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[Einstein Toolkit] #1764: Error with compilation of HWLOC
by Einstein Toolkit 15 May '15

15 May '15

#1764: Error with compilation of HWLOC -----------------------------------+---------------------------------------- Reporter: maxim.barkov@… | Owner: Type: defect | Status: new Priority: blocker | Milestone: Component: Other | Version: development version Keywords: HWLOC | -----------------------------------+---------------------------------------- I updated the ET nightly version. The configuration works fine on the local Ubuntu gcc PC, but it fails to compile at CFCA CRAY XC30 cluster with Intel environment. I do not see error message. {{{ Using configuration: test ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not loaded ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not loaded ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not loaded ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not loaded ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not loaded Reconfiguring test Writing configuration to: /work/barkovmm/ET/Cactus/configs/test/OptionList ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not loaded Cactus - version: 4.2.3 Reconfiguring test. Using configuration options from configure line Setting fds to '4,5 -j --' End of options from configure line Adding configuration options from '/work/barkovmm/ET/Cactus/configs/test/OptionList'... Setting VERSION to 'cfca-2015-04-03' Setting CPP to 'cpp' Setting FPP to 'cpp' Setting CC to 'cc' Setting CXX to 'CC' Setting F77 to 'ftn' Setting F90 to 'ftn' Setting CPPFLAGS to '-g' Setting FPPFLAGS to '-g -traditional' Setting CFLAGS to '-g -debug all -traceback -xHost -align -std=gnu99 -ansi-alias' Setting CXXFLAGS to '-g -debug all -traceback -xHost -align -std=gnu++0x -ansi-alias -D__builtin_signbit=__signbit' Setting F77FLAGS to '-g -debug all -traceback -xHost -align -pad -safe_cray_ptr' Setting F90FLAGS to '-g -debug all -traceback -xHost -align -pad -safe_cray_ptr' Setting C_LINE_DIRECTIVES to 'yes' Setting F_LINE_DIRECTIVES to 'yes' Setting VECTORISE to 'yes' Setting VECTORISE_ALIGNED_ARRAYS to 'no' Setting VECTORISE_INLINE to 'no' Setting DEBUG to 'no' Setting CPP_DEBUG_FLAGS to '-DCARPET_DEBUG' Setting FPP_DEBUG_FLAGS to '-DCARPET_DEBUG' Setting C_DEBUG_FLAGS to '' Setting CXX_DEBUG_FLAGS to '' Setting F77_DEBUG_FLAGS to '-check bounds -check format' Setting F90_DEBUG_FLAGS to '-check bounds -check format' Setting OPTIMISE to 'yes' Setting CPP_OPTIMISE_FLAGS to '' Setting FPP_OPTIMISE_FLAGS to '' Setting C_OPTIMISE_FLAGS to '-O2 -no-prec-div' Setting CXX_OPTIMISE_FLAGS to '-Ofast' Setting F77_OPTIMISE_FLAGS to '-Ofast' Setting F90_OPTIMISE_FLAGS to '-Ofast' Setting C_NO_OPTIMISE_FLAGS to '-O0' Setting CXX_NO_OPTIMISE_FLAGS to '-O0' Setting F77_NO_OPTIMISE_FLAGS to '-O0' Setting F90_NO_OPTIMISE_FLAGS to '-O0' Setting PROFILE to 'no' Setting CPP_PROFILE_FLAGS to '' Setting FPP_PROFILE_FLAGS to '' Setting C_PROFILE_FLAGS to '-pg' Setting CXX_PROFILE_FLAGS to '-pg' Setting F77_PROFILE_FLAGS to '-pg' Setting F90_PROFILE_FLAGS to '-pg' Setting OPENMP to 'yes' Setting CPP_OPENMP_FLAGS to '-openmp' Setting FPP_OPENMP_FLAGS to '-fopenmp' Setting C_OPENMP_FLAGS to '-openmp' Setting CXX_OPENMP_FLAGS to '-openmp' Setting F77_OPENMP_FLAGS to '-openmp' Setting F90_OPENMP_FLAGS to '-openmp' Setting WARN to 'yes' Setting CPP_WARN_FLAGS to '' Setting FPP_WARN_FLAGS to '-Wall' Setting C_WARN_FLAGS to '' Setting CXX_WARN_FLAGS to '' Setting F90_WARN_FLAGS to '' Setting F77_WARN_FLAGS to '' Setting BLAS_DIR to 'NO_BUILD' Setting BOOST_DIR to 'BUILD' Setting FFTW_DIR to '/opt/fftw/3.3.4.0/haswell/' Setting GSL_DIR to '/work/ap/GSL/gsl-1.15/intel/' Setting GSL_INC_DIRS to '/work/ap/GSL/gsl-1.15/intel/include' Setting GSL_LIB_DIRS to '/work/ap/GSL/gsl-1.15/intel/lib' Setting HDF5_DIR to '/opt/cray/hdf5/1.8.13' Setting HWLOC_DIR to 'BUILD' Setting LAPACK_DIR to 'NO_BUILD' Setting MPI_DIR to 'NONE' Setting OPENBLAS_DIR to 'NO_BUILD' Setting OPENBLAS_LIBS to '' Setting PAPI_DIR to '/opt/cray/papi/5.3.2' Setting PETSC_DIR to '/opt/cray/petsc/3.5.1.0/real/INTEL/140/haswell/' Setting PTHREADS to 'yes' Setting ZLIB_DIR to 'BUILD' End of options from '/work/barkovmm/ET/Cactus/configs/test/OptionList'. }}} {{{ checking for stdint.h... (cached) yes checking sys/mman.h usability... yes checking sys/mman.h presence... yes checking for sys/mman.h... yes checking for KAFFINITY... no checking for PROCESSOR_CACHE_TYPE... no checking