06d006/tools/getfem-4.0.0/interface/src/matlab'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/sfs1/phd/ee06d006/tools/getfem-4.0.0/interface/src' make[2]: ***
[all-recursive] Error 1
make[2]: Leaving directory
`/sfs1/phd/ee06d006/tools/getfem-4.0.0/interface' make[1]: ***
[all-recursive] Error 1
make[1]: Leaving directory `/sfs1/phd/ee06d006/tools/getfem-4.0.0'
make: *** [all] Error 2
I would be very happy if anyone has inputs on how I should proceed.
Regards
Arvind
_______________________________________________
Getfem-users mailing list
[email protected]
https://mail.gna.org/listinfo/getfem-users
--
Yves Renard ([email protected]) tel : (33) 04.72.43.87.08
Pole de Mathematiques, INSA-Lyon fax : (33) 04.72.43.85.29
20, rue Albert Einstein
69621 Villeurbanne Cedex, FRANCE
http://math.univ-lyon1.fr/~renard
---------
/* -*- c++ -*- (enables emacs c++ mode) */
/*========================================================================
Copyright (C) 2006-2006 Yves Renard, Julien Pommier.
This file is a part of GETFEM++
Getfem++ is free software; you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as
published by the Free Software Foundation; either version 2.1 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301,
USA.
========================================================================*/
#include <assert.h>
#include <signal.h>
#include <string.h>
#include "gfm_common.h"
const char*
mxClassID2string(mxClassID id) {
switch (id) {
case mxUNKNOWN_CLASS: return "UNKNOWN";
case mxCELL_CLASS: return "CELL";
case mxSTRUCT_CLASS: return "STRUCT";
case mxOBJECT_CLASS: return "OBJECT";
case mxCHAR_CLASS: return "CHAR";
case mxDOUBLE_CLASS: return "DOUBLE";
case mxSINGLE_CLASS: return "SINGLE";
case mxINT8_CLASS: return "INT8";
case mxUINT8_CLASS: return "UINT8";
case mxINT16_CLASS: return "INT16";
case mxUINT16_CLASS: return "UINT16";
case mxINT32_CLASS: return "INT32";
case mxUINT32_CLASS: return "UINT32";
case mxINT64_CLASS: return "INT64";
case mxUINT64_CLASS: return "UINT64";
case mxSPARSE_CLASS: return "SPARSE";
#ifdef LOGICAL_IS_A_TYPE
case mxLOGICAL_CLASS: return "LOGICAL";
#endif
case mxOPAQUE_CLASS: return "OPAQUE_CLASS";
default:
#if MATLAB_RELEASE >= 14
if (id != (mxClassID)(-1))
return "OBJECT";
else
#endif
return "unknown class...did you use the correct mex version ?";
}
}
int
mxarray_to_gfi_array(const mxArray *mx, gfi_array *t)
{
int n = mxGetNumberOfElements(mx);
assert(t);
switch (mxGetClassID(mx)) {
case mxCELL_CLASS: {
int i;
t->storage.type = GFI_CELL;
t->storage.gfi_storage_u.data_cell.data_cell_len = n;
t->storage.gfi_storage_u.data_cell.data_cell_val = (gfi_array**)mxCalloc(n, sizeof(gfi_array*));
for (i = 0; i < n; ++i) {
if (mxGetCell(mx,i)) {
t->storage.gfi_storage_u.data_cell.data_cell_val[i] = mxCalloc(1,sizeof(gfi_array));
