Index: /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/src/code/Makefile =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/src/code/Makefile (revision 26155) +++ /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/src/code/Makefile (revision 26156) @@ -1,16 +1,14 @@ -ifeq "$(origin AR)" "undefined" - AR = ar -endif - -ifeq "$(origin RANLIB)" "undefined" - RANLIB = ranlib -endif - DEST_DIR = ../exec DEST= ${DEST_DIR}/chaco CC = gcc -IFLAG = -Imain -CFLAGS = -fpic -fno-omit-frame-pointer -pthread -fexceptions -g -I/mingw64/x86_64-w64-mingw32/include -Wno-implicit-function-declaration +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 \ @@ -96,5 +94,89 @@ 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) @@ -103,8 +185,8 @@ chaco.a: ${FILES.o} - ${AR} cr $@ ${FILES.o} ; ${RANLIB} $@ + ${AR} $@ ${FILES.o} ; ${RANLIB} $@ chacominusblas.a: ${FILESMINUSBLAS.o} - ${AR} cr $@ ${FILESMINUSBLAS.o} ; ${RANLIB} $@ + ${AR} $@ ${FILESMINUSBLAS.o} ; ${RANLIB} $@ lint: Index: /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/src/code/util/seconds.c =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/src/code/util/seconds.c (revision 26155) +++ /issm/trunk-jpl/externalpackages/chaco/configs/win/msys2/mingw64/src/code/util/seconds.c (revision 26156) @@ -3,21 +3,10 @@ * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ -/** - * NOTE: Under MSYS2 MinGW, we do not want to have to depend on the MSYS2 - * runtime for our distributable packages. Unfortunately, sys/resource.h - * is not currently available for MinGW (standalone) targets under MSYS2. - * this further means that, - * - * -I/mingw64/x86_64-w64-mingw32/include - * - * should be included in CFLAGS, and that, - * - * -I/usr/include - * - * should be avoided. - */ -//#include -//#include +#if defined(_INTEL_WIN_) || defined(_MSYS2_) #include +#else +#include +#include +#endif double seconds() @@ -25,15 +14,15 @@ double curtime; -// #ifdef RUSAGE_SELF +#ifdef RUSAGE_SELF -// /* This timer is faster and more robust (if it exists). */ -// struct rusage rusage; -// int getrusage(); +/* 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)); + 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 +#else /* ANSI timer, but lower resolution & wraps around after ~36 minutes. */ @@ -41,5 +30,5 @@ curtime = clock()/((double) CLOCKS_PER_SEC); -// #endif +#endif return (curtime); Index: /issm/trunk-jpl/externalpackages/semic/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/semic/install.sh (revision 26155) +++ /issm/trunk-jpl/externalpackages/semic/install.sh (revision 26156) @@ -9,5 +9,5 @@ # Cleanup rm -rf ${PREFIX} src -mkdir -p ${PREFIX} +mkdir -p ${PREFIX}/lib # Download source @@ -35,5 +35,5 @@ FFLAGS=$FFLAGS install: libutils.\$(LIB_EXT) - cp libutils.\$(LIB_EXT) ${PREFIX} + cp libutils.\$(LIB_EXT) ${PREFIX}/lib cp utils.mod ${PREFIX} OBJECTS= utils.o @@ -59,5 +59,5 @@ FFLAGS=$FFLAGS install: libsurface_physics.\$(LIB_EXT) - cp libsurface_physics.\$(LIB_EXT) ${PREFIX} + cp libsurface_physics.\$(LIB_EXT) ${PREFIX}/lib cp surface_physics.mod ${PREFIX} OBJECTS= surface_physics.o Index: /issm/trunk-jpl/jenkins/ross-win-msys2-mingw-msmpi-basic =================================================================== --- /issm/trunk-jpl/jenkins/ross-win-msys2-mingw-msmpi-basic (revision 26155) +++ /issm/trunk-jpl/jenkins/ross-win-msys2-mingw-msmpi-basic (revision 26156) @@ -63,4 +63,7 @@ # See documentation in test/NightlyRun/runme.* for more information # -MATLAB_NROPTIONS="'id',[101,102,201,202]" +# NOTE: +# - test701 is skipped because it uses full Stokes equations +# +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),435,701,702,703]" PYTHON_NROPTIONS="" Index: /issm/trunk-jpl/m4/issm_options.m4 =================================================================== --- /issm/trunk-jpl/m4/issm_options.m4 (revision 26155) +++ /issm/trunk-jpl/m4/issm_options.m4 (revision 26156) @@ -320,4 +320,5 @@ AC_DEFINE([_HAVE_RESTRICT_], [1], [with restrict buffers]) elif test "${VENDOR}" == "win-msys2"; then + export CXXFLAGS="-D_MSYS2_" export LDFLAGS="${LDFLAGS} -no-undefined" export OSLIBS="-Wl,-L/mingw64/lib/gcc/x86_64-w64-mingw32/10.2.0 -Wl,-L/mingw64/x86_64-w64-mingw32/lib -Wl,-lstdc++ -Wl,-lgfortran -Wl,-lmingw32 -Wl,-lgcc_s -Wl,-lmoldname -Wl,-lmingwex -Wl,-lmsvcrt -Wl,-lm -Wl,-lpthread -Wl,-lshell32 -Wl,-luser32 -Wl,-lgdi32 -Wl,-luser32 -Wl,-ladvapi32 -Wl,-lkernel32 -Wl,-lquadmath -Wl,-lstdc++ -Wl,-lgcc" @@ -901,6 +902,10 @@ dnl Chaco libraries and header files if test "x${HAVE_CHACO}" == "xyes"; then - CHACOINCL=-I${CHACO_ROOT}/include - CHACOLIB="-L${CHACO_ROOT}/lib -lchacominusblas" + CHACOINCL="-I${CHACO_ROOT}/include" + if test "${IS_MSYS2}" == "yes"; then + CHACOLIB="-Wl,-L${CHACO_ROOT}/lib -Wl,-lchacominusblas" + else + CHACOLIB="-L${CHACO_ROOT}/lib -lchacominusblas" + fi AC_DEFINE([_HAVE_CHACO_], [1], [with Chaco in ISSM src]) AC_SUBST([CHACOINCL]) @@ -1663,5 +1668,9 @@ dnl M1QN3 libraries and header files if test "x${HAVE_M1QN3}" == "xyes"; then - M1QN3LIB="${M1QN3_ROOT}/libm1qn3.a ${M1QN3_ROOT}/libddot.a" + if test "${IS_MSYS2}" == "yes"; then + M1QN3LIB="-Wl,${M1QN3_ROOT}/libm1qn3.a -Wl,${M1QN3_ROOT}/libddot.a" + else + M1QN3LIB="${M1QN3_ROOT}/libm1qn3.a ${M1QN3_ROOT}/libddot.a" + fi AC_DEFINE([_HAVE_M1QN3_], [1], [with M1QN3 in ISSM src]) AC_SUBST([M1QN3LIB]) @@ -2117,6 +2126,10 @@ if test "x${HAVE_SEMIC}" == "xyes"; then SEMICINCL="-I${SEMIC_ROOT}" + if test "${IS_MSYS2}" == "yes"; then + SEMICLIB="-Wl,-L${SEMIC_ROOT}/lib -Wl,-lsurface_physics -Wl,-lutils" + else + SEMICLIB="-L${SEMIC_ROOT}/lib -lsurface_physics -lutils" + fi AC_DEFINE([_HAVE_SEMIC_], [1], [with SEMIC in ISSM src]) - SEMICLIB="-L${SEMIC_ROOT} -lsurface_physics -lutils" AC_SUBST([SEMICLIB]) AC_SUBST([SEMICINCL]) Index: /issm/trunk-jpl/src/c/Makefile.am =================================================================== --- /issm/trunk-jpl/src/c/Makefile.am (revision 26155) +++ /issm/trunk-jpl/src/c/Makefile.am (revision 26156) @@ -707,5 +707,5 @@ if !WINDOWS if !STANDALONE_LIBRARIES -libISSMCore_la_LIBADD = $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(CHACOLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS) +libISSMCore_la_LIBADD = $(CHACOLIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS) if FORTRAN libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB) @@ -733,5 +733,5 @@ libISSMModules_la_LIBADD = ./libISSMCore.la else -libISSMModules_la_LIBADD = ./libISSMCore.la $(TRIANGLELIB) $(CHACOLIB) +libISSMModules_la_LIBADD = ./libISSMCore.la $(TRIANGLELIB) $(CHACOLIB) $(BLASLAPACKLIB) $(OSLIBS) endif endif @@ -823,5 +823,5 @@ #External packages -LDADD += $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(CHACOLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS) +LDADD += $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS) if FORTRAN Index: /issm/trunk-jpl/src/c/modules/Chacox/chaco_seconds.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/Chacox/chaco_seconds.cpp (revision 26155) +++ /issm/trunk-jpl/src/c/modules/Chacox/chaco_seconds.cpp (revision 26156) @@ -1,5 +1,5 @@ /*This is needed, because the chaco library defines a "C" function seconds that conflicts with the Metis version.: */ -#ifdef _INTEL_WIN_ +#if defined(_INTEL_WIN_) || defined(_MSYS2_) #include #else Index: /issm/trunk-jpl/test/NightlyRun/IdFromString.m =================================================================== --- /issm/trunk-jpl/test/NightlyRun/IdFromString.m (revision 26155) +++ /issm/trunk-jpl/test/NightlyRun/IdFromString.m (revision 26156) @@ -20,7 +20,12 @@ %Grep string if strcmp(string,'*'), - [dummy ids_raw]=system(['find ./ -name "test[0-9]*.m" | xargs grep "%Test Name:" | sed -e "s/test/ /g" -e "s/\.m:/ /g" | awk {''print $2''}']); + [dummy ids_raw]=system(['find ./ -name "test[0-9]*.m" | xargs grep "%Test Name:" | sed -e "s/test/ /g" -e "s/\.m:/ /g" | cut -d" " -f 2']); else - [dummy ids_raw]=system(['find ./ -name "test[0-9]*.m" | xargs grep "%Test Name:" | grep ' string ' | sed -e "s/test/ /g" -e "s/\.m:/ /g" | awk {''print $2''}']); + [dummy ids_raw]=system(['find ./ -name "test[0-9]*.m" | xargs grep "%Test Name:" | grep ' string ' | sed -e "s/test/ /g" -e "s/\.m:/ /g" | cut -d" " -f 2']); +end + +%Check for error +if dummy~=0, + error(['system call failed:' newline ids_raw]); end