Index: sm/trunk/externalpackages/chaco/mex/mlchaco_README.txt
===================================================================
--- /issm/trunk/externalpackages/chaco/mex/mlchaco_README.txt	(revision 4632)
+++ 	(revision )
@@ -1,136 +1,0 @@
-mlchaco (from meshpartdist.tar, 2/08/02)
-http://www.cerfacs.fr/algor/Softs/MESHPART/
-
-
-[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c
-34a35  [CLK_TCK undefined, so use CLOCKS_PER_SEC]
-> #include <time.h>      /*  CLOCKS_PER_SEC  */
-56,61c57,62  [update for current Matlab]
-< void mexFunction(    
-<     int         nlhs,           /* number of expected outputs */
-<     Matrix      *plhs[],        /* matrix pointer array returning outputs */
-<     int         nrhs,           /* number of inputs */
-<     Matrix      *prhs[]         /* matrix pointer array for inputs */
-<     )
----
-> void mexFunction(
->     int           nlhs,           /* number of expected outputs */
->     mxArray       *plhs[],        /* array of pointers to output arguments
->     */
->     int           nrhs,           /* number of inputs */
->     const mxArray *prhs[]         /* array of pointers to input arguments */
-> )
-87a89  [update for current Matlab]
->     mwIndex *mwstart,*mwadjacency;
-104c106,110  [update for current Matlab]
-<     start = mxGetJc(A_in);
----
-> /*    start = mxGetJc(A_in);*/
->     mwstart = mxGetJc(A_in);
->     start = mxMalloc((mxGetN(A_in)+1)*sizeof(int));
->     for (i=0; i<(mxGetN(A_in)+1); i++)
->         start[i]= (int)mwstart[i];
-106c112,116  [update for current Matlab]
-<     adjacency = mxGetIr(A_in);
----
-> /*    adjacency = mxGetIr(A_in);*/
->     mwadjacency = mxGetIr(A_in);
->     adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int));
->     for (i=0; i<mxGetNzmax(A_in); i++)
->         adjacency[i]= (int)mwadjacency[i];
-131,132c141,144  [provide default filenames, since no way to input]
-<     outassignname = NULL;
-<     outfilename = NULL;
----
-> /*    outassignname = NULL;
->     outfilename = NULL;*/
->     outassignname = "chaco_assign.txt";
->     outfilename = "chaco_out.txt";
-169c181  [update for current Matlab]
-<       plhs [1] = mxCreateFull (1, 1, REAL) ;
----
->       plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ;
-173c185  [CLK_TCK undefined, so use CLOCKS_PER_SEC]
-<       ((double) CLK_TCK) ;
----
->       ((double) CLOCKS_PER_SEC) ;
-179c191  [update for current Matlab]
-<         map_out = mxCreateFull(1,nvtxs,REAL);
----
->         map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL);
-185a198,199  [update for current Matlab]
->     if (start != NULL) mxFree((char *) start);
->     if (adjacency != NULL) mxFree((char *) adjacency);
-
-
-[jschierm@astrid chaco]$ diff Makefile_old Makefile
-27c27,28  [current Matlab location]
-< MATLAB =        /usr/local/libexec/matlab
----
-> #MATLAB =        /usr/local/libexec/matlab
-> MATLAB =        /usr/local/pkgs/matlab-7.6
-30c31,32  [current Chaco 2.2 location]
-< CHACO =         ../../Chaco-2.0/code
----
-> #CHACO =         ../../Chaco-2.0/code
-> CHACO =         ../../Chaco-2.2/code
-34,35c36,37  [use gcc instead of cc]
-< #CC =            gcc 
-< CC =            cc 
----
-> CC =            gcc 
-> #CC =            cc 
-37c39,40  [add MATLAB flag to compile for mex-function]
-< CFLAGS =        -Xa -G -xO4 -xcg92
----
-> #CFLAGS =        -Xa -G -xO4 -xcg92
