Changeset 28138

Timestamp:

03/13/24 11:46:12 (12 months ago)

Author:

jdquinn

Message:

CHG: Fixes for latest version of Xcode

Location:

issm/trunk-jpl

Files:

• etc/environment.sh (modified) (2 diffs)
• externalpackages/chaco/chaco.patch (modified) (16 diffs)
• externalpackages/chaco/patches/Makefile.mac-sierra.patch (deleted)
• externalpackages/chaco/patches/Makefile.patch (modified) (1 diff)
• externalpackages/cmake/configs (deleted)
• externalpackages/cmake/install-macosx64-highsierra.sh (deleted)
• externalpackages/cmake/install-macosx64-snowleopard.sh (deleted)
• externalpackages/cmake/install.sh (modified) (1 diff)
• externalpackages/dakota/install-6.2-mac.sh (modified) (2 diffs)
• externalpackages/gmsh/configs/4.12.2 (copied) (copied from issm/trunk-jpl/externalpackages/gmsh/configs/4.10.5 )
• externalpackages/gsl/install.sh (modified) (1 diff)
• externalpackages/m1qn3/install-mac.sh (modified) (1 diff)
• externalpackages/petsc/install-3.20-mac-intel.sh (modified) (3 diffs)
• externalpackages/petsc/install-3.20-mac-silicon.sh (modified) (2 diffs)
• jenkins/mac-intel-full (modified) (3 diffs)

issm/trunk-jpl/etc/environment.sh

@@ -186 +186 @@
 #######################
 
+OS_NAME=$(uname -s)
+
+## macOS
+#
+if [[ ${OS_NAME} == "Darwin" ]]; then
+        BUILD_TOOL_PATH=$(xcode-select -p)
+
+        if [[ ${BUILD_TOOL_PATH} == "/Applications/Xcode.app/Contents/Developer" ]]; then
+                BUILD_TOOL_VER=$(xcodebuild -version | /usr/bin/grep "Xcode" | sed -e 's/Xcode //' | cut -d. -f1)
+        elif [[ ${BUILD_TOOL_PATH} == "/Library/Developer/CommandLineTools" ]]; then
+                BUILD_TOOL_VER=$(pkgutil --pkg-info=com.apple.pkg.CLTools_Executables | /usr/bin/grep "version" | sed -e 's/version: //' | cut -d. -f1)
+        else
+                echo "Error: On macOS, either Xcode or the Command Line Tools must be installed!"
+                exit 1
+        fi
+
+        if [[ ${BUILD_TOOL_VER} -ge 15 ]]; then
+                export LDFLAGS="-Wl,-ld_classic"
+        fi
+fi
+
+## Windows
+#
 MINGW=0
-if [[ $(uname -s) == MINGW* ]]; then
+if [[ ${OS_NAME} == MINGW* ]]; then
         MINGW=1
         MSMPI_ROOT="${ISSM_EXT_DIR}/msmpi/install"
@@ -205 +228 @@
 fi
 
-# Windows compilers
-if [[ "${ISSM_ARCH}" == "cygwin-intel" ]]; then
-        source ${ISSM_DIR}/externalpackages/windows/windows_environment.sh
-fi
+# # Windows compilers
+# if [[ "${ISSM_ARCH}" == "cygwin-intel" ]]; then
+#       source ${ISSM_DIR}/externalpackages/windows/windows_environment.sh
+# fi
 
 #########################

issm/trunk-jpl/externalpackages/chaco/chaco.patch

@@ -1 +1 @@
 Only in src/code/assign: assign.o
 diff -rc src/code/assign/assign_out.c old/code/assign/assign_out.c
-*** src/code/assign/assign_out.c        2010-07-16 16:28:47.352242454 -0700
---- old/code/assign/assign_out.c        1995-08-08 14:32:10.000000000 -0700
+*** src/code/assign/assign_out.c  2010-07-16 16:28:47.352242454 -0700
+--- old/code/assign/assign_out.c  1995-08-08 14:32:10.000000000 -0700
 ***************
 *** 3,9 ****
    * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */
   