for CACHE_DESCRIPTOR... no checking for LOGICAL_PROCESSOR_RELATIONSHIP... no checking for RelationProcessorPackage... no checking for SYSTEM_LOGICAL_PROCESSOR_INFORMATION... no checking for GROUP_AFFINITY... no checking for PROCESSOR_RELATIONSHIP... no checking for NUMA_NODE_RELATIONSHIP... no checking for CACHE_RELATIONSHIP... no checking for PROCESSOR_GROUP_INFO... no checking for GROUP_RELATIONSHIP... no checking for SYSTEM_LOGICAL_PROCESSOR_INFORMATION_EX... no checking for PSAPI_WORKING_SET_EX_BLOCK... no checking for PSAPI_WORKING_SET_EX_INFORMATION... no checking for main in -lgdi32... no checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking sys/lgrp_user.h usability... no checking sys/lgrp_user.h presence... no checking for sys/lgrp_user.h... no checking kstat.h usability... no checking kstat.h presence... no checking for kstat.h... no checking whether fabsf is declared... yes checking for fabsf in -lm... icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' yes checking picl.h usability... no checking picl.h presence... no checking for picl.h... no checking whether _SC_NPROCESSORS_ONLN is declared... yes checking whether _SC_NPROCESSORS_CONF is declared... yes checking whether _SC_NPROC_ONLN is declared... no checking whether _SC_NPROC_CONF is declared... no checking whether _SC_PAGESIZE is declared... yes checking whether _SC_PAGE_SIZE is declared... yes checking whether _SC_LARGE_PAGESIZE is declared... no checking mach/mach_host.h usability... no checking mach/mach_host.h presence... no checking for mach/mach_host.h... no checking mach/mach_init.h usability... no checking mach/mach_init.h presence... no checking for mach/mach_init.h... no checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for sys/sysctl.h... yes checking whether CTL_HW is declared... no checking whether HW_NCPU is declared... no checking whether strtoull is declared... icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' yes checking for sysctl... icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' yes checking for sysctlbyname... no checking for pthread_t... yes checking whether function sched_setaffinity is declared... yes checking for old prototype of sched_setaffinity... no checking for working CPU_SET... yes checking for working CPU_SET_S... yes checking for working _syscall3... no checking for KERRIGHED... no checking for lib... no checking for bash... /bin/sh checking for ffs... yes checking whether function ffs is declared... yes checking for ffsl... yes checking whether function ffsl is declared... yes checking for fls... no checking for flsl... no checking for clz... no checking for clzl... no checking for openat... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for getpagesize... yes checking for memalign... yes checking for posix_memalign... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking for uname... yes checking pthread_np.h usability... no checking pthread_np.h presence... no checking for pthread_np.h... no checking whether pthread_setaffinity_np is declared... yes checking whether pthread_getaffinity_np is declared... yes checking for sched_setaffinity... yes checking for sys/cpuset.h... no checking for cpuset_setaffinity... no checking for library containing pthread_getthrds_np... no checking for cpuset_setid... no checking numaif.h usability... yes checking numaif.h presence... yes checking for numaif.h... yes checking for numa_available in -lnuma... no checking nvml.h usability... no checking nvml.h presence... no checking for nvml.h... no checking X11/Xlib.h usability... yes checking X11/Xlib.h presence... yes checking for X11/Xlib.h... yes checking for XOpenDisplay in -lX11... no checking NVCtrl/NVCtrl.h usability... no checking NVCtrl/NVCtrl.h presence... no checking for NVCtrl/NVCtrl.h... no checking for cpuid... yes checking for pthread_mutex_lock... yes checking if plugin support is enabled... no checking components to build statically... noos xml synthetic custom xml_nolibxml linux x86 checking components to build as plugins... checking for X... no ### ### Configuring hwloc documentation ### checking if this is a developer build... no (doxygen generation is optional) checking for doxygen... /usr/bin/doxygen checking for pdflatex... no checking for makeindex... no checking for fig2dev... no checking for gs... /usr/bin/gs checking for epstopdf... no checking if can build doxygen docs... no checking for a sed that does not truncate output... /usr/bin/sed checking if the sed -i option requires an argument... no checking for w3m... /usr/bin/w3m checking for lynx... no checking if can build top-level README... yes checking if will build doxygen docs... no checking if will install doxygen docs... yes checking whether to enable "picky" compiler mode... no (default) ### ### Configuring hwloc command line utilities ### checking for wchar_t... yes checking for putwc... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking for setlocale... (cached) yes checking for uselocale... yes checking xlocale.h usability... yes checking xlocale.h presence... yes checking for xlocale.h... yes checking for setlocale... (cached) yes checking for uselocale... (cached) yes checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking for nl_langinfo... yes checking termcap support using ncurses and ... no checking termcap support using ncurses and -ltermcap... no checking termcap support using ncurses and -lncursesw... yes checking whether diff accepts -u... -u checking whether diff accepts -w... -w ### ### Configuring hwloc tests ### checking for pthread_self in -lpthread... yes checking whether numa_bitmask_alloc is declared... yes checking infiniband/verbs.h usability... yes checking infiniband/verbs.h presence... yes checking for infiniband/verbs.h... yes checking for ibv_open_device in -libverbs... no checking myriexpress.h usability... no checking myriexpress.h presence... no checking for myriexpress.h... no checking for xmllint... xmllint checking for bunzip2... bunzip2 checking if CXX works... yes checking whether diff accepts -u... -u ### ### Performing final hwloc configuration ### checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3458764513820540925 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-linux-gnu file names to x86_64 -unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from cc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... yes checking whether a program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... CC -E checking for ld used by CC... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance checking whether the CC linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for CC option to produce PIC... -fPIC -DPIC checking if CC PIC flag -fPIC -DPIC works... yes checking if CC static flag -static works... yes checking if CC supports -c -o file.o... yes checking if CC supports -c -o file.o... (cached) yes checking whether the CC linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating include/Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating doc/doxygen-config.cfg config.status: creating utils/Makefile config.status: creating hwloc.pc config.status: creating tests/Makefile config.status: creating tests/linux/Makefile config.status: creating tests/linux/gather/Makefile config.status: creating tests/xml/Makefile config.status: creating tests/ports/Makefile config.status: creating tests/rename/Makefile config.status: creating tests/linux/hwloc-gather-topology config.status: creating tests/linux/gather/test-gather-topology.sh config.status: creating tests/linux/test-topology.sh config.status: creating tests/xml/test-topology.sh config.status: creating tests/wrapper.sh config.status: creating utils/hwloc-assembler-remote config.status: creating utils/test-hwloc-annotate.sh config.status: creating utils/test-hwloc-assembler.sh config.status: creating utils/test-hwloc-calc.sh config.status: creating utils/test-hwloc-distances.sh config.status: creating utils/test-hwloc-distrib.sh config.status: creating utils/test-hwloc-info.sh config.status: creating utils/test-hwloc-ls.sh config.status: creating utils/test-fake-plugin.sh config.status: creating include/private/autogen/config.h config.status: creating include/hwloc/autogen/config.h config.status: linking src/topology-solaris.c to tests/ports/topology- solaris.c config.status: linking src/topology-solaris-chiptype.c to tests/ports /topology-solaris-chiptype.c config.status: linking src/topology-aix.c to tests/ports/topology-aix.c config.status: linking src/topology-osf.c to tests/ports/topology-osf.c config.status: linking src/topology-windows.c to tests/ports/topology- windows.c config.status: linking src/topology-darwin.c to tests/ports/topology- darwin.c config.status: linking src/topology-freebsd.c to tests/ports/topology- freebsd.c config.status: linking src/topology-netbsd.c to tests/ports/topology- netbsd.c config.status: linking src/topology-hpux.c to tests/ports/topology-hpux.c config.status: linking src/topology-bgq.c