svn commit: r559900 - in head/science/abinit: . files
Yuri Victorovich
yuri at FreeBSD.org
Sat Jan 2 00:42:02 UTC 2021
Author: yuri
Date: Sat Jan 2 00:42:00 2021
New Revision: 559900
URL: https://svnweb.freebsd.org/changeset/ports/559900
Log:
science/abinit: Update 8.10.3 -> 9.2.2
PR: 252221
Submitted by: thierry
Added:
head/science/abinit/files/patch-config_m4_sd__levmar.m4 (contents, props changed)
head/science/abinit/files/patch-config_scripts_makemake (contents, props changed)
head/science/abinit/files/patch-shared__common__src__02_clib__md5.c (contents, props changed)
head/science/abinit/files/patch-shared_common_src_02__clib_calling__levmar.c (contents, props changed)
Deleted:
head/science/abinit/files/patch-Makefile.in
head/science/abinit/files/patch-src_02__clib_md5.c
Modified:
head/science/abinit/Makefile
head/science/abinit/distinfo
head/science/abinit/pkg-plist
Modified: head/science/abinit/Makefile
==============================================================================
--- head/science/abinit/Makefile Sat Jan 2 00:39:14 2021 (r559899)
+++ head/science/abinit/Makefile Sat Jan 2 00:42:00 2021 (r559900)
@@ -2,10 +2,8 @@
# $FreeBSD$
PORTNAME= abinit
-DISTVERSION= 8.10.3
-PORTREVISION= 6
+DISTVERSION= 9.2.2
CATEGORIES= science
-MASTER_SITES= LOCAL/yuri/ # https://www.abinit.org/sites/default/files/packages/ has the updated 8.10.3 tarball that doesn't compile
MAINTAINER= yuri at FreeBSD.org
COMMENT= Full-featured atomic-scale first-principles simulation software
@@ -13,33 +11,86 @@ COMMENT= Full-featured atomic-scale first-principles s
LICENSE= GPLv3
LICENSE_FILE= ${WRKSRC}/COPYING
-ONLY_FOR_ARCHS= amd64 i386
-BROKEN= fails to build
-BROKEN_i386= Type mismatch in argument 'block_displ', see https://github.com/abinit/abinit/issues/19
+ONLY_FOR_ARCHS= amd64
-LIB_DEPENDS= liblapack.so:math/lapack \
- libblas.so:math/blas
+BUILD_DEPENDS= gm4:devel/m4 \
+ ${PYNUMPY} \
+ ${PY_PYGMENTS} \
+ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}graphviz>0:graphics/py-graphviz@${PY_FLAVOR}
+LIB_DEPENDS= libelpa.so:math/elpa \
+ libsz.so:science/szip \
+ libelpa.so:math/elpa \
+ libxc.so:science/libxc \
+ libfftw3.so:math/fftw3 \
+ libhdf5.so:science/hdf5 \
+ libxml2.so:textproc/libxml2 \
+ libnetcdf.so:science/netcdf \
+ libxmlf90.so:textproc/xmlf90 \
+ libwannier.so:science/wannier90 \
+ libnetcdff.so:science/netcdf-fortran
RUN_DEPENDS= atompaw:science/atompaw
+TEST_DEPENDS= ${PYNUMPY} \
+ libyaml>0:textproc/libyaml
-USES= fortran gmake localbase:ldflags
+USES= autoreconf:build blaslapack:netlib fortran gmake gnome localbase:ldflags \
+ python:3.6+ shebangfix
+USE_GITHUB= yes
+USE_GNOME= libxml2
+SHEBANG_FILES= config/scripts/* doc/tutorial/paral_gspw_assets/abinit.sub.*
+SHEBANG_GLOB= *.py
GNU_CONFIGURE= yes
-
-CONFIGURE_ENV= CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" FC_LDFLAGS="${LDFLAGS}"
-CONFIGURE_ARGS= --enable-shared --disable-static
+CONFIGURE_ENV= CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" FC_LDFLAGS="${LDFLAGS}" \
+ LINALG_FCFLAGS="-I${LOCALBASE}/include/elpa-2019.05.002/modules" \
+ LINALG_LIBS="${BLASLIB} ${LAPACKLIB} -lelpa" \