-  #include      <stdio.h>
-- #include      "defs.h"
+  #include  <stdio.h>
+- #include  "defs.h"
   
   static void assign_out_normal(), assign_out_inv();
@@ -54 +54 @@
 Only in src/code/eigen: eigensolve.o
 diff -rc src/code/eigen/get_extval.c old/code/eigen/get_extval.c
-*** src/code/eigen/get_extval.c 2010-07-16 16:28:47.353242463 -0700
---- old/code/eigen/get_extval.c 1995-08-08 14:32:20.000000000 -0700
+*** src/code/eigen/get_extval.c 2010-07-16 16:28:47.353242463 -0700
+--- old/code/eigen/get_extval.c 1995-08-08 14:32:20.000000000 -0700
 ***************
 *** 4,10 ****
@@ -143 +143 @@
 Only in src/code/klvspiff: make_sep_list.o
 diff -rc src/code/klvspiff/matching.c old/code/klvspiff/matching.c
-*** src/code/klvspiff/matching.c        2010-07-16 16:28:47.356242493 -0700
---- old/code/klvspiff/matching.c        1996-03-11 10:24:25.000000000 -0800
+*** src/code/klvspiff/matching.c  2010-07-16 16:28:47.356242493 -0700
+--- old/code/klvspiff/matching.c  1996-03-11 10:24:25.000000000 -0800
 ***************
 *** 6,12 ****
@@ -158 +158 @@
 Only in src/code/klvspiff: nway_klv.o
 diff -rc src/code/main/defs.h old/code/main/defs.h
-*** src/code/main/defs.h        2010-07-16 16:28:47.359242522 -0700
---- old/code/main/defs.h        1995-08-08 14:32:41.000000000 -0700
+*** src/code/main/defs.h  2010-07-16 16:28:47.359242522 -0700
+--- old/code/main/defs.h  1995-08-08 14:32:41.000000000 -0700
 ***************
 *** 1,39 ****
@@ -165 +165 @@
 ! #define _CHACO_DEFS_H_
 ! 
-  #define TRUE          1
-  #define FALSE         0
+  #define TRUE    1
+  #define FALSE   0
   
 ! #ifndef _HAVE_CHACO_ //protect ISSM compilation. This symbol is defined when we compile ISSM
 ! 
-!       #define max(A, B)       ((A) > (B) ? (A) : (B))
-!       #define min(A, B)       ((A) < (B) ? (A) : (B))
-!       #define sign(A)         ((A) <  0  ? -1  :  1)
-!       #define absval(A)       ((A) <  0  ? -(A): (A))
-! 
-!       /* Define constants that are needed in various places */
-!       #define PI      3.141592653589793
-!       #define TWOPI   6.283185307179586
-!       #define HALFPI  1.570796326794896
+!   #define max(A, B) ((A) > (B) ? (A) : (B))
+!   #define min(A, B) ((A) < (B) ? (A) : (B))
+!   #define sign(A)   ((A) <  0  ? -1  :  1)
+!   #define absval(A) ((A) <  0  ? -(A): (A))
+! 
+!   /* Define constants that are needed in various places */
+!   #define PI  3.141592653589793
+!   #define TWOPI 6.283185307179586
+!   #define HALFPI  1.570796326794896
 ! 
 !     #define check_graph chaco_check_graph
 ! 
 ! 
-!       #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 exit(status) mexErrMsgTxt("exit=" #status)
-! 
-!       #endif
+!   #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 exit(status) mexErrMsgTxt("exit=" #status)
+! 
+!   #endif
 ! 
 ! #endif  //#ifndef _HAVE_CHACO_ 
@@ -202 +202 @@
 ! #endif //ifndef _CHACO_DEFS_H_
 --- 1,11 ----
-! #define       max(A, B)       ((A) > (B) ? (A) : (B))
-! #define       min(A, B)       ((A) < (B) ? (A) : (B))
-! #define sign(A)               ((A) <  0  ? -1  :  1)
-! #define absval(A)     ((A) <  0  ? -(A): (A))
-  #define TRUE          1
-  #define FALSE         0
+! #define max(A, B) ((A) > (B) ? (A) : (B))
+! #define min(A, B) ((A) < (B) ? (A) : (B))
+! #define sign(A)   ((A) <  0  ? -1  :  1)
+! #define absval(A) ((A) <  0  ? -(A): (A))
+  #define TRUE    1
+  #define FALSE   0
   
