debian/0000755000000000000000000000000012241216424007164 5ustar debian/control0000644000000000000000000000267412241216327010602 0ustar Source: ccseapps Section: science Priority: optional Maintainer: Alastair McKinstry Build-Depends: debhelper (>= 9), gfortran Standards-Version: 3.9.4 Homepage: https://ccse.lbl.gov/Software/index.html Package: libbox-dev Section: libdevel Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends}, ${misc:Depends} Description: Boxlib: C++ Block-structured finite difference algorithms library BoxLib is a foundation library of C++ classes that facilitate the development of block-structured finite difference algorithms such as arise in the solution of systems of partial differential equations. BoxLib is particularly useful in designing and building adaptive algorithms. BoxLib contains rich data structures for describing operations which take place on data defined in regions of index space that are unions of non-intersecting rectangles. Because we are interested in unsteady problems where the regions of interest may change in response to an evolving solution, support is provided in BoxLib for efficiently building and destroying the data structures. All constructs in BoxLib are designed to run efficiently in parallel. . BoxLib is the foundation library for the PMAMR (porous media) , (low Mach number combustion), CASTRO (compressible astrophysics) codes. and NYX (cosmology) codes. An analogous version of BoxLib written entirely in Fortran90 is the foundation library for the MAESTRO code, for example. debian/source/0000755000000000000000000000000011670365660010500 5ustar debian/source/format0000644000000000000000000000001411670365660011706 0ustar 3.0 (quilt) debian/patches/0000755000000000000000000000000011670365660010627 5ustar debian/patches/series0000644000000000000000000000006411670365660012044 0ustar arch-support.patch byte-order.patch gnu-build.patch debian/patches/gnu-build.patch0000644000000000000000000000351111670365660013536 0ustar Description: build fixes needed for GNU gcc/gfortran Author: Alastair McKinstry Last-Updated: 2011-12-09 Forwarded: no --- boxlib-1.0.orig/CCSEApps/mk/Make.defs +++ boxlib-1.0/CCSEApps/mk/Make.defs @@ -112,11 +112,11 @@ ifndef DIM endif ifndef COMP - COMP = CC + COMP = cc endif ifndef FCOMP - FCOMP = f77 + FCOMP = gfortran endif ifndef USE_THREADS @@ -134,8 +134,8 @@ endif # # Set some reasonable defaults. # -CXX = CC -FC = f77 +CXX = c++ +FC = gfortran CC = cc # # Defaults for BoxLib style programs. --- boxlib-1.0.orig/CCSEApps/BoxLib/GNUmakefile +++ boxlib-1.0/CCSEApps/BoxLib/GNUmakefile @@ -9,10 +9,12 @@ TOP = $(PBOXLIB_HOME) PRECISION = DOUBLE DEBUG = TRUE DIM = 3 -COMP = KCC -USE_MPI = TRUE +COMP = gcc +USE_MPI = FALSE #NAMESPACE = TRUE NAMESPACE = FALSE +CC = gcc +fC = gfortran # # The base name of the library we're building. --- boxlib-1.0.orig/CCSEApps/BoxLib/VisMF.cpp +++ boxlib-1.0/CCSEApps/BoxLib/VisMF.cpp @@ -343,7 +343,7 @@ VisMF::BaseName (const std::string& file { BL_ASSERT(filename[filename.length() - 1] != '/'); - if (char* slash = strrchr(filename.c_str(), '/')) + if (const char* slash = strrchr(filename.c_str(), '/')) { // // Got at least one slash -- give'm the following tail. @@ -368,7 +368,7 @@ VisMF::DirName (const std::string& filen const char* str = filename.c_str(); - if (char* slash = strrchr(str, '/')) + if (const char* slash = strrchr(str, '/')) { // // Got at least