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Einstein Toolkit Meeting Reminder
by Frank Loeffler 20 Jun '11

20 Jun '11

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Points of discussion: 1) Inclusion of CCE code into the Einstein Toolkit 2) ET paper Frank Loeffler

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HDF5 compile issues w/ or w/o CactusExternal/HDF5
by Scott Hawley 19 Jun '11

19 Jun '11

Hi. I'm unable to get HDF5 capability to install. If I set HDF5_DIR=/sw, which is the installation already on my machine, I get the error message that I need a thorn that implements HDF5. ("CST error 1: -> Thorn 'CarpetIOHDF5' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'CarpetIOHDF5' from it !") If I leave HDF5_DIR unset (and all other "HDF5" flags unset as well) and include CactusExternal/HDF5 in my Thornlist, then I also get an error message saying it's unable to compile, as shown below. To be clear, the options settings which are either left in the file or commented out via "#", are: HDF5 = YES HDF5_DIR = /sw ZLIB_DIR = /sw I tried searching online for previous users messages about this or instructions and have not found them. What am I doing wrong? Thanks, -Scott example of compilation with no HDF5 flags set: % gmake texmex ...skipping... + echo 'HDF5 selected, but HDF5_DIR not set. Checking some places...' + echo 'END MESSAGE' ++ '[' gfortran '!=' none ']' ++ echo lib/libhdf5_fortran.a + FILES='include/hdf5.h lib/libhdf5.a lib/libhdf5_cpp.a lib/libhdf5_fortran.a lib/libhdf5_hl.a lib/libhdf5_hl_cpp.a' + DIRS='/usr /usr/local /usr/local/hdf5 /usr/local/packages/hdf5 /usr/local/apps/hdf5 /opt/local /Users/shawley /Users/shawley/hdf5 c:/packages/hdf5' + for dir in '$DIRS' + HDF5_DIR=/usr + for file in '$FILES' + '[' '!' -r /usr/include/hdf5.h ']' + unset HDF5_DIR + break + '[' -n '' ']' + for dir in '$DIRS' + HDF5_DIR=/usr/local + for file in '$FILES' + '[' '!' -r /usr/local/include/hdf5.h ']' + unset HDF5_DIR + break + '[' -n '' ']' + for dir in '$DIRS' + HDF5_DIR=/usr/local/hdf5 + for file in '$FILES' + '[' '!' -r /usr/local/hdf5/include/hdf5.h ']' + unset HDF5_DIR + break + '[' -n '' ']' + for dir in '$DIRS' + HDF5_DIR=/usr/local/packages/hdf5 + for file in '$FILES' + '[' '!' -r /usr/local/packages/hdf5/include/hdf5.h ']' + unset HDF5_DIR + break + '[' -n '' ']' + for dir in '$DIRS' + HDF5_DIR=/usr/local/apps/hdf5 + for file in '$FILES' + '[' '!' -r /usr/local/apps/hdf5/include/hdf5.h ']' + unset HDF5_DIR + break + '[' -n '' ']' + for dir in '$DIRS' + HDF5_DIR=/opt/local + for file in '$FILES' + '[' '!' -r /opt/local/include/hdf5.h ']' + unset HDF5_DIR + break + '[' -n '' ']' + for dir in '$DIRS' + HDF5_DIR=/Users/shawley + for file in '$FILES' + '[' '!' -r /Users/shawley/include/hdf5.h ']' + unset HDF5_DIR + break + '[' -n '' ']' + for dir in '$DIRS' + HDF5_DIR=/Users/shawley/hdf5 + for file in '$FILES' + '[' '!' -r /Users/shawley/hdf5/include/hdf5.h ']' + unset HDF5_DIR + break + '[' -n '' ']' + for dir in '$DIRS' + HDF5_DIR=c:/packages/hdf5 + for file in '$FILES' + '[' '!' -r c:/packages/hdf5/include/hdf5.h ']' + unset HDF5_DIR + break + '[' -n '' ']' + '[' -z '' ']' + echo 'BEGIN MESSAGE' + echo 'HDF5 not found' + echo 'END MESSAGE' + '[' -z '' -o '' = BUILD ']' + echo 'BEGIN MESSAGE' + echo 'Building HDF5...' + echo 'END MESSAGE' + THORN=HDF5 + NAME=hdf5-1.8.6 ++ dirname /Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5/HDF5.sh + SRCDIR=/Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5 + BUILD_DIR=/Users/shawley/Cactus/configs/texmex/scratch/build/HDF5 + INSTALL_DIR=/Users/shawley/Cactus/configs/texmex/scratch/external/HDF5 + DONE_FILE=/Users/shawley/Cactus/configs/texmex/scratch/done/HDF5 + HDF5_DIR=/Users/shawley/Cactus/configs/texmex/scratch/external/HDF5 + exec + set -x + set -e + cd /Users/shawley/Cactus/configs/texmex/scratch + '[' -e /Users/shawley/Cactus/configs/texmex/scratch/done/HDF5 -a /Users/shawley/Cactus/configs/texmex/scratch/done/HDF5 -nt /Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5/dist/hdf5-1.8.6.tar.gz -a /Users/shawley/Cactus/configs/texmex/scratch/done/HDF5 -nt /Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5/HDF5.sh ']' + echo 'HDF5: Building enclosed HDF5 library' HDF5: Building enclosed HDF5 library ++ gmake --help ++ echo make + MAKE=make ++ gtar --help ++ echo gtar + TAR=gtar + '[' -z patch ']' + '[' gfortran = none ']' + export FC=gfortran + FC=gfortran + export FCFLAGS=-m64 + FCFLAGS=-m64 + export LDFLAGS + unset LIBS + unset RPATH + echo '' rucs + grep 64 + echo 'HDF5: Preparing directory structure...' HDF5: Preparing directory structure... + mkdir build external done + true + rm -rf /Users/shawley/Cactus/configs/texmex/scratch/build/HDF5 /Users/shawley/Cactus/configs/texmex/scratch/external/HDF5 + mkdir /Users/shawley/Cactus/configs/texmex/scratch/build/HDF5 /Users/shawley/Cactus/configs/texmex/scratch/external/HDF5 + echo 'HDF5: Unpacking archive...' HDF5: Unpacking archive... + pushd /Users/shawley/Cactus/configs/texmex/scratch/build/HDF5 ~/Cactus/configs/texmex/scratch/build/HDF5 ~/Cactus/configs/texmex/scratch + gtar xzf /Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5/dist/hdf5-1.8.6.tar.gz + patch -p0 patching file hdf5-1.8.6/test/dt_arith.c + echo 'HDF5: Configuring...' HDF5: Configuring... + cd hdf5-1.8.6 ++ '[' -n gfortran ']' ++ echo '' --enable-fortran + ./configure --prefix=/Users/shawley/Cactus/configs/texmex/scratch/external/HDF5 --with-zlib=/Users/shawley/Cactus/configs/texmex/scratch/external/zlib --enable-cxx --enable-fortran checking for a BSD-compatible install... usage: install installation-prefix Example: install /usr/local Note: See script source for user-modifiable environment variables that may need to be tailored to your desired compilation environment. /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... bin/install-sh -c -d checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... i386-apple-darwin10.7.4 checking