 ! /* Define constants that are needed in various places */
-! #define       PI      3.141592653589793
-! #define       TWOPI   6.283185307179586
+! #define PI  3.141592653589793
+! #define TWOPI 6.283185307179586
 ! #define HALFPI  1.570796326794896
 Only in src/code/main: interface.o
 Only in src/code/main: main.o
 diff -rc src/code/main/params.h old/code/main/params.h
-*** src/code/main/params.h      2010-07-16 16:28:47.361242541 -0700
---- old/code/main/params.h      1995-08-08 14:32:43.000000000 -0700
+*** src/code/main/params.h  2010-07-16 16:28:47.361242541 -0700
+--- old/code/main/params.h  1995-08-08 14:32:43.000000000 -0700
 ***************
 *** 1,12 ****
@@ -224 +224 @@
 - 
 - 
-  #define NAME_LENGTH   80      /* Maximum length of file name */
-  #define LINE_LENGTH   200     /* Length of input files read at once */
-  
-  #define MAXDIMS               3       /* Most cuts allowed at one time */
-  #define MAXSETS               8       /* 2^MAXDIMS */
+  #define NAME_LENGTH 80  /* Maximum length of file name */
+  #define LINE_LENGTH 200 /* Length of input files read at once */
+  
+  #define MAXDIMS   3 /* Most cuts allowed at one time */
+  #define MAXSETS   8 /* 2^MAXDIMS */
 - 
 - 
@@ -234 +234 @@
 --- 1,5 ----
 Only in src/code/main: user_params.o
-diff -rc src/code/Makefile old/code/Makefile
-*** src/code/Makefile   2010-07-21 18:22:19.909939194 -0700
---- old/code/Makefile   1997-10-02 10:23:22.000000000 -0700
-***************
-*** 2,18 ****
-  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 -g
-! #CFLAGS =     -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB
-! OFLAGS =      -O2 
-! #AR =             /usr/ccs/bin/ar rcv   # for solaris 2
-! AR =             /usr/bin/ar rcv
-! #RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
-! RANLIB =         /usr/bin/ranlib
-  
-  FILES.c=      main/user_params.c main/interface.c main/main.c \
-                submain/balance.c submain/divide.c submain/submain.c \
---- 2,9 ----
-  DEST=         ${DEST_DIR}/chaco
-  CC =          gcc
-  IFLAG =               -Imain
-! CFLAGS =      -O2
-! OFLAGS =      -O2
-  
-  FILES.c=      main/user_params.c main/interface.c main/main.c \
-                submain/balance.c submain/divide.c submain/submain.c \
-***************
-*** 96,196 ****
-                util/update.c  util/vecout.c util/vecran.c \
-                  util/vecscale.c 
-  
-- 
-- FILESMINUSBLAS.c=     main/user_params.c main/interface.c main/main.c \
--               submain/balance.c submain/divide.c submain/submain.c \
--               input/input_assign.c \
--               input/check_input.c input/input.c input/input_geom.c \
--               input/input_graph.c input/read_params.c input/reflect_input.c \
--               input/read_val.c \
--               graph/check_graph.c graph/free_graph.c \
--               graph/reformat.c graph/subgraph.c graph/graph_out.c \
--               inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \
--               inertial/inertial1d.c inertial/inertial2d.c \
--               inertial/inertial3d.c inertial/make_subgeom.c \
--               klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \
--               klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \
--               klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \
--               klspiff/klspiff.c klspiff/make_bndy_list.c \
--               klspiff/make_kl_list.c klspiff/nway_kl.c \
--               klvspiff/bpm_improve.c klvspiff/bucketsv.c \
--               klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \
--               klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \
--               klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \
--               klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \
--               klvspiff/flatten.c \
--               coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \
--               coarsen/makeccoords.c \
--               coarsen/coarsen1.c coarsen/makev2cv.c \
--               coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \
--               coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \
--               connect/add_edges.c connect/connected.c connect/find_edges.c \
--               eigen/bidir.c eigen/bisect.c eigen/checkeig.c \
--               eigen/checkeig_ext.c \
--               eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\
--               eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \
--               eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \
--               eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\
--               eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \
--               eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \
--               eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \
--               eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \
--                 eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \
--               eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \
--               symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \
--               symmlq/symmlq.c  \
--               tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \
--               optimize/determinant.c optimize/func2d.c \
--               optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \
--               assign/assign.c assign/assign_out.c assign/mapper.c \
--               assign/median.c assign/merge_assign.c \
--               assign/rec_median.c assign/rotate.c assign/y2x.c \
--               bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \
--               bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \
--               bpmatch/map3d.c bpmatch/movevtxs.c \
--               bpmatch/sorts2d.c bpmatch/sorts3d.c \
--               refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \
--               refine_map/refine_cube.c refine_map/update_cube_edata.c \
--               refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \
--               refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \
--               refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \
--               refine_map/init_mesh_edata.c refine_map/refine_mesh.c \
--               refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \
--               refine_map/refine_map.c refine_map/make_comm_graph.c \
--               refine_part/refine_part.c refine_part/kl_refine.c \
--               refine_part/make_maps_ref.c refine_part/make_terms_ref.c \
--               internal/force_internal.c internal/improve_internal.c \
--               internal/check_internal.c \
--               misc/define_subcubes.c misc/define_submeshes.c \
--               misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \
--               misc/count.c misc/countup.c misc/countup_cube.c \
--               misc/countup_mesh.c misc/make_subgoal.c \
--               misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \
--               misc/sequence.c misc/perturb.c misc/simple_part.c \
--               misc/time_kernels.c misc/timing.c \
--               util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \
--               util/checkpnt.c util/cpvec.c util/dot.c \
--               util/doubleout.c util/input_int.c util/gray.c \
--               util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \
--                 util/normalize.c util/mergesort.c \
--                 util/randomize.c util/smalloc.c util/bail.c \
--               util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \
--               util/strout.c util/tri_prod.c util/true_or_false.c \
--               util/update.c  util/vecout.c util/vecran.c \
--                 util/vecscale.c 
-- 
-  FILES.o=      $(FILES.c:.c=.o) 
-- FILESMINUSBLAS.o=     $(FILESMINUSBLAS.c:.c=.o) 
-- 
-- 
-- ${DEST}:      ${FILES.c} chaco.a Makefile
--               ${CC} ${OFLAGS} chaco.a -lm -o ${DEST}
-  
-- chaco.a:      ${FILES.o}
--               ${AR} chaco.a ${FILES.o} ; ${RANLIB} chaco.a
-  
-! chacominusblas.a:     ${FILESMINUSBLAS.o}
-!               ${AR} chacominusblas.a ${FILESMINUSBLAS.o} ; ${RANLIB} chacominusblas.a
-  
-  lint:
-                lint ${IFLAG} ${FILES.c} -lm
---- 87,97 ----
-                util/update.c  util/vecout.c util/vecran.c \
-                  util/vecscale.c 
-  
-  FILES.o=      $(FILES.c:.c=.o) 
-  
-  
-! ${DEST}:      ${FILES.o} Makefile
-!               ${CC} ${OFLAGS} ${FILES.o} -lm -o ${DEST}
-  
-  lint:
-                lint ${IFLAG} ${FILES.c} -lm
 Only in src/code/misc: count.o
 Only in src/code/misc: countup_cube.o
@@ -398 +252 @@
 Only in src/code/misc: time_kernels.o
 diff -rc src/code/misc/timing.c old/code/misc/timing.c
-*** src/code/misc/timing.c      2010-07-16 16:28:47.366242590 -0700
---- old/code/misc/timing.c      1997-01-03 09:10:52.000000000 -0800
+*** src/code/misc/timing.c  2010-07-16 16:28:47.366242590 -0700
+--- old/code/misc/timing.c  1997-01-03 09:10:52.000000000 -0800
 ***************
 *** 3,9 ****
@@ -443 +297 @@
 Only in src/code/symmlq: pow_dd.o
 diff -rc src/code/symmlq/symmlqblas.f old/code/symmlq/symmlqblas.f
-*** src/code/symmlq/symmlqblas.f        2010-07-21 18:09:10.370123273 -0700
---- old/code/symmlq/symmlqblas.f        2010-07-21 14:02:09.633743650 -0700
+*** src/code/symmlq/symmlqblas.f  2010-07-21 18:09:10.370123273 -0700
+--- old/code/symmlq/symmlqblas.f  2010-07-21 14:02:09.633743650 -0700
 ***************
 *** 16,22 ****
@@ -470 +324 @@
 Only in src/code/util: array_alloc_2D.o
 diff -rc src/code/util/bail.c old/code/util/bail.c
-*** src/code/util/bail.c        2010-07-16 16:28:47.368242609 -0700
---- old/code/util/bail.c        1995-08-08 14:33:01.000000000 -0700
+*** src/code/util/bail.c  2010-07-16 16:28:47.368242609 -0700
+--- old/code/util/bail.c  1995-08-08 14:33:01.000000000 -0700
 ***************
 *** 4,10 ****
   
