Index: /issm/trunk-jpl/externalpackages/chaco/configs/mac/code/util/smalloc.c.patch =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/configs/mac/code/util/smalloc.c.patch (revision 27456) +++ /issm/trunk-jpl/externalpackages/chaco/configs/mac/code/util/smalloc.c.patch (revision 27456) @@ -0,0 +1,4 @@ +6c6 +< #include +--- +> #include Index: /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/Makefile =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/Makefile (revision 27456) +++ /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/Makefile (revision 27456) @@ -0,0 +1,202 @@ +DEST_DIR = ../exec +DEST= ${DEST_DIR}/chaco +CC = gcc +IFLAG = -Imain -I/mingw64/x86_64-w64-mingw32/include +CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -Wno-implicit-function-declaration -D_MSYS2_ +OFLAGS = -O2 +#AR = /usr/ccs/bin/ar rcv # for solaris 2 +#AR = /usr/bin/ar rcv +AR = ar cr +#RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +#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 \ + 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) +FILESMINUSBLAS.o= $(FILESMINUSBLAS.c:.c=.o) + + +${DEST}: ${FILES.c} chaco.a Makefile + ${CC} ${OFLAGS} chaco.a -lm -o ${DEST} + +chaco.a: ${FILES.o} + ${AR} $@ ${FILES.o} ; ${RANLIB} $@ + +chacominusblas.a: ${FILESMINUSBLAS.o} + ${AR} $@ ${FILESMINUSBLAS.o} ; ${RANLIB} $@ + +lint: + lint ${IFLAG} ${FILES.c} -lm + +alint: + alint ${IFLAG} ${FILES.c} -lm + +clean: + rm -f */*.o ${DEST_DIR}/core + +.c.o: + ${CC} -c ${IFLAG} ${CFLAGS} -o $*.o $*.c Index: /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/main/interface.c =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/main/interface.c (revision 27456) +++ /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/main/interface.c (revision 27456) @@ -0,0 +1,234 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#include +#include "defs.h" +#include "structs.h" + +int Using_Main = FALSE; /* Is main routine being called? */ + +int interface(nvtxs, start, adjacency, vwgts, ewgts, x, y, z, + outassignname, outfilename, + assignment, + architecture, ndims_tot, mesh_dims, goal, + global_method, local_method, rqi_flag, vmax, ndims, + eigtol, seed) +int nvtxs; /* number of vertices in full graph */ +int *start; /* start of edge list for each vertex */ +int *adjacency; /* edge list data */ +int *vwgts; /* weights for all vertices */ +float *ewgts; /* weights for all edges */ +float *x, *y, *z; /* coordinates for inertial method */ +char *outassignname; /* name of assignment output file */ +char *outfilename; /* output file name */ +short *assignment; /* set number of each vtx (length n) */ +int architecture; /* 0 => hypercube, d => d-dimensional mesh */ +int ndims_tot; /* total number of cube dimensions to divide */ +int mesh_dims[3]; /* dimensions of mesh of processors */ +double *goal; /* desired set sizes for each set */ +int global_method; /* global partitioning algorithm */ +int local_method; /* local partitioning algorithm */ +int rqi_flag; /* should I use RQI/Symmlq eigensolver? */ +int vmax; /* how many vertices to coarsen down to? */ +int ndims; /* number of eigenvectors (2^d sets) */ +double eigtol; /* tolerance on eigenvectors */ +long seed; /* for random graph mutations */ +{ + extern char *PARAMS_FILENAME; /* name of file with parameter updates */ + extern int MAKE_VWGTS; /* make vertex weights equal to degrees? */ + extern int MATCH_TYPE; /* matching routine to use */ + extern int FREE_GRAPH; /* free graph data structure after reformat? */ + extern int DEBUG_PARAMS; /* debug flag for reading parameters */ + extern int DEBUG_TRACE; /* trace main execution path */ + extern double start_time; /* time routine is entered */ + extern double reformat_time;/* time spent reformatting graph */ + FILE *params_file; /* file for reading new parameters */ + struct vtx_data **graph; /* graph data structure */ + double vwgt_sum; /* sum of vertex weights */ + double time; /* timing variable */ + float **coords; /* coordinates for vertices if used */ + int *vptr; /* loops through vertex weights */ + int flag; /* return code from balance */ + int nedges; /* number of edges in graph */ + int using_vwgts; /* are vertex weights being used? */ + int using_ewgts; /* are edge weights being used? */ + int nsets_tot; /* total number of sets being created */ + int igeom; /* geometric dimension for inertial method */ + int default_goal; /* using default goals? */ + int i; /* loop counter */ + double seconds(); + double *smalloc_ret(); + int sfree(), submain(), reformat(); + void free_graph(), read_params(), strout(); + + if (DEBUG_TRACE > 0) { + printf("\n"); + } + + flag = 0; + graph = NULL; + coords = NULL; + + if (!Using_Main) { /* If not using main, need to read parameters file. */ + start_time = seconds(); + params_file = fopen(PARAMS_FILENAME, "r"); + if (params_file == NULL && DEBUG_PARAMS > 1) { + printf("Parameter file `%s' not found; using default parameters.