host system type... i386-apple-darwin10.7.4 checking shell variables initial values... done checking if basename works... yes checking if xargs works... yes checking for cached host... none checking for config i386-apple-darwin10.7.4... no checking for config i386-apple-darwin10.7.4... no checking for config apple-darwin10.7.4... no checking for config apple-darwin10.7.4... no checking for config i386-darwin10.7.4... no checking for config i386-darwin10.7.4... no checking for config i386-apple... no checking for config darwin10.7.4... no checking for config darwin10.7.4... no checking for config apple... found compiler '/sw/bin/mpicc' is GNU gcc-4.2.1 compiler 'gfortran' is GNU gfortran-4.4.4 Warning: shared libraries are not supported with Fortran Disabling shared libraries No match to get cc_version_info for /sw/bin/mpicc No match to get cxx_version_info for /sw/bin/mpic++ checking for config ./config/site-specific/host-provision.local... no checking for config ./config/site-specific/host-local... no checking for gcc... /sw/bin/mpicc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /sw/bin/mpicc accepts -g... yes checking for /sw/bin/mpicc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of /sw/bin/mpicc... gcc3 checking if Fortran interface enabled... yes checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking for Fortran flag to compile .f90 files... none checking whether we are using the GNU Fortran compiler... (cached) yes checking whether gfortran accepts -g... (cached) yes checking what gfortran does with modules... MODULE.mod checking how gfortran finds modules... -I checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/sw/lib -L/Users/shawley/lib -L/Users/shawley/texmex/lib -L/sw/lib/gcc4.4/lib/ -L/sw/lib/gcc4.4/lib/gcc/x86_64-apple-darwin10.7.3/4.4.4 -L/sw/lib/gcc4.4/lib/gcc/x86_64-apple-darwin10.7.3/4.4.4/../../.. -lgfortranbegin -lgfortran checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking if Fortran compiler supports intrinsic SIZEOF... yes checking if Fortran default REAL is DOUBLE PRECISION... no checking whether we are using the GNU C++ compiler... yes checking whether /sw/bin/mpic++ accepts -g... yes checking dependency style of /sw/bin/mpic++... gcc3 checking how to run the C++ preprocessor... /sw/bin/mpic++ -E checking if c++ interface enabled... yes checking if /sw/bin/mpic++ needs old style header files in includes... no checking if /sw/bin/mpic++ can handle namespaces... yes checking if /sw/bin/mpic++ supports std... yes checking if /sw/bin/mpic++ supports bool types... yes checking if /sw/bin/mpic++ has offsetof extension... yes checking if /sw/bin/mpic++ can handle static cast... yes checking for perl... perl checking whether make sets $(MAKE)... (cached) yes checking for tr... /usr/bin/tr checking if srcdir= and time commands work together... yes checking for mpiexec... none checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by /sw/bin/mpicc... /sw/bin/mpic++ checking if the linker (/sw/bin/mpic++) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /sw/bin/mpic++ option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from /sw/bin/mpicc object... ok checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... /usr/bin/cpp checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if /sw/bin/mpicc supports -fno-rtti -fno-exceptions... no checking for /sw/bin/mpicc option to produce PIC... -fno-common -DPIC checking if /sw/bin/mpicc PIC flag -fno-common -DPIC works... yes checking if /sw/bin/mpicc static flag -static works... no checking if /sw/bin/mpicc supports -c -o file.o... yes checking if /sw/bin/mpicc supports -c -o file.o... (cached) yes checking whether the /sw/bin/mpicc linker (/sw/bin/mpic++) supports shared libraries... yes checking dynamic linker characteristics... darwin10.7.4 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... /sw/bin/mpic++ -E checking for ld used by /sw/bin/mpic++... /sw/bin/mpic++ checking if the linker (/sw/bin/mpic++) is GNU ld... no checking whether the /sw/bin/mpic++ linker (/sw/bin/mpic++) supports shared libraries... yes checking for /sw/bin/mpic++ option to produce PIC... -fno-common -DPIC checking if /sw/bin/mpic++ PIC flag -fno-common -DPIC works... yes checking if /sw/bin/mpic++ static flag -static works... no checking if /sw/bin/mpic++ supports -c -o file.o... yes checking if /sw/bin/mpic++ supports -c -o file.o... (cached) yes checking whether the /sw/bin/mpic++ linker (/sw/bin/mpic++) supports shared libraries... yes checking dynamic linker characteristics... darwin10.7.4 dyld checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fno-common checking if gfortran PIC flag -fno-common works... yes checking if gfortran static flag -static works... no checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/sw/bin/mpic++) supports shared libraries... yes checking dynamic linker characteristics... darwin10.7.4 dyld checking how to hardcode library paths into programs... immediate checking if we should install only statically linked executables... no checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes checking make... checking how make searches directories... VPATH=DIR1 DIR2 ... checking whether make will build with undefined variables... yes checking for production mode... production checking for ceil in -lm... yes checking for ANSI C header files... (cached) yes checking whether time.h and sys/time.h may both be included... yes checking for difftime... yes checking for gettimeofday... yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking sys/ioctl.h usability... yes checking sys/ioctl.h presence... yes checking for sys/ioctl.h... yes checking for sys/stat.h... (cached) yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for sys/types.h... (cached) yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking setjmp.h usability... yes checking setjmp.h presence... yes checking for setjmp.h... yes checking features.h usability... no checking features.h presence... no checking for features.h... no checking for stdint.h... (cached) yes checking io.h usability... no checking io.h presence... no checking for io.h... no checking winsock.h usability... no checking winsock.h presence... no checking for winsock.h... no checking sys/timeb.h usability... yes checking sys/timeb.h presence... yes checking for sys/timeb.h... yes checking if configure should try to set up large file support... