diff --git a/CMakeLists.txt b/CMakeLists.txt index 02a93d5..4aa704c 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -10,6 +10,8 @@ include(FindPkgConfig) include(FindPackageHandleStandardArgs) include(color_msg) +find_package(MPI) + option(BUILD_SHARED_LIBS "Build shared libraries." OFF) option(BUILD_STATIC_LIBS "Build static libraries." ON) option(ENABLE_SHARP "Enable SHARP support." ON) @@ -42,18 +44,6 @@ ENDIF(BUILD_PYTHON) MESSAGE(STATUS "Using the target ${CosmoTool_local} to build python module") -find_package(ZLIB) -find_library(ZLIB_LIBRARY z) -find_library(DL_LIBRARY dl) -find_library(RT_LIBRARY rt) -if (RT_LIBRARY) - SET(RT_DEP rt) - message(STATUS "RT found, linking against it") -else() - SET(RT_DEP) -endif() -find_library(MATH_LIBRARY m) - include(${CMAKE_SOURCE_DIR}/external/external_build.cmake) IF(YORICK_SUPPORT) @@ -67,6 +57,9 @@ IF(YORICK_SUPPORT) ENDIF(YORICK_SUPPORT) find_program(CYTHON NAMES cython3 cython) +find_library(ZLIB_LIBRARY z) +find_library(DL_LIBRARY dl) +find_library(MATH_LIBRARY m) set(NETCDF_FIND_REQUIRED ${YORICK_SUPPORT}) set(GSL_FIND_REQUIRED TRUE) @@ -79,12 +72,14 @@ SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A toolbox for impatient cosmologists") SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux") SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2") SET(CPACK_PACKAGE_VERSION_MAJOR "1") -SET(CPACK_PACKAGE_VERSION_MINOR "3") -SET(CPACK_PACKAGE_VERSION_PATCH "4${EXTRA_VERSION}") +SET(CPACK_PACKAGE_VERSION_MINOR "2") +SET(CPACK_PACKAGE_VERSION_PATCH "3${EXTRA_VERSION}") SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}") SET(CPACK_STRIP_FILES "lib/libCosmoTool.so") -SET(CPACK_SOURCE_IGNORE_FILES -"/CVS/;/\\\\.git/;/\\\\.svn/;\\\\.swp$;\\\\.#;/#;.*~;cscope.*;/CMakeFiles/;.*\\\\.cmake;Makefile") +SET(CPACK_SOURCE_IGNORE_FILES "/CVS/;/\\\\.git/;/\\\\.svn/;\\\\.swp$;\\\\.#;/#;.*~;cscope.*;/CMakeFiles/;.*\\\\.cmake;Makefile") + +include_directories( ${MPI_C_INCLUDE_PATH}) + add_subdirectory(src) add_subdirectory(sample) diff --git a/MANIFEST.in b/MANIFEST.in index 105a2d6..5c4f363 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,5 +1,4 @@ include .gitignore -include pyproject.toml include CMakeLists.txt include FindNumPy.cmake include FindPyLibs.cmake @@ -17,17 +16,14 @@ include doc/source/cpplibrary.rst include doc/source/index.rst include doc/source/intro.rst include doc/source/pythonmodule.rst -include external/config.guess -include external/config.sub include external/external_build.cmake -include external/libsharp-8d51946.tar.gz +include external/libsharp-6077806.tar.gz include external/omptl-20120422.tar.bz2 include external/patch-omptl include python/CMakeLists.txt include python/_cosmo_bispectrum.cpp include python/_cosmo_cic.pyx include python/_cosmo_power.pyx -include python/_cosmomath.pyx include python/_cosmotool.pyx include python/_fast_interp.pyx include python/_project.pyx @@ -97,7 +93,6 @@ include sample/testkd3.cpp include setup.py include src/CMakeLists.txt include src/algo.hpp -include src/numpy_adaptors.hpp include src/bqueue.hpp include src/bqueue.tcc include src/bsp_simple.hpp diff --git a/builder/build-wheels.sh b/builder/build-wheels.sh index 8f529dd..ac343fe 100755 --- a/builder/build-wheels.sh +++ b/builder/build-wheels.sh @@ -8,15 +8,12 @@ export CC CXX # Install a system package required by our library #yum install -y atlas-devel -yum install -y cmake3 gsl-devel zlib-devel fftw3-devel libffi-devel hdf5 hdf5-devel +yum install -y cmake3 gsl-devel zlib-devel fftw3-devel ln -fs /usr/bin/cmake3 /usr/bin/cmake -test -d /io/wheelhouse || mkdir /io/wheelhouse -test -d /io/wheelhouse/fix || mkdir /io/wheelhouse/fix - -ALL_PYTHON="cp39-cp39 cp310-cp310" +ALL_PYTHON="cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39" # Compile wheels for pkg in $ALL_PYTHON; do @@ -24,12 +21,12 @@ for pkg in $ALL_PYTHON; do # "${PYBIN}/pip" install -r /io/dev-requirements.txt "${PYBIN}/pip" install setuptools wheel Cython "${PYBIN}/pip" install -r /io/requirements.txt - "${PYBIN}/pip" wheel -vvv /io/ -w /io/wheelhouse/ + "${PYBIN}/pip" wheel -vvv /io/ -w wheelhouse/ done # Bundle external shared libraries into the wheels -for whl in /io/wheelhouse/cosmotool*linux*.whl; do - auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/fix +for whl in wheelhouse/cosmotool*.whl; do + auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/ done # Install packages and test diff --git a/builder/start.sh b/builder/start.sh index 31f95f0..9fbc185 100755 --- a/builder/start.sh +++ b/builder/start.sh @@ -9,4 +9,4 @@ if ! [ -e ${d}/setup.py ] ; then exit 1 fi -podman run -ti --rm -e PLAT=manylinux2014_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2014_x86_64 /io/builder/build-wheels.sh +podman run -ti --rm -e PLAT=manylinux2010_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2010_x86_64 /io/builder/build-wheels.sh diff --git a/conda/meta.yaml b/conda/meta.yaml index 3f62832..333a565 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -1,6 +1,6 @@ package: name: cosmotool - version: "1.3.0" + version: "1.2.3" source: git_rev: a86c9a8 diff --git a/external/config.guess b/external/config.guess deleted file mode 100755 index 7f76b62..0000000 --- a/external/config.guess +++ /dev/null @@ -1,1754 +0,0 @@ -#! /bin/sh -# Attempt to guess a canonical system name. -# Copyright 1992-2022 Free Software Foundation, Inc. - -# shellcheck disable=SC2006,SC2268 # see below for rationale - -timestamp='2022-01-09' - -# This file is free software; you can redistribute it and/or modify it -# under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; if not, see . -# -# As a special exception to the GNU General Public License, if you -# distribute this file as part of a program that contains a -# configuration script generated by Autoconf, you may include it under -# the same distribution terms that you use for the rest of that -# program. This Exception is an additional permission under section 7 -# of the GNU General Public License, version 3 ("GPLv3"). -# -# Originally written by Per Bothner; maintained since 2000 by Ben Elliston. -# -# You can get the latest version of this script from: -# https://git.savannah.gnu.org/cgit/config.git/plain/config.guess -# -# Please send patches to . - - -# The "shellcheck disable" line above the timestamp inhibits complaints -# about features and limitations of the classic Bourne shell that were -# superseded or lifted in POSIX. 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- 2020:CLIX:*:* | 2430:CLIX:*:*) - GUESS=clipper-intergraph-clix$UNAME_RELEASE - ;; - mips:*:*:UMIPS | mips:*:*:RISCos) - set_cc_for_build - sed 's/^ //' << EOF > "$dummy.c" -#ifdef __cplusplus -#include /* for printf() prototype */ - int main (int argc, char *argv[]) { -#else - int main (argc, argv) int argc; char *argv[]; { -#endif - #if defined (host_mips) && defined (MIPSEB) - #if defined (SYSTYPE_SYSV) - printf ("mips-mips-riscos%ssysv\\n", argv[1]); exit (0); - #endif - #if defined (SYSTYPE_SVR4) - printf ("mips-mips-riscos%ssvr4\\n", argv[1]); exit (0); - #endif - #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) - printf ("mips-mips-riscos%sbsd\\n", argv[1]); exit (0); - #endif - #endif - exit (-1); - } -EOF - $CC_FOR_BUILD -o "$dummy" "$dummy.c" && - dummyarg=`echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p'` && - SYSTEM_NAME=`"$dummy" "$dummyarg"` && - { echo "$SYSTEM_NAME"; exit; } - GUESS=mips-mips-riscos$UNAME_RELEASE - ;; - Motorola:PowerMAX_OS:*:*) - GUESS=powerpc-motorola-powermax - ;; - Motorola:*:4.3:PL8-*) - GUESS=powerpc-harris-powermax - ;; - Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) - GUESS=powerpc-harris-powermax - ;; - Night_Hawk:Power_UNIX:*:*) - GUESS=powerpc-harris-powerunix - ;; - m88k:CX/UX:7*:*) - GUESS=m88k-harris-cxux7 - ;; - m88k:*:4*:R4*) - GUESS=m88k-motorola-sysv4 - ;; - m88k:*:3*:R3*) - GUESS=m88k-motorola-sysv3 - ;; - AViiON:dgux:*:*) - # DG/UX returns AViiON for all architectures - UNAME_PROCESSOR=`/usr/bin/uname -p` - if test "$UNAME_PROCESSOR" = mc88100 || test "$UNAME_PROCESSOR" = mc88110 - then - if test "$TARGET_BINARY_INTERFACE"x = m88kdguxelfx || \ - test "$TARGET_BINARY_INTERFACE"x = x - then - GUESS=m88k-dg-dgux$UNAME_RELEASE - else - GUESS=m88k-dg-dguxbcs$UNAME_RELEASE - fi - else - GUESS=i586-dg-dgux$UNAME_RELEASE - fi - ;; - M88*:DolphinOS:*:*) # DolphinOS (SVR3) - GUESS=m88k-dolphin-sysv3 - ;; - M88*:*:R3*:*) - # Delta 88k system running SVR3 - GUESS=m88k-motorola-sysv3 - ;; - XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) - GUESS=m88k-tektronix-sysv3 - ;; - Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) - GUESS=m68k-tektronix-bsd - ;; - *:IRIX*:*:*) - IRIX_REL=`echo "$UNAME_RELEASE" | sed -e 's/-/_/g'` - GUESS=mips-sgi-irix$IRIX_REL - ;; - ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. - GUESS=romp-ibm-aix # uname -m gives an 8 hex-code CPU id - ;; # Note that: echo "'`uname -s`'" gives 'AIX ' - i*86:AIX:*:*) - GUESS=i386-ibm-aix - ;; - ia64:AIX:*:*) - if test -x /usr/bin/oslevel ; then - IBM_REV=`/usr/bin/oslevel` - else - IBM_REV=$UNAME_VERSION.$UNAME_RELEASE - fi - GUESS=$UNAME_MACHINE-ibm-aix$IBM_REV - ;; - *:AIX:2:3) - if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then - set_cc_for_build - sed 's/^ //' << EOF > "$dummy.c" - #include - - main() - { - if (!__power_pc()) - exit(1); - puts("powerpc-ibm-aix3.2.5"); - exit(0); - } -EOF - if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` - then - GUESS=$SYSTEM_NAME - else - GUESS=rs6000-ibm-aix3.2.5 - fi - elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then - GUESS=rs6000-ibm-aix3.2.4 - else - GUESS=rs6000-ibm-aix3.2 - fi - ;; - *:AIX:*:[4567]) - IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` - if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then - IBM_ARCH=rs6000 - else - IBM_ARCH=powerpc - fi - if test -x /usr/bin/lslpp ; then - IBM_REV=`/usr/bin/lslpp -Lqc bos.rte.libc | \ - awk -F: '{ print $3 }' | sed s/[0-9]*$/0/` - else - IBM_REV=$UNAME_VERSION.$UNAME_RELEASE - fi - GUESS=$IBM_ARCH-ibm-aix$IBM_REV - ;; - *:AIX:*:*) - GUESS=rs6000-ibm-aix - ;; - ibmrt:4.4BSD:*|romp-ibm:4.4BSD:*) - GUESS=romp-ibm-bsd4.4 - ;; - ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and - GUESS=romp-ibm-bsd$UNAME_RELEASE # 4.3 with uname added to - ;; # report: romp-ibm BSD 4.3 - *:BOSX:*:*) - GUESS=rs6000-bull-bosx - ;; - DPX/2?00:B.O.S.:*:*) - GUESS=m68k-bull-sysv3 - ;; - 9000/[34]??:4.3bsd:1.*:*) - GUESS=m68k-hp-bsd - ;; - hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) - GUESS=m68k-hp-bsd4.4 - ;; - 9000/[34678]??:HP-UX:*:*) - HPUX_REV=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*.[0B]*//'` - case $UNAME_MACHINE in - 9000/31?) HP_ARCH=m68000 ;; - 9000/[34]??) HP_ARCH=m68k ;; - 9000/[678][0-9][0-9]) - if test -x /usr/bin/getconf; then - sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` - sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` - case $sc_cpu_version in - 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0 - 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1 - 532) # CPU_PA_RISC2_0 - case $sc_kernel_bits in - 32) HP_ARCH=hppa2.0n ;; - 64) HP_ARCH=hppa2.0w ;; - '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20 - esac ;; - esac - fi - if test "$HP_ARCH" = ""; then - set_cc_for_build - sed 's/^ //' << EOF > "$dummy.c" - - #define _HPUX_SOURCE - #include - #include - - int main () - { - #if defined(_SC_KERNEL_BITS) - long bits = sysconf(_SC_KERNEL_BITS); - #endif - long cpu = sysconf (_SC_CPU_VERSION); - - switch (cpu) - { - case CPU_PA_RISC1_0: puts ("hppa1.0"); break; - case CPU_PA_RISC1_1: puts ("hppa1.1"); break; - case CPU_PA_RISC2_0: - #if defined(_SC_KERNEL_BITS) - switch (bits) - { - case 64: puts ("hppa2.0w"); break; - case 32: puts ("hppa2.0n"); break; - default: puts ("hppa2.0"); break; - } break; - #else /* !defined(_SC_KERNEL_BITS) */ - puts ("hppa2.0"); break; - #endif - default: puts ("hppa1.0"); break; - } - exit (0); - } -EOF - (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=`"$dummy"` - test -z "$HP_ARCH" && HP_ARCH=hppa - fi ;; - esac - if test "$HP_ARCH" = hppa2.0w - then - set_cc_for_build - - # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating - # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler - # generating 64-bit code. GNU and HP use different nomenclature: - # - # $ CC_FOR_BUILD=cc ./config.guess - # => hppa2.0w-hp-hpux11.23 - # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess - # => hppa64-hp-hpux11.23 - - if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | - grep -q __LP64__ - then - HP_ARCH=hppa2.0w - else - HP_ARCH=hppa64 - fi - fi - GUESS=$HP_ARCH-hp-hpux$HPUX_REV - ;; - ia64:HP-UX:*:*) - HPUX_REV=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*.[0B]*//'` - GUESS=ia64-hp-hpux$HPUX_REV - ;; - 3050*:HI-UX:*:*) - set_cc_for_build - sed 's/^ //' << EOF > "$dummy.c" - #include - int - main () - { - long cpu = sysconf (_SC_CPU_VERSION); - /* The order matters, because CPU_IS_HP_MC68K erroneously returns - true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct - results, however. */ - if (CPU_IS_PA_RISC (cpu)) - { - switch (cpu) - { - case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; - case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; - case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; - default: puts ("hppa-hitachi-hiuxwe2"); break; - } - } - else if (CPU_IS_HP_MC68K (cpu)) - puts ("m68k-hitachi-hiuxwe2"); - else puts ("unknown-hitachi-hiuxwe2"); - exit (0); - } -EOF - $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` && - { echo "$SYSTEM_NAME"; exit; } - GUESS=unknown-hitachi-hiuxwe2 - ;; - 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:*) - GUESS=hppa1.1-hp-bsd - ;; - 9000/8??:4.3bsd:*:*) - GUESS=hppa1.0-hp-bsd - ;; - *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) - GUESS=hppa1.0-hp-mpeix - ;; - hp7??:OSF1:*:* | hp8?[79]:OSF1:*:*) - GUESS=hppa1.1-hp-osf - ;; - hp8??:OSF1:*:*) - GUESS=hppa1.0-hp-osf - ;; - i*86:OSF1:*:*) - if test -x /usr/sbin/sysversion ; then - GUESS=$UNAME_MACHINE-unknown-osf1mk - else - GUESS=$UNAME_MACHINE-unknown-osf1 - fi - ;; - parisc*:Lites*:*:*) - GUESS=hppa1.1-hp-lites - ;; - C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) - GUESS=c1-convex-bsd - ;; - C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) - if getsysinfo -f scalar_acc - then echo c32-convex-bsd - else echo c2-convex-bsd - fi - exit ;; - C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) - GUESS=c34-convex-bsd - ;; - C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) - GUESS=c38-convex-bsd - ;; - C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) - GUESS=c4-convex-bsd - ;; - CRAY*Y-MP:*:*:*) - CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` - GUESS=ymp-cray-unicos$CRAY_REL - ;; - CRAY*[A-Z]90:*:*:*) - echo "$UNAME_MACHINE"-cray-unicos"$UNAME_RELEASE" \ - | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ - -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ - -e 's/\.