\n", + PARAMS_FILENAME); + } + read_params(params_file); + } + + if (goal == NULL) { /* If not passed in, default goals have equal set sizes. */ + default_goal = TRUE; + if (architecture == 0) + nsets_tot = 1 << ndims_tot; + else if (architecture == 1) + nsets_tot = mesh_dims[0]; + else if (architecture == 2) + nsets_tot = mesh_dims[0] * mesh_dims[1]; + else if (architecture > 2) + nsets_tot = mesh_dims[0] * mesh_dims[1] * mesh_dims[2]; + + if (MAKE_VWGTS && start != NULL) { + vwgt_sum = start[nvtxs] - start[0] + nvtxs; + } + else if (vwgts == NULL) { + vwgt_sum = nvtxs; + } + else { + vwgt_sum = 0; + vptr = vwgts; + for (i = nvtxs; i; i--) + vwgt_sum += *(vptr++); + } + + vwgt_sum /= nsets_tot; + goal = (double *) smalloc_ret((unsigned) nsets_tot * sizeof(double)); + if (goal == NULL) { + strout("\nERROR: No room to make goals.\n"); + flag = 1; + goto skip; + } + for (i = 0; i < nsets_tot; i++) + goal[i] = vwgt_sum; + } + else { + default_goal = FALSE; + } + + if (MAKE_VWGTS) { + /* Generate vertex weights equal to degree of node. */ + if (vwgts != NULL) { + strout("WARNING: Vertex weights being overwritten by vertex degrees."); + } + vwgts = (int *) smalloc_ret((unsigned) nvtxs * sizeof(int)); + if (vwgts == NULL) { + strout("\nERROR: No room to make vertex weights.\n"); + flag = 1; + goto skip; + } + if (start != NULL) { + for (i = 0; i < nvtxs; i++) + vwgts[i] = 1 + start[i + 1] - start[i]; + } + else { + for (i = 0; i < nvtxs; i++) + vwgts[i] = 1; + } + } + + using_vwgts = (vwgts != NULL); + using_ewgts = (ewgts != NULL); + + if (start != NULL || vwgts != NULL) { /* Reformat into our data structure. */ + time = seconds(); + flag = reformat(start, adjacency, nvtxs, &nedges, vwgts, ewgts, &graph); + + if (flag) { + strout("\nERROR: No room to reformat graph.\n"); + goto skip; + } + + reformat_time += seconds() - time; + } + else { + nedges = 0; + } + + if (FREE_GRAPH) { /* Free old graph data structures. */ + sfree((char *) start); + sfree((char *) adjacency); + if (vwgts != NULL) + sfree((char *) vwgts); + if (ewgts != NULL) + sfree((char *) ewgts); + start = NULL; + adjacency = NULL; + vwgts = NULL; + ewgts = NULL; + } + + + if (global_method == 3 || + (MATCH_TYPE == 5 && (global_method == 1 || + (global_method == 2 && rqi_flag)))) { + if (x == NULL) { + igeom = 0; + } + else { /* Set up coordinate data structure. */ + coords = (float **) smalloc_ret((unsigned) 3 * sizeof(float *)); + if (coords == NULL) { + strout("\nERROR: No room to make coordinate array.\n"); + flag = 1; + goto skip; + } + /* Minus 1's are to allow remainder of program to index with 1. */ + coords[0] = x - 1; + igeom = 1; + if (y != NULL) { + coords[1] = y - 1; + igeom = 2; + if (z != NULL) { + coords[2] = z - 1; + igeom = 3; + } + } + } + } + else { + igeom = 0; + } + + /* Subtract from assignment to allow code to index from 1. */ + assignment = assignment - 1; + flag = submain(graph, nvtxs, nedges, using_vwgts, using_ewgts, igeom, coords, + outassignname, outfilename, + assignment, goal, + architecture, ndims_tot, mesh_dims, + global_method, local_method, rqi_flag, vmax, ndims, + eigtol, seed); + +skip: + if (coords != NULL) + sfree((char *) coords); + + if (default_goal) + sfree((char *) goal); + + if (graph != NULL) + free_graph(graph); + + if (flag && FREE_GRAPH) { + sfree((char *) start); + sfree((char *) adjacency); + sfree((char *) vwgts); + sfree((char *) ewgts); + } + + if (!Using_Main && params_file != NULL) + fclose(params_file); + + return (flag); +} Index: /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/util/bail.c =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/util/bail.c (revision 27456) +++ /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/util/bail.c (revision 27456) @@ -0,0 +1,27 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#include +#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 + termination following detection of some problem. Call with bail(NULL,status) + to suppress message. */ +void bail(msg, status) +char *msg; +int status; +{ + extern FILE *Output_File; /* Output file or NULL */ + + if (msg != NULL && (int) strlen(msg) > 0) { + printf("%s\n", msg); + if (Output_File != NULL) { + fprintf(Output_File, "%s\n", msg); + } + } + exit(status); +} Index: /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/util/seconds.c =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/util/seconds.c (revision 27456) +++ /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/code/util/seconds.c (revision 27456) @@ -0,0 +1,35 