-> CFLAGS =        -Xa -G -xO4 -xcg92 -DMATLAB
-39,40c42,45  [current function locations]
-< AR =             /usr/ccs/bin/ar rcv   # for solaris 2
-< RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
----
-> #AR =             /usr/ccs/bin/ar rcv   # for solaris 2
-> AR =             /usr/bin/ar rcv   # for solaris 2
-> #RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
-> RANLIB =         /usr/bin/ranlib   # for solaris 2
-45,47d49  [use Chaco versions with MATLAB switch rather than local versions]
-<               ${MLCHACO}/chaco_check_graph.c \
-<               ${MLCHACO}/check_input.c \
-<                 ${MLCHACO}/smalloc.c \
-48a51,53
-> #             ${MLCHACO}/chaco_check_graph.c \
-> #             ${MLCHACO}/check_input.c \
-> #                ${MLCHACO}/smalloc.c \
-55a61  [update CHLIST to match Chaco 2.2]
->               ${CHACO}/input/check_input.c \
-61a68  [update CHLIST to match Chaco 2.2]
->               ${CHACO}/graph/check_graph.c \
-91a99  [update CHLIST to match Chaco 2.2]
->               ${CHACO}/klvspiff/flow.c \
-97a106  [update CHLIST to match Chaco 2.2]
->               ${CHACO}/klvspiff/flatten.c \
-100c109,110  [update CHLIST to match Chaco 2.2]
-<               ${CHACO}/coarsen/makecgraph.c \
----
->               ${CHACO}/coarsen/makefgraph.c \
->               ${CHACO}/coarsen/makeccoords.c \
-102d111  [update CHLIST to match Chaco 2.2]
-<               ${CHACO}/coarsen/countcedges.c \
-108a118  [update CHLIST to match Chaco 2.2]
->               ${CHACO}/coarsen/maxmatch5.c \
-234a245  [update CHLIST to match Chaco 2.2]
->               ${CHACO}/util/smalloc.c \
-245a257,258  [use local versions rather than Chaco versions (added for clarity)]
-> #             ${CHACO}/main/user_params.c \
-> #             ${CHACO}/util/bail.c \
-254a268,271  [update for current mex]
-> #mlchaco:     ${MLFILES.c} chaco.a Makefile
-> #             mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
-> #             mv mlchaco.mex* ${DEST_DIR}
-> 
-256c273  [update for current mex]
-<               mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
----
->               mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c}
->               chaco.a -I${CHACO}/main
-
Index: sm/trunk/externalpackages/chaco/mex/mlchaco_jes_notes.txt
===================================================================
--- /issm/trunk/externalpackages/chaco/mex/mlchaco_jes_notes.txt	(revision 4632)
+++ 	(revision )
@@ -1,182 +1,0 @@
-7/15/09:
-
-[jschierm@astrid chaco]$ diff Makefile_old Makefile
-27c27,28
-< MATLAB =        /usr/local/libexec/matlab
----
-> #MATLAB =        /usr/local/libexec/matlab
-> MATLAB =        /usr/local/matlab780
-30c31,32
-< CHACO =         ../../Chaco-2.0/code
----
-> #CHACO =         ../../Chaco-2.0/code
-> CHACO =         ../../Chaco-2.2/code
-34,35c36,37
-< #CC =            gcc 
-< CC =            cc 
----
-> CC =            gcc 
-> #CC =            cc 
-39,40c41,44
-< AR =             /usr/ccs/bin/ar rcv   # for solaris 2
-< RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
----
-> #AR =             /usr/ccs/bin/ar rcv   # for solaris 2
-> AR =             /usr/bin/ar rcv   # for solaris 2
-> #RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
-> RANLIB =         /usr/bin/ranlib   # for solaris 2
-91a96,97  [missing symbols]
->               ${CHACO}/klvspiff/flatten.c \
->               ${CHACO}/klvspiff/flow.c \