to tests/ports/topology-bgq.c config.status: linking src/topology-opencl.c to tests/ports/topology- opencl.c config.status: linking src/topology-cuda.c to tests/ports/topology-cuda.c config.status: linking src/topology-nvml.c to tests/ports/topology-nvml.c config.status: linking src/topology-gl.c to tests/ports/topology-gl.c config.status: executing depfiles commands config.status: executing chmoding-scripts commands config.status: executing libtool commands ----------------------------------------------------------------------------- Hwloc optional build support status (more details can be found above): Probe / display I/O devices: no Graphical output (Cairo): no XML input / output: basic libnuma memory support: no Plugin support: no ----------------------------------------------------------------------------- hwloc: Building... Making all in src CC topology.lo CC traversal.lo CC distances.lo CC components.lo CC bind.lo CC bitmap.lo CC misc.lo CC base64.lo icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CC topology-noos.lo CC topology-synthetic.lo CC topology-custom.lo CC topology-xml.lo icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CC topology-xml-nolibxml.lo icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CC topology-linux.lo icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CC topology-x86.lo icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CCLD libhwloc.la Making all in include Making all in utils CC lstopo_no_graphics-lstopo.o CC lstopo_no_graphics-lstopo-color.o CC lstopo_no_graphics-lstopo-text.o CC lstopo_no_graphics-lstopo-draw.o CC lstopo_no_graphics-lstopo-fig.o CC lstopo_no_graphics-lstopo-xml.o CC hwloc-annotate.o CC hwloc-assembler.o icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CC hwloc-calc.o CC hwloc-bind.o CC hwloc-distances.o CC hwloc-distrib.o icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CC hwloc-info.o icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CC hwloc-ps.o icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' Creating hwloc.7 man page... Creating lstopo.1 man page... Creating hwloc-annotate.1 man page... Creating hwloc-bind.1 man page... Creating hwloc-calc.1 man page... Creating hwloc-distances.1 man page... Creating hwloc-distrib.1 man page... Creating hwloc-info.1 man page... Creating hwloc-ps.1 man page... Creating hwloc-assembler.1 man page... Creating hwloc-assembler-remote.1 man page... icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' Creating hwloc-gather-topology.1 man page... CCLD hwloc-annotate CCLD hwloc-assembler CCLD hwloc-distances icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CCLD hwloc-distrib CCLD hwloc-ps icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CCLD hwloc-calc icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' CCLD hwloc-bind ld: attempted static link of dynamic object `/work/barkovmm/ET/Cactus/configs/cid_rg/scratch/build/hwloc/hwloc-1.7.2/src/.libs/libhwloc.so' ld: attempted static link of dynamic object `/work/barkovmm/ET/Cactus/configs/cid_rg/scratch/build/hwloc/hwloc-1.7.2/src/.libs/libhwloc.so' make[5]: *** [hwloc-assembler] Error 1 make[5]: *** Waiting for unfinished jobs.... make[5]: *** [hwloc-annotate] Error 1 icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' ld: attempted static link of dynamic object `/work/barkovmm/ET/Cactus/configs/cid_rg/scratch/build/hwloc/hwloc-1.7.2/src/.libs/libhwloc.so' make[5]: *** [hwloc-distances] Error 1 icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' ld: attempted static link of dynamic object `/work/barkovmm/ET/Cactus/configs/cid_rg/scratch/build/hwloc/hwloc-1.7.2/src/.libs/libhwloc.so' make[5]: *** [hwloc-distrib] Error 1 ld: attempted static link of dynamic object `/work/barkovmm/ET/Cactus/configs/cid_rg/scratch/build/hwloc/hwloc-1.7.2/src/.libs/libhwloc.so' make[5]: *** [hwloc-ps] Error 1 ld: attempted static link of dynamic object `/work/barkovmm/ET/Cactus/configs/cid_rg/scratch/build/hwloc/hwloc-1.7.2/src/.libs/libhwloc.so' make[5]: *** [hwloc-calc] Error 1 ld: attempted static link of dynamic object `/work/barkovmm/ET/Cactus/configs/cid_rg/scratch/build/hwloc/hwloc-1.7.2/src/.libs/libhwloc.so' make[5]: *** [hwloc-bind] Error 1 make[4]: *** [all-recursive] Error 1 make[2]: *** [make.checked] Error 2 make[1]: *** [/work/barkovmm/ET/Cactus/configs/cid_rg/lib/libthorn_hwloc.a] Error 2 make: *** [cid_rg] Error 2 }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1764> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

