diff --git a/.cvsignore b/.cvsignore deleted file mode 100644 index dad4ed2..0000000 --- a/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -apbs-1.1.0-source.tar.gz diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..fe06b17 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +apbs-1.1.0-source.tar.gz +/apbs-1.2.1-source.tar.gz diff --git a/Makefile b/Makefile deleted file mode 100644 index 623b8bf..0000000 --- a/Makefile +++ /dev/null @@ -1,21 +0,0 @@ -# Makefile for source rpm: apbs -# $Id$ -NAME := apbs -SPECFILE = $(firstword $(wildcard *.spec)) - -define find-makefile-common -for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done -endef - -MAKEFILE_COMMON := $(shell $(find-makefile-common)) - -ifeq ($(MAKEFILE_COMMON),) -# attept a checkout -define checkout-makefile-common -test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2 -endef - -MAKEFILE_COMMON := $(shell $(checkout-makefile-common)) -endif - -include $(MAKEFILE_COMMON) diff --git a/apbs-configure.ac.patch b/apbs-configure.ac.patch index 162d141..7f882f7 100644 --- a/apbs-configure.ac.patch +++ b/apbs-configure.ac.patch @@ -1,6 +1,37 @@ ---- configure.ac_orig 2009-07-10 11:37:12.000000000 -0700 -+++ configure.ac 2009-07-10 16:02:33.000000000 -0700 -@@ -390,7 +390,7 @@ +--- configure.ac_orig 2009-11-25 12:23:02.275659561 -0800 ++++ configure.ac 2009-11-29 23:16:42.319661207 -0800 +@@ -230,14 +230,16 @@ + CXXFLAGS=`echo ${CXXFLAGS} | sed 's/-g//g'`; + fi + fi +-AC_F77_NOFORMAIN ++# AC_F77_NOFORMAIN + FFLAGS="${FLIBS} ${FFLAGS}" +-if test "${CC}" != "icl"; then +- AC_F77_FCN_MANGLE() +-fi ++# this macro is broken, so be sure to set -DVF77_ONEUNDERSCORE ++# if test "${CC}" != "icl"; then ++# AC_F77_FCN_MANGLE() ++# fi + AC_LANG_C + AC_PROG_CPP +-AC_DISABLE_SHARED ++# AC_DISABLE_SHARED ++AC_DISABLE_STATIC + AM_PROG_LIBTOOL + + dnl ########################################################################## +@@ -308,7 +310,7 @@ + dnl # HANDLE COMPILER FLOATING POINT ERROR + dnl # ------------------------------------ + +-AC_FPERROR ++# AC_FPERROR + + dnl ########################################################################## + dnl 8. checks for library functions +@@ -390,7 +392,7 @@ if test -n "${USE_FETK_LIBRARY}"; then maloc_lib_path="${fetk_library_path}" @@ -9,7 +40,7 @@ if test -z "${maloc_lib}"; then AC_MSG_ERROR([Error... Couldn't find FETK library files in the location you specified]) fi -@@ -806,7 +806,7 @@ +@@ -810,7 +812,7 @@ fi LDFLAGS=${LDFLAGS_SAVE}; CPPFLAGS=${CPPFLAGS_SAVE}; @@ -18,7 +49,7 @@ dnl # BEGIN FETK LIBRARY/HEADER TEST BLOCK dnl # ----------------------- -@@ -1028,6 +1028,7 @@ +@@ -1032,6 +1034,7 @@ blas_lib=${contrib_path}/blas/.libs/libapbsblas.a fi AC_SUBST(apbs_do_blas) @@ -26,7 +57,7 @@ dnl # ----------------------- dnl # If using Portland compilers, do not compile -@@ -1206,7 +1207,9 @@ +@@ -1258,7 +1261,9 @@ else apbs_build_libraries="${top_apbsdir}/bin/libapbsmainroutines.la \ ${top_apbsdir}/src/aaa_lib/libapbs.la \ diff --git a/apbs-makefile.am.patch b/apbs-makefile.am.patch index 9f8bda0..16463fc 100644 --- a/apbs-makefile.am.patch +++ b/apbs-makefile.am.patch @@ -1,73 +1,16 @@ ---- ./tools/python/Makefile.am_orig 2009-07-23 12:08:49.000000000 -0700 -+++ ./tools/python/Makefile.am 2009-07-23 13:20:16.000000000 -0700 -@@ -16,4 +16,5 @@ - noinst_PROGRAMS = _apbslib.so - _apbslib_so_SOURCES = apbslib.c - _apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED) --_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) -+_apbslib_so_LDFLAGS = @maloc_lib@ @blas_lib@ $(PY_LDFLAGS) -+_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so ---- ./tools/python/vgrid/Makefile.am_orig 2009-03-05 12:30:03.000000000 -0800 -+++ ./tools/python/vgrid/Makefile.am 2009-07-23 13:20:08.000000000 -0700 -@@ -16,5 +16,6 @@ - noinst_PROGRAMS = _vgrid.so - _vgrid_so_SOURCES = vgridlib.c - _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED) -- _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@ -+ _vgrid_so_LDFLAGS = $(PY_LDFLAGS) @maloc_lib@ @lib_list@ -+ _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so - endif ---- ./tools/arpack/Makefile.am_orig 2009-07-23 13:20:45.000000000 -0700 -+++ ./tools/arpack/Makefile.am 2009-07-23 13:20:47.000000000 -0700 -@@ -12,7 +12,7 @@ +--- ./contrib/opal/Makefile.am_orig 2009-11-24 18:56:20.564534299 -0800 ++++ ./contrib/opal/Makefile.am 2009-11-24 18:59:57.836534326 -0800 +@@ -9,7 +9,7 @@ + AUTOMAKE_OPTIONS = no-dependencies + SUFFIXES = .H .h .C .c .f .o - noinst_PROGRAMS = driver - driver_SOURCES = driver.c readhb.f ardriv.f --driver_LDADD = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@ -+driver_LDADD = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@ -latlas - INCLUDES = @inc_list@ - AM_CFLAGS = @CFLAGS@ - AM_LDFLAGS = @LDFLAGS@ @FFLAGS@ ---- ./bin/Makefile.am_orig 2009-07-22 22:08:44.000000000 -0700 -+++ ./bin/Makefile.am 2009-07-22 22:11:07.000000000 -0700 -@@ -12,24 +12,24 @@ +-always_built_SUBDIRS = ZSI ++# always_built_SUBDIRS = ZSI - build_libraries = @apbs_build_libraries@ + SUBDIRS = $(always_built_SUBDIRS) . --bindir = ${prefix}/bin -+# bindir = ${prefix}/bin - bin_PROGRAMS = apbs - apbs_SOURCES = main.c --apbs_LDADD = ${build_libraries} -+apbs_LDADD = ${build_libraries} ./libapbsmainroutines.la - --libdir = ${prefix}/lib -+# libdir = ${prefix}/lib - lib_LTLIBRARIES = libapbsmainroutines.la - libapbsmainroutines_la_SOURCES = routines.c --libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION} -+libapbsmainroutines_la_LDFLAGS = @maloc_lib@ ../src/aaa_lib/libapbs.la -version-info ${APBS_VERSION} - - INCLUDES = @inc_list@ - AM_CFLAGS= @wall_pedantic@ - AM_LDFLAGS = @LDFLAGS@ @FFLAGS@ - --includedir = ${prefix}/include/apbs --include_HEADERS = routines.h -+# includedir = ${prefix}/include/apbs -+# include_HEADERS = routines.h - --install-data-local: -- -cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin -- -chmod 755 ${prefix}/bin/ApbsClient.py -- -rm -f ${prefix}/bin/wsdl2py -\ No newline at end of file -+#install-data-local: -+# -cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin -+# -chmod 755 ${prefix}/bin/ApbsClient.py -+# -rm -f ${prefix}/bin/wsdl2py ---- ./src/aaa_lib/Makefile.am_orig 2009-07-22 22:08:57.000000000 -0700 -+++ ./src/aaa_lib/Makefile.am 2009-07-22 