-99a106  [missing symbols]
->               ${CHACO}/coarsen/makeccoords.c \
-102a110  [missing symbols]
->               ${CHACO}/coarsen/makefgraph.c \
-108a117  [missing symbols]
->               ${CHACO}/coarsen/maxmatch5.c \
-254a264,267
-> #mlchaco:     ${MLFILES.c} chaco.a Makefile
-> #             mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
-> #             mv mlchaco.mex* ${DEST_DIR}
-> 
-256c269
-<               mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
----
->               mex -output mlchaco -largeArrayDims ${MLFILES.c} chaco.a -I${CHACO}/main
-
-[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c
-34a35
-> #include <time.h>      /*  CLOCKS_PER_SEC  */
-56,61c57,62
-< void mexFunction(    
-<     int         nlhs,           /* number of expected outputs */
-<     Matrix      *plhs[],        /* matrix pointer array returning outputs */
-<     int         nrhs,           /* number of inputs */
-<     Matrix      *prhs[]         /* matrix pointer array for inputs */
-<     )
----
-> void mexFunction(
->     int           nlhs,           /* number of expected outputs */
->     mxArray       *plhs[],        /* array of pointers to output arguments
->     */
->     int           nrhs,           /* number of inputs */
->     const mxArray *prhs[]         /* array of pointers to input arguments */
-> )
-87a89
->     mwIndex *mwstart,*mwadjacency;
-104c106,110
-<     start = mxGetJc(A_in);
----
-> /*    start = mxGetJc(A_in);*/
->     mwstart = mxGetJc(A_in);
->     start = mxMalloc((mxGetN(A_in)+1)*sizeof(int));
->     for (i=0; i<(mxGetN(A_in)+1); i++)
->         start[i]= (int)mwstart[i];
-106c112,116
-<     adjacency = mxGetIr(A_in);
----
-> /*    adjacency = mxGetIr(A_in);*/
->     mwadjacency = mxGetIr(A_in);
->     adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int));
->     for (i=0; i<mxGetNzmax(A_in); i++)
->         adjacency[i]= (int)mwadjacency[i];
-169c181
-<       plhs [1] = mxCreateFull (1, 1, REAL) ;
----
->       plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ;
-173c185
-<       ((double) CLK_TCK) ;
----
->       ((double) CLOCKS_PER_SEC) ;
-179c191
-<         map_out = mxCreateFull(1,nvtxs,REAL);
----
->         map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL);
-185a198,199
->     if (start != NULL) mxFree((char *) start);
->     if (adjacency != NULL) mxFree((char *) adjacency);
-
-
-7/29/09:
-
-[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c
-131,132c141,144
-<     outassignname = NULL;
-<     outfilename = NULL;
----
-> /*    outassignname = NULL;
->     outfilename = NULL;*/
->     outassignname = "chaco_assign.txt";
->     outfilename = "chaco_out.txt";
-
-7/30/09:
-
-[jschierm@astrid chaco]$ diff Makefile_old Makefile
-27c27,28
-< MATLAB =        /usr/local/libexec/matlab
----
-> #MATLAB =        /usr/local/libexec/matlab
-> MATLAB =        /usr/local/pkgs/matlab-7.6
-37c39,40
-< CFLAGS =        -Xa -G -xO4 -xcg92
----
-> #CFLAGS =        -Xa -G -xO4 -xcg92
-> CFLAGS =        -Xa -G -xO4 -xcg92 -DMATLAB
-45,47d49  [using Chaco versions with MATLAB switch]
-<               ${MLCHACO}/chaco_check_graph.c \
-<               ${MLCHACO}/check_input.c \
-<                 ${MLCHACO}/smalloc.c \
-48a51,53
-> #             ${MLCHACO}/chaco_check_graph.c \
-> #             ${MLCHACO}/check_input.c \
-> #                ${MLCHACO}/smalloc.c \
-55a61