if (mxarray_to_gfi_array(mxGetCell(mx,i), t->storage.gfi_storage_u.data_cell.data_cell_val[i]) != 0) return 1;
} else t->storage.gfi_storage_u.data_cell.data_cell_val[i] = NULL;
}
} break;
case mxCHAR_CLASS: {
t->storage.type = GFI_CHAR;
t->storage.gfi_storage_u.data_char.data_char_len = n;
t->storage.gfi_storage_u.data_char.data_char_val = mxCalloc(n+1,sizeof(char));
mxGetString(mx,t->storage.gfi_storage_u.data_char.data_char_val,n+1);
} break;
case mxINT32_CLASS: {
t->storage.type = GFI_INT32;
t->storage.gfi_storage_u.data_int32.data_int32_len = n;
t->storage.gfi_storage_u.data_int32.data_int32_val = mxGetData(mx);
} break;
#ifdef LOGICAL_IS_A_TYPE
case mxLOGICAL_CLASS: {
int i;
mxLogical *p = (mxLogical*)mxGetData(mx);
t->storage.type = GFI_INT32;
t->storage.gfi_storage_u.data_int32.data_int32_len = n;
t->storage.gfi_storage_u.data_int32.data_int32_val = (int*)mxCalloc(n,sizeof(int));
for (i = 0; i < n; ++i)
t->storage.gfi_storage_u.data_int32.data_int32_val[i] = (p[i] ? 1 : 0);
} break;
#endif
case mxUINT32_CLASS: {
t->storage.type = GFI_UINT32;
t->storage.gfi_storage_u.data_uint32.data_uint32_len = n;
t->storage.gfi_storage_u.data_uint32.data_uint32_val = mxGetData(mx);
} break;
case mxSPARSE_CLASS: /* for older (i.e. 6.1) matlab versions... */
case mxDOUBLE_CLASS: {
int is_complex = mxIsComplex(mx);
if (!mxIsSparse(mx)) {
t->storage.type = GFI_DOUBLE;
t->storage.gfi_storage_u.data_double.is_complex = is_complex;
t->storage.gfi_storage_u.data_double.data_double_len = n * (is_complex ? 2 : 1);
if (!is_complex) {
t->storage.gfi_storage_u.data_double.data_double_val = mxGetData(mx);
} else {
double *pr = mxGetData(mx), *pi = mxGetImagData(mx);
int i;
t->storage.gfi_storage_u.data_double.data_double_val = mxCalloc(n,sizeof(double)*2);
for (i=0; i < n; ++i) {
t->storage.gfi_storage_u.data_double.data_double_val[i*2] = pr[i];
t->storage.gfi_storage_u.data_double.data_double_val[i*2+1] = pi[i];
}
}
} else {
int nnz = mxGetNzmax(mx);
t->storage.type = GFI_SPARSE;
t->storage.gfi_storage_u.sp.is_complex = is_complex;
t->storage.gfi_storage_u.sp.ir.ir_len = nnz; t->storage.gfi_storage_u.sp.ir.ir_val = mxGetIr(mx);
t->storage.gfi_storage_u.sp.jc.jc_len = mxGetN(mx)+1; t->storage.gfi_storage_u.sp.jc.jc_val = mxGetJc(mx);
t->storage.gfi_storage_u.sp.pr.pr_len = nnz * (is_complex ? 2 : 1);
if (!is_complex) {
t->storage.gfi_storage_u.sp.pr.pr_val = mxGetPr(mx);
} else {
double *pr = mxGetPr(mx), *pi = mxGetPi(mx);
int i;
t->storage.gfi_storage_u.sp.pr.pr_val = mxCalloc(nnz,sizeof(double)*2);
for (i=0; i < nnz; ++i) {
t->storage.gfi_storage_u.sp.pr.pr_val[i*2] = pr[i];
t->storage.gfi_storage_u.sp.pr.pr_val[i*2+1] = pi[i];
}
}
}
} break;
case mxOBJECT_CLASS:
case mxSTRUCT_CLASS:
#if MATLAB_RELEASE >= 14
default:
#endif
{
mxArray *fid = mxGetField(mx, 0, "id");