22:12:12.000000000 -0700 +--- ./src/aaa_lib/Makefile.am_orig 2009-11-24 18:57:31.108534078 -0800 ++++ ./src/aaa_lib/Makefile.am 2009-11-29 22:09:14.931662428 -0800 @@ -18,12 +18,12 @@ AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la BLAS_LIBS = @blas_lib@ @@ -83,14 +26,85 @@ INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@ AM_CFLAGS = @wall_pedantic@ ---- ./contrib/opal/Makefile.am_orig 2009-07-23 17:40:40.000000000 -0700 -+++ ./contrib/opal/Makefile.am 2009-07-23 17:40:08.000000000 -0700 -@@ -9,7 +9,7 @@ - AUTOMAKE_OPTIONS = no-dependencies - SUFFIXES = .H .h .C .c .f .o +--- ./tools/arpack/Makefile.am_orig 2009-11-24 18:57:41.564534258 -0800 ++++ ./tools/arpack/Makefile.am 2009-11-24 18:59:57.837534477 -0800 +@@ -12,7 +12,7 @@ --always_built_SUBDIRS = ZSI -+# always_built_SUBDIRS = ZSI + noinst_PROGRAMS = driver + driver_SOURCES = driver.c readhb.f ardriv.f +-driver_LDADD = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@ ++driver_LDADD = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@ -latlas + INCLUDES = @inc_list@ + AM_CFLAGS = @CFLAGS@ + AM_LDFLAGS = @LDFLAGS@ +--- ./tools/python/vgrid/Makefile.am_orig 2009-11-24 18:57:54.604534072 -0800 ++++ ./tools/python/vgrid/Makefile.am 2009-11-24 18:59:57.837534477 -0800 +@@ -16,5 +16,6 @@ + noinst_PROGRAMS = _vgrid.so + _vgrid_so_SOURCES = vgridlib.c + _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED) +- _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@ ++ _vgrid_so_LDFLAGS = $(PY_LDFLAGS) @maloc_lib@ @lib_list@ ++ _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so + endif +--- ./tools/python/Makefile.am_orig 2009-11-24 18:58:01.740534012 -0800 ++++ ./tools/python/Makefile.am 2009-11-24 18:59:57.838534348 -0800 +@@ -16,4 +16,5 @@ + noinst_PROGRAMS = _apbslib.so + _apbslib_so_SOURCES = apbslib.c + _apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED) +-_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) ++_apbslib_so_LDFLAGS = @maloc_lib@ @blas_lib@ $(PY_LDFLAGS) ++_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so +--- ./bin/Makefile.am_orig 2009-11-24 18:58:07.772534219 -0800 ++++ ./bin/Makefile.am 2009-11-24 19:09:09.452534035 -0800 +@@ -12,34 +12,35 @@ - SUBDIRS = $(always_built_SUBDIRS) . + build_libraries = @apbs_build_libraries@ +-bindir = ${prefix}/bin ++# bindir = ${prefix}/bin + bin_PROGRAMS = apbs + apbs_SOURCES = main.c +-apbs_LDADD = ${build_libraries} ++apbs_LDADD = ${build_libraries} ./libapbsmainroutines.la + + # This is a hack I suspect, but needed to force apbs to be + # rebuilt anytime the make command is issued + # Problem before is that there is no dependency between source file + # recompilation and relinking the binary. There is probably + # a cleaner way to do this, I can't find it, however. +-BUILT_SOURCES = rm.apbs + +-rm.apbs: Makefile +- -rm -f apbs ++# BUILT_SOURCES = rm.apbs + +-libdir = ${prefix}/lib ++# rm.apbs: Makefile ++# -rm -f apbs ++ ++# libdir = ${prefix}/lib + lib_LTLIBRARIES = libapbsmainroutines.la + libapbsmainroutines_la_SOURCES = routines.c +-libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION} ++libapbsmainroutines_la_LDFLAGS = @maloc_lib@ ../src/aaa_lib/libapbs.la -version-info ${APBS_VERSION} + + INCLUDES = @inc_list@ + AM_CFLAGS= @wall_pedantic@ + AM_LDFLAGS = @LDFLAGS@ @FFLAGS@ + +-includedir = ${prefix}/include/apbs +-include_HEADERS = routines.h ++# includedir = ${prefix}/include/apbs ++# include_HEADERS = routines.h + +-install-data-local: +- -cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin +- -chmod 755 ${prefix}/bin/ApbsClient.py +- -rm -f ${prefix}/bin/wsdl2py +\ No newline at end of file ++#install-data-local: ++# -cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin ++# -chmod 755 ${prefix}/bin/ApbsClient.py ++# -rm -f ${prefix}/bin/wsdl2py diff --git a/apbs.spec b/apbs.spec index 46a0a17..2da13b4 100644 --- a/apbs.spec +++ b/apbs.spec @@ -2,8 +2,8 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver -Version: 1.1.0 -Release: 7%{?dist} +Version: 1.2.1 +Release: 3%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -15,12 +15,10 @@ Patch0: apbs-configure.ac.patch # removes hardcoded prefix setting so DESTDIR works Patch1: apbs-makefile.am.patch Buildroot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) -BuildRequires: autoconf -BuildRequires: automake +BuildRequires: gcc-gfortran BuildRequires: libtool BuildRequires: arpack-devel BuildRequires: atlas-devel -BuildRequires: blas-devel BuildRequires: maloc-devel BuildRequires: python-devel Requires: python-ZSI @@ -72,7 +70,7 @@ library. %setup -q -n %{name}-%{version}-source %patch0 -p0 %patch1 -p0 -libtoolize --automake +libtoolize --automake --force aclocal autoheader automake --gnu @@ -91,7 +89,7 @@ rm doc/programmer/html/vpee_8h__incl.map rm doc/programmer/html/dummy_8c__incl.map %build -%configure --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --enable-shared --disable-static FFLAGS="-I/usr/include/atlas" +%configure --with-blas-name=cblas --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lcblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --enable-shared FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" # die, rpath, die. sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool @@ -172,6 +170,22 @@ rm -rf %{buildroot} %doc doc/programmer/ %changelog +* Wed Mar 16 2011 Dominik Mierzejewski - 1.2.1-3 +- fix build on EL-5 (add missing BR: gcc-gfortran, run libtoolize with --force) +- link only to atlas-provided blas for performance + +* Tue Dec 01 2009 Tim Fenn - 1.2.1-2 +- add RPM_OPT_FLAGS + +* Wed Nov 25 2009 Tim Fenn - 1.2.1-1 +- update to 1.2.1 + +* Tue Nov 24 2009 Tim Fenn - 1.2.0-2 +- fix broken source + +* Thu Nov 04 2009 Tim Fenn - 1.2.0-1 +- update to 1.2.0 + * Mon Jul 27 2009 Tim Fenn - 1.1.0-7 - remove python byte compiled files in bindir - loop to add tools diff --git a/import.log b/import.log deleted file mode 100644 index 4304fcb..0000000 --- a/import.log +++ /dev/null @@ -1 +0,0 @@ -apbs-1_1_0-7_fc10:HEAD:apbs-1.1.0-7.fc10.src.rpm:1250887770 diff --git a/sources b/sources index ca113f8..a83d832 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -ca31ba09714e4fc9acce91e7961569cd apbs-1.1.0-source.tar.gz +831d85e90083ec639451657195ff90da apbs-1.2.1-source.tar.gz