->               ${CHACO}/input/check_input.c \
-61a68
->               ${CHACO}/graph/check_graph.c \
-91a99  [compared CHFILES with Chaco Makefile CHFILES]
->               ${CHACO}/klvspiff/flow.c \
-97a106  [compared CHFILES with Chaco Makefile CHFILES]
->               ${CHACO}/klvspiff/flatten.c \
-100c109,110  [compared CHFILES with Chaco Makefile CHFILES]
-<               ${CHACO}/coarsen/makecgraph.c \
----
->               ${CHACO}/coarsen/makefgraph.c \
->               ${CHACO}/coarsen/makeccoords.c \
-102d111  [compared CHFILES with Chaco Makefile CHFILES]
-<               ${CHACO}/coarsen/countcedges.c \
-108a118  [compared CHFILES with Chaco Makefile CHFILES]
->               ${CHACO}/coarsen/maxmatch5.c \
-234a245
->               ${CHACO}/util/smalloc.c \
-245a257,258
-> #             ${CHACO}/main/user_params.c \
-> #             ${CHACO}/util/bail.c \
-254a268,271
-> #mlchaco:     ${MLFILES.c} chaco.a Makefile
-> #             mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
-> #             mv mlchaco.mex* ${DEST_DIR}
-> 
-256c273
-<               mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
----
->               mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c}
->               chaco.a -I${CHACO}/main
-
-5/25/10:
-
-- reorganized chaco.m and mlchaco.c drivers into Chaco.c matlab-layer (independent of chaco) and Chacox.c x-layer (independent of matlab).
-
-5/26/10:
-
-- added mexchaco target to Makefile (and related changes).
-
-5/27/10
-
-- added define for exit(status) to ${CHACO}/main/defs.h so that local bail.c is
-  unnecessary.
-
-6/15/10:
-
-- separated chaco x-layer from meshpart build.
-
Index: /issm/trunk/externalpackages/chaco/mlchaco_README.txt
===================================================================
--- /issm/trunk/externalpackages/chaco/mlchaco_README.txt	(revision 4633)
+++ /issm/trunk/externalpackages/chaco/mlchaco_README.txt	(revision 4633)
@@ -0,0 +1,136 @@
+mlchaco (from meshpartdist.tar, 2/08/02)
+http://www.cerfacs.fr/algor/Softs/MESHPART/
+
+
+[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c
+34a35  [CLK_TCK undefined, so use CLOCKS_PER_SEC]
+> #include <time.h>      /*  CLOCKS_PER_SEC  */
+56,61c57,62  [update for current Matlab]
+< void mexFunction(    
+<     int         nlhs,           /* number of expected outputs */
+<     Matrix      *plhs[],        /* matrix pointer array returning outputs */
+<     int         nrhs,           /* number of inputs */
+<     Matrix      *prhs[]         /* matrix pointer array for inputs */
+<     )
+---
+> void mexFunction(
+>     int           nlhs,           /* number of expected outputs */
+>     mxArray       *plhs[],        /* array of pointers to output arguments
+>     */
+>     int           nrhs,           /* number of inputs */
+>     const mxArray *prhs[]         /* array of pointers to input arguments */
+> )
+87a89  [update for current Matlab]
+>     mwIndex *mwstart,*mwadjacency;
+104c106,110  [update for current Matlab]
+<     start = mxGetJc(A_in);
+---
+> /*    start = mxGetJc(A_in);*/
+>     mwstart = mxGetJc(A_in);
+>     start = mxMalloc((mxGetN(A_in)+1)*sizeof(int));
+>     for (i=0; i<(mxGetN(A_in)+1); i++)
+>         start[i]= (int)mwstart[i];
+106c112,116  [update for current Matlab]
+<     adjacency = mxGetIr(A_in);
+---
+> /*    adjacency = mxGetIr(A_in);*/
+>     mwadjacency = mxGetIr(A_in);