one slash -- give'm the dirname including last slash. --- boxlib-1.0.orig/CCSEApps/BoxLib/std/limits +++ boxlib-1.0/CCSEApps/BoxLib/std/limits @@ -23,7 +23,7 @@ #include #include -#include +// #include __STL_BEGIN_NAMESPACE debian/patches/byte-order.patch0000644000000000000000000000563311670365660013733 0ustar Author: Alastair McKinstry Description: Use __BYTE_ORDER to build on non-specfied architectures Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650558 Last-Updated: 2011-12-09 Forwarded: no Index: ccseapps/CCSEApps/BoxLib/FPC.cpp =================================================================== --- ccseapps.orig/CCSEApps/BoxLib/FPC.cpp 2006-01-11 19:13:06.000000000 +0000 +++ ccseapps/CCSEApps/BoxLib/FPC.cpp 2011-12-09 10:48:46.000000000 +0000 @@ -25,6 +25,7 @@ // #include +#include // // FP orders. // @@ -51,11 +52,14 @@ // +// For non-specifically defined systems, assume that middle-endian ordering is no longer +// used, and rely on __BYTE_ORDER working + const IntDescriptor& FPC::NativeLongDescriptor () { -#if defined(__alpha) || defined(__i486__) || defined(WIN32) || defined(i386) || defined(__i386__) || defined(__ia64__) || defined(__x86_64__) +#if (defined(__alpha) || defined(__i486__) || defined(WIN32) || defined(i386) || defined(__i386__) || defined(__ia64__) || defined(__x86_64__)) || (__BYTE_ORDER == __LITTLE_ENDIAN) static const IntDescriptor nld(sizeof(long), IntDescriptor::ReverseOrder); #endif @@ -63,11 +67,14 @@ static const IntDescriptor nld(sizeof(long), IntDescriptor::NormalOrder); #endif -#if defined(__sgi) || \ +#if ( defined(__sgi) || \ defined(__sun) || \ defined(_AIX) || \ defined(_CRAYT3E) || \ - defined(__hpux) + defined(__hpux) || \ + defined(__hppa__) || \ + defined(__m68k__) ) || \ + ( __BYTE_ORDER == __BIG_ENDIAN ) static const IntDescriptor nld(sizeof(long), IntDescriptor::NormalOrder); #endif @@ -78,7 +85,7 @@ RealDescriptor& FPC::NativeRealDescriptor () { -#if defined(__alpha) || defined(__i486__) || defined(WIN32) || defined(i386) || defined(__i386__) || defined(__ia64__) || defined(__x86_64__) +#if (defined(__alpha) || defined(__i486__) || defined(WIN32) || defined(i386) || defined(__i386__) || defined(__ia64__) || defined(__x86_64__)) || ( __BYTE_ORDER == __LITTLE_ENDIAN) #ifdef BL_USE_FLOAT static const RealDescriptor nrd(ieee_float, reverse_float_order, 4); #else @@ -90,11 +97,11 @@ static const RealDescriptor nrd(cray_float, cray_float_order, 8); #endif -#if defined(__sgi) || \ +#if (defined(__sgi) || \ defined(__sun) || \ defined(_AIX) || \ defined(_CRAYT3E) || \ - defined(__hpux) + defined(__hpux) ) || ( __BYTE_ORDER == __BIG_ENDIAN) #ifdef BL_USE_FLOAT static const RealDescriptor nrd(ieee_float, normal_float_order, 4); #else @@ -129,7 +136,6 @@ return i64rd; } - // // TODO -- add more machine descriptions. // @@ -145,7 +151,8 @@ defined(__x86_64__) || \ defined(__hpux) || \ defined(_MSC_VER) || \ - defined(_AIX)) -#error We do not yet support FAB I/O on this machine + defined(_AIX)) +#warning "Assuming floating-point order from byte-order" + #endif debian/patches/debian-changes-1.0-10000644000000000000000000000523411670365660014040 0ustar Description: Upstream changes introduced in version 1.0-1 This patch has been created by dpkg-source during the package build. Here's the last changelog entry, hopefully it gives details on why those changes were made: . boxlib (1.0-1) UNRELEASED; urgency=low . * Initial