Index: sm/trunk/externalpackages/chaco/Makefile.patch =================================================================== --- /issm/trunk/externalpackages/chaco/Makefile.patch (revision 3010) +++ (revision ) @@ -1,8 +1,0 @@ -5c5,9 -< CFLAGS = -O2 ---- -> #IFLAG = -Imain -I/usr/local/pkgs/matlab-7.8/extern/include -> #CFLAGS = -O2 -> #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions -> CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -> #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB Index: sm/trunk/externalpackages/chaco/assign_out.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/assign_out.c.patch (revision 3010) +++ (revision ) @@ -1,2 +1,0 @@ -5a6 -> #include "defs.h" Index: sm/trunk/externalpackages/chaco/bail.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/bail.c.patch (revision 3010) +++ (revision ) @@ -1,2 +1,0 @@ -6a7 -> #include "defs.h" Index: /issm/trunk/externalpackages/chaco/chaco.patch =================================================================== --- /issm/trunk/externalpackages/chaco/chaco.patch (revision 3011) +++ /issm/trunk/externalpackages/chaco/chaco.patch (revision 3011) @@ -0,0 +1,171 @@ +Only in /home/jschierm/Libs/Chaco-2.2: chaco_jes_notes.txt +Only in /home/jschierm/Libs/Chaco-2.2: chaco_README.txt +diff -rc src/code/assign/assign_out.c /home/jschierm/Libs/Chaco-2.2/code/assign/assign_out.c +*** src/code/assign/assign_out.c 1995-08-08 14:32:10.000000000 -0700 +--- /home/jschierm/Libs/Chaco-2.2/code/assign/assign_out.c 2009-07-30 09:37:34.781348564 -0700 +*************** +*** 3,8 **** +--- 3,9 ---- + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include ++ #include "defs.h" + + static void assign_out_normal(), assign_out_inv(); + +diff -rc src/code/eigen/get_extval.c /home/jschierm/Libs/Chaco-2.2/code/eigen/get_extval.c +*** src/code/eigen/get_extval.c 1995-08-08 14:32:20.000000000 -0700 +--- /home/jschierm/Libs/Chaco-2.2/code/eigen/get_extval.c 2009-07-30 09:43:00.511686903 -0700 +*************** +*** 4,9 **** +--- 4,10 ---- + + #include + #include ++ #include "defs.h" + + /* Finds first extended eigenpair of system corresponding to + tridiagonal T using using Rafael's bisection technique. */ +diff -rc src/code/klvspiff/matching.c /home/jschierm/Libs/Chaco-2.2/code/klvspiff/matching.c +*** src/code/klvspiff/matching.c 1996-03-11 10:24:25.000000000 -0800 +--- /home/jschierm/Libs/Chaco-2.2/code/klvspiff/matching.c 2009-07-30 09:43:11.604702814 -0700 +*************** +*** 6,11 **** +--- 6,12 ---- + code provided by Ed Rothberg at SGI. */ + + #include ++ #include "defs.h" + + #define TRUE 1 + #define FALSE 0 +diff -rc src/code/main/defs.h /home/jschierm/Libs/Chaco-2.2/code/main/defs.h +*** src/code/main/defs.h 1995-08-08 14:32:41.000000000 -0700 +--- /home/jschierm/Libs/Chaco-2.2/code/main/defs.h 2009-08-25 10:02:57.088970763 -0700 +*************** +*** 9,11 **** +--- 9,27 ---- + #define PI 3.141592653589793 + #define TWOPI 6.283185307179586 + #define HALFPI 1.570796326794896 ++ ++ #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 ++ +Only in /home/jschierm/Libs/Chaco-2.2/code/main: defs_old.h +diff -rc src/code/Makefile /home/jschierm/Libs/Chaco-2.2/code/Makefile +*** src/code/Makefile 1997-10-02 10:23:22.000000000 -0700 +--- /home/jschierm/Libs/Chaco-2.2/code/Makefile 2010-02-10 14:05:56.986149785 -0800 +*************** +*** 2,8 **** + DEST= ${DEST_DIR}/chaco + CC = gcc + IFLAG = -Imain +! CFLAGS = -O2 + OFLAGS = -O2 + + FILES.c= main/user_params.c main/interface.c main/main.c \ +--- 2,13 ---- + DEST= ${DEST_DIR}/chaco + CC = gcc + IFLAG = -Imain +! #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 +! #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB + OFLAGS = -O2 + + FILES.c= main/user_params.c main/interface.c main/main.c \ +Only in /home/jschierm/Libs/Chaco-2.2/code: Makefile_old +diff -rc src/code/misc/timing.c /home/jschierm/Libs/Chaco-2.2/code/misc/timing.c +*** src/code/misc/timing.c 1997-01-03 09:10:52.000000000 -0800 +--- /home/jschierm/Libs/Chaco-2.2/code/misc/timing.c 2009-07-30 09:43:19.954714766 -0700 +*************** +*** 3,8 **** +--- 3,9 ---- + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include ++ #include "defs.h" + + /* Timing parameters. */ + +diff -rc src/code/util/bail.c /home/jschierm/Libs/Chaco-2.2/code/util/bail.c +*** src/code/util/bail.c 1995-08-08 14:33:01.000000000 -0700 +--- /home/jschierm/Libs/Chaco-2.2/code/util/bail.c 2009-07-30 09:43:24.495721262 -0700 +*************** +*** 4,9 **** +--- 4,10 ---- + + #include + #include ++ #include "defs.h" + + /* Wrapper for exit() - print message and exit with status code. Exit code + of 0 indicates normal termination. Exit code of 1 indicates early +diff -rc src/code/util/checkpnt.c /home/jschierm/Libs/Chaco-2.2/code/util/checkpnt.c +*** src/code/util/checkpnt.c 1995-08-08 14:33:01.000000000 -0700 +--- /home/jschierm/Libs/Chaco-2.2/code/util/checkpnt.c 2009-07-30 09:43:28.190726549 -0700 +*************** +*** 4,9 **** +--- 4,10 ---- + + #include + #include ++ #include "defs.h" + + /* Debug break point. */ + void checkpnt(tag) +diff -rc src/code/util/doubleout.c /home/jschierm/Libs/Chaco-2.2/code/util/doubleout.c +*** src/code/util/doubleout.c 1995-08-08 14:33:02.000000000 -0700 +--- /home/jschierm/Libs/Chaco-2.2/code/util/doubleout.c 2009-07-30 09:43:34.192735135 -0700 +*************** +*** 3,8 **** +--- 3,9 ---- + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include ++ #include "defs.h" + + /* Print a double precision number with filtering format to screen. */ + void doubleout(number, mode) +diff -rc src/code/util/smalloc.c /home/jschierm/Libs/Chaco-2.2/code/util/smalloc.c +*** src/code/util/smalloc.c 1996-03-11 10:44:07.000000000 -0800 +--- /home/jschierm/Libs/Chaco-2.2/code/util/smalloc.c 2009-07-30 09:43:39.722743047 -0700 +*************** +*** 4,9 **** +--- 4,10 ---- + + #include + #include ++ #include "defs.h" + + static int nmalloc = 0; /* number of calls to malloc */ + static int nfree = 0; /* number of calls to free */ +diff -rc src/code/util/strout.c /home/jschierm/Libs/Chaco-2.2/code/util/strout.c +*** src/code/util/strout.c 1995-08-08 14:33:05.000000000 -0700 +--- /home/jschierm/Libs/Chaco-2.2/code/util/strout.c 2009-07-30 09:43:47.607754325 -0700 +*************** +*** 4,9 **** +--- 4,10 ---- + + #include + #include ++ #include "defs.h" + + /* Wrapper for a printf statement with a string as only arg. + Prints to screen and to output file if there is one. */ Index: sm/trunk/externalpackages/chaco/checkpnt.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/checkpnt.c.patch (revision 3010) +++ (revision ) @@ -1,2 +1,0 @@ -6a7 -> #include "defs.h" Index: sm/trunk/externalpackages/chaco/defs.h.patch =================================================================== --- /issm/trunk/externalpackages/chaco/defs.h.patch (revision 3010) +++ (revision ) @@ -1,17 +1,0 @@ -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 -> Index: sm/trunk/externalpackages/chaco/doubleout.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/doubleout.c.patch (revision 3010) +++ (revision ) @@ -1,2 +1,0 @@ -5a6 -> #include "defs.h" Index: sm/trunk/externalpackages/chaco/get_extval.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/get_extval.c.patch (revision 3010) +++ (revision ) @@ -1,2 +1,0 @@ -6a7 -> #include "defs.h" Index: /issm/trunk/externalpackages/chaco/install.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install.sh (revision 3010) +++ /issm/trunk/externalpackages/chaco/install.sh (revision 3011) @@ -1,36 +1,27 @@ #!/bin/bash -#Some cleanup +# Some cleanup rm -rf Chaco-2.2 rm -rf src rm -rf install -#Create src and install directories +# Create src and install directories mkdir src install -#Untar +# Untar tar -xvzf Chaco-2.2.tar.gz -#Move chaco to src directory +# Move chaco to src directory mv Chaco-2.2/* src rm -rf Chaco-2.2 -#Apply patches -patch src/code/main/defs.h defs.h.patch -patch src/code/assign/assign_out.c assign_out.c.patch -patch src/code/eigen/get_extval.c get_extval.c.patch -patch src/code/klvspiff/matching.c matching.c.patch -patch src/code/misc/timing.c timing.c.patch -patch src/code/util/bail.c bail.c.patch -patch src/code/util/checkpnt.c checkpnt.c.patch -patch src/code/util/doubleout.c doubleout.c.patch -patch src/code/util/smalloc.c smalloc.c.patch -patch src/code/util/strout.c strout.c.patch -patch src/code/Makefile Makefile.patch +# Apply patches (all at once) +# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch) +patch -p0 < chaco.patch -#Build chaco +# Build chaco cd src/code make -#Clean up, so that meshpart creates its own objects for mlchaco +# Clean up, so that meshpart creates its own objects for mlchaco make clean cd ../.. Index: sm/trunk/externalpackages/chaco/matching.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/matching.c.patch (revision 3010) +++ (revision ) @@ -1,2 +1,0 @@ -8a9 -> #include "defs.h" Index: sm/trunk/externalpackages/chaco/smalloc.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/smalloc.c.patch (revision 3010) +++ (revision ) @@ -1,2 +1,0 @@ -6a7 -> #include "defs.h" Index: sm/trunk/externalpackages/chaco/strout.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/strout.c.patch (revision 3010) +++ (revision ) @@ -1,2 +1,0 @@ -6a7 -> #include "defs.h" Index: sm/trunk/externalpackages/chaco/timing.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/timing.c.patch (revision 3010) +++ (revision ) @@ -1,2 +1,0 @@ -5a6 -> #include "defs.h"