+>     adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int));
+>     for (i=0; i<mxGetNzmax(A_in); i++)
+>         adjacency[i]= (int)mwadjacency[i];
+131,132c141,144  [provide default filenames, since no way to input]
+<     outassignname = NULL;
+<     outfilename = NULL;
+---
+> /*    outassignname = NULL;
+>     outfilename = NULL;*/
+>     outassignname = "chaco_assign.txt";
+>     outfilename = "chaco_out.txt";
+169c181  [update for current Matlab]
+<       plhs [1] = mxCreateFull (1, 1, REAL) ;
+---
+>       plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ;
+173c185  [CLK_TCK undefined, so use CLOCKS_PER_SEC]
+<       ((double) CLK_TCK) ;
+---
+>       ((double) CLOCKS_PER_SEC) ;
+179c191  [update for current Matlab]
+<         map_out = mxCreateFull(1,nvtxs,REAL);
+---
+>         map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL);
+185a198,199  [update for current Matlab]
+>     if (start != NULL) mxFree((char *) start);
+>     if (adjacency != NULL) mxFree((char *) adjacency);
+
+
+[jschierm@astrid chaco]$ diff Makefile_old Makefile
+27c27,28  [current Matlab location]
+< MATLAB =        /usr/local/libexec/matlab
+---
+> #MATLAB =        /usr/local/libexec/matlab
+> MATLAB =        /usr/local/pkgs/matlab-7.6
+30c31,32  [current Chaco 2.2 location]
+< CHACO =         ../../Chaco-2.0/code
+---
+> #CHACO =         ../../Chaco-2.0/code
+> CHACO =         ../../Chaco-2.2/code
+34,35c36,37  [use gcc instead of cc]
+< #CC =            gcc 
+< CC =            cc 
+---
+> CC =            gcc 
+> #CC =            cc 
+37c39,40  [add MATLAB flag to compile for mex-function]
+< CFLAGS =        -Xa -G -xO4 -xcg92
+---
+> #CFLAGS =        -Xa -G -xO4 -xcg92
+> CFLAGS =        -Xa -G -xO4 -xcg92 -DMATLAB
+39,40c42,45  [current function locations]
+< AR =             /usr/ccs/bin/ar rcv   # for solaris 2
+< RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
+---
+> #AR =             /usr/ccs/bin/ar rcv   # for solaris 2
+> AR =             /usr/bin/ar rcv   # for solaris 2
+> #RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
+> RANLIB =         /usr/bin/ranlib   # for solaris 2
+45,47d49  [use Chaco versions with MATLAB switch rather than local versions]
+<               ${MLCHACO}/chaco_check_graph.c \
+<               ${MLCHACO}/check_input.c \
+<                 ${MLCHACO}/smalloc.c \
+48a51,53
+> #             ${MLCHACO}/chaco_check_graph.c \
+> #             ${MLCHACO}/check_input.c \
+> #                ${MLCHACO}/smalloc.c \
+55a61  [update CHLIST to match Chaco 2.2]
+>               ${CHACO}/input/check_input.c \
+61a68  [update CHLIST to match Chaco 2.2]
+>               ${CHACO}/graph/check_graph.c \
+91a99  [update CHLIST to match Chaco 2.2]
+>               ${CHACO}/klvspiff/flow.c \
+97a106  [update CHLIST to match Chaco 2.2]
+>               ${CHACO}/klvspiff/flatten.c \
+100c109,110  [update CHLIST to match Chaco 2.2]
+<               ${CHACO}/coarsen/makecgraph.c \
+---
+>               ${CHACO}/coarsen/makefgraph.c \
+>               ${CHACO}/coarsen/makeccoords.c \
+102d111  [update CHLIST to match Chaco 2.2]
+<               ${CHACO}/coarsen/countcedges.c \
+108a118  [update CHLIST to match Chaco 2.2]
+>               ${CHACO}/coarsen/maxmatch5.c \
+234a245  [update CHLIST to match Chaco 2.2]
+>               ${CHACO}/util/smalloc.c \
+245a257,258  [use local versions rather than Chaco versions (added for clarity)]