release. (Closes: #XXXXXX) . The person named in the Author field signed this changelog entry. Author: Alastair McKinstry --- The information above should follow the Patch Tagging Guidelines, please checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here are templates for supplementary fields that you might want to add: Origin: , Bug: Bug-Debian: http://bugs.debian.org/ Bug-Ubuntu: https://launchpad.net/bugs/ Forwarded: Reviewed-By: Last-Update: --- boxlib-1.0.orig/CCSEApps/mk/Make.defs +++ boxlib-1.0/CCSEApps/mk/Make.defs @@ -112,11 +112,11 @@ ifndef DIM endif ifndef COMP - COMP = CC + COMP = cc endif ifndef FCOMP - FCOMP = f77 + FCOMP = gfortran endif ifndef USE_THREADS @@ -134,8 +134,8 @@ endif # # Set some reasonable defaults. # -CXX = CC -FC = f77 +CXX = c++ +FC = gfortran CC = cc # # Defaults for BoxLib style programs. --- boxlib-1.0.orig/CCSEApps/BoxLib/GNUmakefile +++ boxlib-1.0/CCSEApps/BoxLib/GNUmakefile @@ -9,10 +9,12 @@ TOP = $(PBOXLIB_HOME) PRECISION = DOUBLE DEBUG = TRUE DIM = 3 -COMP = KCC -USE_MPI = TRUE +COMP = gcc +USE_MPI = FALSE #NAMESPACE = TRUE NAMESPACE = FALSE +CC = gcc +fC = gfortran # # The base name of the library we're building. --- boxlib-1.0.orig/CCSEApps/BoxLib/VisMF.cpp +++ boxlib-1.0/CCSEApps/BoxLib/VisMF.cpp @@ -343,7 +343,7 @@ VisMF::BaseName (const std::string& file { BL_ASSERT(filename[filename.length() - 1] != '/'); - if (char* slash = strrchr(filename.c_str(), '/')) + if (const char* slash = strrchr(filename.c_str(), '/')) { // // Got at least one slash -- give'm the following tail. @@ -368,7 +368,7 @@ VisMF::DirName (const std::string& filen const char* str = filename.c_str(); - if (char* slash = strrchr(str, '/')) + if (const char* slash = strrchr(str, '/')) { // // Got at least one slash -- give'm the dirname including last slash. --- boxlib-1.0.orig/CCSEApps/BoxLib/std/limits +++ boxlib-1.0/CCSEApps/BoxLib/std/limits @@ -23,7 +23,7 @@ #include #include -#include +// #include __STL_BEGIN_NAMESPACE debian/patches/arch-support.patch0000644000000000000000000001240411670365660014300 0ustar Author: Alastair McKinstry Description: Build on Non-Linux Debian systems (Gnu Hurd and Gnu-KFreeBSD) Last-Updated: 2011-10-22 Forwarded: no Index: ccseapps/CCSEApps/mk/Make.GNU =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 +++ ccseapps/CCSEApps/mk/Make.GNU 2011-10-22 18:14:51.000000000 +0100 @@ -0,0 +1,100 @@ +# Make for GNU/Hurd. + +# Lets pretend these compilers are available for Hurd .. + +ifeq ($(COMP),KCC) + CXX = KCC + CXXOPTF += -O1 +K1 + CXXDEBF += +K0 + FULLWARN := --strict_warnings +else +ifeq ($(COMP),PGI) + CXX = pgCC + CXXOPTF += + CXXDEBF += -g +else +endif +endif + +FORT_CPP := gcc -E -traditional + +ifeq ($(FCOMP),Lahey) + FC := lf95 --ml cdecl + fC := $(FC) + # FDEBF += -H aesu + # FOPTF += -K fast + # fDEBF += -H aesu + # fOPTF += -K fast + LIBRARY_LOCATIONS += /usr/local/lf9561/lib + override XTRALIBS += -lfj9f6 -lfj9i6 -lfj9e6 +else +ifeq ($(FCOMP),Absoft) + FC := f90 -B108 -YEXT_NAMES=LCS + fC := $(FC) + LIBRARY_LOCATIONS += /usr/absoft/lib + override XTRALIBS += -lfio -lf77math + #override FORTLINK := LOWERCASE +else +ifeq ($(FCOMP),PGI) + FC := pgf90 + fC := $(FC) + FOPTF += -fast + fOPTF += -fast + FDEBF += -g + fDEBF += -g + LIBRARY_LOCATIONS += /usr/pgi/linux86/lib + override XTRALIBS += -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lpgc +else +ifeq ($(FCOMP),Intel) + # mostly in