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking if large (64-bit) files are supported on this system.... yes skipping test for lseek64(), fseeko64 , ftello64, ftruncate64() because off64_t is not defined checking for fseeko... yes checking for ftello... yes checking for stat64... yes checking for fstat64... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for ptrdiff_t... yes checking whether byte ordering is bigendian... no checking size of char... 1 checking size of short... 2 checking size of int... 4 checking size of unsigned... 4 checking size of long... 8 checking size of long long... 8 checking size of __int64... 0 checking size of float... 4 checking size of double... 8 checking size of long double... 16 checking size of int8_t... 1 checking size of uint8_t... 1 checking size of int_least8_t... 1 checking size of uint_least8_t... 1 checking size of int_fast8_t... 1 checking size of uint_fast8_t... 1 checking size of int16_t... 2 checking size of uint16_t... 2 checking size of int_least16_t... 2 checking size of uint_least16_t... 2 checking size of int_fast16_t... 2 checking size of uint_fast16_t... 2 checking size of int32_t... 4 checking size of uint32_t... 4 checking size of int_least32_t... 4 checking size of uint_least32_t... 4 checking size of int_fast32_t... 4 checking size of uint_fast32_t... 4 checking size of int64_t... 8 checking size of uint64_t... 8 checking size of int_least64_t... 8 checking size of uint_least64_t... 8 checking size of int_fast64_t... 8 checking size of uint_fast64_t... 8 checking size of size_t... 8 checking size of ssize_t... 8 checking size of ptrdiff_t... 8 checking size of off_t... 8 checking size of off64_t... 0 checking if dev_t is scalar... yes checking for dmalloc library... suppressed checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for compress2 in -lz... yes checking for compress2... yes checking for szlib... suppressed checking for pthread... suppressed checking for thread safe support... no checking for tm_gmtoff in struct tm... yes checking for __tm_gmtoff in struct tm... no checking for global timezone variable... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for struct tm.tm_zone... yes checking for struct timezone... yes checking whether gettimeofday() gives timezone... yes checking for st_blocks in struct stat... yes checking for _getvideoconfig... no checking for gettextinfo... no checking for GetConsoleScreenBufferInfo... no checking for _scrsize... no checking for ioctl... yes checking for struct videoconfig... no checking for struct text_info... no checking for TIOCGWINSZ... yes checking for TIOCGETD... yes checking for alarm... yes checking for BSDgettimeofday... no checking for fork... yes checking for frexpf... yes checking for frexpl... yes checking for gethostname... yes checking for getpwuid... yes checking for getrusage... yes checking for lstat... yes checking for rand_r... yes checking for random... yes checking for setsysinfo... no checking for signal... yes checking for longjmp... yes checking for setjmp... yes checking for siglongjmp... yes checking for sigsetjmp... yes checking for sigprocmask... yes checking for snprintf... yes checking for srandom... yes checking for strdup... yes checking for symlink... yes checking for system... yes checking for tmpfile... yes checking for vasprintf... yes checking for waitpid... yes checking for vsnprintf... yes checking if vsnprintf returns correct value... yes checking if lone colon can be used as an argument... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for __attribute__ extension... yes checking for __func__ extension... yes checking for __FUNCTION__ extension... yes checking for C99 designated initialization support... yes checking how to print long long... %ld and %lu checking Threads support system scope... yes checking for gpfs... suppressed checking for debug flags... none checking whether function stack tracking is enabled... no checking whether metadata trace file code is enabled... no checking for API tracing... no checking for instrumented library... no checking whether to clear file buffers... yes checking whether a memory checking tool will be used... no configure: error: An MPI compiler is being used; --enable-cxx is not allowed + (( 1 )) + echo 'BEGIN ERROR' + echo 'Error while building HDF5. Aborting.' + echo 'END ERROR' + exit 1 HDF5 selected, but HDF5_DIR not set. Checking some places... HDF5 not found Building HDF5... CST error 1: -> Configuration script for thorn HDF5 returned exit code 1 Error message: 'Error while building HDF5. Aborting.' Checking consistency... Creating Thorn-Flesh bindings... Creating implementation bindings... Creating parameter bindings... Creating variable bindings... Creating schedule bindings... Creating function bindings... ------------------------------------------------------ There was 1 error during execution of the CST This must be corrected before compilation can proceed ------------------------------------------------------ ------------------------------------------------------ Warnings were generated during execution of the CST ------------------------------------------------------ CST error 1: -> Configuration script for thorn HDF5 returned exit code 1 Error message: 'Error while building HDF5. Aborting.' ------------------------------------------------------ make[1]: *** [/Users/shawley/Cactus/configs/texmex/config-data/make.thornlist] Error 1 make: *** [texmex] Error 2 provision.local 19>