mxArray *fcid = mxGetField(mx, 0, "cid");
if (fid && mxGetClassID(fid) == mxUINT32_CLASS &&
fcid && mxGetClassID(fcid) == mxUINT32_CLASS) {
int n = mxGetNumberOfElements(fid),i;
assert(n == mxGetNumberOfElements(fcid));
if (mxGetNumberOfElements(fid) >= 1) {
t->storage.type = GFI_OBJID;
t->storage.gfi_storage_u.objid.objid_len = mxGetNumberOfElements(fid);
t->storage.gfi_storage_u.objid.objid_val = mxCalloc(n, sizeof(gfi_object_id));
for (i=0; i < n; ++i) {
t->storage.gfi_storage_u.objid.objid_val[i].id = ((int*)mxGetData(fid))[i];
t->storage.gfi_storage_u.objid.objid_val[i].cid = ((int*)mxGetData(fcid))[i];
}
} else {
mexPrintf("empty arrays of getfem object ids not handled"); return 1;
}
} else {
mexPrintf("matlab structures (except getfem object ids) not handled"); return 1;
}
} break;
#if MATLAB_RELEASE < 14
default: {
mexPrintf("unhandled class type : %s\n", mxClassID2string(mxGetClassID(mx)));
return 1;
} break;
#endif
}
t->dim.dim_len = mxGetNumberOfDimensions(mx);
t->dim.dim_val = (u_int*)mxGetDimensions(mx);
return 0;
}
mxArray*
gfi_array_to_mxarray(gfi_array *t) {
mxArray *m;
assert(t);
/* Matlab represent scalars as an array of size one */
/* while gfi_array represents "scalar" values with 0-dimension array */
int ndim = (t->dim.dim_len == 0 ? 1 : t->dim.dim_len);
static const int one = 1;
const int *dim = (t->dim.dim_len == 0 ? &one : (const int *)t->dim.dim_val);
switch (t->storage.type) {
case GFI_UINT32:
case GFI_INT32: {
m = mxCreateNumericArray(ndim, dim, (t->storage.type == GFI_UINT32) ? mxUINT32_CLASS:mxINT32_CLASS, mxREAL);
memcpy(mxGetData(m), t->storage.gfi_storage_u.data_int32.data_int32_val, sizeof(int)*t->storage.gfi_storage_u.data_int32.data_int32_len);
} break;
case GFI_DOUBLE: {
if (!gfi_array_is_complex(t)) {
m = mxCreateNumericArray(ndim, dim, mxDOUBLE_CLASS, mxREAL);
memcpy(mxGetData(m), t->storage.gfi_storage_u.data_double.data_double_val, sizeof(double)*t->storage.gfi_storage_u.data_double.data_double_len);
} else {
double *pr, *pi; int i;
m = mxCreateNumericArray(ndim, dim, mxDOUBLE_CLASS, mxCOMPLEX);
pr = mxGetData(m); pi = mxGetImagData(m);
for (i=0; i < t->storage.gfi_storage_u.data_double.data_double_len; ) {
*pr++ = t->storage.gfi_storage_u.data_double.data_double_val[i++];
*pi++ = t->storage.gfi_storage_u.data_double.data_double_val[i++];
}
}
} break;
case GFI_CHAR: {
char *s = calloc(t->storage.gfi_storage_u.data_char.data_char_len+1,1);
strncpy(s,t->storage.gfi_storage_u.data_char.data_char_val,t->storage.gfi_storage_u.data_char.data_char_len);
m = mxCreateString(s); free(s);
} break;
case GFI_CELL: {
unsigned i;
m = mxCreateCellArray(ndim, dim);
for (i=0; i < t->storage.gfi_storage_u.data_cell.data_cell_len; ++i)
mxSetCell(m,i,gfi_array_to_mxarray(t->storage.gfi_storage_u.data_cell.data_cell_val[i]));
} break;
case GFI_OBJID: {