Make.defs + FDEBF += $(INTEL_EXTRA_DEBUG_FLAGS) + FOPTF += $(INTEL_EXTRA_OPT_FLAGS) + fDEBF += $(INTEL_EXTRA_DEBUG_FLAGS) + fOPTF += $(INTEL_EXTRA_OPT_FLAGS) +else +ifeq ($(FCOMP),f77) + FC := g77 -fno-second-underscore + fC := $(FC) + # default g77/f77 version + FOPTF += -O + fOPTF += -O + FDEBF += -g + fDEBF += -g + #DEFINES += -DBL_FORT_USE_UNDERSCORE + #override XTRALIBS += -lf2c +# LIBRARY_LOCATIONS += /usr/lib/gcc-lib/i386-redhat-linux/2.96 + override XTRALIBS += -lg2c + FDEBF += -ffortran-bounds-check + FDEBF += -Wimplicit + fDEBF += -Wimplicit + fDEBF += -ffortran-bounds-check +endif +endif +endif +endif +endif + +CXXPRFF += -pg +FPRF += -pg + +override XTRALIBS += -lm + +ifeq ($(WHICHLINUX), PCCLUSTER) + LIBRARY_LOCATIONS += /usr/local/pkg/gcc/lib/gcc-lib/i686-pc-linux-gnu/2.95.1 + # this should be made into a link to the current version ^^^^^^ +endif + +ifeq ($(WHICHLINUX), ALPHACLUSTER) + FC := fort -assume nounderscore +# FC := fort + fC := $(FC) + override FORTLINK := LOWERCASE + #FOPTF += -O5 -fast -transform_loops -speculate all -automatic + FOPTF = -O5 -fast + FOPTF = -O2 + fOPTF = -O5 -fast + fOPTF = -O2 + LIBRARY_LOCATIONS += /usr/local/pkg/gcc-2.95.1-generic/lib/gcc-lib/alpha-redhat-linux/2.95.1 + # this should be made into a link to the current version ^^^^^^ + LIBRARIES += -lfor +endif Index: ccseapps/CCSEApps/mk/Make.defs =================================================================== --- ccseapps.orig/CCSEApps/mk/Make.defs 2003-03-14 23:44:57.000000000 +0000 +++ ccseapps/CCSEApps/mk/Make.defs 2011-10-22 18:18:48.000000000 +0100 @@ -51,6 +51,10 @@ MACHINE := $(shell uname) endif +# Drop the GNU/kFreeBSD to kFreeBSD +ifeq ($(findstring kFreeBSD, $(MACHINE)), kFreeBSD) + MACHINE := kFreeBSD +endif # # We'd also like to distinguish between SunOS and Solaris. # Index: ccseapps/CCSEApps/mk/Make.kFreeBSD =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 +++ ccseapps/CCSEApps/mk/Make.kFreeBSD 2011-10-22 18:15:47.000000000 +0100 @@ -0,0 +1,79 @@ +# Make for Debian GNU/kFreeBSD + +ifeq ($(COMP),KCC) + CXX = KCC + CXXOPTF += -O1 +K1 + CXXDEBF += +K0 + FULLWARN := --strict_warnings +else +ifeq ($(COMP),PGI) + CXX = pgCC + CXXOPTF += + CXXDEBF += -g +else +endif +endif + +FORT_CPP := gcc -E -traditional + +ifeq ($(FCOMP),Lahey) + FC := lf95 --ml cdecl + fC := $(FC) + # FDEBF += -H aesu + # FOPTF += -K fast + # fDEBF += -H aesu + # fOPTF += -K fast + LIBRARY_LOCATIONS += /usr/local/lf9561/lib + override XTRALIBS += -lfj9f6 -lfj9i6 -lfj9e6 +else +ifeq ($(FCOMP),Absoft) + FC := f90 -B108 -YEXT_NAMES=LCS + fC := $(FC) + LIBRARY_LOCATIONS += /usr/absoft/lib + override XTRALIBS += -lfio -lf77math + #override FORTLINK := LOWERCASE +else +ifeq ($(FCOMP),PGI) + FC := pgf90 + fC := $(FC) + FOPTF += -fast + fOPTF += -fast + FDEBF += -g + fDEBF += -g + LIBRARY_LOCATIONS += /usr/pgi/linux86/lib + override XTRALIBS += -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lpgc +else +ifeq ($(FCOMP),Intel) + # mostly in Make.defs + FDEBF += $(INTEL_EXTRA_DEBUG_FLAGS) + FOPTF += $(INTEL_EXTRA_OPT_FLAGS) + fDEBF += $(INTEL_EXTRA_DEBUG_FLAGS) + fOPTF += $(INTEL_EXTRA_OPT_FLAGS) +else +ifeq ($(FCOMP),f77) + FC := g77 -fno-second-underscore + fC := $(FC) + # default g77/f77 version + FOPTF += -O + fOPTF += -O + FDEBF += -g + fDEBF += -g + #DEFINES += -DBL_FORT_USE_UNDERSCORE + #override XTRALIBS += -lf2c +# LIBRARY_LOCATIONS += /usr/lib/gcc-lib/i386-redhat-linux/2.96 + override XTRALIBS += -lg2c + FDEBF += -ffortran-bounds-check + FDEBF += -Wimplicit + fDEBF += -Wimplicit + fDEBF += -ffortran-bounds-check +endif +endif +endif +endif +endif + +CXXPRFF += -pg +FPRF += -pg + +override XTRALIBS += -lm + debian/rules0000755000000000000000000000176511670365660010271 0ustar #!