-  #include      <stdio.h>
-  #include      <string.h>
-- #include      "defs.h"
+  #include  <stdio.h>
+  #include  <string.h>
+- #include  "defs.h"
   
   /* Wrapper for exit() - print message and exit with status code. Exit code
@@ -487 +341 @@
   int       status;
   {
-      extern FILE *Output_File;         /* Output file or NULL */
+      extern FILE *Output_File;   /* Output file or NULL */
 +     void      exit();
   
@@ -495 +349 @@
 Only in src/code/util: bit_reverse.o
 diff -rc src/code/util/checkpnt.c old/code/util/checkpnt.c
-*** src/code/util/checkpnt.c    2010-07-16 16:28:47.370242629 -0700
---- old/code/util/checkpnt.c    1995-08-08 14:33:01.000000000 -0700
+*** src/code/util/checkpnt.c  2010-07-16 16:28:47.370242629 -0700
+--- old/code/util/checkpnt.c  1995-08-08 14:33:01.000000000 -0700
 ***************
 *** 4,10 ****
   
-  #include      <stdio.h>
-  #include      <string.h>
-- #include      "defs.h"
+  #include  <stdio.h>
+  #include  <string.h>
+- #include  "defs.h"
   
   /* Debug break point. */
@@ -511 +365 @@
 Only in src/code/util: dot.o
 diff -rc src/code/util/doubleout.c old/code/util/doubleout.c
-*** src/code/util/doubleout.c   2010-07-16 16:28:47.372242648 -0700
---- old/code/util/doubleout.c   1995-08-08 14:33:02.000000000 -0700
+*** src/code/util/doubleout.c 2010-07-16 16:28:47.372242648 -0700
+--- old/code/util/doubleout.c 1995-08-08 14:33:02.000000000 -0700
 ***************
 *** 3,9 ****
@@ -538 +392 @@
 Only in src/code/util: shell_sort.o
 diff -rc src/code/util/smalloc.c old/code/util/smalloc.c
-*** src/code/util/smalloc.c     2010-07-16 16:28:47.375242677 -0700
---- old/code/util/smalloc.c     1996-03-11 10:44:07.000000000 -0800
+*** src/code/util/smalloc.c 2010-07-16 16:28:47.375242677 -0700
+--- old/code/util/smalloc.c 1996-03-11 10:44:07.000000000 -0800
 ***************
 *** 4,10 ****
@@ -547 +401 @@
 - #include "defs.h"
   
-  static int nmalloc = 0;               /* number of calls to malloc */
-  static int nfree = 0;         /* number of calls to free */
+  static int nmalloc = 0;   /* number of calls to malloc */
+  static int nfree = 0;   /* number of calls to free */
 --- 4,9 ----
 Only in src/code/util: smalloc.o
 diff -rc src/code/util/strout.c old/code/util/strout.c
-*** src/code/util/strout.c      2010-07-16 16:28:47.377242697 -0700
---- old/code/util/strout.c      1995-08-08 14:33:05.000000000 -0700
+*** src/code/util/strout.c  2010-07-16 16:28:47.377242697 -0700
+--- old/code/util/strout.c  1995-08-08 14:33:05.000000000 -0700
 ***************
 *** 4,10 ****
   
-  #include      <stdio.h>
-  #include      <string.h>
-- #include      "defs.h"
+  #include  <stdio.h>
+  #include  <string.h>
+- #include  "defs.h"
   
   /* Wrapper for a printf statement with a string as only arg.

issm/trunk-jpl/externalpackages/chaco/patches/Makefile.patch

@@ -1 @@
-cat Makefile.patch 
---- Makefile.bak        2023-12-16 14:13:20.545167957 -0500
-+++ src/code/Makefile   2023-12-16 14:15:23.204795093 -0500
-@@ -6,13 +6,15 @@
- #CFLAGS =      -O2
- #OFLAGS =      -O2
- #CFLAGS =      -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions
--CFLAGS =       -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g
-+CFLAGS =       -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/include/malloc -Wno-implicit-function-declaration
- #CFLAGS =      -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB
- OFLAGS =       -O2 
- #AR =             /usr/ccs/bin/ar rcv   # for solaris 2
--AR =             /usr/bin/ar rcv
-+#AR =             /usr/bin/ar rcv
+--- ./src/code/Makefile 1997-10-02 10:23:22
++++ ./Makefile  2024-03-12 14:07:55
+@@ -1,106 +1,117 @@
+-DEST_DIR =     ../exec
+-DEST=          ${DEST_DIR}/chaco
+-CC =           gcc
++DEST_DIR =     ../exec
++DEST =         ${DEST_DIR}/chaco
++CC =           gcc
+ IFLAG =                -Imain
+-CFLAGS =       -O2
+-OFLAGS =       -O2
++CFLAGS =       -fPIC -pthread -fexceptions -g -I/usr/include/malloc -w -Wno-error=implicit-int -Wno-error=implicit-function-declaration
++OFLAGS =       -O2 -fno-omit-frame-pointer
 +AR =           ar rcv
- #RANLIB =         /usr/ccs/bin/ranlib   # for solaris 2
--RANLIB =         /usr/bin/ranlib
-+#RANLIB =         /usr/bin/ranlib
 +RANLIB =       ranlib
  