+> #             ${CHACO}/main/user_params.c \
+> #             ${CHACO}/util/bail.c \
+254a268,271  [update for current mex]
+> #mlchaco:     ${MLFILES.c} chaco.a Makefile
+> #             mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
+> #             mv mlchaco.mex* ${DEST_DIR}
+> 
+256c273  [update for current mex]
+<               mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
+---
+>               mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c}
+>               chaco.a -I${CHACO}/main
+
Index: /issm/trunk/externalpackages/chaco/mlchaco_jes_notes.txt
===================================================================
--- /issm/trunk/externalpackages/chaco/mlchaco_jes_notes.txt	(revision 4633)
+++ /issm/trunk/externalpackages/chaco/mlchaco_jes_notes.txt	(revision 4633)
@@ -0,0 +1,182 @@
+7/15/09:
+
+[jschierm@astrid chaco]$ diff Makefile_old Makefile
+27c27,28
+< MATLAB =        /usr/local/libexec/matlab
+---
+> #MATLAB =        /usr/local/libexec/matlab
+> MATLAB =        /usr/local/matlab780
+30c31,32
+< CHACO =         ../../Chaco-2.0/code
+---
+> #CHACO =         ../../Chaco-2.0/code
+> CHACO =         ../../Chaco-2.2/code
+34,35c36,37
+< #CC =            gcc 
+< CC =            cc 
+---
+> CC =            gcc 
+> #CC =            cc 
+39,40c41,44
+< AR =             /usr/ccs/bin/ar rcv   # for solaris 2
+< RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
+---
+> #AR =             /usr/ccs/bin/ar rcv   # for solaris 2
+> AR =             /usr/bin/ar rcv   # for solaris 2
+> #RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
+> RANLIB =         /usr/bin/ranlib   # for solaris 2
+91a96,97  [missing symbols]
+>               ${CHACO}/klvspiff/flatten.c \
+>               ${CHACO}/klvspiff/flow.c \
+99a106  [missing symbols]
+>               ${CHACO}/coarsen/makeccoords.c \
+102a110  [missing symbols]
+>               ${CHACO}/coarsen/makefgraph.c \
+108a117  [missing symbols]
+>               ${CHACO}/coarsen/maxmatch5.c \
+254a264,267
+> #mlchaco:     ${MLFILES.c} chaco.a Makefile
+> #             mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
+> #             mv mlchaco.mex* ${DEST_DIR}
+> 
+256c269
+<               mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
+---
+>               mex -output mlchaco -largeArrayDims ${MLFILES.c} chaco.a -I${CHACO}/main
+
+[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c
+34a35
+> #include <time.h>      /*  CLOCKS_PER_SEC  */
+56,61c57,62
+< void mexFunction(    
+<     int         nlhs,           /* number of expected outputs */
+<     Matrix      *plhs[],        /* matrix pointer array returning outputs */
+<     int         nrhs,           /* number of inputs */
+<     Matrix      *prhs[]         /* matrix pointer array for inputs */
+<     )
+---
+> void mexFunction(
+>     int           nlhs,           /* number of expected outputs */
+>     mxArray       *plhs[],        /* array of pointers to output arguments
+>     */
+>     int           nrhs,           /* number of inputs */
+>     const mxArray *prhs[]         /* array of pointers to input arguments */
+> )
+87a89
+>     mwIndex *mwstart,*mwadjacency;
+104c106,110
+<     start = mxGetJc(A_in);
+---
+> /*    start = mxGetJc(A_in);*/
+>     mwstart = mxGetJc(A_in);
+>     start = mxMalloc((mxGetN(A_in)+1)*sizeof(int));
+>     for (i=0; i<(mxGetN(A_in)+1); i++)
+>         start[i]= (int)mwstart[i];
+106c112,116
+<     adjacency = mxGetIr(A_in);
+---
+> /*    adjacency = mxGetIr(A_in);*/
+>     mwadjacency = mxGetIr(A_in);
+>     adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int));
+>     for (i=0; i<mxGetNzmax(A_in); i++)
+>         adjacency[i]= (int)mwadjacency[i];
+169c181
+<       plhs [1] = mxCreateFull (1, 1, REAL) ;
+---
+>       plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ;
+173c185
+<       ((double) CLK_TCK) ;
+---
+>       ((double) CLOCKS_PER_SEC) ;
+179c191
+<         map_out = mxCreateFull(1,nvtxs,REAL);
+---
+>         map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL);
+185a198,199
+>     if (start != NULL) mxFree((char *) start);
+>     if (adjacency != NULL) mxFree((char *) adjacency);
+
+
+7/29/09:
+
+[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c
+131,132c141,144
+<     outassignname = NULL;
+<     outfilename = NULL;
+---
+> /*    outassignname = NULL;
+>     outfilename = NULL;*/
+>     outassignname = "chaco_assign.txt";
+>     outfilename = "chaco_out.txt";
+
+7/30/09:
+
+[jschierm@astrid chaco]$ diff Makefile_old Makefile
+27c27,28
+< MATLAB =        /usr/local/libexec/matlab
+---
+> #MATLAB =        /usr/local/libexec/matlab
+> MATLAB =        /usr/local/pkgs/matlab-7.6
+37c39,40
+< CFLAGS =        -Xa -G -xO4 -xcg92
+---
+> #CFLAGS =        -Xa -G -xO4 -xcg92
+> CFLAGS =        -Xa -G -xO4 -xcg92 -DMATLAB
+45,47d49  [using Chaco versions with MATLAB switch]
+<               ${MLCHACO}/chaco_check_graph.c \
+<               ${MLCHACO}/check_input.c \
+<                 ${MLCHACO}/smalloc.c \
+48a51,53
+> #             ${MLCHACO}/chaco_check_graph.c \
+> #             ${MLCHACO}/check_input.c \
+> #                ${MLCHACO}/smalloc.c \
+55a61
+>               ${CHACO}/input/check_input.c \
+61a68
+>               ${CHACO}/graph/check_graph.c \
+91a99  [compared CHFILES with Chaco Makefile CHFILES]
+>               ${CHACO}/klvspiff/flow.c \
+97a106  [compared CHFILES with Chaco Makefile CHFILES]
+>               ${CHACO}/klvspiff/flatten.c \
+100c109,110  [compared CHFILES with Chaco Makefile CHFILES]
+<               ${CHACO}/coarsen/makecgraph.c \
+---
+>               ${CHACO}/coarsen/makefgraph.c \
+>               ${CHACO}/coarsen/makeccoords.c \
+102d111  [compared CHFILES with Chaco Makefile CHFILES]
+<               ${CHACO}/coarsen/countcedges.c \
+108a118  [compared CHFILES with Chaco Makefile CHFILES]
+>               ${CHACO}/coarsen/maxmatch5.c \
+234a245
+>               ${CHACO}/util/smalloc.c \
+245a257,258
+> #             ${CHACO}/main/user_params.c \
+> #             ${CHACO}/util/bail.c \
+254a268,271
+> #mlchaco:     ${MLFILES.c} chaco.a Makefile
+> #             mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
+> #             mv mlchaco.mex* ${DEST_DIR}
+> 
+256c273
+<               mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main
+---
+>               mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c}
+>               chaco.a -I${CHACO}/main
+
+5/25/10:
+
+- reorganized chaco.m and mlchaco.c drivers into Chaco.c matlab-layer (independent of chaco) and Chacox.c x-layer (independent of matlab).
+
+5/26/10:
+
+- added mexchaco target to Makefile (and related changes).
+
+5/27/10
+
+- added define for exit(status) to ${CHACO}/main/defs.h so that local bail.c is
+  unnecessary.
+
+6/15/10:
+
+- separated chaco x-layer from meshpart build.
+