+ NETCDF_FORTRAN_FCFLAGS=-I${LOCALBASE}/include \
+ XMLF90_FCFLAGS=-I${LOCALBASE}/include \
+ WANNIER90_LIBS="${BLASLIB} ${LAPACKLIB} -lwannier"
+CONFIGURE_ARGS= --with-fft --with-libxc --with-libxml2 --with-netcdf \
+ --with-netcdf-fortran --with-wannier90 --with-xmlf90
FCFLAGS+= -ffree-line-length-none
+TEST_TARGET= tests_abirules tests_buildsys
+TEST_WRKSRC= ${WRKSRC}/abichecks
+PORTDOCS= *
-OPTIONS_DEFINE= OPENMP MPI
+OPTIONS_DEFINE= DOCS OPENMP MPI
OPTIONS_DEFAULT= OPENMP MPI
OPENMP_CONFIGURE_ENABLE= openmp
OPENMP_LDFLAGS= -lomp
-MPI_CONFIGURE_ENABLE= mpi
-MPI_VARS= FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include
-MPI_LDFLAGS= ${LOCALBASE}/lib/libmpich.so ${LOCALBASE}/lib/libmpicxx.so ${LOCALBASE}/lib/libmpifort.so
-MPI_LIB_DEPENDS= libmpi.so:net/mpich
+MPI_CONFIGURE_WITH= mpi=yes
+# fftw3 not enabled because libfftw3_mpi is required but not packaged
+MPI_VARS= FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include \
+ CONFIGURE_ENV+=MPI_LIBS="`pkg-config --libs mpich` -lmpifort" \
+ CONFIGURE_ENV+MPI_LDFLAGS="`pkg-config --libs mpich` -lmpifort"
+MPI_BUILD_DEPENDS= mpich>0:net/mpich
+MPI_RUN_DEPENDS= mpich>0:net/mpich
-do-test:
- @cd ${WRKSRC}/tests && ./configure && ${GMAKE} check
+.if defined(WITH_LEVMAR)
+# --with-levmar seems deprecated
+LIB_DEPENDS+= liblevmar.so:math/levmar
+CONFIGURE_ENV+= LEVMAR_LIBS="-llevmar ${BLASLIB} ${LAPACKLIB}"
+CONFIGURE_ARGS+= --with-levmar
+.endif
-.include <bsd.port.mk>
+.include <bsd.port.pre.mk>
+
+.if ${GCC_DEFAULT} >= 10
+FCFLAGS+= -fallow-argument-mismatch # see https://github.com/abinit/abinit/issues/41
+.endif
+
+pre-configure:
+ (cd ${WRKSRC} && ./autogen.sh)
+
+post-install-DOCS-on:
+ ${REINPLACE_CMD} -e 's|/usr/bin/env python|${PYTHON_CMD}|' \
+ ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py
+ ${RM} ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py.bak
+ @${MKDIR} ${STAGEDIR}${DOCSDIR}
+ ${CP} -R ${WRKSRC}/doc/tutorial ${STAGEDIR}${DOCSDIR}
+
+pre-test:
+ ${TOUCH} ${TEST_WRKSRC}/make.log
+
+.include <bsd.port.post.mk>
Modified: head/science/abinit/distinfo
==============================================================================
--- head/science/abinit/distinfo Sat Jan 2 00:39:14 2021 (r559899)
+++ head/science/abinit/distinfo Sat Jan 2 00:42:00 2021 (r559900)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1550812825
-SHA256 (abinit-8.10.3.tar.gz) = 922e38edab95e1763c4d504a927f7ea4e19da3143e5b33c5d6e4b41210bf5a9d
-SIZE (abinit-8.10.3.tar.gz) = 88310400
+TIMESTAMP = 1608996405
+SHA256 (abinit-abinit-9.2.2_GH0.tar.gz) = 29511bbc4f4e318cf3676aafdfea48ce2beb8ab6bd64062bd38d516fc02a8543
+SIZE (abinit-abinit-9.2.2_GH0.tar.gz) = 98949530
Added: head/science/abinit/files/patch-config_m4_sd__levmar.m4
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/abinit/files/patch-config_m4_sd__levmar.m4 Sat Jan 2 00:42:00 2021 (r559900)
@@ -0,0 +1,10 @@
+--- config/m4/sd_levmar.m4.orig 2020-11-10 12:21:53 UTC
++++ config/m4/sd_levmar.m4
+@@ -239,6 +239,7 @@ AC_DEFUN([_SD_LEVMAR_CHECK_USE], [
+ AC_LANG_PUSH([C])
+ AC_LINK_IFELSE([AC_LANG_PROGRAM(
+ [[
++# include <stddef.h>