[^.]*$/.X/' - exit ;; - CRAY*TS:*:*:*) - CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` - GUESS=t90-cray-unicos$CRAY_REL - ;; - CRAY*T3E:*:*:*) - CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` - GUESS=alphaev5-cray-unicosmk$CRAY_REL - ;; - CRAY*SV1:*:*:*) - CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` - GUESS=sv1-cray-unicos$CRAY_REL - ;; - *:UNICOS/mp:*:*) - CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'` - GUESS=craynv-cray-unicosmp$CRAY_REL - ;; - F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) - FUJITSU_PROC=`uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz` - FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'` - FUJITSU_REL=`echo "$UNAME_RELEASE" | sed -e 's/ /_/'` - GUESS=${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL} - ;; - 5000:UNIX_System_V:4.*:*) - FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'` - FUJITSU_REL=`echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'` - GUESS=sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL} - ;; - i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) - GUESS=$UNAME_MACHINE-pc-bsdi$UNAME_RELEASE - ;; - sparc*:BSD/OS:*:*) - GUESS=sparc-unknown-bsdi$UNAME_RELEASE - ;; - *:BSD/OS:*:*) - GUESS=$UNAME_MACHINE-unknown-bsdi$UNAME_RELEASE - ;; - arm:FreeBSD:*:*) - UNAME_PROCESSOR=`uname -p` - set_cc_for_build - if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ - | grep -q __ARM_PCS_VFP - then - FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` - GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL-gnueabi - else - FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` - GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL-gnueabihf - fi - ;; - *:FreeBSD:*:*) - UNAME_PROCESSOR=`/usr/bin/uname -p` - case $UNAME_PROCESSOR in - amd64) - UNAME_PROCESSOR=x86_64 ;; - i386) - UNAME_PROCESSOR=i586 ;; - esac - FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` - GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL - ;; - i*:CYGWIN*:*) - GUESS=$UNAME_MACHINE-pc-cygwin - ;; - *:MINGW64*:*) - GUESS=$UNAME_MACHINE-pc-mingw64 - ;; - *:MINGW*:*) - GUESS=$UNAME_MACHINE-pc-mingw32 - ;; - *:MSYS*:*) - GUESS=$UNAME_MACHINE-pc-msys - ;; - i*:PW*:*) - GUESS=$UNAME_MACHINE-pc-pw32 - ;; - *:SerenityOS:*:*) - GUESS=$UNAME_MACHINE-pc-serenity - ;; - *:Interix*:*) - case $UNAME_MACHINE in - x86) - GUESS=i586-pc-interix$UNAME_RELEASE - ;; - authenticamd | genuineintel | EM64T) - GUESS=x86_64-unknown-interix$UNAME_RELEASE - ;; - IA64) - GUESS=ia64-unknown-interix$UNAME_RELEASE - ;; - esac ;; - i*:UWIN*:*) - GUESS=$UNAME_MACHINE-pc-uwin - ;; - amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) - GUESS=x86_64-pc-cygwin - ;; - prep*:SunOS:5.*:*) - SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'` - GUESS=powerpcle-unknown-solaris2$SUN_REL - ;; - *:GNU:*:*) - # the GNU system - GNU_ARCH=`echo "$UNAME_MACHINE" | sed -e 's,[-/].*$,,'` - GNU_REL=`echo "$UNAME_RELEASE" | sed -e 's,/.*$,,'` - GUESS=$GNU_ARCH-unknown-$LIBC$GNU_REL - ;; - *:GNU/*:*:*) - # other systems with GNU libc and userland - GNU_SYS=`echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"` - GNU_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` - GUESS=$UNAME_MACHINE-unknown-$GNU_SYS$GNU_REL-$LIBC - ;; - *:Minix:*:*) - GUESS=$UNAME_MACHINE-unknown-minix - ;; - aarch64:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - aarch64_be:Linux:*:*) - UNAME_MACHINE=aarch64_be - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - alpha:Linux:*:*) - case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' /proc/cpuinfo 2>/dev/null` in - EV5) UNAME_MACHINE=alphaev5 ;; - EV56) UNAME_MACHINE=alphaev56 ;; - PCA56) UNAME_MACHINE=alphapca56 ;; - PCA57) UNAME_MACHINE=alphapca56 ;; - EV6) UNAME_MACHINE=alphaev6 ;; - EV67) UNAME_MACHINE=alphaev67 ;; - EV68*) UNAME_MACHINE=alphaev68 ;; - esac - objdump --private-headers /bin/sh | grep -q ld.so.1 - if test "$?" = 0 ; then LIBC=gnulibc1 ; fi - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - arc:Linux:*:* | arceb:Linux:*:* | arc32:Linux:*:* | arc64:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - arm*:Linux:*:*) - set_cc_for_build - if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ - | grep -q __ARM_EABI__ - then - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - else - if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ - | grep -q __ARM_PCS_VFP - then - GUESS=$UNAME_MACHINE-unknown-linux-${LIBC}eabi - else - GUESS=$UNAME_MACHINE-unknown-linux-${LIBC}eabihf - fi - fi - ;; - avr32*:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - cris:Linux:*:*) - GUESS=$UNAME_MACHINE-axis-linux-$LIBC - ;; - crisv32:Linux:*:*) - GUESS=$UNAME_MACHINE-axis-linux-$LIBC - ;; - e2k:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - frv:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - hexagon:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - i*86:Linux:*:*) - GUESS=$UNAME_MACHINE-pc-linux-$LIBC - ;; - ia64:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - k1om:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - loongarch32:Linux:*:* | loongarch64:Linux:*:* | loongarchx32:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - m32r*:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - m68*:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - mips:Linux:*:* | mips64:Linux:*:*) - set_cc_for_build - IS_GLIBC=0 - test x"${LIBC}" = xgnu && IS_GLIBC=1 - sed 's/^ //' << EOF > "$dummy.c" - #undef CPU - #undef mips - #undef mipsel - #undef mips64 - #undef mips64el - #if ${IS_GLIBC} && defined(_ABI64) - LIBCABI=gnuabi64 - #else - #if ${IS_GLIBC} && defined(_ABIN32) - LIBCABI=gnuabin32 - #else - LIBCABI=${LIBC} - #endif - #endif - - #if ${IS_GLIBC} && defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 - CPU=mipsisa64r6 - #else - #if ${IS_GLIBC} && !defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 - CPU=mipsisa32r6 - #else - #if defined(__mips64) - CPU=mips64 - #else - CPU=mips - #endif - #endif - #endif - - #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) - MIPS_ENDIAN=el - #else - #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) - MIPS_ENDIAN= - #else - MIPS_ENDIAN= - #endif - #endif -EOF - cc_set_vars=`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU\|^MIPS_ENDIAN\|^LIBCABI'` - eval "$cc_set_vars" - test "x$CPU" != x && { echo "$CPU${MIPS_ENDIAN}-unknown-linux-$LIBCABI"; exit; } - ;; - mips64el:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - openrisc*:Linux:*:*) - GUESS=or1k-unknown-linux-$LIBC - ;; - or32:Linux:*:* | or1k*:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - padre:Linux:*:*) - GUESS=sparc-unknown-linux-$LIBC - ;; - parisc64:Linux:*:* | hppa64:Linux:*:*) - GUESS=hppa64-unknown-linux-$LIBC - ;; - parisc:Linux:*:* | hppa:Linux:*:*) - # Look for CPU level - case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in - PA7*) GUESS=hppa1.1-unknown-linux-$LIBC ;; - PA8*) GUESS=hppa2.0-unknown-linux-$LIBC ;; - *) GUESS=hppa-unknown-linux-$LIBC ;; - esac - ;; - ppc64:Linux:*:*) - GUESS=powerpc64-unknown-linux-$LIBC - ;; - ppc:Linux:*:*) - GUESS=powerpc-unknown-linux-$LIBC - ;; - ppc64le:Linux:*:*) - GUESS=powerpc64le-unknown-linux-$LIBC - ;; - ppcle:Linux:*:*) - GUESS=powerpcle-unknown-linux-$LIBC - ;; - riscv32:Linux:*:* | riscv32be:Linux:*:* | riscv64:Linux:*:* | riscv64be:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - s390:Linux:*:* | s390x:Linux:*:*) - GUESS=$UNAME_MACHINE-ibm-linux-$LIBC - ;; - sh64*:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - sh*:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - sparc:Linux:*:* | sparc64:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - tile*:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - vax:Linux:*:*) - GUESS=$UNAME_MACHINE-dec-linux-$LIBC - ;; - x86_64:Linux:*:*) - set_cc_for_build - LIBCABI=$LIBC - if test "$CC_FOR_BUILD" != no_compiler_found; then - if (echo '#ifdef __ILP32__'; echo IS_X32; echo '#endif') | \ - (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ - grep IS_X32 >/dev/null - then - LIBCABI=${LIBC}x32 - fi - fi - GUESS=$UNAME_MACHINE-pc-linux-$LIBCABI - ;; - xtensa*:Linux:*:*) - GUESS=$UNAME_MACHINE-unknown-linux-$LIBC - ;; - i*86:DYNIX/ptx:4*:*) - # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. - # earlier versions are messed up and put the nodename in both - # sysname and nodename. - GUESS=i386-sequent-sysv4 - ;; - i*86:UNIX_SV:4.2MP:2.*) - # Unixware is an offshoot of SVR4, but it has its own version - # number series starting with 2... - # I am not positive that other SVR4 systems won't match this, - # I just have to hope. -- rms. - # Use sysv4.2uw... so that sysv4* matches it. - GUESS=$UNAME_MACHINE-pc-sysv4.2uw$UNAME_VERSION - ;; - i*86:OS/2:*:*) - # If we were able to find `uname', then EMX Unix compatibility - # is probably installed. - GUESS=$UNAME_MACHINE-pc-os2-emx - ;; - i*86:XTS-300:*:STOP) - GUESS=$UNAME_MACHINE-unknown-stop - ;; - i*86:atheos:*:*) - GUESS=$UNAME_MACHINE-unknown-atheos - ;; - i*86:syllable:*:*) - GUESS=$UNAME_MACHINE-pc-syllable - ;; - i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) - GUESS=i386-unknown-lynxos$UNAME_RELEASE - ;; - i*86:*DOS:*:*) - GUESS=$UNAME_MACHINE-pc-msdosdjgpp - ;; - i*86:*:4.*:*) - UNAME_REL=`echo "$UNAME_RELEASE" | sed 's/\/MP$//'` - if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then - GUESS=$UNAME_MACHINE-univel-sysv$UNAME_REL - else - GUESS=$UNAME_MACHINE-pc-sysv$UNAME_REL - fi - ;; - i*86:*:5:[678]*) - # UnixWare 7.x, OpenUNIX and OpenServer 6. - case `/bin/uname -X | grep "^Machine"` in - *486*) UNAME_MACHINE=i486 ;; - *Pentium) UNAME_MACHINE=i586 ;; - *Pent*|*Celeron) UNAME_MACHINE=i686 ;; - esac - GUESS=$UNAME_MACHINE-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} - ;; - i*86:*:3.2:*) - if test -f /usr/options/cb.name; then - UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then - UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` - (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 - (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ - && UNAME_MACHINE=i586 - (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ - && UNAME_MACHINE=i686 - (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ - && UNAME_MACHINE=i686 - GUESS=$UNAME_MACHINE-pc-sco$UNAME_REL - else - GUESS=$UNAME_MACHINE-pc-sysv32 - fi - ;; - pc:*:*:*) - # Left here for compatibility: - # uname -m prints for DJGPP always 'pc', but it prints nothing about - # the processor, so we play safe by assuming i586. - # Note: whatever this is, it MUST be the same as what config.sub - # prints for the "djgpp" host, or else GDB configure will decide that - # this is a cross-build. - GUESS=i586-pc-msdosdjgpp - ;; - Intel:Mach:3*:*) - GUESS=i386-pc-mach3 - ;; - paragon:*:*:*) - GUESS=i860-intel-osf1 - ;; - i860:*:4.*:*) # i860-SVR4 - if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then - GUESS=i860-stardent-sysv$UNAME_RELEASE # Stardent Vistra i860-SVR4 - else # Add other i860-SVR4 vendors below as they are discovered. - GUESS=i860-unknown-sysv$UNAME_RELEASE # Unknown i860-SVR4 - fi - ;; - mini*:CTIX:SYS*5:*) - # "miniframe" - GUESS=m68010-convergent-sysv - ;; - mc68k:UNIX:SYSTEM5:3.51m) - GUESS=m68k-convergent-sysv - ;; - M680?0:D-NIX:5.3:*) - GUESS=m68k-diab-dnix - ;; - M68*:*:R3V[5678]*:*) - test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; - 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) - OS_REL='' - test -r /etc/.relid \ - && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` - /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ - && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } - /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ - && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; - 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) - /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ - && { echo i486-ncr-sysv4; exit; } ;; - NCR*:*:4.2:* | MPRAS*:*:4.2:*) - OS_REL='.3' - test -r /etc/.relid \ - && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` - /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ - && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } - /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ - && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } - /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ - && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; - m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) - GUESS=m68k-unknown-lynxos$UNAME_RELEASE - ;; - mc68030:UNIX_System_V:4.*:*) - GUESS=m68k-atari-sysv4 - ;; - TSUNAMI:LynxOS:2.*:*) - GUESS=sparc-unknown-lynxos$UNAME_RELEASE - ;; - rs6000:LynxOS:2.