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VECTORISE_ALIGNED_ARRAYS
by Erik Schnetter 17 Jun '11

17 Jun '11

In the light of recent events I would like to point out again that you should not be using the configuration option VECTORISE_ALIGNED_ARRAYS. Some time ago, I accidentally committed (and later undid) a corresponding change to SimFactory. This option enables experimental changes in the Mercurial version of Carpet and is likely to lead to nans or other inconsistencies in your simulations. Please check your configuration options... Apologies, -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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CarpetMask compilation errors
by jhar131＠cct.lsu.edu 16 Jun '11

16 Jun '11

Hello, I'm having problems with CarpetMask when I attempt to build a simulation. Included are my error messages. Does anyone have any suggestions? Preprocessing /home/joshua/Cactus/arrangements/Carpet/CarpetMask/src/mask_surface.cc Compiling /home/joshua/Cactus/arrangements/Carpet/CarpetMask/src/mask_surface.cc /home/joshua/Cactus/arrangements/Carpet/CarpetMask/src/mask_surface.cc: In function ?void CarpetMask::CarpetSurfaceSetup(cGH*)?: /home/joshua/Cactus/arrangements/Carpet/CarpetMask/src/mask_surface.cc:111:19: error: call of overloaded ?isnan(double&)? is ambiguous /home/joshua/Cactus/arrangements/Carpet/CarpetMask/src/mask_surface.cc:111:19: note: candidates are: /usr/include/bits/mathcalls.h:235:1: note: int isnan(double) /usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/cmath:558:3: note: bool std::isnan(long double) /usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/cmath:554:3: note: bool std::isnan(double) /usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/cmath:550:3: note: bool std::isnan(float) /home/joshua/Cactus/arrangements/Carpet/CarpetMask/src/mask_surface.cc:128:19: error: call of overloaded ?isnan(double&)? is ambiguous /home/joshua/Cactus/arrangements/Carpet/CarpetMask/src/mask_surface.cc:128:19: note: candidates are: /usr/include/bits/mathcalls.h:235:1: note: int isnan(double) /usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/cmath:558:3: note: bool std::isnan(long double) /usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/cmath:554:3: note: bool std::isnan(double) /usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/cmath:550:3: note: bool std::isnan(float) make[3]: *** [mask_surface.cc.o] Error 1 make[2]: *** [make.checked] Error 2 make[1]: *** [/home/joshua/Cactus/configs/ConfigName/lib/libthorn_CarpetMask.a] Error 2 make[1]: *** Waiting for unfinished jobs.... Sincerely, Joshua Harris

