Fix typo in BR: gcc-gfortran.

- link only to atlas-provided blas for performance

.cvsignore

@@ -1 +0,0 @@
-apbs-1.1.0-source.tar.gz

.gitignore

@@ -0,0 +1,2 @@
+apbs-1.1.0-source.tar.gz
+/apbs-1.2.1-source.tar.gz

Makefile

@@ -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)

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 \

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 

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 <rpm@greysector.net> - 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 <fenn@stanford.edu> - 1.2.1-2
+- add RPM_OPT_FLAGS
+
+* Wed Nov 25 2009 Tim Fenn <fenn@stanford.edu> - 1.2.1-1
+- update to 1.2.1
+
+* Tue Nov 24 2009 Tim Fenn <fenn@stanford.edu> - 1.2.0-2
+- fix broken source
+
+* Thu Nov 04 2009 Tim Fenn <fenn@stanford.edu> - 1.2.0-1
+- update to 1.2.0
+
 * Mon Jul 27 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-7
 - remove python byte compiled files in bindir
 - loop to add tools

import.log

@@ -1 +0,0 @@
-apbs-1_1_0-7_fc10:HEAD:apbs-1.1.0-7.fc10.src.rpm:1250887770

sources

@@ -1 +1 @@
-ca31ba09714e4fc9acce91e7961569cd  apbs-1.1.0-source.tar.gz
+831d85e90083ec639451657195ff90da  apbs-1.2.1-source.tar.gz