*:*) - GUESS=rs6000-unknown-lynxos$UNAME_RELEASE - ;; - PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) - GUESS=powerpc-unknown-lynxos$UNAME_RELEASE - ;; - SM[BE]S:UNIX_SV:*:*) - GUESS=mips-dde-sysv$UNAME_RELEASE - ;; - RM*:ReliantUNIX-*:*:*) - GUESS=mips-sni-sysv4 - ;; - RM*:SINIX-*:*:*) - GUESS=mips-sni-sysv4 - ;; - *:SINIX-*:*:*) - if uname -p 2>/dev/null >/dev/null ; then - UNAME_MACHINE=`(uname -p) 2>/dev/null` - GUESS=$UNAME_MACHINE-sni-sysv4 - else - GUESS=ns32k-sni-sysv - fi - ;; - PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort - # says - GUESS=i586-unisys-sysv4 - ;; - *:UNIX_System_V:4*:FTX*) - # From Gerald Hewes . - # How about differentiating between stratus architectures? -djm - GUESS=hppa1.1-stratus-sysv4 - ;; - *:*:*:FTX*) - # From seanf@swdc.stratus.com. - GUESS=i860-stratus-sysv4 - ;; - i*86:VOS:*:*) - # From Paul.Green@stratus.com. - GUESS=$UNAME_MACHINE-stratus-vos - ;; - *:VOS:*:*) - # From Paul.Green@stratus.com. - GUESS=hppa1.1-stratus-vos - ;; - mc68*:A/UX:*:*) - GUESS=m68k-apple-aux$UNAME_RELEASE - ;; - news*:NEWS-OS:6*:*) - GUESS=mips-sony-newsos6 - ;; - R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) - if test -d /usr/nec; then - GUESS=mips-nec-sysv$UNAME_RELEASE - else - GUESS=mips-unknown-sysv$UNAME_RELEASE - fi - ;; - BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. - GUESS=powerpc-be-beos - ;; - BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. - GUESS=powerpc-apple-beos - ;; - BePC:BeOS:*:*) # BeOS running on Intel PC compatible. - GUESS=i586-pc-beos - ;; - BePC:Haiku:*:*) # Haiku running on Intel PC compatible. - GUESS=i586-pc-haiku - ;; - x86_64:Haiku:*:*) - GUESS=x86_64-unknown-haiku - ;; - SX-4:SUPER-UX:*:*) - GUESS=sx4-nec-superux$UNAME_RELEASE - ;; - SX-5:SUPER-UX:*:*) - GUESS=sx5-nec-superux$UNAME_RELEASE - ;; - SX-6:SUPER-UX:*:*) - GUESS=sx6-nec-superux$UNAME_RELEASE - ;; - SX-7:SUPER-UX:*:*) - GUESS=sx7-nec-superux$UNAME_RELEASE - ;; - SX-8:SUPER-UX:*:*) - GUESS=sx8-nec-superux$UNAME_RELEASE - ;; - SX-8R:SUPER-UX:*:*) - GUESS=sx8r-nec-superux$UNAME_RELEASE - ;; - SX-ACE:SUPER-UX:*:*) - GUESS=sxace-nec-superux$UNAME_RELEASE - ;; - Power*:Rhapsody:*:*) - GUESS=powerpc-apple-rhapsody$UNAME_RELEASE - ;; - *:Rhapsody:*:*) - GUESS=$UNAME_MACHINE-apple-rhapsody$UNAME_RELEASE - ;; - arm64:Darwin:*:*) - GUESS=aarch64-apple-darwin$UNAME_RELEASE - ;; - *:Darwin:*:*) - UNAME_PROCESSOR=`uname -p` - case $UNAME_PROCESSOR in - unknown) UNAME_PROCESSOR=powerpc ;; - esac - if command -v xcode-select > /dev/null 2> /dev/null && \ - ! xcode-select --print-path > /dev/null 2> /dev/null ; then - # Avoid executing cc if there is no toolchain installed as - # cc will be a stub that puts up a graphical alert - # prompting the user to install developer tools. - CC_FOR_BUILD=no_compiler_found - else - set_cc_for_build - fi - if test "$CC_FOR_BUILD" != no_compiler_found; then - if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ - (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ - grep IS_64BIT_ARCH >/dev/null - then - case $UNAME_PROCESSOR in - i386) UNAME_PROCESSOR=x86_64 ;; - powerpc) UNAME_PROCESSOR=powerpc64 ;; - esac - fi - # On 10.4-10.6 one might compile for PowerPC via gcc -arch ppc - if (echo '#ifdef __POWERPC__'; echo IS_PPC; echo '#endif') | \ - (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ - grep IS_PPC >/dev/null - then - UNAME_PROCESSOR=powerpc - fi - elif test "$UNAME_PROCESSOR" = i386 ; then - # uname -m returns i386 or x86_64 - UNAME_PROCESSOR=$UNAME_MACHINE - fi - GUESS=$UNAME_PROCESSOR-apple-darwin$UNAME_RELEASE - ;; - *:procnto*:*:* | *:QNX:[0123456789]*:*) - UNAME_PROCESSOR=`uname -p` - if test "$UNAME_PROCESSOR" = x86; then - UNAME_PROCESSOR=i386 - UNAME_MACHINE=pc - fi - GUESS=$UNAME_PROCESSOR-$UNAME_MACHINE-nto-qnx$UNAME_RELEASE - ;; - *:QNX:*:4*) - GUESS=i386-pc-qnx - ;; - NEO-*:NONSTOP_KERNEL:*:*) - GUESS=neo-tandem-nsk$UNAME_RELEASE - ;; - NSE-*:NONSTOP_KERNEL:*:*) - GUESS=nse-tandem-nsk$UNAME_RELEASE - ;; - NSR-*:NONSTOP_KERNEL:*:*) - GUESS=nsr-tandem-nsk$UNAME_RELEASE - ;; - NSV-*:NONSTOP_KERNEL:*:*) - GUESS=nsv-tandem-nsk$UNAME_RELEASE - ;; - NSX-*:NONSTOP_KERNEL:*:*) - GUESS=nsx-tandem-nsk$UNAME_RELEASE - ;; - *:NonStop-UX:*:*) - GUESS=mips-compaq-nonstopux - ;; - BS2000:POSIX*:*:*) - GUESS=bs2000-siemens-sysv - ;; - DS/*:UNIX_System_V:*:*) - GUESS=$UNAME_MACHINE-$UNAME_SYSTEM-$UNAME_RELEASE - ;; - *:Plan9:*:*) - # "uname -m" is not consistent, so use $cputype instead. 386 - # is converted to i386 for consistency with other x86 - # operating systems. - if test "${cputype-}" = 386; then - UNAME_MACHINE=i386 - elif test "x${cputype-}" != x; then - UNAME_MACHINE=$cputype - fi - GUESS=$UNAME_MACHINE-unknown-plan9 - ;; - *:TOPS-10:*:*) - GUESS=pdp10-unknown-tops10 - ;; - *:TENEX:*:*) - GUESS=pdp10-unknown-tenex - ;; - KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) - GUESS=pdp10-dec-tops20 - ;; - XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) - GUESS=pdp10-xkl-tops20 - ;; - *:TOPS-20:*:*) - GUESS=pdp10-unknown-tops20 - ;; - *:ITS:*:*) - GUESS=pdp10-unknown-its - ;; - SEI:*:*:SEIUX) - GUESS=mips-sei-seiux$UNAME_RELEASE - ;; - *:DragonFly:*:*) - DRAGONFLY_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'` - GUESS=$UNAME_MACHINE-unknown-dragonfly$DRAGONFLY_REL - ;; - *:*VMS:*:*) - UNAME_MACHINE=`(uname -p) 2>/dev/null` - case $UNAME_MACHINE in - A*) GUESS=alpha-dec-vms ;; - I*) GUESS=ia64-dec-vms ;; - V*) GUESS=vax-dec-vms ;; - esac ;; - *:XENIX:*:SysV) - GUESS=i386-pc-xenix - ;; - i*86:skyos:*:*) - SKYOS_REL=`echo "$UNAME_RELEASE" | sed -e 's/ .*$//'` - GUESS=$UNAME_MACHINE-pc-skyos$SKYOS_REL - ;; - i*86:rdos:*:*) - GUESS=$UNAME_MACHINE-pc-rdos - ;; - i*86:Fiwix:*:*) - GUESS=$UNAME_MACHINE-pc-fiwix - ;; - *:AROS:*:*) - GUESS=$UNAME_MACHINE-unknown-aros - ;; - x86_64:VMkernel:*:*) - GUESS=$UNAME_MACHINE-unknown-esx - ;; - amd64:Isilon\ OneFS:*:*) - GUESS=x86_64-unknown-onefs - ;; - *:Unleashed:*:*) - GUESS=$UNAME_MACHINE-unknown-unleashed$UNAME_RELEASE - ;; -esac - -# Do we have a guess based on uname results? -if test "x$GUESS" != x; then - echo "$GUESS" - exit -fi - -# No uname command or uname output not recognized. -set_cc_for_build -cat > "$dummy.c" < -#include -#endif -#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) -#if defined (vax) || defined (__vax) || defined (__vax__) || defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) -#include -#if defined(_SIZE_T_) || defined(SIGLOST) -#include -#endif -#endif -#endif -main () -{ -#if defined (sony) -#if defined (MIPSEB) - /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, - I don't know.... */ - printf ("mips-sony-bsd\n"); exit (0); -#else -#include - printf ("m68k-sony-newsos%s\n", -#ifdef NEWSOS4 - "4" -#else - "" -#endif - ); exit (0); -#endif -#endif - -#if defined (NeXT) -#if !defined (__ARCHITECTURE__) -#define __ARCHITECTURE__ "m68k" -#endif - int version; - version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; - if (version < 4) - printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); - else - printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); - exit (0); -#endif - -#if defined (MULTIMAX) || defined (n16) -#if defined (UMAXV) - printf ("ns32k-encore-sysv\n"); exit (0); -#else -#if defined (CMU) - printf ("ns32k-encore-mach\n"); exit (0); -#else - printf ("ns32k-encore-bsd\n"); exit (0); -#endif -#endif -#endif - -#if defined (__386BSD__) - printf ("i386-pc-bsd\n"); exit (0); -#endif - -#if defined (sequent) -#if defined (i386) - printf ("i386-sequent-dynix\n"); exit (0); -#endif -#if defined (ns32000) - printf ("ns32k-sequent-dynix\n"); exit (0); -#endif -#endif - -#if defined (_SEQUENT_) - struct utsname un; - - uname(&un); - if (strncmp(un.version, "V2", 2) == 0) { - printf ("i386-sequent-ptx2\n"); exit (0); - } - if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ - printf ("i386-sequent-ptx1\n"); exit (0); - } - printf ("i386-sequent-ptx\n"); exit (0); -#endif - -#if defined (vax) -#if !defined (ultrix) -#include -#if defined (BSD) -#if BSD == 43 - printf ("vax-dec-bsd4.3\n"); exit (0); -#else -#if BSD == 199006 - printf ("vax-dec-bsd4.3reno\n"); exit (0); -#else - printf ("vax-dec-bsd\n"); exit (0); -#endif -#endif -#else - printf ("vax-dec-bsd\n"); exit (0); -#endif -#else -#if defined(_SIZE_T_) || defined(SIGLOST) - struct utsname un; - uname (&un); - printf ("vax-dec-ultrix%s\n", un.release); exit (0); -#else - printf ("vax-dec-ultrix\n"); exit (0); -#endif -#endif -#endif -#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) -#if defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) -#if defined(_SIZE_T_) || defined(SIGLOST) - struct utsname *un; - uname (&un); - printf ("mips-dec-ultrix%s\n", un.release); exit (0); -#else - printf ("mips-dec-ultrix\n"); exit (0); -#endif -#endif -#endif - -#if defined (alliant) && defined (i860) - printf ("i860-alliant-bsd\n"); exit (0); -#endif - - exit (1); -} -EOF - -$CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null && SYSTEM_NAME=`"$dummy"` && - { echo "$SYSTEM_NAME"; exit; } - -# Apollos put the system type in the environment. -test -d /usr/apollo && { echo "$ISP-apollo-$SYSTYPE"; exit; } - -echo "$0: unable to guess system type" >&2 - -case $UNAME_MACHINE:$UNAME_SYSTEM in - mips:Linux | mips64:Linux) - # If we got here on MIPS GNU/Linux, output extra information. - cat >&2 <&2 <&2 </dev/null || echo unknown` -uname -r = `(uname -r) 2>/dev/null || echo unknown` -uname -s = `(uname -s) 2>/dev/null || echo unknown` -uname -v = `(uname -v) 2>/dev/null || echo unknown` - -/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` -/bin/uname -X = `(/bin/uname -X) 2>/dev/null` - -hostinfo = `(hostinfo) 2>/dev/null` -/bin/universe = `(/bin/universe) 2>/dev/null` -/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` -/bin/arch = `(/bin/arch) 2>/dev/null` -/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` -/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` - -UNAME_MACHINE = "$UNAME_MACHINE" -UNAME_RELEASE = "$UNAME_RELEASE" -UNAME_SYSTEM = "$UNAME_SYSTEM" -UNAME_VERSION = "$UNAME_VERSION" -EOF -fi - -exit 1 - -# Local variables: -# eval: (add-hook 'before-save-hook 'time-stamp) -# time-stamp-start: "timestamp='" -# time-stamp-format: "%:y-%02m-%02d" -# time-stamp-end: "'" -# End: diff --git a/external/config.sub b/external/config.sub deleted file mode 100755 index dba16e8..0000000 --- a/external/config.sub +++ /dev/null @@ -1,1890 +0,0 @@ -#! /bin/sh -# Configuration validation subroutine script. -# Copyright 1992-2022 Free Software Foundation, Inc. - -# shellcheck disable=SC2006,SC2268 # see below for rationale - -timestamp='2022-01-03' - -# This file is free software; you can redistribute it and/or modify it -# under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; if not, see . -# -# As a special exception to the GNU General Public License, if you -# distribute this file as part of a program that contains a -# configuration script generated by Autoconf, you may include it under -# the same distribution terms that you use for the rest of that -# program. This Exception is an additional permission under section 7 -# of the GNU General Public License, version 3 ("GPLv3"). - - -# Please send patches to . -# -# Configuration subroutine to validate and canonicalize a configuration type. -# Supply the specified configuration type as an argument. -# If it is invalid, we print an error message on stderr and exit with code 1. -# Otherwise, we print the canonical config type on stdout and succeed. - -# You can get the latest version of this script from: -# https://git.savannah.gnu.org/cgit/config.git/plain/config.sub - -# This file is supposed to be the same for all GNU packages -# and recognize all the CPU types, system types and aliases -# that are meaningful with *any* GNU software. -# Each package is responsible for reporting which valid configurations -# it does not support. The user should be able to distinguish -# a failure to support a valid configuration from a meaningless -# configuration. - -# The goal of this file is to map all the various variations of a given -# machine specification into a single specification in the form: -# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM -# or in some cases, the newer four-part form: -# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM -# It is wrong to echo any other type of specification. - -# The "shellcheck disable" line above the timestamp inhibits complaints -# about features and limitations of the classic Bourne shell that were -# superseded or lifted in POSIX. However, this script identifies a wide -# variety of pre-POSIX systems that do not have POSIX shells at all, and -# even some reasonably current systems (Solaris 10 as case-in-point) still -# have a pre-POSIX /bin/sh. - -me=`echo "$0" | sed -e 's,.*/,,'` - -usage="\ -Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS - -Canonicalize a configuration name. - -Options: - -h, --help print this help, then exit - -t, --time-stamp print date of last modification, then exit - -v, --version print version number, then exit - -Report bugs and patches to ." - -version="\ -GNU config.sub ($timestamp) - -Copyright 1992-2022 Free Software Foundation, Inc. - -This is free software; see the source for copying conditions. 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- kfreebsd*-gnu* | kopensolaris*-gnu*) - ;; - vxworks-simlinux | vxworks-simwindows | vxworks-spe) - ;; - nto-qnx*) - ;; - os2-emx) - ;; - *-eabi* | *-gnueabi*) - ;; - -*) - # Blank kernel with real OS is always fine. - ;; - *-*) - echo "Invalid configuration \`$1': Kernel \`$kernel' not known to work with OS \`$os'." 1>&2 - exit 1 - ;; -esac - -# Here we handle the case where we know the os, and the CPU type, but not the -# manufacturer. We pick the logical manufacturer. -case $vendor in - unknown) - case $cpu-$os in - *-riscix*) - vendor=acorn - ;; - *-sunos*) - vendor=sun - ;; - *-cnk* | *-aix*) - vendor=ibm - ;; - *-beos*) - vendor=be - ;; - *-hpux*) - vendor=hp - ;; - *-mpeix*) - vendor=hp - ;; - *-hiux*) - vendor=hitachi - ;; - *-unos*) - vendor=crds - ;; - *-dgux*) - vendor=dg - ;; - *-luna*) - vendor=omron - ;; - *-genix*) - vendor=ns - ;; - *-clix*) - vendor=intergraph - ;; - *-mvs* | *-opened*) - vendor=ibm - ;; - *-os400*) - vendor=ibm - ;; - s390-* | s390x-*) - vendor=ibm - ;; - *-ptx*) - vendor=sequent - ;; - *-tpf*) - vendor=ibm - ;; - *-vxsim* | *-vxworks* | *-windiss*) - vendor=wrs - ;; - *-aux*) - vendor=apple - ;; - *-hms*) - vendor=hitachi - ;; - *-mpw* | *-macos*) - vendor=apple - ;; - *-*mint | *-mint[0-9]* | *-*MiNT | *-MiNT[0-9]*) - vendor=atari - ;; - *-vos*) - vendor=stratus - ;; - esac - ;; -esac - -echo "$cpu-$vendor-${kernel:+$kernel-}$os" -exit - -# Local variables: -# eval: (add-hook 'before-save-hook 'time-stamp) -# time-stamp-start: "timestamp='" -# time-stamp-format: "%:y-%02m-%02d" -# time-stamp-end: "'" -# End: diff --git a/external/external_build.cmake b/external/external_build.cmake index 997cc4d..bbe3e77 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -2,19 +2,16 @@ include(FindOpenMP) OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF) -SET(SOURCE_PREFIX ${CMAKE_SOURCE_DIR}) SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE STRING "URL to download FFTW from") SET(EIGEN_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" CACHE STRING "URL to download Eigen from") SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from") -SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.2/src/hdf5-1.12.2.tar.gz" CACHE STRING "URL to download HDF5 from") -SET(NETCDF_URL "https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz" CACHE STRING "URL to download NetCDF from") -SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.1.tar.gz" CACHE STRING "URL to download NetCDF-C++ from") -SET(BOOST_URL "https://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/boost_1_82_0.tar.gz" CACHE STRING "URL to download Boost from") -SET(GSL_URL "https://ftpmirror.gnu.org/gsl/gsl-2.7.tar.gz" CACHE STRING "URL to download GSL from ") +SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from") +SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz" CACHE STRING "URL to download NetCDF from") +SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.0.tar.gz" CACHE STRING "URL to download NetCDF-C++ from") +SET(BOOST_URL "https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.bz2" CACHE STRING "URL to download Boost