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#if defined(_INTEL_WIN_) || defined(_MSYS2_) +#include +#else +#include +#include +#endif + +double seconds() +{ + double curtime; + +#ifdef RUSAGE_SELF + +/* This timer is faster and more robust (if it exists). */ + struct rusage rusage; + int getrusage(); + + getrusage(RUSAGE_SELF, &rusage); + curtime = ((rusage.ru_utime.tv_sec + rusage.ru_stime.tv_sec) + + 1.0e-6 * (rusage.ru_utime.tv_usec + rusage.ru_stime.tv_usec)); + +#else + +/* ANSI timer, but lower resolution & wraps around after ~36 minutes. */ + + curtime = clock()/((double) CLOCKS_PER_SEC); + +#endif + + return (curtime); +} Index: /issm/trunk-jpl/externalpackages/chaco/install-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/install-linux.sh (revision 27456) +++ /issm/trunk-jpl/externalpackages/chaco/install-linux.sh (revision 27456) @@ -0,0 +1,60 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER=2.2 + +PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed + +## Environment +# +export CFLAGS="-Wno-error=implicit-function-declaration" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf" + +# Unpack source +tar -xvzf Chaco-${VER}.tar.gz + +# Move source to 'src' directory +mv Chaco-${VER}/* src +rm -rf Chaco-${VER} + +# Apply patches +patch -R -p0 < chaco.patch # Written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch +patch src/code/Makefile < patches/Makefile.patch + +# Compile +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Install +cp -p src/exec/README ${PREFIX} +cp -p src/exec/User_Params ${PREFIX} +cp -p src/exec/*.coords ${PREFIX} +cp -p src/exec/*.graph ${PREFIX} +mkdir ${PREFIX}/include +cp -p src/code/main/defs.h ${PREFIX}/include/defs.h +cp -p src/code/main/params.h ${PREFIX}/include/params.h +cp -p chaco.h ${PREFIX}/include/chaco.h +mkdir ${PREFIX}/lib +mv src/code/chaco.a ${PREFIX}/lib/libchaco.a +mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a +mkdir ${PREFIX}/exec +mv src/exec/chaco ${PREFIX}/exec Index: sm/trunk-jpl/externalpackages/chaco/install-mac-sierra.sh =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/install-mac-sierra.sh (revision 27455) +++ (revision ) @@ -1,55 +1,0 @@ -#!/bin/bash -set -eu - -# Some cleanup -rm -rf Chaco-2.2 -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz' -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf' - -# Untar -tar -xvzf Chaco-2.2.tar.gz - -# Move chaco to src directory -mv Chaco-2.2/* src -rm -rf Chaco-2.2 - -# Apply patches (all at once) -# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch) -patch -R -p0 < chaco.patch - -# Patch src/code/Makefile -patch ./src/code/Makefile ./patches/Makefile.mac-sierra.patch - - -# Build chaco -cd src/code -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make chacominusblas.a - -# Clean up objects (but not library or executable) -make clean -cd ../.. - -# Populate install directory -cp -p src/exec/README install -cp -p src/exec/User_Params install -cp -p src/exec/*.coords install -cp -p src/exec/*.graph install -mkdir install/include -cp -p src/code/main/defs.h install/include/defs.h -cp -p src/code/main/params.h install/include/params.h -cp -p chaco.h install/include/chaco.h -mkdir install/lib -mv src/code/chaco.a install/lib/libchaco.a -mv src/code/chacominusblas.a install/lib/libchacominusblas.a -mkdir install/exec -mv src/exec/chaco install/exec Index: /issm/trunk-jpl/externalpackages/chaco/install-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/install-mac.sh (revision 27456) +++ /issm/trunk-jpl/externalpackages/chaco/install-mac.sh (revision 27456) @@ -0,0 +1,61 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER=2.2 + +PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed + +## Environment +# +export CFLAGS="-Wno-error=implicit-function-declaration" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf" + +# Unpack source +tar -xvzf Chaco-${VER}.tar.gz + +# Move source to 'src' directory +mv Chaco-${VER}/* src +rm -rf Chaco-${VER} + +# Apply patches +patch -R -p0 < chaco.patch # Written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch +patch src/code/Makefile < patches/Makefile.patch +parch src/code/util/smalloc.c < configs/mac/code/util/smalloc.c.patch + +# Compile +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Install +cp -p src/exec/README ${PREFIX} +cp -p src/exec/User_Params ${PREFIX} +cp -p src/exec/*.coords ${PREFIX} +cp -p src/exec/*.graph ${PREFIX} +mkdir ${PREFIX}/include +cp -p src/code/main/defs.h ${PREFIX}/include/defs.h +cp -p src/code/main/params.h ${PREFIX}/include/params.h +cp -p chaco.h ${PREFIX}/include/chaco.h +mkdir ${PREFIX}/lib +mv src/code/chaco.a ${PREFIX}/lib/libchaco.a +mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a +mkdir ${PREFIX}/exec +mv src/exec/chaco ${PREFIX}/exec Index: /issm/trunk-jpl/externalpackages/chaco/install-win-msys2-mingw.sh =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/install-win-msys2-mingw.sh (revision 27455) +++ /issm/trunk-jpl/externalpackages/chaco/install-win-msys2-mingw.sh (revision 27456) @@ -24,13 +24,12 @@ rm -rf Chaco-${VER} -# Apply patches (all at once) -# (written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch) -patch -R -p0 < chaco.patch +# Apply patches +patch -R -p0 < chaco.patch # Written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch # Copy customized source and configuration files to 'src' directory -cp configs/win/msys2/mingw64/src/code/Makefile src/code -cp configs/win/msys2/mingw64/src/code/main/interface.c src/code/main -cp configs/win/msys2/mingw64/src/code/util/bail.c src/code/util -cp configs/win/msys2/mingw64/src/code/util/seconds.c src/code/util +cp configs/win/msys2/mingw64/code/Makefile src/code +cp configs/win/msys2/mingw64/code/main/interface.c src/code/main +cp configs/win/msys2/mingw64/code/util/bail.c src/code/util +cp configs/win/msys2/mingw64/code/util/seconds.c src/code/util # Compile Index: sm/trunk-jpl/externalpackages/chaco/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/install.sh (revision 27455) +++ (revision ) @@ -1,61 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER=2.2 - -PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed - -## Environment -# -export CFLAGS="-Wno-error=implicit-function-declaration" - -# Cleanup -rm -rf ${PREFIX} src -mkdir -p ${PREFIX} src - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz" -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf" - -# Unpack source -tar -xvzf Chaco-${VER}.tar.gz - -# Move source to 'src' directory -mv Chaco-${VER}/* src -rm -rf Chaco-${VER} - -# Apply patches (all at once) -# (written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch) -patch -R -p0 < chaco.patch -patch src/code/Makefile patches/Makefile.patch - -# Compile -cd src/code -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make chacominusblas.a - -# Clean up objects (but not library or executable) -make clean -cd ../.. - -# Install -cp -p src/exec/README ${PREFIX} -cp -p src/exec/User_Params ${PREFIX} -cp -p src/exec/*.coords ${PREFIX} -cp -p src/exec/*.graph ${PREFIX} -mkdir ${PREFIX}/include -cp -p src/code/main/defs.h ${PREFIX}/include/defs.h -cp -p src/code/main/params.h ${PREFIX}/include/params.h -cp -p chaco.h ${PREFIX}/include/chaco.h -mkdir ${PREFIX}/lib -mv src/code/chaco.a ${PREFIX}/lib/libchaco.a -mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a -mkdir ${PREFIX}/exec -mv src/exec/chaco ${PREFIX}/exec Index: /issm/trunk-jpl/jenkins/aws-amazon_linux-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/aws-amazon_linux-solid_earth (revision 27455) +++ /issm/trunk-jpl/jenkins/aws-amazon_linux-solid_earth (revision 27456) @@ -36,5 +36,5 @@ petsc install-3.12-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/eis-daskhub-python-modules =================================================================== --- /issm/trunk-jpl/jenkins/eis-daskhub-python-modules (revision 27455) +++ /issm/trunk-jpl/jenkins/eis-daskhub-python-modules (revision 27456) @@ -54,5 +54,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/eis-smce-binaries =================================================================== --- /issm/trunk-jpl/jenkins/eis-smce-binaries (revision 27455) +++ /issm/trunk-jpl/jenkins/eis-smce-binaries (revision 27456) @@ -53,5 +53,5 @@ gmsh install-4.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/linux64_caladan =================================================================== --- /issm/trunk-jpl/jenkins/linux64_caladan (revision 27455) +++ /issm/trunk-jpl/jenkins/linux64_caladan (revision 27456) @@ -47,5 +47,5 @@ boost install-1.7-linux.sh dakota install-6.2-linux64.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh shell2junit install.sh" Index: /issm/trunk-jpl/jenkins/pine_island-mac-basic =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-basic (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-basic (revision 27456) @@ -37,5 +37,5 @@ petsc install-3.12-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-binaries-matlab =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-matlab (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-binaries-matlab (revision 27456) @@ -58,5 +58,5 @@ gmsh install-4-mac-static.sh triangle install-mac-static.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python-2 =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python-2 (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python-2 (revision 27456) @@ -50,4 +50,5 @@ curl install-7-mac-static.sh netcdf install-4.7-parallel-static.sh + sqlite install-static.sh proj install-6-static.sh gdal install-3-python-static.sh @@ -56,5 +57,5 @@ gmsh install-4-mac-static.sh triangle install-mac-static.