2 4

WaveMoL
by Babiuc-Hamilton, Maria 16 Jun '11

16 Jun '11

Hello, Is there a newer version of the WaveMoL that would work with the current release of the Einstein Toolkit? I found one on the cactus code webpage, but it gives me this error: conflicting types for ' ' previous declaration of ' ' thanks, Maria

1 0

Tutorial config error on QueenBee
by Scott Hawley 16 Jun '11

16 Jun '11

Hi. Apparently there's a problem with MPICH on QueenBee? queebee options obtained from https://svn.cct.lsu.edu/repos/cactus/tutorials/introduction/examples/Cactus… -Scott [shawley@qb3 ~/Cactus]$ gmake etk THORNLIST=manifest/einsteintoolkit.th options=queenbee.options ________________________________________________________________________ Cactus - version: 4.0.b17 Setup configuration etk (yes)? yes Setting up new configuration etk Completely new cactus build. Creating config database Creating new configuration etk. Using configuration options from configure line Setting THORNLIST to 'manifest/einsteintoolkit.th' End of options from configure line Adding configuration options from 'queenbee.options'... Setting VERSION to '2009-06-19' Setting CPP to 'cpp' Setting FPP to 'cpp' Setting CC to 'icc' Setting CXX to 'icpc' Setting F77 to 'ifort' Setting F90 to 'ifort' Setting CFLAGS to '-g -std=gnu99 -ansi_alias' Setting CXXFLAGS to '-g -std=gnu99 -restrict' Setting CPPFLAGS to '-g -DMPICH_IGNORE_CXX_SEEK' Setting LDFLAGS to '-g -Wl,-rpath,/home/eschnett/hdf5-1.8.2/lib -Wl,-rpath,/usr/local/packages/gsl-1.9-intel9.1/lib' Setting DEBUG to 'no' Setting PROFILE to 'no' Setting WARN to 'yes' Setting OPTIMISE to 'yes' Setting C_OPTIMISE_FLAGS to '-O2' Setting CXX_OPTIMISE_FLAGS to '-O2' Setting F77_OPTIMISE_FLAGS to '-O2' Setting F90_OPTIMISE_FLAGS to '-O2' Setting GSL_DIR to '/usr/local/packages/gsl-1.9-intel9.1' Setting HDF5 to 'yes' Setting HDF5_DIR to '/home/eschnett/hdf5-1.8.2' Setting MPI to 'MPICH' Setting MPICH_DIR to '/usr/local/packages/mvapich-0.98-intel10.1' Setting MPICH_DEVICE to 'ch_gen2' Setting PTHREADS to 'yes' Setting LIBXML2_DIR to '/home/knarf/utils' End of options from 'queenbee.options'. creating cache ./config.cache checking host system type... x86_64-unknown-linux-gnu checking whether make sets ${MAKE}... yes checking whether the C compiler (icc -g -std=gnu99 -ansi_alias -g -Wl,-rpath,/home/eschnett/hdf5-1.8.2/lib -Wl,-rpath,/usr/local/packages/gsl-1.9-intel9.1/lib) works... yes checking whether the C compiler (icc -g -std=gnu99 -ansi_alias -g -Wl,-rpath,/home/eschnett/hdf5-1.8.2/lib -Wl,-rpath,/usr/local/packages/gsl-1.9-intel9.1/lib) is a cross-compiler... no checking whether we are using GNU C... yes checking whether the C++ compiler (icpc -g -std=gnu99 -restrict -g -Wl,-rpath,/home/eschnett/hdf5-1.8.2/lib -Wl,-rpath,/usr/local/packages/gsl-1.9-intel9.1/lib) works... yes checking whether the C++ compiler (icpc -g -std=gnu99 -restrict -g -Wl,-rpath,/home/eschnett/hdf5-1.8.2/lib -Wl,-rpath,/usr/local/packages/gsl-1.9-intel9.1/lib) is a cross-compiler... no checking whether we are using GNU C++... yes checking for ranlib... ranlib checking for nvcc... no checking for perl... perl checking for gtar... gtar checking for gzip... gzip checking for gpatch... no checking for patch... patch checking for git... git checking for ar... ar checking for mkdir... mkdir checking for bash... /bin/sh Setting CACHELINE_BYTES to 64 Setting CACHE_SIZE to 6144*1024 bytes checking how to run the C preprocessor... cpp checking for ANSI C header files... yes checking whether byte ordering is bigendian... no checking size of long long... 8 checking size of long int... 8 checking size of int... 4 checking size of short int... 2 checking size of long double... 16 checking size of double... 8 checking size of float... 4 checking size of char *... 8 checking for the null device... /dev/null checking for gethostbyname... yes checking whether mode_t is defined... yes checking for availability of gettimeofday timing... yes checking if gettimeofday needs timezone... yes checking for availability of getrusage timing... yes checking for availability of _ftime timing... no checking for time.h... yes checking for sys/time.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for string.h... yes checking for assert.h... yes checking for tgmath.h... yes checking for sys/stat.h... yes checking for getopt.h... yes checking for dirent.h... yes checking for c_asm.h... no checking for intrinsics.h... no checking for mach/mach_time.h... no checking for regex.h... yes checking for sys/filio.h... no checking for sys/ioctl.h... yes checking for sys/socket.h... yes checking for netinet/in.h... yes checking for netdb.h... yes checking for arpa/inet.h... yes checking for winsock2.h... no checking for crypt.h... yes checking for signal.h... yes checking for malloc.h... yes checking whether time.h and sys/time.h may both be included... yes checking whether socklen_t is defined... yes checking whether SOCKET is defined... no checking for hrtime_t... no checking for gethrtime... no checking for read_real_time... no checking for time_base_to_time... no checking for clock_gettime... no checking for mach_absolute_time... no checking for _rtc intrinsic... no checking for mallinfo... yes checking for mallopt... yes checking whether M_MMAP_THRESHOLD is defined... yes checking if __int64 is defined... yes checking for vector... yes checking for vector.h... yes checking for getopt_long_only... yes checking for working const... yes checking for C inline... inline checking for C static inline... static inline checking for C restrict... restrict checking for C++ restrict... restrict checking for C bool... no checking for CXX bool... yes checking for C _Pragma... yes checking for C function __attribute__((__noinline__))... yes checking for CXX function __attribute__((__noinline__))... yes checking for CXX member function __attribute__((__noinline__))... yes checking for C __attribute__((__unused__))... yes checking for CXX __attribute__((__unused__))... yes checking for C __attribute__((__aligned__(...)))... yes checking for CXX __attribute__((__aligned__(...)))... yes checking for Fortran REAL*4... yes checking for Fortran REAL*8... yes checking for Fortran REAL*16... yes checking for Fortran COMPLEX*8... yes checking for Fortran COMPLEX*16... yes checking for Fortran COMPLEX*32... yes checking for crypt... no checking for crypt in library crypt... yes checking for finite... yes checking for isnan... yes checking for isinf... yes checking for mkstemp... yes checking for va_copy... yes checking for main in library c_r... no checking for main in library pthread... yes Configuring with HDF5. Using HDF5 package in /home/eschnett/hdf5-1.8.2 Configuring with MPI MPICH selected Cannot execute /usr/local/packages/mvapich-0.98-intel10.1/bin/tarch Error creating configuration etk gmake: *** [etk] Error 2