from") +SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ") mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL) -file(MAKE_DIRECTORY ${SOURCE_PREFIX}/downloads) - SET(all_deps) MACRO(CHECK_CHANGE_STATE VAR) @@ -39,13 +36,12 @@ CHECK_CHANGE_STATE(INTERNAL_DLIB DLIB_INCLUDE_DIR DLIB_LIBRARIES) IF(ENABLE_OPENMP) IF (NOT OPENMP_FOUND) - MESSAGE(NOTICE "No known compiler option for enabling OpenMP") - ELSE() - SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") - SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") - SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS}") + MESSAGE(ERROR "No known compiler option for enabling OpenMP") ENDIF(NOT OPENMP_FOUND) + SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS}") ENDIF(ENABLE_OPENMP) @@ -59,25 +55,17 @@ if (ENABLE_SHARP) SET(DEP_BUILD ${BUILD_PREFIX}/sharp-prefix/src/sharp/auto) IF(NOT ENABLE_OPENMP) SET(SHARP_OPENMP --disable-openmp) - ELSE() - SET(SHARP_OPENMP) ENDIF() SET(CUTILS_LIBRARY ${DEP_BUILD}/lib/libc_utils.a) SET(FFTPACK_LIBRARY ${DEP_BUILD}/lib/libfftpack.a) SET(SHARP_LIBRARY ${DEP_BUILD}/lib/libsharp.a) SET(SHARP_LIBRARIES ${SHARP_LIBRARY} ${FFTPACK_LIBRARY} ${CUTILS_LIBRARY}) SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include) - message(STATUS "Flags: ${CMAKE_C_FLAGS}") ExternalProject_Add(sharp - URL ${CMAKE_SOURCE_DIR}/external/libsharp-8d51946.tar.gz + URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz PREFIX ${BUILD_PREFIX}/sharp-prefix - DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND - cp -f ${CMAKE_SOURCE_DIR}/external/config.guess . && - cp -f ${CMAKE_SOURCE_DIR}/external/config.sub . && - autoconf && - ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" "CFLAGS=${CMAKE_C_FLAGS}" "LDFLAGS=${CMAKE_EXE_LINKER_FLAGS}" --prefix=${DEP_BUILD} ${SHARP_OPENMP} + CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP} INSTALL_COMMAND echo "No install" BUILD_BYPRODUCTS ${SHARP_LIBRARIES} ) @@ -94,23 +82,27 @@ if (INTERNAL_HDF5) ExternalProject_Add(hdf5 PREFIX ${BUILD_PREFIX}/hdf5-prefix URL ${HDF5_URL} - URL_HASH MD5=30172c75e436d7f2180e274071a4ca97 - DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads - CONFIGURE_COMMAND - ${HDF5_SOURCE_DIR}/configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" "CFLAGS=${CMAKE_C_FLAGS}" "LDFLAGS=${CMAKE_EXE_LINKER_FLAGS}" --prefix=${HDF5_BIN_DIR} --disable-shared --enable-cxx --enable-hl --enable-tools --with-pic - INSTALL_COMMAND make install + URL_HASH MD5=29117bf488887f89888f9304c8ebea0b + CMAKE_ARGS + -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} + -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} + -DHDF5_BUILD_CPP_LIB=ON + -DHDF5_BUILD_TOOLS=ON + -DHDF5_BUILD_HL_LIB=ON + -DBUILD_SHARED_LIBS=OFF ) SET(cosmotool_DEPS ${cosmotool_DEPS} hdf5) SET(hdf5_built hdf5) SET(ENV{HDF5_ROOT} ${HDF5_BIN_DIR}) SET(HDF5_ROOTDIR ${HDF5_BIN_DIR}) SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib") - SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl ${RT_LIBRARY}") - set(HDF5_C_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5.a) - set(HDF5_HL_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl.a) - set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE) - set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl.a CACHE STRING "HDF5 HL lib" FORCE) - set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp.a CACHE STRING "HDF5 C++ lib" FORCE) + SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl") + set(HDF5_C_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5-static.a) + set(HDF5_HL_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl-static.a) + set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5-static.a CACHE STRING "HDF5 lib" FORCE) + set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl-static.a CACHE STRING "HDF5 HL lib" FORCE) + set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp-static.a CACHE STRING "HDF5 C++ lib" FORCE) SET(HDF5_INCLUDE_DIRS ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE) mark_as_advanced(HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIRS) @@ -168,52 +160,43 @@ if (INTERNAL_NETCDF) SET(NETCDF_CONFIG_COMMAND ${NETCDF_SOURCE_DIR}/configure --prefix=${NETCDF_BIN_DIR} --libdir=${NETCDF_BIN_DIR}/lib --enable-netcdf-4 --with-pic --disable-shared --disable-dap - --disable-byterange --disable-cdmremote --disable-rpc --enable-cxx-4 + --disable-cdmremote --disable-rpc --enable-cxx-4 --disable-examples ${EXTRA_NC_FLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}) list(INSERT CMAKE_PREFIX_PATH 0 ${EXT_INSTALL}) string(REPLACE ";" "|" CMAKE_PREFIX_PATH_ALT_SEP "${CMAKE_PREFIX_PATH}") ExternalProject_Add(netcdf DEPENDS ${hdf5_built} - URL_HASH MD5=f48ee01534365006934f0c63d4055ea0 PREFIX ${BUILD_PREFIX}/netcdf-prefix - DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads URL ${NETCDF_URL} - LIST_SEPARATOR | - CMAKE_ARGS + LIST_SEPARATOR | + CMAKE_ARGS -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH_ALT_SEP} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} - -DNC_EXTRA_DEPS=${RT_DEP} -DBUILD_SHARED_LIBS=OFF -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=Release -DENABLE_NETCDF4=ON - -DENABLE_BYTERANGE=FALSE - -DCMAKE_POSITION_INDEPENDENT_CODE=ON - -DENABLE_DAP=OFF + -DCMAKE_POSITION_INDEPENDENT_CODE=ON + -DENABLE_DAP=OFF -DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR} -DHDF5_C_LIBRARY=${HDF5_C_STATIC_LIBRARY} -DHDF5_HL_LIBRARY=${HDF5_HL_STATIC_LIBRARY} -DHDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIRS} - -DCMAKE_INSTALL_LIBDIR=lib + -DCMAKE_INSTALL_LIBDIR=lib ) SET(NETCDFCXX_SOURCE_DIR ${BUILD_PREFIX}/netcdf-c++-prefix/src/netcdf-c++) ExternalProject_Add(netcdf-c++ DEPENDS ${hdf5_built} netcdf PREFIX ${BUILD_PREFIX}/netcdf-c++-prefix - DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads URL ${NETCDFCXX_URL} CMAKE_ARGS - -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH_ALT_SEP} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DBUILD_SHARED_LIBS=OFF - -DCMAKE_POSITION_INDEPENDENT_CODE=ON - -DHDF5_C_LIBRARY=${HDF5_C_STATIC_LIBRARY} - -DHDF5_HL_LIBRARY=${HDF5_HL_STATIC_LIBRARY} - -DHDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIRS} + -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR} @@ -251,8 +234,7 @@ if (INTERNAL_BOOST) ExternalProject_Add(boost URL ${BOOST_URL} PREFIX ${BUILD_PREFIX}/boost-prefix - DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads - URL_HASH MD5=f7050f554a65f6a42ece221eaeec1660 + URL_HASH MD5=da07ca30dd1c0d1fdedbd487efee01bd CONFIGURE_COMMAND ${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost BUILD_IN_SOURCE 1 @@ -295,7 +277,6 @@ IF(INTERNAL_GSL) ExternalProject_Add(gsl URL ${GSL_URL} PREFIX ${BUILD_PREFIX}/gsl-prefix - DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads CONFIGURE_COMMAND ${GSL_SOURCE_DIR}/configure --prefix=${EXT_INSTALL} --disable-shared --with-pic @@ -348,7 +329,6 @@ IF(INTERNAL_FFTW) ExternalProject_Add(fftw URL ${FFTW_URL} PREFIX ${BUILD_PREFIX}/fftw-prefix - DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads CONFIGURE_COMMAND ${FFTW_SOURCE}/configure --prefix=${EXT_INSTALL} @@ -378,7 +358,6 @@ IF (INTERNAL_EIGEN) ExternalProject_Add(eigen URL ${EIGEN_URL} URL_HASH MD5=b9e98a200d2455f06db9c661c5610496 - DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads PREFIX ${BUILD_PREFIX}/eigen-prefix CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} @@ -411,7 +390,6 @@ SET(cosmotool_DEPS ${cosmotool_DEPS} omptl) SET(OMPTL_BUILD_DIR ${BUILD_PREFIX}/omptl-prefix/src/omptl) ExternalProject_Add(omptl PREFIX ${BUILD_PREFIX}/omptl-prefix - DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads URL ${CMAKE_SOURCE_DIR}/external/omptl-20120422.tar.bz2 CONFIGURE_COMMAND echo "No configure" BUILD_COMMAND echo "No build" diff --git a/external/libsharp-8d51946.tar.gz b/external/libsharp-8d51946.tar.gz deleted file mode 100644 index 7ca7602..0000000 Binary files a/external/libsharp-8d51946.tar.gz and /dev/null differ diff --git a/external/patch-omptl b/external/patch-omptl index 1386247..9ea9d28 100644 --- a/external/patch-omptl +++ b/external/patch-omptl @@ -1,6 +1,6 @@ diff -ur omptl.old/omptl_algorithm omptl/omptl_algorithm ---- omptl.old/omptl_algorithm 2022-06-19 08:21:39.815498672 +0200 -+++ omptl/omptl_algorithm 2022-06-19 08:21:52.953544672 +0200 +--- omptl.old/omptl_algorithm 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_algorithm 2021-06-20 15:40:29.000000000 +0200 @@ -20,7 +20,7 @@ #define OMPTL_ALGORITHM 1 @@ -23,13 +23,11 @@ diff -ur omptl.old/omptl_algorithm omptl/omptl_algorithm #endif /* OMPTL_ALGORITHM */ diff -ur omptl.old/omptl_algorithm_par.h omptl/omptl_algorithm_par.h ---- omptl.old/omptl_algorithm_par.h 2022-06-19 08:21:39.816498675 +0200 -+++ omptl/omptl_algorithm_par.h 2022-06-19 08:23:50.705956964 +0200 -@@ -20,9 +20,10 @@ - #include +--- omptl.old/omptl_algorithm_par.h 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_algorithm_par.h 2021-06-20 15:40:50.000000000 +0200 +@@ -21,8 +21,8 @@ #include #include -+#include -#include -#include @@ -38,78 +36,7 @@ diff -ur omptl.old/omptl_algorithm_par.h omptl/omptl_algorithm_par.h #include -@@ -510,7 +511,7 @@ - - typename std::vector::iterator result = - std::find_if(results.begin(),results.end(), -- std::bind2nd(std::not_equal_to(), last) ); -+ std::bind(std::not_equal_to(), std::placeholders::_1, last) ); - - if ( result != results.end() ) - return *result; -@@ -569,7 +570,7 @@ - - const typename std::vector::iterator result - = std::find_if(results.begin(), results.end(), -- std::bind2nd(std::not_equal_to(), last) ); -+ std::bind(std::not_equal_to(), std::placeholders::_1, last) ); - - if ( result != results.end() ) - return *result; -@@ -654,7 +655,7 @@ - - const typename std::vector::iterator - result = std::find_if(results.begin(), results.end(), -- std::bind2nd(std::not_equal_to(), last1)); -+ std::bind(std::not_equal_to(), std::placeholders::_1, last1)); - - if ( result != results.end() ) - return *result; -@@ -953,7 +954,7 @@ - results[t] = std::lower_bound(partitions[t].first, partitions[t].second, value, comp); - - const typename std::vector::iterator result = -- std::find_if(results.begin(), results.end(), std::bind2nd(std::not_equal_to(), last) ); -+ std::find_if(results.begin(), results.end(), std::bind(std::not_equal_to(), std::placeholders::_1, last) ); - - if (result != results.end()) - return *result; -@@ -1179,7 +1180,7 @@ - - namespace detail - { -- -+ - template - Iterator _pivot_range(Iterator first, Iterator last, - const typename std::iterator_traits::value_type pivot, -@@ -1309,14 +1310,14 @@ - void random_shuffle(RandomAccessIterator first, RandomAccessIterator last, - const unsigned P) - { -- std::random_shuffle(first, last); -+ std::shuffle(first, last, std::mt19937(std::random_device()())); - } - - template - void random_shuffle(RandomAccessIterator first, RandomAccessIterator last, - RandomNumberGenerator& rgen, const unsigned P) - { -- std::random_shuffle(first, last, rgen); -+ std::shuffle(first, last, std::mt19937(std::random_device()())); - } - - // Not (yet) parallelized, not straightforward due to possible dependencies -@@ -1472,7 +1473,7 @@ - const T& new_value, const unsigned P) - { - return ::omptl::replace_copy_if(first, last, result, -- std::bind2nd(std::equal_to(), old_value), new_value, P); -+ std::bind(std::equal_to(), std::placeholders::_1, old_value), new_value, P); - } - - template -@@ -1700,7 +1701,7 @@ +@@ -1700,7 +1700,7 @@ std::vector pivot_used(pivots.size(), false); // can't be bool due to parallel write @@ -118,56 +45,9 @@ diff -ur omptl.old/omptl_algorithm_par.h omptl/omptl_algorithm_par.h assert(1u << max_depth <= P); for (unsigned i = 0; i < max_depth; ++i) { -@@ -1781,7 +1782,7 @@ - std::cout << std::endl; - - std::cout << borders.size() << " " << partitions.size() << " " << P << std::endl; --*/ -+*/ - // Round one: sort final partitions, split remaining - #pragma omp parallel for - for (int i = 0; i < int(partitions.size()); ++i) -@@ -1814,7 +1815,7 @@ - - const RandomAccessIterator begin = partitions[i].first; - const RandomAccessIterator end = partitions[i].second; -- -+ - const RandomAccessIterator middle = - detail::_pivot_range(begin, end, pivots[pivot_index], comp); - partitions[i ] = std::make_pair(begin, middle); -diff -ur omptl.old/omptl_algorithm_ser.h omptl/omptl_algorithm_ser.h ---- omptl.old/omptl_algorithm_ser.h 2022-06-19 08:21:39.815498672 +0200 -+++ omptl/omptl_algorithm_ser.h 2022-06-19 08:21:52.960544697 +0200 -@@ -14,7 +14,7 @@ - // You should have received a copy of the GNU Lesser General Public - // License along with this library; if not, write to the Free Software - // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA -- -+#include - - namespace omptl - { -@@ -463,14 +463,14 @@ - void random_shuffle(RandomAccessIterator first, RandomAccessIterator last, - const unsigned P) - { -- return ::std::random_shuffle(first, last); -+ return ::std::shuffle(first, last, std::mt19937(std::random_device()())); - } - - template - void random_shuffle(RandomAccessIterator first, RandomAccessIterator last, - RandomNumberGenerator &rgen, const unsigned P) - { -- return ::std::random_shuffle(first, last, rgen); -+ return ::std::shuffle(first, last, std::mt19937(std::random_device()())); - } - - template diff -ur omptl.old/omptl_numeric omptl/omptl_numeric ---- omptl.old/omptl_numeric 2022-06-19 08:21:39.816498675 +0200 -+++ omptl/omptl_numeric 2022-06-19 08:21:52.955544679 +0200 +--- omptl.old/omptl_numeric 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_numeric 2021-06-20 15:40:29.000000000 +0200 @@ -19,7 +19,7 @@ #define OMPTL_NUMERIC 1 @@ -193,8 +73,8 @@ diff -ur omptl.old/omptl_numeric omptl/omptl_numeric #endif /* OMPTL_NUMERIC */ diff -ur omptl.old/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h ---- omptl.old/omptl_numeric_extensions.h 2022-06-19 08:21:39.815498672 +0200 -+++ omptl/omptl_numeric_extensions.h 2022-06-19 08:21:52.956544683 +0200 +--- omptl.old/omptl_numeric_extensions.h 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_numeric_extensions.h 2021-06-20 15:40:29.000000000 +0200 @@ -51,9 +51,9 @@ } // namespace @@ -208,8 +88,8 @@ diff -ur omptl.old/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h namespace omptl diff -ur omptl.old/omptl_numeric_par.h omptl/omptl_numeric_par.h ---- omptl.old/omptl_numeric_par.h 2022-06-19 08:21:39.816498675 +0200 -+++ omptl/omptl_numeric_par.h 2022-06-19 08:21:52.957544686 +0200 +--- omptl.old/omptl_numeric_par.h 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_numeric_par.h 2021-06-20 15:40:29.000000000 +0200 @@ -23,8 +23,8 @@ #include #include @@ -222,8 +102,8 @@ diff -ur omptl.old/omptl_numeric_par.h omptl/omptl_numeric_par.h namespace omptl { diff -ur