- FILES.c=       main/user_params.c main/interface.c main/main.c \
-                submain/balance.c submain/divide.c submain/submain.c \
+-FILES.c=       main/user_params.c main/interface.c main/main.c \
+-               submain/balance.c submain/divide.c submain/submain.c \
+-               input/input_assign.c \
+-               input/check_input.c input/input.c input/input_geom.c \
+-               input/input_graph.c input/read_params.c input/reflect_input.c \
+-               input/read_val.c \
+-               graph/check_graph.c graph/free_graph.c \
+-               graph/reformat.c graph/subgraph.c graph/graph_out.c \
+-               inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \
+-               inertial/inertial1d.c inertial/inertial2d.c \
+-               inertial/inertial3d.c inertial/make_subgeom.c \
+-               klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \
+-               klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \
+-               klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \
+-               klspiff/klspiff.c klspiff/make_bndy_list.c \
+-               klspiff/make_kl_list.c klspiff/nway_kl.c \
+-               klvspiff/bpm_improve.c klvspiff/bucketsv.c \
+-               klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \
+-               klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \
+-               klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \
+-               klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \
+-               klvspiff/flatten.c \
+-               coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \
+-               coarsen/makeccoords.c \
+-               coarsen/coarsen1.c coarsen/makev2cv.c \
+-               coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \
+-               coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \
+-               connect/add_edges.c connect/connected.c connect/find_edges.c \
+-               eigen/bidir.c eigen/bisect.c eigen/checkeig.c \
+-               eigen/checkeig_ext.c \
+-               eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\
+-               eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \
+-               eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \
+-               eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\
+-               eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \
+-               eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \
+-               eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \
+-               eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \
+-                eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \
+-               eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \
+-               symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \
+-               symmlq/symmlq.c symmlq/symmlqblas.c \
+-               tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \
+-               optimize/determinant.c optimize/func2d.c \
+-               optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \
+-               assign/assign.c assign/assign_out.c assign/mapper.c \
+-               assign/median.c assign/merge_assign.c \
+-               assign/rec_median.c assign/rotate.c assign/y2x.c \
+-               bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \
+-               bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \
+-               bpmatch/map3d.c bpmatch/movevtxs.c \
+-               bpmatch/sorts2d.c bpmatch/sorts3d.c \
+-               refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \
+-               refine_map/refine_cube.c refine_map/update_cube_edata.c \
+-               refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \
+-               refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \
+-               refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \
+-               refine_map/init_mesh_edata.c refine_map/refine_mesh.c \
+-               refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \
+-               refine_map/refine_map.c refine_map/make_comm_graph.c \
+-               refine_part/refine_part.c refine_part/kl_refine.c \
+-               refine_part/make_maps_ref.c refine_part/make_terms_ref.c \
+-               internal/force_internal.c internal/improve_internal.c \
+-               internal/check_internal.c \
+-               misc/define_subcubes.c misc/define_submeshes.c \
+-               misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \
+-               misc/count.c misc/countup.c misc/countup_cube.c \
+-               misc/countup_mesh.c misc/make_subgoal.c \
+-               misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \
+-               misc/sequence.c misc/perturb.c misc/simple_part.c \
+-               misc/time_kernels.c misc/timing.c \
+-               util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \
+-               util/checkpnt.c util/cpvec.c util/dot.c \
+-               util/doubleout.c util/input_int.c util/gray.c \
+-               util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \
+-                util/normalize.c util/mergesort.c \
+-                util/randomize.c util/smalloc.c util/bail.c \
+-               util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \
+-               util/strout.c util/tri_prod.c util/true_or_false.c \
+-               util/update.c  util/vecout.c util/vecran.c \
+-                util/vecscale.c 
++FILESMINUSBLAS.c = \
++       main/user_params.c main/interface.c main/main.c \