unsigned i,j=1;
static const char *fields[] = {"id","cid"};
mxArray *mxid, *mxcid;
m = mxCreateStructArray(1, (const int*)&t->storage.gfi_storage_u.objid.objid_len, 2, fields);
for (i=0; i < t->storage.gfi_storage_u.objid.objid_len; ++i) {
mxid = mxCreateNumericArray(1, (const int*)&j, mxUINT32_CLASS, mxREAL);
*(int*)mxGetData(mxid) = t->storage.gfi_storage_u.objid.objid_val[i].id;
mxSetField(m,i,fields[0], mxid);
mxcid = mxCreateNumericArray(1, (const int*)&j, mxUINT32_CLASS, mxREAL);
*(int*)mxGetData(mxcid) = t->storage.gfi_storage_u.objid.objid_val[i].cid;
mxSetField(m,i,fields[1], mxcid);
}
} break;
case GFI_SPARSE: {
assert(ndim == 2);
m = mxCreateSparse(t->dim.dim_val[0], t->dim.dim_val[1],
t->storage.gfi_storage_u.sp.pr.pr_len,
gfi_array_is_complex(t) ? mxCOMPLEX : mxREAL);
memcpy(mxGetIr(m),
t->storage.gfi_storage_u.sp.ir.ir_val,
t->storage.gfi_storage_u.sp.ir.ir_len * sizeof(int));
memcpy(mxGetJc(m),
t->storage.gfi_storage_u.sp.jc.jc_val,
t->storage.gfi_storage_u.sp.jc.jc_len * sizeof(int));
if (!gfi_array_is_complex(t)) {
memcpy(mxGetPr(m), t->storage.gfi_storage_u.sp.pr.pr_val, t->storage.gfi_storage_u.sp.pr.pr_len * sizeof(double));
} else {
double *pr, *pi; int i;
pr = mxGetPr(m); pi = mxGetPi(m);
for (i=0; i < t->storage.gfi_storage_u.sp.pr.pr_len; ) {
*pr++ = t->storage.gfi_storage_u.sp.pr.pr_val[i++];
*pi++ = t->storage.gfi_storage_u.sp.pr.pr_val[i++];
}
}
} break;
default: {
assert(0);
} break;
}
return m;
}
gfi_array_list *
build_gfi_array_list(int nrhs, const mxArray *prhs[]) {
gfi_array_list *l;
int i;
l = mxCalloc(1,sizeof(gfi_array_list));
l->arg.arg_len = nrhs;
l->arg.arg_val = mxCalloc(nrhs, sizeof(gfi_array));
for (i=0; i < nrhs; ++i) {
if (mxarray_to_gfi_array(prhs[i], &l->arg.arg_val[i]) != 0) return NULL;
}
return l;
}
#ifndef WIN32
struct sigaction old_sigint;
#endif
static int sigint_hit = 0;
static getfem_sigint_handler_t sigint_callback;
static void sigint(int sig) {
sigint_callback(sig);
remove_custom_sigint(0);
sigint_hit++;
}
void install_custom_sigint(getfem_sigint_handler_t h) {
#ifndef WIN32 /* matlab on win does not use signals so.. */
struct sigaction new_sigint;
new_sigint.sa_handler = sigint;
sigint_callback = h;
sigemptyset(&new_sigint.sa_mask);
new_sigint.sa_flags = 0;
sigaction (SIGINT, NULL, &old_sigint);
if (old_sigint.sa_handler != SIG_IGN)
sigaction(SIGINT, &new_sigint, NULL);
sigint_hit = 0;
#endif
}
void remove_custom_sigint(int allow_rethrow) {
#ifndef WIN32
struct sigaction act;
sigaction (SIGINT, NULL, &act);
if (act.sa_handler == sigint) {
sigaction(SIGINT, &old_sigint, NULL);
}
if (allow_rethrow && sigint_hit) {
fprintf(stderr, "ready, raising SIGINT now\n");
raise(SIGINT);
}
sigint_hit = 0;
#endif
}
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https://mail.gna.org/listinfo/getfem-users