omptl.old/omptl_tools.h omptl/omptl_tools.h ---- omptl.old/omptl_tools.h 2022-06-19 08:21:39.816498675 +0200 -+++ omptl/omptl_tools.h 2022-06-19 08:21:52.957544686 +0200 +--- omptl.old/omptl_tools.h 2012-04-22 16:29:41.000000000 +0200 ++++ omptl/omptl_tools.h 2021-06-20 15:40:42.000000000 +0200 @@ -25,7 +25,7 @@ #include #include diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 7a031e7..0000000 --- a/pyproject.toml +++ /dev/null @@ -1,8 +0,0 @@ -[build-system] -requires = ["setuptools","wheel","cython"] -build-backend = "setuptools.build_meta" - - -[tool.towncrier] -directory = "changes" - diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt index 1b3fe10..7eda7ac 100644 --- a/python/CMakeLists.txt +++ b/python/CMakeLists.txt @@ -2,7 +2,7 @@ set(CMAKE_SHARED_MODULE_PREFIX) set(PYTHON_INCLUDES ${NUMPY_INCLUDE_DIRS} ${PYTHON_INCLUDE_PATH} ${CMAKE_SOURCE_DIR}/python) -include_directories(${CMAKE_SOURCE_DIR}/python ${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src) +include_directories(${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src) IF(CYTHON) add_custom_command( @@ -69,10 +69,13 @@ target_link_libraries(_fast_interp PRIVATE ${CosmoTool_local} ) SET(ct_TARGETS _cosmotool _project _cosmo_power _cosmo_cic _fast_interp _cosmomath) if (Boost_FOUND) - message(STATUS "Building bispectrum support") + message(STATUS "Building bispectrum support (path = ${Boost_INCLUDE_DIRS})") include_directories(${Boost_INCLUDE_DIRS}) add_library(_cosmo_bispectrum MODULE _cosmo_bispectrum.cpp) target_link_libraries(_cosmo_bispectrum ${MATH_LIBRARY}) + if(ENABLE_OPENMP) + set_target_properties(_cosmo_bispectrum PROPERTIES COMPILE_FLAGS "${OpenMP_CXX_FLAGS}" LINK_FLAGS "${OpenMP_CXX_FLAGS}") + endif() if (Boost_DEP) add_dependencies(_cosmo_bispectrum ${Boost_DEP}) endif() diff --git a/python/_cosmomath.pyx b/python/_cosmomath.pyx index fc4b3b6..e5ab880 100644 --- a/python/_cosmomath.pyx +++ b/python/_cosmomath.pyx @@ -12,7 +12,7 @@ cdef extern from "numpy/npy_common.h": ctypedef npy_intp cdef extern from "special_math.hpp" namespace "CosmoTool": - T log_modified_bessel_first_kind[T](T v, T z) except + nogil + T log_modified_bessel_first_kind[T](T v, T z) nogil except + cdef extern from "numpy_adaptors.hpp" namespace "CosmoTool": void parallel_ufunc_dd_d[T,IT](char **args, IT* dimensions, IT* steps, void *func) diff --git a/python/_cosmotool.pyx b/python/_cosmotool.pyx index 7f2bc76..b2494bd 100644 --- a/python/_cosmotool.pyx +++ b/python/_cosmotool.pyx @@ -39,7 +39,7 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool": cdef extern from "loadGadget.hpp" namespace "CosmoTool": - SimuData *loadGadgetMulti(const char *fname, int id, int flags, int gformat) except + nogil + SimuData *loadGadgetMulti(const char *fname, int id, int flags, int gformat) nogil except + void cxx_writeGadget "CosmoTool::writeGadget" (const char * s, SimuData *data) except + cdef extern from "safe_gadget.hpp": @@ -313,13 +313,6 @@ tries to get an array from the object.""" references to the object are gone. """ pass - -cdef extern from "numpy/arrayobject.h": - # a little bit awkward: the reference to obj will be stolen - # using PyObject* to signal that Cython cannot handle it automatically - int PyArray_SetBaseObject(np.ndarray arr, PyObject *obj) except -1 # -1 means there was an error - - cdef object wrap_array(void *p, np.uint64_t s, int typ): cdef np.ndarray ndarray cdef ArrayWrapper wrapper @@ -327,8 +320,7 @@ cdef object wrap_array(void *p, np.uint64_t s, int typ): wrapper = ArrayWrapper() wrapper.set_data(s, typ, p) ndarray = np.array(wrapper, copy=False) - #ndarray.base = wrapper - PyArray_SetBaseObject(ndarray, wrapper) + ndarray.base = wrapper Py_INCREF(wrapper) return ndarray diff --git a/python/_project.pyx b/python/_project.pyx index 726ed0c..bd64667 100644 --- a/python/_project.pyx +++ b/python/_project.pyx @@ -727,7 +727,7 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density, cdef int iu0[3] cdef int i cdef int N = density.shape[0] - cdef int half_N = density.shape[0]//2 + cdef int half_N = density.shape[0]/2 cdef int completed cdef DTYPE_t I0, d, dist2, delta, s, max_distance2 cdef int jumper[1] diff --git a/requirements.txt b/requirements.txt index 922eaeb..3a4577b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,5 @@ -numpy<1.22 +numpy<1.19 cffi numexpr -cython<3 +pyfftw +cython diff --git a/sample/CMakeLists.txt b/sample/CMakeLists.txt index 6d019a7..839b37f 100644 --- a/sample/CMakeLists.txt +++ b/sample/CMakeLists.txt @@ -1,8 +1,4 @@ SET(tolink ${CosmoTool_local} ${CosmoTool_LIBS} ${GSL_LIBRARIES} ${DL_LIBRARY}) -if (RT_LIBRARY) - SET(tolink ${tolink} ${RT_LIBRARY}) -endif() - include_directories(${CMAKE_SOURCE_DIR}/src) include_directories(${FFTW3_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS} ${GSL_INCLUDE_PATH}) if(YORICK_SUPPORT) @@ -91,7 +87,7 @@ if (Boost_FOUND) ENDIF (YORICK_SUPPORT) if (HDF5_FOUND) add_executable(simple3DFilter simple3DFilter.cpp) - target_link_libraries(simple3DFilter ${tolink}) + target_link_libraries(simple3DFilter ${tolink} ${MPI_C_LIBRARIES}) add_executable(simpleDistanceFilter simpleDistanceFilter.cpp) target_link_libraries(simpleDistanceFilter ${tolink}) @@ -105,7 +101,7 @@ if (Boost_FOUND) add_executable(gadgetToArray gadgetToArray.cpp) target_link_libraries(gadgetToArray ${tolink}) - + add_executable(testHDF5 testHDF5.cpp) target_link_libraries(testHDF5 ${tolink}) diff --git a/sample/simple3DFilter.cpp b/sample/simple3DFilter.cpp index 2dbde42..ace6ecb 100644 --- a/sample/simple3DFilter.cpp +++ b/sample/simple3DFilter.cpp @@ -1,3 +1,11 @@ +#include +#include + +#include +#include +#include +#include + #include "hdf5_array.hpp" #include "miniargs.hpp" #include "mykdtree.hpp" @@ -5,11 +13,6 @@ #include "openmp.hpp" #include "sphSmooth.hpp" #include "yorick.hpp" -#include -#include -#include -#include -#include using namespace std; using namespace CosmoTool; @@ -27,37 +30,32 @@ typedef boost::multi_array array_type; typedef boost::multi_array array3_type; typedef boost::multi_array array4_type; -ComputePrecision getVelocity(const VCoord &v, int i) { return v.mass * v.v[i]; } +ComputePrecision getVelocity(const VCoord& v, int i) { return v.mass * v.v[i]; } -ComputePrecision getMass(const VCoord &v) { return v.mass; } +ComputePrecision getMass(const VCoord& v) { return v.mass; } typedef SPHSmooth MySmooth; typedef MySmooth::SPHTree MyTree; typedef MyTree::Cell MyCell; template -void computeInterpolatedField(MyTree *tree1, double boxsize, int Nres, +void computeInterpolatedField(MyTree* tree1, double boxsize, int Nres, double cx, double cy, double cz, - array3_type &bins, array3_type &arr, FuncT func, + array3_type& bins, array3_type& arr, FuncT func, double rLimit2) { - int rz_max = 0; -#pragma omp parallel shared(rz_max) +#pragma omp parallel { MySmooth smooth1(tree1, N_SPH); -#pragma omp for collapse(3) schedule(dynamic) +#pragma omp for schedule(dynamic) for (int rz = 0; rz < Nres; rz++) { + double pz = (rz)*boxsize / Nres - cz; + cout << format("[%d] %d / %d") % smp_get_thread_id() % rz % Nres << endl; for (int ry = 0; ry < Nres; ry++) { + double py = (ry)*boxsize / Nres - cy; for (int rx = 0; rx < Nres; rx++) { - if (rz > rz_max) { - rz_max = rz; - cout << format("[%d] %d / %d") % smp_get_thread_id() % rz % Nres - << endl; - } double px = (rx)*boxsize / Nres - cx; - double py = (ry)*boxsize / Nres - cy; - double pz = (rz)*boxsize / Nres - cz; MyTree::coords c = {float(px), float(py), float(pz)}; @@ -80,11 +78,18 @@ void computeInterpolatedField(MyTree *tree1, double boxsize, int Nres, } } -int main(int argc, char **argv) { - char *fname1, *outFile; +int main(int argc, char** argv) { + int provided; + MPI_Init_thread(&argc, &argv, MPI_THREAD_FUNNELED, &provided); + if (provided < MPI_THREAD_FUNNELED) { + std::cerr << "Cannot mix MPI and Threads here. Please recompile with " + "OpenMP or MPI switched off." + << std::endl; + MPI_Abort(MPI_COMM_WORLD, 99); + } + char *fname1, *fname2; double rLimit, boxsize, rLimit2, cx, cy, cz; int Nres; - int periodic; MiniArgDesc args[] = {{"INPUT DATA1", &fname1, MINIARG_STRING}, {"RADIUS LIMIT", &rLimit, MINIARG_DOUBLE}, @@ -93,17 +98,17 @@ int main(int argc, char **argv) { {"CX", &cx, MINIARG_DOUBLE}, {"CY", &cy, MINIARG_DOUBLE}, {"CZ", &cz, MINIARG_DOUBLE}, - {"OUTPUT FILE", &outFile, MINIARG_STRING}, - {"PERIODIC", &periodic, MINIARG_INT}, {0, 0, MINIARG_NULL}}; - if (!parseMiniArgs(argc, argv, args)) - return 1; + if (!parseMiniArgs(argc, argv, args)) return 1; + int rank, size; + MPI_Comm_rank(MPI_COMM_WORLD, &rank); + MPI_Comm_size(MPI_COMM_WORLD, &size); H5::H5File in_f(fname1, 0); - H5::H5File out_f(outFile, H5F_ACC_TRUNC); + H5::H5File out_f(boost::str(boost::format("fields_%d.h5", rank), H5F_ACC_TRUNC); array_type v1_data; - uint64_t N1_points, N2_points; + uint32_t N1_points, N2_points; array3_type bins(boost::extents[Nres][Nres][Nres]); @@ -116,17 +121,15 @@ int main(int argc, char **argv) { cout << "Got " << N1_points << " in the first file." << endl; - MyCell *allCells_1 = new MyCell[N1_points]; + MyCell* allCells_1 = new MyCell[N1_points]; #pragma omp parallel for schedule(static) - for (uint32_t i = 0; i < Nres * Nres * Nres; i++) - bins.data()[i] = 0; + for (long i = 0; i < Nres * Nres * Nres; i++) bins.data()[i] = 0; cout << "Shuffling data in cells..." << endl; #pragma omp parallel for schedule(static) - for (uint64_t i = 0; i < N1_points; i++) { - for (int j = 0; j < 3; j++) - allCells_1[i].coord[j] = v1_data[i][j]; + for (int i = 0; i < N1_points; i++) { + for (int j = 0; j < 3; j++) allCells_1[i].coord[j] = v1_data[i][j]; for (int k = 0; k < 3; k++) allCells_1[i].val.pValue.v[k] = v1_data[i][3 + k]; allCells_1[i].val.pValue.mass = v1_data[i][6]; @@ -140,9 +143,8 @@ int main(int argc, char **argv) { if (rx < 0 || rx >= Nres || ry < 0 || ry >= Nres || rz < 0 || rz >= Nres) continue; - auto &b = bins[rx][ry][rz]; -#pragma omp atomic - b++; + //#pragma omp atomic update + bins[rx][ry][rz]++; } v1_data.resize(boost::extents[1][1]); @@ -150,7 +152,6 @@ int main(int argc, char **argv) { cout << "Building trees..." << endl; MyTree tree1(allCells_1, N1_points); - tree1.setPeriodic(periodic != 0, boxsize); cout << "Creating smoothing filter..." << endl; @@ -158,21 +159,18 @@ int main(int argc, char **argv) { cout << "Weighing..." << endl; - int rz_max = 0; -#pragma omp parallel shared(rz_max) +#pragma omp parallel { MySmooth smooth1(&tree1, N_SPH); -#pragma omp for collapse(3) schedule(dynamic, 8) +#pragma omp for schedule(dynamic) for (int rz = 0; rz < Nres; rz++) { + double pz = (rz)*boxsize / Nres - cz; + + (cout << rz << " / " << Nres << endl).flush(); for (int ry = 0; ry < Nres; ry++) { + double py = (ry)*boxsize / Nres - cy; for (int rx = 0; rx < Nres; rx++) { - if (rz > rz_max) { - rz_max = rz; - (cout << rz << " / " << Nres << endl).flush(); - } - double pz = (rz)*boxsize / Nres - cz; - double py = (ry)*boxsize / Nres - cy; double px = (rx)*boxsize / Nres - cx; MyTree::coords c = {float(px), float(py), float(pz)}; @@ -187,11 +185,30 @@ int main(int argc, char **argv) { smooth1.fetchNeighbours(c, numInCell); else smooth1.fetchNeighbours(c); +#pragma omp critical smooth1.addGridSite(c); } } + (cout << " Done " << rz << endl).flush(); } } + // + // Reduction on the cell.weight in the tree. + // MPI_Allreduce to act on contiguous arrays. + auto tree = smooth1.getTree(); + auto nodes = tree->getAllNodes(); + double *weight_array = new double[N1_points]; + for (size_t c = 0; c < N1_points; c++) { + weight_array[c] = allCells[c].val.weight; + } + MPI_Allreduce(MPI_IN_PLACE, weight_array, N1_points, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); + for (size_t c = 0; c < N1_points; c++) { + allCells[c].val.weight = weight_array[c]; + } + delete[] weight_array; + + // cell.weights -> build a 1d array of the particles weight -> MPI_Allreduce -> resend the new weights to the particles + // cout << "Interpolating..." << endl; diff --git a/setup.py b/setup.py index 0b98cce..da984f3 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,6 @@ import stat import os import sys import shutil -from sysconfig import get_config_var from distutils.command.install_data import install_data import pathlib from setuptools import find_packages, setup, Extension @@ -77,9 +76,9 @@ class InstallCMakeLibs(install_lib): # # your files are moved to the appropriate location when the installation # # is run # -# libs = [os.path.join(bin_dir, _lib) for _lib in -# os.listdir(bin_dir) if -# os.path.isfile(os.path.join(bin_dir, _lib)) and +# libs = [os.path.join(bin_dir, _lib) for _lib in +# os.listdir(bin_dir) if +# os.path.isfile(os.path.join(bin_dir, _lib)) and # os.path.splitext(_lib)[1] in [".dll", ".so"] # and not (_lib.startswith("python") or _lib.startswith(PACKAGE_NAME))] # @@ -88,16 +87,16 @@ class InstallCMakeLibs(install_lib): # shutil.move(lib, os.path.join(self.build_dir, # os.path.basename(lib))) # -# # Mark the libs for installation, adding them to -# # distribution.data_files seems to ensure that setuptools' record +# # Mark the libs for installation, adding them to +# # distribution.data_files seems to ensure that setuptools' record # # writer appends them to installed-files.txt in the package's egg-info # # -# # Also tried adding the libraries to the distribution.libraries list, -# # but that never seemed to add them to the installed-files.txt in the -# # egg-info, and the online recommendation seems to be adding libraries -# # into eager_resources in the call to setup(), which I think puts them -# # in data_files anyways. -# # +# # Also tried adding the libraries to the distribution.libraries list, +# # but that never seemed to add them to the installed-files.txt in the +# # egg-info, and the online recommendation seems to be adding libraries +# # into eager_resources in the call to setup(), which I think puts them +# # in data_files anyways. +# # # # What is the best way? # # # These are the additional installation files that should be @@ -105,7 +104,7 @@ class InstallCMakeLibs(install_lib): # # step; depending on the files that are generated from your cmake # # build chain, you may need to modify the below code # -# self.distribution.data_files = [os.path.join(self.install_dir, +# self.distribution.data_files = [os.path.join(self.install_dir, # os.path.basename(lib)) # for lib in libs] # print(self.distribution.data_files) @@ -168,24 +167,17 @@ class BuildCMakeExt(build_ext): # Change your cmake arguments below as necessary # Below is just an example set of arguments for building Blender as a Python module - c_compiler=os.environ.get('CC', get_config_var("CC")) - cxx_compiler=os.environ.get('CXX', get_config_var("CXX")) - compilers=[] fill_up_settings=[ - ("CMAKE_C_COMPILER", "CC", get_config_var("CC")), - ("CMAKE_CXX_COMPILER", "CXX", get_config_var("CXX")), - ("CMAKE_C_FLAGS", "CFLAGS", None), - ("CMAKE_CXX_FLAGS", "CXXFLAGS", None), - ("CMAKE_EXE_LINKER_FLAGS_INIT", "LDFLAGS", None), - ("CMAKE_SHARED_LINKER_FLAGS_INIT", "LDFLAGS", None), - ("CMAKE_MODULE_LINKER_FLAGS_INIT", "LDFLAGS", None)] - for cmake_flag, os_flag, default_flag in fill_up_settings: - if os_flag in os.environ or default_flag is not None: - c = os.environ.get(os_flag, default_flag) - if not c is None: - compilers.append(f"-D{cmake_flag}={c}") - print(compilers) + ("CMAKE_C_COMPILER", "CC"), + ("CMAKE_CXX_COMPILER", "CXX"), + ("CMAKE_C_FLAGS", "CFLAGS"), + ("CMAKE_EXE_LINKER_FLAGS_INIT", "LDFLAGS"), + ("CMAKE_SHARED_LINKER_FLAGS_INIT", "LDFLAGS"), + ("CMAKE_MODULE_LINKER_FLAGS_INIT", "LDFLAGS")] + for cmake_flag, os_flag in fill_up_settings: + if os_flag in os.environ: + compilers.append(f"-D{cmake_flag}={os.environ[os_flag]}") self.spawn(['cmake', '-H'+SOURCE_DIR, '-B'+self.build_temp, '-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON', @@ -221,7 +213,7 @@ class BuildCMakeExt(build_ext): if _pyd_top[0].startswith(PACKAGE_NAME): if os.path.splitext(_pyd)[1] in [".pyd", ".so"] or _pyd_top[-1] == 'config.py': pyd_path.append((_pyd_top,_pyd)) - + for top,p in pyd_path: _,n = os.path.split(p) @@ -237,10 +229,10 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.3.6', + version='1.2.3', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, - install_requires=['cython','numpy','cffi','numexpr','h5py'], + install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], setup_requires=['cython','cffi','numpy','numexpr'], ext_modules=[CosmoTool_extension], description='A small cosmotool box of useful functions', diff --git a/src/cosmopower.cpp b/src/cosmopower.cpp index 7ecaf2d..5e58c2c 100644 --- a/src/cosmopower.cpp +++ b/src/cosmopower.cpp @@ -212,30 +212,6 @@ double CosmoPower::powerHuWiggles(double k) return normPower * pow(k,n) * T_k * T_k; } -double CosmoPower::BAO_Tk(double k){ - - double no_wiggle_tk = noWiggleTk(k); - - double A = 0; - double r_s = 10; - double k_D = 2 * M_PI / 100; - - //sqrt as we want to make the parameterization part of the transfer function - double param = sqrt(1 + A * sin(k * r_s) * exp(- k / k_D)); - return no_wiggle_tk * param; - -} - -double CosmoPower::sample_BAO(double k) -{ - // BAO wiggle parameterization for reconstruction - // Babic et al. 2022, https://arxiv.org/abs/2203.06177 - - double T_k = BAO_Tk(k); - - return normPower * pow(k,n) * T_k * T_k; - } - double CosmoPower::primordialPowerSpectrum(double k) { //Primordial power spectrum, needed for PNG @@ -273,19 +249,6 @@ double CosmoPower::matterTransferFunctionHu(double k) return T_k; } -double CosmoPower::noWiggleTk(double k) -{ - double s = 44.5 * log(9.83 / OmegaEff) / (sqrt(1 + 10 * pow(OMEGA_B * h * h, 0.75))); - double alpha_Gamma = 1 - 0.328 * log(431 * OmegaEff) * OMEGA_B / OMEGA_0 + 0.38 * log(22.3 * OmegaEff) * pow(OMEGA_B / OMEGA_0, 2); - double GammaEff = OMEGA_0 * h * (alpha_Gamma + (1 - alpha_Gamma)/(1 + pow(0.43 * k * s, 4))); - double q = k/(h*GammaEff) * pow(Theta_27, 2); - double L_0 = log(2 * M_E + 1.8 * q); - double C_0 = 14.2 + 731 / (1 + 62.5 * q); - double T0 = L_0 / (L_0 + C_0 * q * q); - - return T0; -} - double CosmoPower::powerHuBaryons(double k) { double s = 44.5 * log(9.83 / OmegaEff) / (sqrt(1 + 10 * pow(OMEGA_B * h * h, 0.75))); @@ -481,18 +444,12 @@ void CosmoPower::setFunction(CosmoFunction f) case POWER_SUGIYAMA: eval = &CosmoPower::powerSugiyama; break; - case SAMPLE_WIGGLES: - eval = &CosmoPower::sample_BAO; - break; case POWER_BDM: eval = &CosmoPower::powerBDM; break; case POWER_TEST: eval = &CosmoPower::powerTest; break; - case BAO_TK: - eval = &CosmoPower::BAO_Tk; - break; default: abort(); } diff --git a/src/cosmopower.hpp b/src/cosmopower.hpp index 86ad8b1..ba0bffc 100644 --- a/src/cosmopower.hpp +++ b/src/cosmopower.hpp @@ -89,9 +89,7 @@ namespace CosmoTool { POWER_SUGIYAMA, POWER_BDM, POWER_TEST, - HU_WIGGLES_ORIGINAL, - SAMPLE_WIGGLES, - BAO_TK + HU_WIGGLES_ORIGINAL }; CosmoPower(); @@ -124,9 +122,6 @@ namespace CosmoTool { double powerBDM(double k); double powerTest(double k); double powerHuWigglesOriginal(double k); - double sample_BAO(double k); - double noWiggleTk(double k); - double BAO_Tk(double k); }; }; diff --git a/src/h5_readFlash.cpp b/src/h5_readFlash.cpp index 6e2ec3a..8e46b89 100644 --- a/src/h5_readFlash.cpp +++ b/src/h5_readFlash.cpp @@ -7,16 +7,16 @@ This software is a computer program whose purpose is to provide a toolbox for co data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...) This software is governed by the CeCILL license under French law and -abiding by the rules of distribution of free software. You can use, +abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL -"http://www.cecill.info". +"http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited -liability. +liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the @@ -25,9 +25,9 @@ that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their -requirements in conditions enabling the security of their systems and/or -data to be ensured and, more generally, to use and operate it in the -same conditions as regards security. +requirements in conditions enabling the security of their systems and/or +data to be ensured and, more generally, to use and operate it in the +same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. @@ -59,8 +59,8 @@ int ipvz_out = 5; /* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */ -/* n*_runtime_parameters should be set by the caller to - the maximum number of runtime parameters to read. +/* n*_runtime_parameters should be set by the caller to + the maximum number of runtime parameters to read. */ void h5_read_runtime_parameters @@ -100,12 +100,12 @@ void h5_read_runtime_parameters nreal_runtime_parameters = MAX_PARM; /* integer runtime parameters */ - int_rt_parms = (int_runtime_params_t *) malloc(nint_runtime_parameters * sizeof(int_runtime_params_t)); + int_rt_parms = (int_runtime_params_t *) malloc(nint_runtime_parameters * sizeof(int_runtime_params_t)); rank = 1; DataSet dataset = file->openDataSet("integer runtime parameters"); - - IntType int_rt_type = dataset.getIntType(); + + IntType int_rt_type = dataset.getIntType(); //int_rt_type = H5Dget_type(dataset); DataSpace dataspace = dataset.getSpace(); @@ -123,7 +123,10 @@ void h5_read_runtime_parameters DataSpace memspace(rank, &dimens_1d); //memspace = H5Screate_simple(rank, &dimens_1d, NULL); - dataset.read(int_rt_parms, int_rt_type, memspace, dataspace); + dataset.read(int_rt_parms, int_rt_type, memspace, dataspace, + H5P_DEFAULT); + //status = H5Dread(dataset, int_rt_type, memspace, dataspace, + // H5P_DEFAULT, int_rt_parms); for (i = 0; i < nint_runtime_parameters; i++) { @@ -142,14 +145,14 @@ void h5_read_runtime_parameters /* reals */ - real_rt_parms = (real_runtime_params_t *) malloc(nreal_runtime_parameters * sizeof(real_runtime_params_t)); - + real_rt_parms = (real_runtime_params_t *) malloc(nreal_runtime_parameters * sizeof(real_runtime_params_t)); + rank = 1; dataset = file->openDataSet("real runtime parameters"); - //dataset = H5Dopen(*file_identifier, "real runtime parameters"); - + //dataset = H5Dopen(*file_identifier, "real runtime parameters"); + dataspace = dataset.getSpace(); - FloatType real_rt_type = dataset.getFloatType(); + FloatType real_rt_type = dataset.getFloatType(); ndims = dataspace.getSimpleExtentDims(&dimens_1d, NULL); //dataspace = H5Dget_space(dataset); //real_rt_type = H5Dget_type(dataset); @@ -164,7 +167,10 @@ void h5_read_runtime_parameters memspace = DataSpace(rank, &dimens_1d); //memspace = H5Screate_simple(rank, &dimens_1d, NULL); - dataset.read(real_rt_parms, real_rt_type, memspace, dataspace); + dataset.read(real_rt_parms, real_rt_type, memspace, dataspace, + H5P_DEFAULT); + //status = H5Dread(dataset, real_rt_type, memspace, dataspace, +// H5P_DEFAULT, real_rt_parms); for (i = 0; i < nreal_runtime_parameters; i++) { @@ -187,7 +193,7 @@ void h5_read_runtime_parameters *LBox = real_runtime_parameter_values[i]; } if (strncmp(real_runtime_parameter_names[i],"hubbleconstant", 14) == 0 ) { - *hubble = real_runtime_parameter_values[i]; + *hubble = real_runtime_parameter_values[i]; } if (strncmp(real_runtime_parameter_names[i],"omegamatter", 11) == 0 ) { *omegam = real_runtime_parameter_values[i]; @@ -199,7 +205,7 @@ void h5_read_runtime_parameters *omegalambda = real_runtime_parameter_values[i]; } } - + for (i = 0; i < nint_runtime_parameters; i++) { if (strncmp(int_runtime_parameter_names[i],"pt_numx",7) == 0 ) { *numPart = int_runtime_parameter_values[i]; @@ -208,7 +214,7 @@ void h5_read_runtime_parameters } } - + /* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*/ void h5_read_flash3_particles (H5File* file, int* totalparticles, @@ -235,8 +241,8 @@ void h5_read_flash3_particles (H5File* file, char *propName; double *partBuffer; char part_names[50][OUTPUT_PROP_LENGTH]; - int string_size; - + int string_size; + // char part_names[NPART_PROPS][OUTPUT_PROP_LENGTH]; hsize_t dimens_2d[2], maxdimens_2d[2]; hsize_t start_2d[2], count_2d[2], stride_2d[2]; @@ -259,12 +265,12 @@ void h5_read_flash3_particles (H5File* file, //total number of particle properties numProps = dimens_2d[0]; - + string_size = OUTPUT_PROP_LENGTH; StrType string_type = H5Tcopy(H5T_C_S1); string_type.setSize(string_size); //status = H5Tset_size(string_type, string_size); - + rank = 2; start_2d[0] = 0; @@ -276,20 +282,22 @@ void h5_read_flash3_particles (H5File* file, count_2d[0] = dimens_2d[0]; count_2d[1] = dimens_2d[1]; - dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d); + dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d); //status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start_2d, // stride_2d, count_2d, NULL); DataSpace memspace(rank, dimens_2d); //memspace = H5Screate_simple(rank, dimens_2d, NULL); - dataset.read(part_names, string_type); - + dataset.read(part_names, string_type, H5S_ALL, H5S_ALL, H5P_DEFAULT); + //status = H5Dread(dataset, string_type, H5S_ALL, H5S_ALL, + // H5P_DEFAULT, part_names); + string_type.close(); memspace.close(); dataspace.close(); - dataset.close(); + dataset.close(); //H5Tclose(string_type); //H5Sclose(memspace); //H5Sclose(dataspace); @@ -305,7 +313,7 @@ void h5_read_flash3_particles (H5File* file, if (strncmp(part_names[i], "velz", 4) == 0) { ipvz = i+1; } } - if ((iptag < 0) || (ipx < 0) || (ipy < 0) || (ipz < 0) || (ipvx < 0) || + if ((iptag < 0) || (ipx < 0) || (ipy < 0) || (ipz < 0) || (ipvx < 0) || (ipvy < 0) || (ipvz < 0) ) { printf("One or more required particle attributes not found in file!\n"); return; @@ -317,7 +325,7 @@ void h5_read_flash3_particles (H5File* file, //read particles dataset = file->openDataSet("tracer particles"); //dataset = H5Dopen(*file_identifier, "tracer particles"); - + FloatType datatype = dataset.getFloatType(); //datatype = H5Dget_type(dataset); @@ -330,7 +338,7 @@ void h5_read_flash3_particles (H5File* file, ndims = dataspace.getSimpleExtentDims(dimens_2d, NULL); //dataspace = H5Dget_space(dataset); //H5Sget_simple_extent_dims(dataspace, dimens_2d, maxdimens_2d); - + /*insert particle properties (numPartBuffer) particles at a time*/ pstack = (*localnp); poffset = 0; @@ -358,7 +366,7 @@ void h5_read_flash3_particles (H5File* file, dimens_2d[0] = (pcount); dimens_2d[1] = (numProps); - dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d); + dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d); //status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start_2d, // stride_2d, count_2d, NULL); @@ -366,7 +374,8 @@ void h5_read_flash3_particles (H5File* file, //memspace = H5Screate_simple(rank, dimens_2d, maxdimens_2d); /* read data from the dataset */ - dataset.read(partBuffer, datatype, memspace, dataspace); + dataset.read(partBuffer, datatype, memspace, dataspace, H5P_DEFAULT); + //status = H5Dread(dataset, datatype, memspace, dataspace, H5P_DEFAULT, partBuffer); /* convert buffer into particle struct */ @@ -382,8 +391,8 @@ void h5_read_flash3_particles (H5File* file, pos3[p+poffset] = (float) *(partBuffer+ipz-1+p*numProps); } } - - + + if (vel1 && vel2 && vel3) { for(p=0; p < (pcount); p++) { vel1[p+poffset] = (float) *(partBuffer+ipvx-1+p*numProps); @@ -414,7 +423,7 @@ void h5_read_flash3_particles (H5File* file, //status = H5Sclose(dataspace); //status = H5Dclose(dataset); } - + /*xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*/ @@ -442,7 +451,7 @@ void h5_read_flash3_header_info(H5File* file, H5std_string DATASET_NAME; - string_type = H5Tcopy(H5T_C_S1); + string_type = H5Tcopy(H5T_C_S1); H5Tset_size(string_type, MAX_STRING_LENGTH); DataSet dataset = file->openDataSet("real scalars"); @@ -458,13 +467,13 @@ void h5_read_flash3_header_info(H5File* file, /* malloc a pointer to a list of real_list_t's */ real_list = (real_list_t *) malloc(dimens_1d * sizeof(real_list_t)); - // create a new simple dataspace of 1 dimension and size of 'dimens_1d' + // create a new simple dataspace of 1 dimension and size of 'dimens_1d' DataSpace memspace(1, &dimens_1d); - // create an empty vessel sized to hold one real_list_t's worth of data + // create an empty vessel sized to hold one real_list_t's worth of data CompType real_list_type( sizeof(real_list_t) ); - // subdivide the empty vessel into its component sections (name and value) + // subdivide the empty vessel into its component sections (name and value) real_list_type.insertMember( "name", HOFFSET(real_list_t, name), @@ -475,8 +484,9 @@ void h5_read_flash3_header_info(H5File* file, HOFFSET(real_list_t, value), PredType::NATIVE_DOUBLE); - // read the data into 'real_list' - dataset.read( real_list, real_list_type, memspace, dataspace); + // read the data into 'real_list' + dataset.read( real_list, real_list_type, memspace, dataspace, + H5P_DEFAULT); if (status < 0) { diff --git a/src/hdf5_array.hpp b/src/hdf5_array.hpp index 55dc87b..db75a33 100644 --- a/src/hdf5_array.hpp +++ b/src/hdf5_array.hpp @@ -426,7 +426,7 @@ namespace CosmoTool { #define CTOOL_HDF5_INSERT_ELEMENT(r, STRUCT, element) \ { \ ::CosmoTool::get_hdf5_data_type t; \ - long position = offsetof(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \ + long position = HOFFSET(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \ const char *field_name = BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 1, element)); \ type.insertMember(field_name, position, t.type()); \ } diff --git a/src/interpolate.cpp b/src/interpolate.cpp index b996f7a..3de19f5 100644 --- a/src/interpolate.cpp +++ b/src/interpolate.cpp @@ -157,7 +157,6 @@ const Interpolate& Interpolate::operator=(const Interpolate& a) gsl_spline_init(spline, a.spline->x, a.spline->y, a.spline->size); logx = a.logx; logy = a.logy; - return *this; } double Interpolate::getMaxX() const diff --git a/src/mykdtree.hpp b/src/mykdtree.hpp index 67908cf..1b36eea 100644 --- a/src/mykdtree.hpp +++ b/src/mykdtree.hpp @@ -1,5 +1,5 @@ /*+ -This is CosmoTool (./src/mykdtree.hpp) -- Copyright (C) Guilhem Lavaux (2007-2022) +This is CosmoTool (./src/mykdtree.