++       submain/balance.c submain/divide.c submain/submain.c \
++       input/input_assign.c \
++       input/check_input.c input/input.c input/input_geom.c \
++       input/input_graph.c input/read_params.c input/reflect_input.c \
++       input/read_val.c \
++       graph/check_graph.c graph/free_graph.c \
++       graph/reformat.c graph/subgraph.c graph/graph_out.c \
++       inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \
++       inertial/inertial1d.c inertial/inertial2d.c \
++       inertial/inertial3d.c inertial/make_subgeom.c \
++       klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \
++       klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \
++       klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \
++       klspiff/klspiff.c klspiff/make_bndy_list.c \
++       klspiff/make_kl_list.c klspiff/nway_kl.c \
++       klvspiff/bpm_improve.c klvspiff/bucketsv.c \
++       klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \
++       klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \
++       klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \
++       klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \
++       klvspiff/flatten.c \
++       coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \
++       coarsen/makeccoords.c \
++       coarsen/coarsen1.c coarsen/makev2cv.c \
++       coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \
++       coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \
++       connect/add_edges.c connect/connected.c connect/find_edges.c \
++       eigen/bidir.c eigen/bisect.c eigen/checkeig.c \
++       eigen/checkeig_ext.c \
++       eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\
++       eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \
++       eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \
++       eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\
++       eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \
++       eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \
++       eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \
++       eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \
++       eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \
++       eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \
++       symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \
++       symmlq/symmlq.c \
++       tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \
++       optimize/determinant.c optimize/func2d.c \
++       optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \
++       assign/assign.c assign/assign_out.c assign/mapper.c \
++       assign/median.c assign/merge_assign.c \
++       assign/rec_median.c assign/rotate.c assign/y2x.c \
++       bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \
++       bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \
++       bpmatch/map3d.c bpmatch/movevtxs.c \
++       bpmatch/sorts2d.c bpmatch/sorts3d.c \
++       refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \
++       refine_map/refine_cube.c refine_map/update_cube_edata.c \
++       refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \
++       refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \
++       refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \
++       refine_map/init_mesh_edata.c refine_map/refine_mesh.c \
++       refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \
++       refine_map/refine_map.c refine_map/make_comm_graph.c \
++       refine_part/refine_part.c refine_part/kl_refine.c \
++       refine_part/make_maps_ref.c refine_part/make_terms_ref.c \
++       internal/force_internal.c internal/improve_internal.c \
++       internal/check_internal.c \
++       misc/define_subcubes.c misc/define_submeshes.c \
++       misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \
++       misc/count.c misc/countup.c misc/countup_cube.c \
++       misc/countup_mesh.c misc/make_subgoal.c \
++       misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \
++       misc/sequence.c misc/perturb.c misc/simple_part.c \
++       misc/time_kernels.c misc/timing.c \
++       util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \
++       util/checkpnt.c util/cpvec.c util/dot.c \
++       util/doubleout.c util/input_int.c util/gray.c \
++       util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \
++       util/normalize.c util/mergesort.c \
++       util/randomize.c util/smalloc.c util/bail.c \
++       util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \
++       util/strout.c util/tri_prod.c util/true_or_false.c \
++       util/update.c util/vecout.c util/vecran.c \
++       util/vecscale.c
+ 
+-FILES.o=       $(FILES.c:.c=.o) 
++FILES.c = $(FILESMINUSBLAS.c) symmlq/symmlqblas.c
+ 
++FILES.o =                      $(FILES.c:.c=.o)
++FILESMINUSBLAS.o =     $(FILESMINUSBLAS.c:.c=.o)
+ 
+-${DEST}:       ${FILES.o} Makefile
+-               ${CC} ${OFLAGS} ${FILES.o} -lm -o ${DEST}
++${DEST}: ${FILES.c} chaco.a Makefile
++       ${CC} ${OFLAGS} chaco.a -lm -o ${DEST}
+ 
++chaco.a: ${FILES.o}
++       ${AR} chaco.a ${FILES.o} ; ${RANLIB} chaco.a
++
++chacominusblas.a: ${FILESMINUSBLAS.o}
++       ${AR} chacominusblas.a ${FILESMINUSBLAS.o} ; ${RANLIB} chacominusblas.a
++
+ lint:
+-               lint ${IFLAG} ${FILES.c} -lm
++       lint ${IFLAG} ${FILES.c} -lm
+ 
+ alint:
+-               alint ${IFLAG} ${FILES.c} -lm
++       alint ${IFLAG} ${FILES.c} -lm
+ 
+ clean:
+-               rm -f */*.o ${DEST_DIR}/core
++       rm -f */*.o ${DEST_DIR}/core
+ 
+ .c.o:
+-               ${CC} -c ${IFLAG} ${CFLAGS} -o $*.o $*.c
++       ${CC} -c ${IFLAG} ${CFLAGS} -o $*.o $*.c