+ # include <levmar.h>
+
+ void dfit_function(double *p, double *y, int m, int n, void *adata)
Added: head/science/abinit/files/patch-config_scripts_makemake
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/abinit/files/patch-config_scripts_makemake Sat Jan 2 00:42:00 2021 (r559900)
@@ -0,0 +1,11 @@
+--- config/scripts/makemake.orig 2020-12-26 16:36:41 UTC
++++ config/scripts/makemake
+@@ -408,7 +408,7 @@ if ( opts.run_clean ):
+ sys.exit(0)
+
+ # Get Autotools versions
+-(m4_ret, m4_version) = getstatusoutput("m4 --version | sed 's/o/ /g' ")
++(m4_ret, m4_version) = getstatusoutput("gm4 --version | sed 's/o/ /g' ")
+ (ac_ret, ac_version) = getstatusoutput("autoconf --version")
+ (am_ret, am_version) = getstatusoutput("automake --version")
+ (lt_ret, lt_version) = getstatusoutput("libtool --version")
Added: head/science/abinit/files/patch-shared__common__src__02_clib__md5.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/abinit/files/patch-shared__common__src__02_clib__md5.c Sat Jan 2 00:42:00 2021 (r559900)
@@ -0,0 +1,11 @@
+--- shared/common/src/02_clib/md5.c.orig 2017-02-28 12:02:53 UTC
++++ shared/common/src/02_clib/md5.c
+@@ -47,7 +47,7 @@
+ #ifdef HAVE_MALLOC_MALLOC_H
+ # include <malloc/malloc.h>
+ #else
+-# include <malloc.h>
++# include <stdlib.h>
+ #endif
+
+ #include "md5.h"
Added: head/science/abinit/files/patch-shared_common_src_02__clib_calling__levmar.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/abinit/files/patch-shared_common_src_02__clib_calling__levmar.c Sat Jan 2 00:42:00 2021 (r559900)
@@ -0,0 +1,20 @@
+--- shared/common/src/02_clib/calling_levmar.c.orig 2020-11-10 12:21:53 UTC
++++ shared/common/src/02_clib/calling_levmar.c
+@@ -150,7 +150,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ];
+ /* invoke the optimisation function with box boundaries*/
+ ret=dlevmar_bc_dif(dim_screening, coeffs, yvals, c_ncoeffs, c_nvals, \
+ lower_bounds, upper_bounds, 3000, opts, info, NULL, NULL, \
+- (void *)&adata); // Box boundary conditions without Jacobian
++ NULL, (void *)&adata); // Box boundary conditions without Jacobian
+ //}
+ //}
+
+@@ -220,7 +220,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ];
+ /* invoke the optimisation function with box boundaries*/
+ ret=dlevmar_bc_dif(dre_and_im_screening, coeffs, yvals, c_ncoeffs, c_nvals, \
+ lower_bounds, upper_bounds, 1000, opts, info, NULL, NULL, \
+- (void *)&adata); // Box boundary conditions without Jacobian
++ NULL, (void *)&adata); // Box boundary conditions without Jacobian
+ //}
+ //}
+
Modified: head/science/abinit/pkg-plist
==============================================================================
--- head/science/abinit/pkg-plist Sat Jan 2 00:39:14 2021 (r559899)
+++ head/science/abinit/pkg-plist Sat Jan 2 00:42:00 2021 (r559900)
@@ -1,8 +1,9 @@
bin/abinit
+bin/abitk
bin/aim
bin/anaddb
+bin/atdep
bin/band2eps
-bin/bsepostproc
bin/conducti
bin/cut3d
bin/dummy_tests
@@ -17,7 +18,7 @@ bin/mrggkk
bin/mrgscr
bin/multibinit
bin/optic
-bin/tdep
+bin/testtransposer
bin/ujdet
bin/vdw_kernelgen
libdata/pkgconfig/abinit.pc
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