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014) guilhem.lavaux@gmail.com @@ -7,16 +7,16 @@ This software is a computer program whose purpose is to provide a toolbox for co data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...) This software is governed by the CeCILL license under French law and -abiding by the rules of distribution of free software. You can use, +abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL -"http://www.cecill.info". +"http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited -liability. +liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the @@ -25,9 +25,9 @@ that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their -requirements in conditions enabling the security of their systems and/or -data to be ensured and, more generally, to use and operate it in the -same conditions as regards security. +requirements in conditions enabling the security of their systems and/or +data to be ensured and, more generally, to use and operate it in the +same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. @@ -48,13 +48,13 @@ namespace CosmoTool { typedef uint64_t NodeIntType; - template + template struct KDDef { typedef CType CoordType; typedef float KDCoordinates[N]; }; - + template struct KDCell { @@ -99,10 +99,10 @@ namespace CosmoTool { typename KDDef::CoordType r, r2; KDCell **cells; typename KDDef::CoordType *distances; - uint64_t currentRank; - uint64_t numCells; + uint32_t currentRank; + uint32_t numCells; }; - + template class RecursionMultipleInfo @@ -114,14 +114,14 @@ namespace CosmoTool { RecursionMultipleInfo(const typename KDDef::KDCoordinates& rx, KDCell **cells, - uint64_t numCells) + uint32_t numCells) : queue(cells, numCells, INFINITY),traversed(0) { std::copy(rx, rx+N, x); } }; - template + template struct KD_default_cell_splitter { void operator()(KDCell **cells, NodeIntType Ncells, NodeIntType& split_index, int axis, typename KDDef::KDCoordinates minBound, typename KDDef::KDCoordinates maxBound); @@ -135,7 +135,7 @@ namespace CosmoTool { typedef typename KDDef::KDCoordinates coords; typedef KDCell Cell; typedef KDTreeNode Node; - + CellSplitter splitter; KDTree(Cell *cells, NodeIntType Ncells); @@ -153,20 +153,20 @@ namespace CosmoTool { std::copy(replicate, replicate+N, this->replicate); } - uint64_t getIntersection(const coords& x, CoordType r, + uint32_t getIntersection(const coords& x, CoordType r, Cell **cells, - uint64_t numCells); - uint64_t getIntersection(const coords& x, CoordType r, + uint32_t numCells); + uint32_t getIntersection(const coords& x, CoordType r, Cell **cells, CoordType *distances, - uint64_t numCells); - uint64_t countCells(const coords& x, CoordType r); + uint32_t numCells); + uint32_t countCells(const coords& x, CoordType r); Cell *getNearestNeighbour(const coords& x); - void getNearestNeighbours(const coords& x, uint64_t NumCells, + void getNearestNeighbours(const coords& x, uint32_t NumCells, Cell **cells); - void getNearestNeighbours(const coords& x, uint64_t NumCells, + void getNearestNeighbours(const coords& x, uint32_t NumCells, Cell **cells, CoordType *distances); @@ -183,7 +183,7 @@ namespace CosmoTool { NodeIntType getNumberInNode(const Node *n) const { return n->numNodes; } #else NodeIntType getNumberInNode(const Node *n) const { - if (n == 0) + if (n == 0) return 0; return 1+getNumberInNode(n->children[0])+getNumberInNode(n->children[1]); } @@ -211,7 +211,7 @@ namespace CosmoTool { uint32_t depth, coords minBound, coords maxBound); - + template void recursiveIntersectionCells(RecursionInfoCells& info, Node *node, @@ -224,7 +224,7 @@ namespace CosmoTool { CoordType& R2, Cell*& cell); void recursiveMultipleNearest(RecursionMultipleInfo& info, Node *node, - int level); + int level); }; diff --git a/src/mykdtree.tcc b/src/mykdtree.tcc index 6b6831d..e3fbdc8 100644 --- a/src/mykdtree.tcc +++ b/src/mykdtree.tcc @@ -33,7 +33,7 @@ namespace CosmoTool { template KDTree::KDTree(Cell *cells, NodeIntType Ncells) { - periodic = false; + periodic = false; base_cell = cells; numNodes = Ncells; @@ -41,7 +41,7 @@ namespace CosmoTool { sortingHelper = new Cell *[Ncells]; for (NodeIntType i = 0; i < Ncells; i++) - sortingHelper[i] = &cells[i]; + sortingHelper[i] = &cells[i]; optimize(); } @@ -73,16 +73,16 @@ namespace CosmoTool { absoluteMax[k] = cell->coord[k]; } } - + std::cout << " rebuilding the tree..." << std::endl; - root = buildTree(sortingHelper, activeCells, 0, absoluteMin, absoluteMax); + root = buildTree(sortingHelper, activeCells, 0, absoluteMin, absoluteMax); std::cout << " done." << std::endl; } template - uint64_t KDTree::getIntersection(const coords& x, CoordType r, + uint32_t KDTree::getIntersection(const coords& x, CoordType r, KDTree::Cell **cells, - uint64_t numCells) + uint32_t numCells) { RecursionInfoCells info; @@ -112,10 +112,10 @@ namespace CosmoTool { } template - uint64_t KDTree::getIntersection(const coords& x, CoordType r, + uint32_t KDTree::getIntersection(const coords& x, CoordType r, Cell **cells, CoordType *distances, - uint64_t numCells) + uint32_t numCells) { RecursionInfoCells info; @@ -144,7 +144,7 @@ namespace CosmoTool { } template - uint64_t KDTree::countCells(const coords& x, CoordType r) + uint32_t KDTree::countCells(const coords& x, CoordType r) { RecursionInfoCells info; @@ -175,7 +175,7 @@ namespace CosmoTool { template template - void KDTree::recursiveIntersectionCells(RecursionInfoCells& info, + void KDTree::recursiveIntersectionCells(RecursionInfoCells& info, Node *node, int level) { @@ -183,7 +183,7 @@ namespace CosmoTool { CoordType d2 = 0; #if __KD_TREE_ACTIVE_CELLS == 1 - if (node->value->active) + if (node->value->active) #endif { for (int j = 0; j < 3; j++) @@ -250,9 +250,9 @@ namespace CosmoTool { } template - void KD_default_cell_splitter::operator()(KDCell **cells, NodeIntType Ncells, + void KD_default_cell_splitter::operator()(KDCell **cells, NodeIntType Ncells, NodeIntType& split_index, int axis, - typename KDDef::KDCoordinates minBound, + typename KDDef::KDCoordinates minBound, typename KDDef::KDCoordinates maxBound) { CellCompare compare(axis); @@ -279,9 +279,9 @@ namespace CosmoTool { //#pragma omp atomic capture nodeId = (this->lastNode)++; - + node = &nodes[nodeId]; - + // Isolate the environment splitter(cell0, Ncells, mid, axis, minBound, maxBound); @@ -297,12 +297,12 @@ namespace CosmoTool { { node->children[0] = buildTree(cell0, mid, depth, minBound, tmpBound); } - + memcpy(tmpBound, minBound, sizeof(coords)); tmpBound[axis] = node->value->coord[axis]; #pragma omp task private(tmpBound) { - node->children[1] = buildTree(cell0+mid+1, Ncells-mid-1, depth, + node->children[1] = buildTree(cell0+mid+1, Ncells-mid-1, depth, tmpBound, maxBound); } @@ -391,17 +391,17 @@ namespace CosmoTool { } return; } - + // Check if current node is not the nearest - CoordType thisR2 = + CoordType thisR2 = computeDistance(node->value, x); - + if (thisR2 < R2) { R2 = thisR2; best = node->value; - } - + } + // Now we found the best. We check whether the hypersphere // intersect the hyperplane of the other branch @@ -435,11 +435,11 @@ namespace CosmoTool { { coords x_new; r.getPosition(x_new); - recursiveNearest(root, 0, x_new, R2, best); + recursiveNearest(root, 0, x_new, R2, best); } while (r.next()); } - + return best; } @@ -474,15 +474,15 @@ namespace CosmoTool { { recursiveMultipleNearest(info, go, level+1); } - + // Check if current node is not the nearest - CoordType thisR2 = + CoordType thisR2 = computeDistance(node->value, info.x); info.queue.push(node->value, thisR2); info.traversed++; // if (go == 0) // return; - + // Now we found the best. We check whether the hypersphere // intersect the hyperplane of the other branch @@ -497,15 +497,15 @@ namespace CosmoTool { { recursiveMultipleNearest(info, other, level+1); } - } + } } template - void KDTree::getNearestNeighbours(const coords& x, uint64_t N2, + void KDTree::getNearestNeighbours(const coords& x, uint32_t N2, Cell **cells) { RecursionMultipleInfo info(x, cells, N2); - + for (int i = 0; i < N2; i++) cells[i] = 0; @@ -527,12 +527,12 @@ namespace CosmoTool { } template - void KDTree::getNearestNeighbours(const coords& x, uint64_t N2, + void KDTree::getNearestNeighbours(const coords& x, uint32_t N2, Cell **cells, CoordType *distances) { RecursionMultipleInfo info(x, cells, N2); - + for (int i = 0; i < N2; i++) cells[i] = 0; @@ -555,14 +555,14 @@ namespace CosmoTool { #ifdef __KD_TREE_SAVE_ON_DISK #define KDTREE_DISK_SIGNATURE "KDTREE" #define KDTREE_DISK_SIGNATURE_LEN 7 - + template struct KDTreeOnDisk { long cell_id; long children_node[2]; typename KDDef::KDCoordinates minBound, maxBound; - }; + }; struct KDTreeHeader { @@ -619,7 +619,7 @@ namespace CosmoTool { { std::cerr << "KDTree Signature invalid" << std::endl; throw InvalidOnDiskKDTree(); - } + } if (h.numCells != Ncells || h.nodesUsed < 0) { std::cerr << "The number of cells has changed (" << h.numCells << " != " << Ncells << ") or nodesUsed=" << h.nodesUsed << std::endl; @@ -643,8 +643,8 @@ namespace CosmoTool { throw InvalidOnDiskKDTree(); } if (node_on_disk.cell_id > numNodes || node_on_disk.cell_id < 0 || - (node_on_disk.children_node[0] >= 0 && node_on_disk.children_node[0] > lastNode) || node_on_disk.children_node[0] < -1 || - (node_on_disk.children_node[1] >= 0 && node_on_disk.children_node[1] > lastNode) || node_on_disk.children_node[1] < -1) + node_on_disk.children_node[0] > lastNode || node_on_disk.children_node[0] < -1 || + node_on_disk.children_node[1] > lastNode || node_on_disk.children_node[1] < -1) { delete[] nodes; std::cerr << "Invalid cell id or children node id invalid" << std::endl; @@ -683,10 +683,10 @@ namespace CosmoTool { } root = &nodes[h.rootId]; - + sortingHelper = new Cell *[Ncells]; for (NodeIntType i = 0; i < Ncells; i++) - sortingHelper[i] = &cells[i]; + sortingHelper[i] = &cells[i]; } #endif diff --git a/src/powerSpectrum.cpp b/src/powerSpectrum.cpp index 7786080..777654c 100644 --- a/src/powerSpectrum.cpp +++ b/src/powerSpectrum.cpp @@ -58,7 +58,6 @@ using namespace std; #define POWER_TEST 8 #define POWER_SPECTRUM POWER_EFSTATHIOU -#define SAMPLE_WIGGLES 9 namespace Cosmology { @@ -207,31 +206,6 @@ double powG(double y) */ double powerSpectrum(double k, double normPower) { -#if POWER_SPECTRUM == SAMPLE_WIGGLES - // BAO wiggle parameterization for reconstruction - // Babic et al. 2022, https://arxiv.org/abs/2203.06177 - - // No-wiggle transfer function - - double s = 44.5 * log(9.83 / OmegaEff) / (sqrt(1 + 10 * pow(OMEGA_B * h * h, 0.75))); - double alpha_Gamma = 1 - 0.328 * log(431 * OmegaEff) * OMEGA_B / OMEGA_0 + 0.38 * log(22.3 * OmegaEff) * pow(OMEGA_B / OMEGA_0, 2); - double GammaEff = OMEGA_0 * h * (alpha_Gamma + (1 - alpha_Gamma)/(1 + pow(0.43 * k * s, 4))); - double q = k/(h*GammaEff) * pow(Theta_27, 2); - double L_0 = log(2 * M_E + 1.8 * q); - double C_0 = 14.2 + 731 / (1 + 62.5 * q); - double T0 = L_0 / (L_0 + C_0 * q * q); - - // Wiggle parameterization - - double A = 0; - double r_s = 10; - double k_D = 2 * M_PI / 100; - - double param = 1 + A * sin(k * r_s) * exp(- k / k_D); - - return normPower * pow(k, n) * T0 * T0 * param; -#endif - #if POWER_SPECTRUM == POWER_EFSTATHIOU double a = 6.4/Gamma0; double b = 3/Gamma0; diff --git a/src/sphSmooth.hpp b/src/sphSmooth.hpp index f9c468b..c364621 100644 --- a/src/sphSmooth.hpp +++ b/src/sphSmooth.hpp @@ -1,5 +1,5 @@ /*+ -This is CosmoTool (./src/sphSmooth.hpp) -- Copyright (C) Guilhem Lavaux (2007-2022) +This is CosmoTool (./src/sphSmooth.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014) guilhem.lavaux@gmail.com @@ -7,16 +7,16 @@ This software is a computer program whose purpose is to provide a toolbox for co data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...) This software is governed by the CeCILL license under French law and -abiding by the rules of distribution of free software. You can use, +abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL -"http://www.cecill.info". +"http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited -liability. +liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the @@ -25,9 +25,9 @@ that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their -requirements in conditions enabling the security of their systems and/or -data to be ensured and, more generally, to use and operate it in the -same conditions as regards security. +requirements in conditions enabling the security of their systems and/or +data to be ensured and, more generally, to use and operate it in the +same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. @@ -39,89 +39,80 @@ knowledge of the CeCILL license and that you accept its terms. #include "config.hpp" #include "mykdtree.hpp" -namespace CosmoTool { +namespace CosmoTool +{ template - class SPHSmooth { + class SPHSmooth + { public: - typedef struct { + typedef struct + { ComputePrecision weight; ValType pValue; } FullType; - typedef KDTree SPHTree; - typedef KDTreeNode SPHNode; - typedef KDCell SPHCell; - typedef typename KDTree::CoordType CoordType; + typedef KDTree SPHTree; + typedef KDTreeNode SPHNode; + typedef KDCell SPHCell; + typedef typename KDTree::CoordType CoordType; - typedef ComputePrecision (*computeParticleValue)(const ValType &t); - typedef void (*runParticleValue)(ValType &t); + typedef ComputePrecision (*computeParticleValue)(const ValType& t); + typedef void (*runParticleValue)(ValType& t); public: typedef SPHCell *P_SPHCell; - struct SPHState { + struct SPHState + { boost::shared_ptr ngb; boost::shared_ptr distances; typename SPHTree::coords currentCenter; int currentNgb; ComputePrecision smoothRadius; }; - + + SPHSmooth(SPHTree *tree, uint32_t Nsph); - virtual ~SPHSmooth(); + virtual ~SPHSmooth(); - void - fetchNeighbours(const typename SPHTree::coords &c, SPHState *state = 0); - - void fetchNeighbours( - const typename SPHTree::coords &c, uint32_t newNsph, - SPHState *state = 0); - void fetchNeighboursOnVolume( - const typename SPHTree::coords &c, ComputePrecision radius); - const typename SPHTree::coords &getCurrentCenter() const { + void fetchNeighbours(const typename SPHTree::coords& c, SPHState *state = 0); + + void fetchNeighbours(const typename SPHTree::coords& c, uint32_t