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Difficulties with ADMMass,CarpetIO,CarpetRegrid2
by Scott Hawley 15 Jun '11

15 Jun '11

Frank et all, I appreciate all your advice. I set up a simple run with one BH using TexMEx, and the AH Finder agrees closely with my result (for a low-resolution run), but ADMMass puts out different values, as shown here: INFO (TexMEx) ADM Mass: thisproc_admmass = 0.12501, total_admmass = 1.000074637580139 INFO (ADMMass): detector 0: ADM mass 0.123574, surface (cube): xmin -30, xmax 30, ymin -30, ymax 30, zmin -30, zmax 30 INFO (ADMMass): detector 0: ADM mass with lapse 0.123574, surface (cube): xmin -30, xmax 30, ymin -30, ymax 30, zmin -30, zmax 30 INFO (ADMMass): detector 0: ADM mass 0.123574, volume (cube): xmin -30, xmax 30, ymin -30, ymax 30, zmin -30, zmax 30 INFO (AHFinderDirect): proc 0: searching for horizon 1/1 INFO (AHFinderDirect): AH 1/1: r=2 at (-0.000000,-0.000000,-0.000000) INFO (AHFinderDirect): AH 1/1: area=50.26535847 m_irreducible=0.9999987667 The closest relevant number comes by multiplying the ADMMass values by 8 (=0.988592), but this still seems greater than the error should be. I don't have more data right now, because none of the CarpetIO routines will compile on my Mac. (e.g. CarpetIOASCII, bottom of this message)... I tried using CarpetRegrid2, but it is not handing over the grid hierarchy to my thorn the way CarpetRegrid did, and I end up getting a giant unigrid run (using the parameters like those in CarpetRegrid2/par/staticbh.par). I may need to coordinate with Erik on this. -Scott gmake texmex SILENT=no ...skipping.... Checking status of thorn CarpetIOASCII ________________________________________________________________________ if [ ! -d ./ ] ; then mkdir -p ./ ; fi cd ./ ; make CCTK_TARGET=make.checked TOP=/Users/shawley/Cactus/configs/texmex CONFIG=/Users/shawley/Cactus/configs/texmex/config-data SRCDIR=/Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src THORN=CarpetIOASCII USESTHORNS="Carpet Carpet CarpetLib CarpetLib IOUtil IOUtil" -f /Users/shawley/Cactus/lib/make/make.subdir Preprocessing /Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src/ioascii.cc { if test no = 'yes'; then echo '#line 1 "'/Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src/ioascii.cc'"'; fi; cat /Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src/ioascii.cc; } | perl -s /Users/shawley/Cactus/lib/sbin/c_file_processor.pl -line_directives=no -source_file_name=/Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src/ioascii.cc /Users/shawley/Cactus/configs/texmex/config-data > ioascii.cc Compiling /Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src/ioascii.cc current_wd=`pwd` ; cd /Users/shawley/Cactus/configs/texmex/scratch ; /sw/bin/mpic++ -m64 -fopenmp -O2 -c -o $current_wd/ioascii.cc.o $current_wd/ioascii.cc -I"/sw/include" -I"/sw/include" -I"/sw/include/openmpi/" -I"/sw/include" -I"/sw/include" -I"/sw/include/openmpi/" -I"/Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src" -I"/Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src/include" -I"/Users/shawley/Cactus/configs/texmex/config-data" -I"/Users/shawley/Cactus/configs/texmex/bindings/include" -I"/Users/shawley/Cactus/src/include" -I"/Users/shawley/Cactus/arrangements" -I"/Users/shawley/Cactus/configs/texmex/bindings/Configuration/Thorns" -I"/Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src" -I"/Users/shawley/Cactus/arrangements/Carpet/CarpetIOASCII/src/include" -DTHORN_IS_CarpetIOASCII -DCCODE /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc: In static member function ‘static void CarpetIOASCII::IOASCII<outdim>::CheckSteerableParameters(const cGH*)’: /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:195: error: cannot convert ‘ioRequest**’ to ‘double’ for argument ‘7’ to ‘void IOUtil_ParseVarsForOutput(const cGH*, const char*, const char*, int, const char*, int, double, ioRequest**)’ /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h: In static member function ‘static int CarpetIOASCII::IOASCII<outdim>::OutputVarAs(const cGH*, const char*, const char*)’: /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h:91: error: too few arguments to function ‘ioRequest* IOUtil_DefaultIORequest(const cGH*, int, int, double)’ /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:391: error: at this point in file /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h: In static member function ‘static int CarpetIOASCII::IOASCII<outdim>::OutputVarAs(const cGH*, const char*, const char*) [with int outdim = 0]’: /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:1381: instantiated from here /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h:91: error: too few arguments to function ‘ioRequest* IOUtil_DefaultIORequest(const cGH*, int, int, double)’ /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:391: error: at this point in file /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc: In static member function ‘static void CarpetIOASCII::IOASCII<outdim>::CheckSteerableParameters(const cGH*) [with int outdim = 0]’: /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:1381: instantiated from here /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:192: error: cannot convert ‘ioRequest**’ to ‘double’ for argument ‘7’ to ‘void IOUtil_ParseVarsForOutput(const cGH*, const char*, const char*, int, const char*, int, double, ioRequest**)’ /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h: In static member function ‘static int CarpetIOASCII::IOASCII<outdim>::OutputVarAs(const cGH*, const char*, const char*) [with int outdim = 1]’: /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:1382: instantiated from here /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h:91: error: too few arguments to function ‘ioRequest* IOUtil_DefaultIORequest(const cGH*, int, int, double)’ /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:391: error: at this point in file /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc: In static member function ‘static void CarpetIOASCII::IOASCII<outdim>::CheckSteerableParameters(const cGH*) [with int outdim = 1]’: /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:1382: instantiated from here /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:192: error: cannot convert ‘ioRequest**’ to ‘double’ for argument ‘7’ to ‘void IOUtil_ParseVarsForOutput(const cGH*, const char*, const char*, int, const char*, int, double, ioRequest**)’ /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h: In static member function ‘static int CarpetIOASCII::IOASCII<outdim>::OutputVarAs(const cGH*, const char*, const char*) [with int outdim = 2]’: /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:1383: instantiated from here /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h:91: error: too few arguments to function ‘ioRequest* IOUtil_DefaultIORequest(const cGH*, int, int, double)’ /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:391: error: at this point in file /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc: In static member function ‘static void CarpetIOASCII::IOASCII<outdim>::CheckSteerableParameters(const cGH*) [with int outdim = 2]’: /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:1383: instantiated from here /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:192: error: cannot convert ‘ioRequest**’ to ‘double’ for argument ‘7’ to ‘void IOUtil_ParseVarsForOutput(const cGH*, const char*, const char*, int, const char*, int, double, ioRequest**)’ /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h: In static member function ‘static int CarpetIOASCII::IOASCII<outdim>::OutputVarAs(const cGH*, const char*, const char*) [with int outdim = 3]’: /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:1384: instantiated from here /Users/shawley/Cactus/arrangements/CactusBase/IOUtil/src/ioutil_Utils.h:91: error: too few arguments to function ‘ioRequest* IOUtil_DefaultIORequest(const cGH*, int, int, double)’ /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:391: error: at this point in file /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc: In static member function ‘static void CarpetIOASCII::IOASCII<outdim>::CheckSteerableParameters(const cGH*) [with int outdim = 3]’: /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:1384: instantiated from here /Users/shawley/Cactus/configs/texmex/build/CarpetIOASCII/ioascii.cc:192: error: cannot convert ‘ioRequest**’ to ‘double’ for argument ‘7’ to ‘void IOUtil_ParseVarsForOutput(const cGH*, const char*, const char*, int, const char*, int, double, ioRequest**)’ make[3]: *** [ioascii.cc.o] Error 1 make[2]: *** [make.checked] Error 2 make[1]: *** [/Users/shawley/Cactus/configs/texmex/lib/libthorn_CarpetIOASCII.a] Error 2 make: *** [texmex] Error 2