1 28

[Einstein Toolkit] #1775: Add Boost to ET
by Einstein Toolkit 15 May '15

15 May '15

#1775: Add Boost to ET -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- There was a request to support Boost in the ET. I suggest to add our Boost thorn, in the same way that we currently support PETSc. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1775> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

1 3

[Einstein Toolkit] #1776: Wrong mpirun copied to utilities directory in MPI thorn
by Einstein Toolkit 13 May '15

13 May '15

#1776: Wrong mpirun copied to utilities directory in MPI thorn -----------------------------------+---------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Other | Version: development version Keywords: ExternalLibraries/MPI | -----------------------------------+---------------------------------------- On Mac OS, if I set MPI_DIR=BUILD in order to build OpenMPI using the MPI thorn, Cactus should copy the built version of mpirun into exe/<config>. However, if it finds one in /usr/local/bin, it copies that one instead. NB: to compile OpenMPI, you need gnu99 or later in CFLAGS, as OpenMPI needs the 'asm' directive, which is a GNU extension. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1776> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

1 3

[Einstein Toolkit] #1763: Several users unsubscribed from mailing lists
by Einstein Toolkit 11 May '15

11 May '15

#1763: Several users unsubscribed from mailing lists ----------------------+----------------------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: critical | Milestone: Component: Other | Version: development version Keywords: | ----------------------+----------------------------------------------------- It looks like I have been accidentally unsubscribed from several ET mailing lists. I received no unsubscription notification; I just stopped receiving the mails. The last posts I have from the users and tickets lists are from 26.03.2015. Eloisa and Oleg apparently also had this problem. I suspect others have also been unsubscribed, so it would be good to look into this and figure out what went wrong, and re-subscribe people. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1763> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1774: CarpetProlongateTest/test_cc_tvd_hi needs too much memory
by Einstein Toolkit 09 May '15

09 May '15

#1774: CarpetProlongateTest/test_cc_tvd_hi needs too much memory --------------------+------------------------------------------------------- Reporter: knarf | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- On a machine (VM) with 1GB RAM this fails, running out of memory. Given the nature of this test we should be able to make it smaller. After the 2015_05 release. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1774> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1751: [Pull request: CactusUtils/WatchDog] new thorn to automatically terminate jobs that hang
by Einstein Toolkit 01 May '15

01 May '15

#1751: [Pull request: CactusUtils/WatchDog] new thorn to automatically terminate jobs that hang -----------------------------------+---------------------------------------- Reporter: dradice@… | Owner: Type: enhancement | Status: new Priority: unset | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- WatchDog is thorn that terminates jobs that do not make progress over a user-defined time frame. Internally, WatchDog updates an internal timer at CCTK_ANALYSIS and uses the pthread library to spawn watcher thread that periodically checks if the timer has been updated. If the timer has not been updated for more than a user-defined time frame, the thread calls "exit()" to terminate the process (and the job). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1751> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1765: CarpetRegrid does not check for incorrect outer boundary size
by Einstein Toolkit 29 Apr '15

29 Apr '15

#1765: CarpetRegrid does not check for incorrect outer boundary size --------------------+------------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: unset | Milestone: Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- The attached parfile trigger an assert for inconsistent grid structure inside of CarpetLib. The issue is that boundary_size is set to 1 instead of 3. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1765> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1761: Problem with building on XC30 CFCA
by Einstein Toolkit 28 Apr '15