issm/trunk-jpl/externalpackages/cmake/install.sh

@@ -5 +5 @@
 ## Constants
 #
-VER="3.19.3"
+VER="3.28.3"
 
 PREFIX="${ISSM_DIR}/externalpackages/cmake/install" # Set to location where external package should be installed

issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh

@@ -74 +74 @@
         -DBUILD_STATIC_LIBS=OFF \
         -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \
-        -DCMAKE_C_FLAGS="-w" \
+        -DCMAKE_C_FLAGS="-w -Wno-error=implicit-int" \
         -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \
         -DCMAKE_CXX_FLAGS="-fdelayed-template-parsing -w" \
@@ -139 +139 @@
 install_name_tool -add_rpath ${LIBGFORTRAN_ROOT} libteuchos.dylib
 install_name_tool -add_rpath ${LIBGFORTRAN_ROOT} liboptpp.dylib
-

issm/trunk-jpl/externalpackages/gsl/install.sh

@@ -37 +37 @@
         make -j $1 install
 fi
+

issm/trunk-jpl/externalpackages/m1qn3/install-mac.sh

@@ -1 +1 @@
 #!/bin/bash
 set -eu
+
 
 ## Constants

issm/trunk-jpl/externalpackages/petsc/install-3.20-mac-intel.sh

@@ -38 +38 @@
         --PETSC_DIR="${PETSC_DIR}" \
         --CFLAGS="-Wno-error=implicit-function-declaration" \
-        --LDFLAGS="-Wl,-ld_classic" \
         --with-debugging=0 \
         --with-valgrind=0 \
@@ -45 +44 @@
         --with-pic=1 \
         --download-fblaslapack=1 \
-        --download-mpich=1 \
+        --download-mpich="https://www.mpich.org/static/downloads/4.2.0/mpich-4.2.0.tar.gz" \
         --download-metis=1 \
         --download-parmetis=1 \
@@ -56 +55 @@
 make install
 
+# Need to make sure classic linker is used (should be able to remove this once MPICH fixes it)
+if [[ ${LDFLAGS} =~ "-Wl,-ld_classic" ]]; then
+        sed -i'' -e 's/-Wl,-commons,use_dylibs//g' ${PREFIX}/bin/mpicc
+        sed -i'' -e 's/-Wl,-commons,use_dylibs//g' ${PREFIX}/bin/mpicxx
+fi

issm/trunk-jpl/externalpackages/petsc/install-3.20-mac-silicon.sh

@@ -5 +5 @@
 ## Constants
 #
-VER="3.20.2"
+VER="3.20.5"
 
 PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
@@ -45 +45 @@
 make
 make install
+
+# Need to make sure classic linker is used (should be able to remove this once MPICH fixes it)
+if [[ ${LDFLAGS} =~ "-Wl,-ld_classic" ]]; then
+        sed -i'' -e 's/-Wl,-commons,use_dylibs//g' ${PREFIX}/bin/mpicc
+        sed -i'' -e 's/-Wl,-commons,use_dylibs//g' ${PREFIX}/bin/mpicxx
+fi

issm/trunk-jpl/jenkins/mac-intel-full

@@ -24 +24 @@
         --with-python-dir=/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \
         --with-python-numpy-dir=/Library/Python/3.9/site-packages/numpy/core/include/numpy \
-        --with-fortran-lib="-L/opt/homebrew/Cellar/gcc/13.1.0/lib/gcc/13 -lgfortran" \
+        --with-fortran-lib="-L/usr/local/Cellar/gcc/13.2.0/lib/gcc/13 -lgfortran" \
         --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
         --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
@@ -51 +51 @@
         autotools       install-mac.sh
         cmake           install.sh
-        petsc           install-3.14-mac.sh
+        petsc           install-3.20-mac-intel.sh
         gsl                     install.sh
         boost           install-1.7-mac.sh
@@ -91 +91 @@
 
 # Nightly run options
-MATLAB_NROPTIONS=""
-PYTHON_NROPTIONS=""
+MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),119,216,274,423,430,433,435,441:442,448,462:464,508,517,544,546,701,702,703,808]"
+PYTHON_NROPTIONS="--exclude Dakota 119 216 274 423 430 433 435 441:442 448 462:464 508 517 544 546 702:703 808"
+