=>> Building science/cardioid build started at Tue Dec 16 16:31:22 EST 2025 port directory: /usr/ports/science/cardioid package name: cardioid-g20211026_4 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p1 FreeBSD 14.3-RELEASE-p1 1403000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1391 Jan 31 2025 /usr/ports/science/cardioid/Makefile Ports top last git commit: 10f7dee57a4c Ports top unclean checkout: no Port dir last git commit: 6cce1f5b223a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 10 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p1 1403000 UNAME_r=14.3-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for cardioid-g20211026_4: MFEM=off: Build with MFEM mesh library OPENMP=on: Parallel processing support via OpenMP ====> MPI (Message Passing Interface) support: you have to select exactly one of them NOMPI=off: Build without parallel processing support MPICH=on: Parallel processing support via MPICH OPENMPI=off: Parallel processing support via Open MPI ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/cardioid/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/cardioid/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/cardioid/work/.cache HOME=/wrkdirs/usr/ports/science/cardioid/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/cardioid/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/cardioid/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/science/cardioid/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/cardioid/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/cardioid/work/.cache HOME=/wrkdirs/usr/ports/science/cardioid/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/cardioid/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/cardioid/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/science/cardioid/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- MFEM="@comment " NO_MFEM="" MPICH="" NO_MPICH="@comment " NOMPI="@comment " NO_NOMPI="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" CMAKE_BUILD_TYPE="release" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cardioid" EXAMPLESDIR="share/examples/cardioid" DATADIR="share/cardioid" WWWDIR="www/cardioid" ETCDIR="etc/cardioid" --End PLIST_SUB-- --SUB_LIST-- MFEM="@comment " NO_MFEM="" MPICH="" NO_MPICH="@comment " NOMPI="@comment " NO_NOMPI="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cardioid DOCSDIR=/usr/local/share/doc/cardioid EXAMPLESDIR=/usr/local/share/examples/cardioid WWWDIR=/usr/local/www/cardioid ETCDIR=/usr/local/etc/cardioid --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cardioid-g20211026_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> cardioid-g20211026_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cardioid-g20211026_4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cardioid-g20211026_4 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cardioid-g20211026_4 for building => SHA256 Checksum OK for LLNL-cardioid-g20211026-2f66d9f_GH0.tar.gz. => SHA256 Checksum OK for mfem-mfem-v4.4_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cardioid-g20211026_4 for building ===> Extracting for cardioid-g20211026_4 => SHA256 Checksum OK for LLNL-cardioid-g20211026-2f66d9f_GH0.tar.gz. => SHA256 Checksum OK for mfem-mfem-v4.4_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for cardioid-g20211026_4 ===> Applying FreeBSD patches for cardioid-g20211026_4 from /usr/ports/science/cardioid/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cardioid-g20211026_4 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.10.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.10... [pkg.DaveG.ca] `-- Installing expat-2.7.3... [pkg.DaveG.ca] `-- Extracting expat-2.7.3: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.51.0... [pkg.DaveG.ca] `-- Extracting libuv-1.51.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.4_2... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] `-- Extracting rhash-1.4.4_2: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.10: .......... done ===> cardioid-g20211026_4 depends on file: /usr/local/bin/cmake - found ===> Returning to build of cardioid-g20211026_4 ===> cardioid-g20211026_4 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.1,4.pkg [pkg.DaveG.ca] Installing ninja-1.13.1,4... [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.1... [pkg.DaveG.ca] | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] Extracting ninja-1.13.1,4: ..... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> cardioid-g20211026_4 depends on executable: ninja - found ===> Returning to build of cardioid-g20211026_4 ===> cardioid-g20211026_4 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> cardioid-g20211026_4 depends on file: /usr/local/bin/ccache - found ===> Returning to build of cardioid-g20211026_4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cardioid-g20211026_4 depends on shared library: libblas.so - not found ===> Installing existing package /packages/All/blas-3.12.1.pkg [pkg.DaveG.ca] Installing blas-3.12.1... [pkg.DaveG.ca] `-- Installing gcc13-13.3.0_3... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc13-13.3.0_3: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg.DaveG.ca] Extracting blas-3.12.1: ..... done ===== Message from gcc13-13.3.0_3: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> cardioid-g20211026_4 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> Returning to build of cardioid-g20211026_4 ===> cardioid-g20211026_4 depends on shared library: liblapack.so - not found ===> Installing existing package /packages/All/lapack-3.12.1.pkg [pkg.DaveG.ca] Installing lapack-3.12.1... [pkg.DaveG.ca] Extracting lapack-3.12.1: .......... done ===> cardioid-g20211026_4 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Returning to build of cardioid-g20211026_4 ===> cardioid-g20211026_4 depends on shared library: libmpich.so - not found ===> Installing existing package /packages/All/mpich-4.3.2.pkg [pkg.DaveG.ca] Installing mpich-4.3.2... [pkg.DaveG.ca] `-- Installing hwloc2-2.12.1_1... [pkg.DaveG.ca] | `-- Installing level-zero-1.26.0... [pkg.DaveG.ca] | | `-- Installing libfmt-12.1.0... [pkg.DaveG.ca] | | `-- Extracting libfmt-12.1.0: .......... done [pkg.DaveG.ca] | | `-- Installing spdlog-1.16.0_1... [pkg.DaveG.ca] | | `-- Extracting spdlog-1.16.0_1: .......... done [pkg.DaveG.ca] | `-- Extracting level-zero-1.26.0: .......... done [pkg.DaveG.ca] | `-- Installing libpciaccess-0.18.1_1... [pkg.DaveG.ca] | | `-- Installing hwdata-0.402,1... [pkg.DaveG.ca] | | `-- Extracting hwdata-0.402,1: ...... done [pkg.DaveG.ca] | `-- Extracting libpciaccess-0.18.1_1: ..... done [pkg.DaveG.ca] | `-- Installing libxml2-2.14.6... [pkg.DaveG.ca] | `-- Extracting libxml2-2.14.6: .......... done [pkg.DaveG.ca] `-- Extracting hwloc2-2.12.1_1: .......... done [pkg.DaveG.ca] `-- Installing json-c-0.18... [pkg.DaveG.ca] `-- Extracting json-c-0.18: .......... done [pkg.DaveG.ca] `-- Installing libepoll-shim-0.0.20240608... [pkg.DaveG.ca] `-- Extracting libepoll-shim-0.0.20240608: .......... done [pkg.DaveG.ca] `-- Installing libfabric-1.15.1_4... [pkg.DaveG.ca] `-- Extracting libfabric-1.15.1_4: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting mpich-4.3.2: .......... done ===> cardioid-g20211026_4 depends on shared library: libmpich.so - found (/usr/local/lib/libmpich.so) ===> Returning to build of cardioid-g20211026_4 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for cardioid-g20211026_4 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/science/cardioid/work/.build CMake Warning (dev) at CMakeLists.txt:32 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is Clang 19.1.7 -- The CXX compiler identification is Clang 19.1.7 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:33 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Could NOT find Git (missing: GIT_EXECUTABLE) -- Git Support is OFF -- MPI Support is ON -- Found MPI_C: /usr/local/lib/libmpi.so (found version "4.1") -- Found MPI_CXX: /usr/local/lib/libmpicxx.so (found version "4.1") -- Found MPI: TRUE (found version "4.1") -- MPI C Compile Flags: -- MPI C Include Path: /usr/local/include/json-c;/usr/local/include/gcc13;/usr/local/include -- MPI C Link Flags: -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -- MPI C Libraries: /usr/local/lib/libmpi.so -- MPI CXX Compile Flags: -- MPI CXX Include Path: /usr/local/include -- MPI CXX Link Flags: -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -- MPI CXX Libraries: /usr/local/lib/libmpicxx.so;/usr/local/lib/libmpi.so -- MPI Executable: /usr/local/bin/mpiexec -- MPI Num Proc Flag: -n -- MPI Command Append: CMake Warning (dev) at blt/cmake/BLTMacros.cmake:314 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): blt/cmake/thirdparty/SetupMPI.cmake:93 (blt_register_library) blt/cmake/thirdparty/SetupThirdParty.cmake:69 (include) blt/SetupBLT.cmake:107 (include) CMakeLists.txt:48 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at blt/cmake/BLTMacros.cmake:331 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): blt/cmake/thirdparty/SetupMPI.cmake:93 (blt_register_library) blt/cmake/thirdparty/SetupThirdParty.cmake:69 (include) blt/SetupBLT.cmake:107 (include) CMakeLists.txt:48 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- CUDA Support is OFF -- ROCM Support is OFF -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Sphinx support is ON -- Failed to locate Sphinx executable (missing: SPHINX_EXECUTABLE) -- Valgrind support is ON -- Failed to locate Valgrind executable (missing: VALGRIND_EXECUTABLE) -- Uncrustify support is ON -- Failed to locate Uncrustify executable (missing: UNCRUSTIFY_EXECUTABLE) -- Cppcheck support is ON -- Failed to locate Cppcheck executable (missing: CPPCHECK_EXECUTABLE) CMake Warning (dev) at blt/SetupBLT.cmake:170 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:48 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at blt/SetupBLT.cmake:172 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:48 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- OpenMP Support is true -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") -- OpenMP CXX Flags: -fopenmp=libomp -- C Compiler family is Clang -- Adding optional BLT definitions and compiler flags -- Standard C++11 selected -- Fortran support disabled. -- CMAKE_C_FLAGS flags are: -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -- CMAKE_CXX_FLAGS flags are: -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -- CMAKE_EXE_LINKER_FLAGS flags are: CMake Warning (dev) at blt/cmake/BLTMacros.cmake:483 (target_sources): Policy CMP0076 is not set: target_sources() command converts relative paths to absolute. Run "cmake --help-policy CMP0076" for policy details. Use the cmake_policy command to set the policy and suppress this warning. An interface source of target "simdops" has a relative path. Call Stack (most recent call first): simdops/CMakeLists.txt:2 (blt_add_library) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at blt/cmake/BLTMacros.cmake:314 (set): implicitly converting 'LIST' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:104 (blt_register_library) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (30.5s) -- Generating done (0.8s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/science/cardioid/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for cardioid-g20211026_4 [ 0% 34/116] /usr/local/libexec/ccache/cc -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong 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deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 249 | set_SP(cnst); | ^ 1 warning generated. [ 16% 34/116] /usr/local/libexec/ccache/cc -DHAVE_LAPACK -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu99 -fPIC -fopenmp=libomp -MD -MT elec/CMakeFiles/ode_cpu_only.dir/svd.c.o -MF elec/CMakeFiles/ode_cpu_only.dir/svd.c.o.d -o elec/CMakeFiles/ode_cpu_only.dir/svd.c.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/svd.c [ 17% 34/116] /usr/local/libexec/ccache/cc -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu99 -fPIC -fopenmp=libomp -MD -MT elec/CMakeFiles/heart_cpu_only.dir/spi_impl.c.o -MF elec/CMakeFiles/heart_cpu_only.dir/spi_impl.c.o.d -o elec/CMakeFiles/heart_cpu_only.dir/spi_impl.c.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/spi_impl.c [ 18% 34/116] /usr/local/libexec/ccache/cc -DHAVE_LAPACK -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu99 -fPIC -fopenmp=libomp -MD -MT elec/CMakeFiles/ode_cpu_only.dir/TT06GatesSimd2.c.o -MF elec/CMakeFiles/ode_cpu_only.dir/TT06GatesSimd2.c.o.d -o elec/CMakeFiles/ode_cpu_only.dir/TT06GatesSimd2.c.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/TT06GatesSimd2.c In file included from /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/TT06GatesSimd2.c:3: /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/portableSIMD.h:68:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 68 | } | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/TT06GatesSimd2.c:39:7: warning: expression result unused [-Wunused-value] 39 | for (jj;jj:9:1: note: expanded from here 9 | "/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/setConductivity.cc" | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/setConductivity.cc:276:7: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 276 | abortAll(1); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include/mpiUtils.h:39:39: note: expanded from macro 'abortAll' 39 | #define abortAll(x) abortAll_core((x),__FILE__,__LINE__) | ^ :11:1: note: expanded from here 11 | "/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/setConductivity.cc" | ^ 2 warnings generated. [ 83% 112/116] /usr/local/libexec/ccache/c++ -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIC -fopenmp=libomp -MD -MT elec/CMakeFiles/heart_gpu_aware.dir/initializeSimulate.cc.o -MF elec/CMakeFiles/heart_gpu_aware.dir/initializeSimulate.cc.o.d -o elec/CMakeFiles/heart_gpu_aware.dir/initializeSimulate.cc.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/initializeSimulate.cc /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/initializeSimulate.cc:342:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 342 | int coord[nDims]; | ^~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/initializeSimulate.cc:342:17: note: read of non-const variable 'nDims' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/initializeSimulate.cc:341:11: note: declared here 341 | int nDims = hi_nTorusDim(); | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/initializeSimulate.cc:349:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 349 | int size[nDims]; | ^~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/initializeSimulate.cc:349:19: note: read of non-const variable 'nDims' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/initializeSimulate.cc:341:11: note: declared here 341 | int nDims = hi_nTorusDim(); | ^ 2 warnings generated. [ 84% 112/116] /usr/local/libexec/ccache/c++ -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIC -fopenmp=libomp -MD -MT elec/CMakeFiles/heart_gpu_aware.dir/FGRDiffusionOMP.cc.o -MF elec/CMakeFiles/heart_gpu_aware.dir/FGRDiffusionOMP.cc.o.d -o elec/CMakeFiles/heart_gpu_aware.dir/FGRDiffusionOMP.cc.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/FGRDiffusionOMP.cc [ 85% 112/116] /usr/local/libexec/ccache/c++ -DDiff_Weight_Type_Single -DHAVE_LAPACK -DWITH_MPI -DWITH_PIO -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simUtil/src/../include -I/wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/simdops/include -isystem /usr/local/include/json-c -isystem /usr/local/include/gcc13 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++11 -fPIE -fopenmp=libomp -MD -MT elec/CMakeFiles/modifyAnatomyFile.dir/modifyAnatomyFile.cc.o -MF elec/CMakeFiles/modifyAnatomyFile.dir/modifyAnatomyFile.cc.o.d -o elec/CMakeFiles/modifyAnatomyFile.dir/modifyAnatomyFile.cc.o -c /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:71:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 71 | double work[lwork]; | ^~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:71:19: note: read of non-const variable 'lwork' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:62:8: note: declared here 62 | int lwork; | ^ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:83:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 83 | double work[lwork]; | ^~~~~ /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:83:19: note: read of non-const variable 'lwork' is not allowed in a constant expression /wrkdirs/usr/ports/science/cardioid/work/cardioid-2f66d9f/elec/modifyAnatomyFile.cc:62:8: note: declared here 62 | int lwork; | ^ 2 warnings generated. 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lib/libthreading.a lib/libheart_cpu_only.a lib/libsimUtil.a /usr/local/lib/liblapack.so /usr/local/lib/libblas.so /usr/local/lib/liblapack.so /usr/local/lib/libblas.so /usr/local/lib/libmpi.so /usr/local/lib/libmpicxx.so /usr/local/lib/libmpi.so /usr/local/lib/libmpicxx.so && : =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cardioid-g20211026_4 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.9.pkg [pkg.DaveG.ca] Installing bash-5.3.9... [pkg.DaveG.ca] Extracting bash-5.3.9: .......... done ===> cardioid-g20211026_4 depends on executable: bash - found ===> Returning to build of cardioid-g20211026_4 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for cardioid-g20211026_4 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/science/cardioid/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/cardioid -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/cardioid" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/singleCell -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/singleCell" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/science/cardioid/work/stage/usr/local/bin/compileReaction ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-16T21:31:22+0000' 'PKG_NOTE_ports_top_git_hash=10f7dee57a4c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=6cce1f5b223a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for cardioid-g20211026_4 ===> Building cardioid-g20211026_4 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for cardioid-g20211026_4 build of science/cardioid | cardioid-g20211026_4 ended at Tue Dec 16 16:33:37 EST 2025 build time: 00:02:16