/usr/bin/make -f export DH_VERBOSE=1 # Magic debhelper rule %: dh $@ DESTDIR=debian/libbox-dev DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH) LIBDIR:=/usr/lib/$(DEB_HOST_MULTIARCH) override_dh_auto_build: $(MAKE) -C CCSEApps/BoxLib DEBUG=FALSE DIM=2 $(MAKE) -C CCSEApps/BoxLib DEBUG=FALSE DIM=3 override_dh_auto_clean: $(MAKE) -C CCSEApps/BoxLib clean find . -size 0 -delete find . -depth -name d -exec rm -rf {} \; find . -depth -name f -exec rm -rf {} \; find . -depth -name o -exec rm -rf {} \; rm -rf CCSEApps/include CCSEApps/lib CCSEApps/*/*.a dh_auto_clean override_dh_auto_test: #$(MAKE) -C CCSEApps/BoxLib/test @echo "Tests currently disabled." override_dh_auto_install: dh_auto_install $(MAKE) -C CCSEApps/BoxLib DIM=2 DEBUG=FALSE install mkdir -p $(DESTDIR)/$(LIBDIR) mv CCSEApps/BoxLib/libbox2d.*.a $(DESTDIR)/$(LIBDIR)/libbox2d.a mv CCSEApps/BoxLib/libbox3d.*.a $(DESTDIR)/$(LIBDIR)/libbox3d.a mv CCSEApps/include/* $(DESTDIR)/usr/include/BoxLib debian/libbox-dev.dirs0000644000000000000000000000003511670365660012114 0ustar /usr/include/BoxLib /usr/lib debian/compat0000644000000000000000000000000212241216414010361 0ustar 9 debian/README.debian0000644000000000000000000000023111670365660011275 0ustar Currently Only the BoxLib library from CCSEApps is built. This may change if there is any demand for the other libraries. * First build is without MPI. debian/changelog0000644000000000000000000000107012241216402011030 0ustar ccseapps (2.5-3) unstable; urgency=low * Move to Standards-Version: 3.9.4 * Add ${misc:Depends} for debhelper dependency. -- Alastair McKinstry Thu, 14 Nov 2013 18:56:27 +0000 ccseapps (2.5-2) unstable; urgency=low * Patch to detect byte order and build on more archs. Closes: #650558. -- Alastair McKinstry Fri, 09 Dec 2011 10:49:04 +0000 ccseapps (2.5-1) unstable; urgency=low * Initial release. (Closes: #624233). -- Alastair McKinstry Sat, 23 Apr 2011 15:05:24 +0100 debian/copyright0000644000000000000000000002434711670365660011145 0ustar SOURCE CODE LICENSE AGREEMENT Software: BoxLib Version: Oct. 12, 2000 Release IMPORTANT - READ CAREFULLY: This License Agreement ("Agreement") is a legal agreement between you (in your capacity as an individual and as an agent for your company, institution or other entity) and The Regents of the University of California, Department of Energy contract-operators of the Ernest Orlando Lawrence Berkeley National Laboratory ("Berkeley Lab"). Downloading, installing, using, or copying of the Software (as defined below) by you or by a third party on your behalf indicates your agreement to be bound by the terms and conditions of this Agreement. If you do not agree to these terms and conditions, do not download, install or use the Software. 1. LICENSE GRANT. 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If you have any questions or feedback concerning this Software, contact the Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 50A-1148, Berkeley, CA 94720 or via email at webmaster@mothra.lbl.gov. Form rev000928 debian/libbox-dev.docs0000644000000000000000000000000611670365660012101 0ustar NOTES