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python-3 =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python-3 (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python-3 (revision 27456) @@ -57,5 +57,5 @@ gmsh install-4-mac-static.sh triangle install-mac-static.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-dakota =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-dakota (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-dakota (revision 27456) @@ -58,5 +58,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-examples =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-examples (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-examples (revision 27456) @@ -59,5 +59,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-full =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-full (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-full (revision 27456) @@ -56,5 +56,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-full-valgrind =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-full-valgrind (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-full-valgrind (revision 27456) @@ -57,5 +57,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-solid_earth (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-solid_earth (revision 27456) @@ -58,5 +58,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-solid_earth-lambert =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-solid_earth-lambert (revision 27455) +++ /issm/trunk-jpl/jenkins/pine_island-mac-solid_earth-lambert (revision 27456) @@ -58,5 +58,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/pleiades-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/pleiades-solid_earth (revision 27455) +++ /issm/trunk-jpl/jenkins/pleiades-solid_earth (revision 27456) @@ -51,5 +51,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-basic =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-basic (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-basic (revision 27456) @@ -35,5 +35,5 @@ petsc install-3.12-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-matlab =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-matlab (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-matlab (revision 27456) @@ -56,5 +56,5 @@ gmsh install-4-linux-static.sh triangle install-linux-static.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python-2 =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python-2 (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python-2 (revision 27456) @@ -56,5 +56,5 @@ gmsh install-4-linux-static.sh triangle install-linux-static.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python-3 =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python-3 (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python-3 (revision 27456) @@ -57,5 +57,5 @@ gmsh install-4-linux-static.sh triangle install-linux-static.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-codipack =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-codipack (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-codipack (revision 27456) @@ -42,5 +42,5 @@ gsl install.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-dakota =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-dakota (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-dakota (revision 27456) @@ -55,5 +55,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-full =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-full (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-full (revision 27456) @@ -56,5 +56,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-full-mplapack =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-full-mplapack (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-full-mplapack (revision 27456) @@ -59,5 +59,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind (revision 27456) @@ -56,5 +56,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-iceocean =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-iceocean (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-iceocean (revision 27456) @@ -36,5 +36,5 @@ petsc install-3.12-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-python =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-python (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-python (revision 27456) @@ -51,5 +51,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth (revision 27455) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth (revision 27456) @@ -53,5 +53,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh