Index: /issm/trunk/externalpackages/chaco/chaco_README.txt
===================================================================
--- /issm/trunk/externalpackages/chaco/chaco_README.txt	(revision 2972)
+++ /issm/trunk/externalpackages/chaco/chaco_README.txt	(revision 2972)
@@ -0,0 +1,55 @@
+Chaco-2.2.tar (5/03/00? -- 2.0 was 2/95)
+http://www.sandia.gov/~bahendr/chaco.html
+
+
+Note that meshpart pulls the object files from here, compiled with
+the MATLAB flag for use in the mlchaco mex function, and assembles
+them into a library in its own directory.  This means that any
+objects compiled for the mlchaco mex function and left here should
+not be used for the stand-alone chaco executable, and vice versa.
+
+
+[jschierm@astrid main]$ diff defs_old.h defs.h
+11a12,27  [for running as a matlab mex function]
+> 
+> #ifdef MATLAB
+>     #include "mat.h"
+>     #include "mex.h"
+>     #include "matrix.h"
+>    
+>     #define printf mexPrintf
+>     #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__))
+>     #define malloc mxMalloc
+>     #define calloc mxCalloc
+>     #define realloc mxRealloc
+>     #define free mxFree
+> 
+>     #define check_graph chaco_check_graph
+> #endif
+> 
+
+
+added #include "defs.h" to the following:
+assign/assign_out.c
+eigen/get_extval.c
+klvspiff/matching.c
+misc/timing.c
+util/bail.c
+util/checkpnt.c
+util/doubleout.c
+util/smalloc.c
+util/strout.c
+
+
+[jschierm@astrid code]$ diff Makefile_old Makefile
+4,5c4,9  [fPIC required, CFLAGS and OFLAGS copied from Cielo gccopts_v75.sh for glnxa64]
+< IFLAG =               -Imain
+< CFLAGS =      -O2
+---
+> IFLAG =               -Imain -I/usr/local/pkgs/matlab-7.6/extern/include
+> #CFLAGS =     -O2
+> #OFLAGS =     -O2
+> #CFLAGS =     -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions
+> CFLAGS =      -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB
+> #CFLAGS =     -fPIC -fno-omit-frame-pointer -pthread -fexceptions
+
Index: /issm/trunk/externalpackages/chaco/chaco_jes_notes.txt
===================================================================
--- /issm/trunk/externalpackages/chaco/chaco_jes_notes.txt	(revision 2972)
+++ /issm/trunk/externalpackages/chaco/chaco_jes_notes.txt	(revision 2972)
@@ -0,0 +1,81 @@
+7/13/09:
+
+[jschierm@astrid Chaco-2.2]$ diff ../chaco/code/Makefile code
+5,6c5,8  [fPIC required, CFLAGS and OFLAGS copied from Cielo gccopts_v75.sh for glnxa64]
+< CFLAGS =      -O2
+< OFLAGS =      -O2
+---
+> #CFLAGS =     -O2
+> #OFLAGS =     -O2
+> CFLAGS =      -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions
+> OFLAGS =      -O -DNDEBUG
+34a37,38  [added for meshpart chaco.a library, specified by its makefile]
+>               coarsen/makecgraph.c \
+>               coarsen/countcedges.c \
+
+7/30/09:
+
+[jschierm@astrid main]$ diff defs_old.h defs.h
+11a12,26  [for running as a matlab mex function]
+> 
+> #ifdef MATLAB
+>     #include "mat.h"
+>     #include "mex.h"
+>     #include "matrix.h"
+>    
+>     #define printf mexPrintf
+>     #define malloc mxMalloc
+>     #define calloc mxCalloc
+>     #define realloc mxRealloc
+>     #define free mxFree
+> 
+>     #define check_graph chaco_check_graph
+> #endif
+> 
+
+added #include "defs.h" to the following:
+assign/assign_out.c
+eigen/get_extval.c
+klvspiff/matching.c
+misc/timing.c
+util/bail.c
+util/checkpnt.c
+util/doubleout.c
+util/smalloc.c
+util/strout.c
+
+[jschierm@astrid code]$ diff Makefile_old Makefile | more
+4,5c4,9
+< IFLAG =               -Imain
+< CFLAGS =      -O2
+---
+> IFLAG =               -Imain -I/usr/local/pkgs/matlab-7.6/extern/include
+> #CFLAGS =     -O2
+> #OFLAGS =     -O2
+> #CFLAGS =     -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread
+> -fexceptions
+> CFLAGS =      -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB
+> #CFLAGS =     -fPIC -fno-omit-frame-pointer -pthread -fexceptions
+
+8/25/09:
+
+added macro for fprintf to capture missing output:
+[jschierm@astrid main]$ diff defs_old.h defs.h
+11a12,27
+> 
+> #ifdef MATLAB
+>     #include "mat.h"
+>     #include "mex.h"
+>     #include "matrix.h"
+>    
+>     #define printf mexPrintf
+>     #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__))
+>     #define malloc mxMalloc
+>     #define calloc mxCalloc
+>     #define realloc mxRealloc
+>     #define free mxFree
+> 
+>     #define check_graph chaco_check_graph
+> #endif
+> 
+