newNsph); + void fetchNeighboursOnVolume(const typename SPHTree::coords& c, ComputePrecision radius); + const typename SPHTree::coords& getCurrentCenter() const + { return internal.currentCenter; } - /** This is the pure SPH smoothing function. It does not reweight by the - * value computed at each grid site. - */ - template - ComputePrecision computeSmoothedValue( - const typename SPHTree::coords &c, FuncT fun, SPHState *state = 0); + template + ComputePrecision computeSmoothedValue(const typename SPHTree::coords& c, + FuncT fun, SPHState *state = 0); + + template + ComputePrecision computeInterpolatedValue(const typename SPHTree::coords& c, + FuncT fun, SPHState *state = 0); + + ComputePrecision getMaxDistance(const typename SPHTree::coords& c, + SPHNode *node) const; - /** This is the weighted SPH smoothing function. It does reweight by the - * value computed at each grid site. This ensures the total sum of the interpolated - * quantity is preserved by interpolating to the target mesh. - */ - template - ComputePrecision computeInterpolatedValue( - const typename SPHTree::coords &c, FuncT fun, SPHState *state = 0); - - /** This is the adjoint gradient of computeInterpolatedValue w.r.t. to the value - * array. FuncT is expected to have the following prototype: - * void((CellValue defined by the user), ComputePrecision weighted_ag_value) - */ - template - void computeAdjointGradientSmoothedValue( - const typename SPHTree::coords &c, ComputePrecision ag_value, FuncT fun, - SPHState *state = 0); - - ComputePrecision - getMaxDistance(const typename SPHTree::coords &c, SPHNode *node) const; - - ComputePrecision getSmoothingLen() const { return internal.smoothRadius; } + ComputePrecision getSmoothingLen() const + { + return internal.smoothRadius; + } // TO USE WITH EXTREME CARE ! - void setSmoothingLen(ComputePrecision len) { internal.smoothRadius = len; } + void setSmoothingLen(ComputePrecision len) + { + internal.smoothRadius = len; + } // END - template + template void runForEachNeighbour(FuncT fun, SPHState *state = 0); - void addGridSite(const typename SPHTree::coords &c, SPHState *state); - void addGridSite(const typename SPHTree::coords &c); + void addGridSite(const typename SPHTree::coords& c); bool hasNeighbours() const; - virtual ComputePrecision getKernel(ComputePrecision d) const; + virtual ComputePrecision getKernel(ComputePrecision d) const; SPHTree *getTree() { return tree; } @@ -134,29 +125,29 @@ namespace CosmoTool { uint32_t getCurrent() const { return internal.currentNgb; } uint32_t getNgb() const { return maxNgb; } - + protected: SPHState internal; uint32_t Nsph; uint32_t deltaNsph; uint32_t maxNgb; SPHTree *tree; - - template - ComputePrecision computeWValue( - const typename SPHTree::coords &c, SPHCell &cell, CoordType d, - FuncT fun, SPHState *state); - - template - void runUnrollNode(SPHNode *node, FuncT fun); + + template + ComputePrecision computeWValue(const typename SPHTree::coords & c, + SPHCell& cell, + CoordType d, + FuncT fun, SPHState *state); + + template + void runUnrollNode(SPHNode *node, + FuncT fun); }; - template - bool operator<( - const SPHSmooth &s1, - const SPHSmooth &s2); + template + bool operator<(const SPHSmooth& s1, const SPHSmooth& s2); -}; // namespace CosmoTool +}; #include "sphSmooth.tcc" diff --git a/src/sphSmooth.tcc b/src/sphSmooth.tcc index 6643dd3..45a3c29 100644 --- a/src/sphSmooth.tcc +++ b/src/sphSmooth.tcc @@ -3,248 +3,225 @@ namespace CosmoTool { - template - SPHSmooth::SPHSmooth(SPHTree *tree, uint32_t Nsph) { - this->Nsph = Nsph; - this->tree = tree; - internal.currentNgb = 0; +template +SPHSmooth::SPHSmooth(SPHTree *tree, uint32_t Nsph) +{ + this->Nsph = Nsph; + this->tree = tree; + internal.currentNgb = 0; - this->maxNgb = Nsph; - internal.ngb = boost::shared_ptr(new SPHCell *[maxNgb]); - internal.distances = boost::shared_ptr(new CoordType[maxNgb]); - } + this->maxNgb = Nsph; + internal.ngb = boost::shared_ptr(new SPHCell *[maxNgb]); + internal.distances = boost::shared_ptr(new CoordType[maxNgb]); +} - template - SPHSmooth::~SPHSmooth() {} +template +SPHSmooth::~SPHSmooth() +{ +} - template - template - ComputePrecision SPHSmooth::computeWValue( - const typename SPHTree::coords &c, SPHCell &cell, CoordType d, FuncT fun, - SPHState *state) { - CoordType weight; +template +template +ComputePrecision SPHSmooth::computeWValue(const typename SPHTree::coords& c, + SPHCell& cell, + CoordType d, + FuncT fun, SPHState *state) +{ + CoordType weight; - d /= state->smoothRadius; - weight = getKernel(d); + d /= state->smoothRadius; + weight = getKernel(d); - if (cell.val.weight != 0) - return weight * fun(cell.val.pValue) / cell.val.weight; - else - return 0; - } + if (cell.val.weight != 0) + return weight * fun(cell.val.pValue) / cell.val.weight; + else + return 0; +} - template - void SPHSmooth::fetchNeighbours( - const typename SPHTree::coords &c, uint32_t newNngb, SPHState *state) { - ComputePrecision d2, max_dist = 0; - uint32_t requested = newNngb; +template +void +SPHSmooth::fetchNeighbours(const typename SPHTree::coords& c, uint32_t newNngb) +{ + ComputePrecision d2, max_dist = 0; + uint32_t requested = newNngb; - if (state != 0) { - state->distances = boost::shared_ptr(new CoordType[newNngb]); - state->ngb = boost::shared_ptr(new SPHCell *[newNngb]); - } else { - state = &internal; - if (requested > maxNgb) { - maxNgb = requested; - internal.ngb = boost::shared_ptr(new P_SPHCell[maxNgb]); - internal.distances = - boost::shared_ptr(new CoordType[maxNgb]); - } + if (requested > maxNgb) + { + maxNgb = requested; + internal.ngb = boost::shared_ptr(new P_SPHCell[maxNgb]); + internal.distances = boost::shared_ptr(new CoordType[maxNgb]); } - memcpy(state->currentCenter, c, sizeof(c)); - tree->getNearestNeighbours( - c, requested, (SPHCell **)state->ngb.get(), - (CoordType *)state->distances.get()); + memcpy(internal.currentCenter, c, sizeof(c)); + tree->getNearestNeighbours(c, requested, (SPHCell **)internal.ngb.get(), (CoordType*)internal.distances.get()); - state->currentNgb = 0; - for (uint32_t i = 0; i < requested && (state->ngb)[i] != 0; - i++, state->currentNgb++) { - state->distances[i] = sqrt(state->distances[i]); - d2 = state->distances[i]; + internal.currentNgb = 0; + for (uint32_t i = 0; i < requested && (internal.ngb)[i] != 0; i++,internal.currentNgb++) + { + internal.distances[i] = sqrt(internal.distances[i]); + d2 = internal.distances[i]; if (d2 > max_dist) max_dist = d2; } - state->smoothRadius = max_dist / 2; - } + internal.smoothRadius = max_dist / 2; +} - template - void SPHSmooth::fetchNeighbours( - const typename SPHTree::coords &c, SPHState *state) { - ComputePrecision d2, max_dist = 0; - uint32_t requested = Nsph; +template +void SPHSmooth::fetchNeighbours(const typename SPHTree::coords& c, SPHState *state) +{ + ComputePrecision d2, max_dist = 0; + uint32_t requested = Nsph; - if (state != 0) { - state->distances = boost::shared_ptr(new CoordType[Nsph]); - state->ngb = boost::shared_ptr(new SPHCell *[Nsph]); - } else - state = &internal; + if (state != 0) { + state->distances = boost::shared_ptr(new CoordType[Nsph]); + state->ngb = boost::shared_ptr(new SPHCell *[Nsph]); + } else + state = &internal; + + memcpy(state->currentCenter, c, sizeof(c)); + + tree->getNearestNeighbours(c, requested, state->ngb.get(), state->distances.get()); - memcpy(state->currentCenter, c, sizeof(c)); - - tree->getNearestNeighbours( - c, requested, state->ngb.get(), state->distances.get()); - - state->currentNgb = 0; - for (uint32_t i = 0; i < requested && state->ngb[i] != 0; - i++, state->currentNgb++) { - d2 = state->distances[i] = sqrt(state->distances[i]); - if (d2 > max_dist) - max_dist = d2; - } - - state->smoothRadius = max_dist / 2; - } - - template - void SPHSmooth::fetchNeighboursOnVolume( - const typename SPHTree::coords &c, ComputePrecision radius) { - uint32_t numPart; - ComputePrecision d2, max_dist = 0; - - memcpy(internal.currentCenter, c, sizeof(c)); - - internal.currentNgb = tree->getIntersection( - c, radius, internal.ngb, internal.distances, maxNgb); - - for (uint32_t i = 0; i < internal.currentNgb; i++) { + state->currentNgb = 0; + for (uint32_t i = 0; i < requested && state->ngb[i] != 0; i++,state->currentNgb++) + { d2 = internal.distances[i] = sqrt(internal.distances[i]); if (d2 > max_dist) max_dist = d2; } - internal.smoothRadius = max_dist / 2; - } - template - template - ComputePrecision SPHSmooth::computeSmoothedValue( - const typename SPHTree::coords &c, FuncT fun, SPHState *state) { - if (state == 0) - state = &internal; + state->smoothRadius = max_dist / 2; +} - ComputePrecision outputValue = 0; - ComputePrecision max_dist = 0; - ComputePrecision r3 = cube(state->smoothRadius); - for (uint32_t i = 0; i < state->currentNgb; i++) { - outputValue += - computeWValue(c, *state->ngb[i], state->distances[i], fun, state); +template +void +SPHSmooth::fetchNeighboursOnVolume(const typename SPHTree::coords& c, + ComputePrecision radius) +{ + uint32_t numPart; + ComputePrecision d2, max_dist = 0; + + memcpy(internal.currentCenter, c, sizeof(c)); + + internal.currentNgb = tree->getIntersection(c, radius, internal.ngb, internal.distances, + maxNgb); + + for (uint32_t i = 0; i < internal.currentNgb; i++) + { + d2 = internal.distances[i] = sqrt(internal.distances[i]); + if (d2 > max_dist) + max_dist = d2; + } + internal.smoothRadius = max_dist / 2; +} + +template +template +ComputePrecision +SPHSmooth::computeSmoothedValue(const typename SPHTree::coords& c, + FuncT fun, SPHState *state) +{ + if (state == 0) + state = &internal; + + ComputePrecision outputValue = 0; + ComputePrecision max_dist = 0; + ComputePrecision r3 = cube(state->smoothRadius); + + for (uint32_t i = 0; i < state->currentNgb; i++) + { + outputValue += computeWValue(c, *state->ngb[i], state->distances[i], fun, state); } - return outputValue / r3; - } + return outputValue / r3; +} - template - ComputePrecision interpolateOne(const ValType &t) { - return 1.0; - } +template +ComputePrecision interpolateOne(const ValType& t) +{ + return 1.0; +} - template - template - void SPHSmooth::computeAdjointGradientSmoothedValue( - const typename SPHTree::coords &c, ComputePrecision ag_value, FuncT fun, - SPHState *state) { - if (state == 0) - state = &internal; +// WARNING ! Cell's weight must be 1 !!! +template +template +ComputePrecision SPHSmooth::computeInterpolatedValue(const typename SPHTree::coords& c, + FuncT fun, SPHState *state) +{ + if (state == 0) + state = &internal; + + ComputePrecision outputValue = 0; + ComputePrecision max_dist = 0; + ComputePrecision weight = 0; - ComputePrecision outputValue = 0; - ComputePrecision max_dist = 0; - ComputePrecision weight = 0; - - for (uint32_t i = 0; i < state->currentNgb; i++) { - weight += - computeWValue(c, *state->ngb[i], state->distances[i], interpolateOne); - } - - for (uint32_t i = 0; i < state->currentNgb; i++) { - auto &cell = *state->ngb[i]; - double partial_ag = - computeWValue( - c, cell, state->distances[i], - [ag_value](ComputePrecision) { return ag_value; }) / - weight; - fun(cell.val.pValue, ag_value); - } - } - - // WARNING ! Cell's weight must be 1 !!! - template - template - ComputePrecision SPHSmooth::computeInterpolatedValue( - const typename SPHTree::coords &c, FuncT fun, SPHState *state) { - if (state == 0) - state = &internal; - - ComputePrecision outputValue = 0; - ComputePrecision max_dist = 0; - ComputePrecision weight = 0; - - for (uint32_t i = 0; i < state->currentNgb; i++) { + for (uint32_t i = 0; i < state->currentNgb; i++) + { outputValue += computeWValue(c, *state->ngb[i], state->distances[i], fun); - weight += - computeWValue(c, *state->ngb[i], state->distances[i], interpolateOne); + weight += computeWValue(c, *state->ngb[i], state->distances[i], interpolateOne); } - return (outputValue == 0) ? 0 : (outputValue / weight); - } + return (outputValue == 0) ? 0 : (outputValue / weight); +} - template - template - void - SPHSmooth::runForEachNeighbour(FuncT fun, SPHState *state) { - if (state == 0) - state = &internal; - - for (uint32_t i = 0; i < state->currentNgb; i++) { +template +template +void SPHSmooth::runForEachNeighbour(FuncT fun, SPHState *state) +{ + if (state == 0) + state = &internal; + + for (uint32_t i = 0; i < state->currentNgb; i++) + { fun(state->ngb[i]); } - } +} - template - void SPHSmooth::addGridSite( - const typename SPHTree::coords &c, SPHState *state) { - ComputePrecision outputValue = 0; - ComputePrecision max_dist = 0; - ComputePrecision r3 = cube(state->smoothRadius); - for (uint32_t i = 0; i < state->currentNgb; i++) { - ComputePrecision d = state->distances[i]; - SPHCell &cell = *(state->ngb[i]); - double kernel_value = getKernel(d / state->smoothRadius) / r3; -#pragma omp atomic update - cell.val.weight += kernel_value; +template +void SPHSmooth::addGridSite(const typename SPHTree::coords& c) +{ + ComputePrecision outputValue = 0; + ComputePrecision max_dist = 0; + + ComputePrecision r3 = cube(internal.smoothRadius); + + for (uint32_t i = 0; i < internal.currentNgb; i++) + { + ComputePrecision d = internal.distances[i]; + SPHCell& cell = *(internal.ngb[i]); + cell.val.weight += getKernel(d/internal.smoothRadius) / r3; } - } +} - template - void - SPHSmooth::addGridSite(const typename SPHTree::coords &c) { - addGridSite(c, &internal); - } - - template - ComputePrecision - SPHSmooth::getKernel(ComputePrecision x) const { - // WARNING !!! This is an unnormalized version of the kernel. - if (x < 1) - return 1 - 1.5 * x * x + 0.75 * x * x * x; - else if (x < 2) { +template +ComputePrecision +SPHSmooth::getKernel(ComputePrecision x) const +{ + // WARNING !!! This is an unnormalized version of the kernel. + if (x < 1) + return 1 - 1.5 * x * x + 0.75 * x * x * x; + else if (x < 2) + { ComputePrecision d = 2 - x; return 0.25 * d * d * d; - } else - return 0; - } + } + else + return 0; +} - template - bool SPHSmooth::hasNeighbours() const { - return (internal.currentNgb != 0); - } +template +bool SPHSmooth::hasNeighbours() const +{ + return (internal.currentNgb != 0); +} - template - bool operator<( - const SPHSmooth &s1, - const SPHSmooth &s2) { - return (s1.getSmoothingLen() < s2.getSmoothingLen()); - } -}; // namespace CosmoTool +template +bool operator<(const SPHSmooth& s1, const SPHSmooth& s2) +{ + return (s1.getSmoothingLen() < s2.getSmoothingLen()); +} + +}; diff --git a/src/yorick_nc3.cpp b/src/yorick_nc3.cpp index 07064c9..b1f09e9 100644 --- a/src/yorick_nc3.cpp +++ b/src/yorick_nc3.cpp @@ -260,6 +260,7 @@ namespace CosmoTool { template void loadArray(const std::string& fname, T*&array, uint32_t *&dimList, uint32_t& rank) + throw (NoSuchFileException) { NcFile f(fname.c_str(), NcFile::ReadOnly);