28 Apr '15

#1761: Problem with building on XC30 CFCA -----------------------------------+---------------------------------------- Reporter: maxim.barkov@… | Owner: Type: task | Status: new Priority: major | Milestone: Component: Cactus | Version: development version Keywords: | -----------------------------------+---------------------------------------- I try to compile ET on CFCA NAOJ cluster Cray XC30. I used as similar system edison in NERSC. So far I have problems with build procedure. CFCA is configured by default for Cray environment. In configuration file I switch programming enviroment to Intel and correct paths to actual ones. Unfortunately simfactory crashed. {{{ libtool: install: /usr/bin/install -c fftw-wisdom /home/barkovmm/ET/Cactus/configs/whisky/scratch/external/FFTW3/bin/fftw- wisdom Making install in m4 ~/ET/Cactus/configs/whisky/scratch FFTW3: Cleaning up... FFTW3: Done. Creating /home/barkovmm/ET/Cactus/configs/whisky/lib/libthorn_FFTW3.a make: *** [whisky] Error 2 }}} If I run comand on the cluster {{{make whisky_11}}} ET continue configuration and crushed on GSL {{{ icc: command line warning #10121: overriding '-xCORE-AVX2' with '-xHost' In file included from results.c(32): /usr/lib64/gcc/x86_64-suse-linux/4.3/include/varargs.h(4): error: #error directive: "GCC no longer implements <varargs.h>." #error "GCC no longer implements <varargs.h>." ^ In file included from results.c(32): /usr/lib64/gcc/x86_64-suse-linux/4.3/include/varargs.h(5): error: #error directive: "Revise your code to use <stdarg.h>." #error "Revise your code to use <stdarg.h>." ^ results.c(95): error #54: too few arguments in invocation of macro "va_start" va_start (ap); ^ results.c(95): error: expected an expression va_start (ap); ^ results.c(155): error #54: too few arguments in invocation of macro "va_start" va_start (ap); ^ results.c(155): error: expected an expression va_start (ap); ^ results.c(232): error #54: too few arguments in invocation of macro "va_start" va_start (ap); ^ results.c(232): error: expected an expression va_start (ap); ^ results.c(309): error #54: too few arguments in invocation of macro "va_start" va_start (ap); ^ results.c(309): error: expected an expression va_start (ap); ^ results.c(364): error #54: too few arguments in invocation of macro "va_start" va_start (ap); ^ results.c(364): error: expected an expression va_start (ap); ^ results.c(408): error #54: too few arguments in invocation of macro "va_start" va_start (ap); ^ results.c(408): error: expected an expression va_start (ap); ^ Internal error: null pointer compilation aborted for results.c (code 4) make[6]: *** [results.lo] Error 1 make[5]: *** [all-recursive] Error 1 make[4]: *** [all] Error 2 make[3]: *** [/work/barkovmm/ET/Cactus/configs/whisky_11/scratch/done/GSL] Error 2 make[2]: *** [make.checked] Error 2 make[1]: *** [/work/barkovmm/ET/Cactus/configs/whisky_11/lib/libthorn_GSL.a] Error 2 make: *** [whisky_11] Error 2 }}} Any help or suggestions are very welcome. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1761> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1768: Output of distrib=constant arrays
by Einstein Toolkit 27 Apr '15

27 Apr '15

#1768: Output of distrib=constant arrays -------------------------+-------------------------------------------------- Reporter: hinder | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: development version Keywords: | -------------------------+-------------------------------------------------- I have a Cactus array with size=1 and distrib=constant. I would like to see its value on all processes. According to http://cactuscode.org/pipermail/users/2014-March/003421.html, it has been observed that CarpetIOASCII (and CarpetIOHDF5) only output the data from process 0, whereas IOASCII outputs the data from all processes. The reason I need this is that I want to see the system swap usage on each process stored in SystemStatistics::process_memory_mb. The data is legitimately different on each process. {{{ REAL process_memory_mb TYPE=array DIM=1 SIZE=1 DISTRIB=constant TAGS='Checkpoint="no"' }}} How hard would it be to add support to CarpetIOASCII for outputting grid array data from all processes for distrib-constant arrays? It already does this for distrib=default. To use the current functionality, one way would be to increase the size of the array and then write code to replicate the data between processes. However, I don't think there is any way to specify that the array should have size=NPROCS, so you would have to specify this using a parameter, and this is a lot of work for something which would more naturally be done in CarpetIOASCII. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1768> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1767: test system does not remove old test data before running new test
by Einstein Toolkit 24 Apr '15

24 Apr '15

#1767: test system does not remove old test data before running new test -----------------------+---------------------------------------------------- Reporter: anonymous | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: development version Keywords: | -----------------------+---------------------------------------------------- When running a test, the test system does not delete the old test output directory first which can hide missing files. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1767> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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