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Some thoughts on the webpage..
by azebrowski＠cct.lsu.edu 13 Jun '11

13 Jun '11

Hi all, I'm currently overhauling some code for a Cactus project, and thought it'd be a good idea to update my install with the newest ET release. Here are a few things I've noticed while looking for the newest release: 1) The "releases" button/page contains a lot of information on the latest release (Curie), but no actual link to either the component list itself or a page detailing download and installation directions. This seems like an oversight that would be easy to correct. 2) The "documentation" header does not contain a link to Cactus tutorials. Perhaps there could be a "Quickstart" label or a "Getting Started" label, which then loads a page that gives a choice between the beginner/advanced tutorials? A new user might click on the "User Guide" from the main menu thinking that's all there is to get started with and feel overwhelmed, when all s/he might want is to just get their hands dirty with an example or two. Anyways, hope this is useful criticism, just saw some things that I thought could be cleared up a bit :) -Ashley Zebrowski

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Error from AEIThorns/ADMMass
by Scott Hawley 13 Jun '11

13 Jun '11

INFO (TexMEx): Done with TexMEx INFO (ADMMacros): Spatial finite differencing order: 4 INFO (ADMMacros): Spatial finite differencing order: 4 INFO (ADMMacros): Spatial finite differencing order: 4 INFO (ADMMacros): Spatial finite differencing order: 4 WARNING level 0 in thorn ADMMass processor 1 host hedges.belmont.edu (line 62 of /home/shawley/Cactus/configs/texmex/build/ADMMass/volume_integral.c): -> Error in obtaining OutsideMask state descriptors The relevant lines from the parameter file are SpaceMask::use_mask = yes LegoExcision::fixed_excision = "sphere" LegoExcision::num_fixed_regions = 2 LegoExcision::fixed_size = 0.9 LegoExcision::fixed_origin_x = -5.0 LegoExcision::fixed2_size = 1.0 LegoExcision::fixed2_origin_x = 5.0 ADMMass::ADMMass_volume_radius[0] = 30 ADMMass::ADMMass_Excise_Horizons = "yes" Does anyone know how to fix this? Thanks, Scott Attachments: Attached are the full parameter file and a full output log. -- Scott H. Hawley, Ph.D. Asst. Prof. of Physics Chemistry & Physics Dept Office: Hitch 100D Belmont University Tel: +1-615-460-6206 Nashville, TN 37212 USA Fax: +1-615-460-5458 PGP Key at http://sks-keyservers.net

2 3

Meeting minutes
by Roland Haas 13 Jun '11

13 Jun '11

Meeting minutes: Present were: Tanja, Roland, Erik, Frank, Josh, Christian, Yosef, Béla Szilágyi, Maria Babiuc CCE code: * thorns will (did) appear today in https://svn.einsteintoolkit.org/incoming/ arrangement suggestions are (as in in Frank's email): SphericalSlice -> CactusNumerical (analog SphericalSurface) new arrangement PITTNull (?) for CCE evolution code WorldTube -> PITTNull (CCE extraction thorn) ADMDerivatives -> EinsteinBase/EinsteinUtils (?) * please look at thorns once they appear and start discussion on mailing list * agree that PITTNull is the correct thorn name (since PITT was used in the papers) * CCE evolution is done in a Cactus thorn that uses PUGH * work cycle is to run the main simulation with an "interface" thorn that writes out initial data for the characteristic evolution, then run a postprocessing run using PUGH and the CCE thorn * two (interface) thorns to initial extract data for CCE ** original extraction code used in 1011.4223 by Yosef (stand-alone ?) *** tested with LazEv, currently being tested with McLachlan ** WorldTube by Christian Reisswig (requires extra infrastructure thorns) *** tested with MacLachlan and the AEI multipatch code (Llama?) * ask Christian Reisswig for short description of WorldTube, then decide whether to ** keep only one thorn ** keep both thorns ** merge them * requested citations for PITTNull are in README: > If you use this code, then we request that you cite the following papers: > > Title: Characteristic Extraction Tool for Gravitational Waveforms > Authors: M.C. Babiuc, B. Szilagyi, J. Winicour, Y. Zlochower > arXiv:1011.4223 > submitted to Physical Review D > > Title: Cauchy-characteristic matching > Authors: N. Bishop, R. Isaacson, R. Gomez, L. Lehner, B. Szilagyi, J. Winicour > arXiv: gr-qc/9801070 > Appeared in "On the Black Hole Trail" > eds. Bala Iyer and Biplab Bhawal (Kluwer) * license still needs to be specified in README file new infrastructure thorns: * SphericalSlice: a mini driver operations on a sphere (IO, coordinates) * ADMDerivatives: computes time and space derivatives of the ADM variables * status of examples in ET paper: ** TOV runs still in queue on QueenBee ** high res single distorted black hole has not been completed yet (there was quite a lot of waiting time on Kraken) but has made some progress (end reworded quote) * stellar collapse example: Christian will work on it fall ET workshop: * Josh will send around old proposal for workshop to be used as starting point * organizers will decide on preliminary budget and speaker list for purposes of writing the skeleton proposal Yours, Roland

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