Attachment #221028 for bug #252221




# $FreeBSD$

PORTNAME=	abinit
DISTVERSION=	9.2.2
PORTREVISION=	6
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@FreeBSD.org
COMMENT=	Full-featured atomic-scale first-principles simulation software

LICENSE=	GPLv3
LICENSE_FILE=	${WRKSRC}/COPYING

ONLY_FOR_ARCHS=	amd64
BROKEN=		fails to build
BROKEN_i386=	Type mismatch in argument 'block_displ', see https://github.com/abinit/abinit/issues/19

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	\
		libwannier90.so:science/wannier90	\
		libnetcdff.so:science/netcdf-fortran
RUN_DEPENDS=	atompaw:science/atompaw
TEST_DEPENDS=	${PYNUMPY}	\
		libyaml>0:textproc/libyaml

USE_GITHUB=	yes

USES=		autoreconf:build blaslapack:netlib fortran gmake gnome localbase:ldflags	\
		python:3.6+ shebangfix
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="${LDFLAGS}"	\
		LINALG_FCFLAGS="-I${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} -lwannier90"
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=			DOCS OPENMP MPI
OPTIONS_DEFAULT=		OPENMP MPI

OPENMP_CONFIGURE_ENABLE=	openmp
OPENMP_LDFLAGS=			-lomp

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_LIB_DEPENDS=		libmpi.so:net/mpich

.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

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.mk>

Lines 1-3 Link Here

(-)science/abinit/distinfo (-3 / +3 lines)
1	TIMESTAMP = 1550812825	1	TIMESTAMP = 1608996405
2	SHA256 (abinit-8.10.3.tar.gz) = 922e38edab95e1763c4d504a927f7ea4e19da3143e5b33c5d6e4b41210bf5a9d	2	SHA256 (abinit-abinit-9.2.2_GH0.tar.gz) = 29511bbc4f4e318cf3676aafdfea48ce2beb8ab6bd64062bd38d516fc02a8543
3	SIZE (abinit-8.10.3.tar.gz) = 88310400	3	SIZE (abinit-abinit-9.2.2_GH0.tar.gz) = 98949530

Lines 1-11 Link Here

(-)science/abinit/files/patch-Makefile.in (-11 lines)
1	--- Makefile.in.orig 2018-06-14 05:16:42 UTC
2	+++ Makefile.in
3	@@ -876,7 +876,7 @@ AM_DISTCHECK_CONFIGURE_FLAGS = \
4	@abi_ac_distcheck@ \
5	PYFLAGS="@PYFLAGS@ -B"
6
7	-SUBDIRS = fallbacks src abichecks tests
8	+SUBDIRS = fallbacks src abichecks
9
10	# Additional files to clean
11	CLEANFILES = config.optim config.fc_info.tmp

Line 0 Link Here

(-)science/abinit/files/patch-config_m4_sd__levmar.m4 (+10 lines)
	1	--- config/m4/sd_levmar.m4.orig 2020-11-10 12:21:53 UTC
	2	+++ config/m4/sd_levmar.m4
	3	@@ -239,6 +239,7 @@ AC_DEFUN([_SD_LEVMAR_CHECK_USE], [
	4	AC_LANG_PUSH([C])
	5	AC_LINK_IFELSE([AC_LANG_PROGRAM(
	6	[[
	7	+# include <stddef.h>
	8	# include <levmar.h>
	9
	10	void dfit_function(double p, double y, int m, int n, void *adata)

Line 0 Link Here

(-)science/abinit/files/patch-config_scripts_makemake (+11 lines)
	1	--- config/scripts/makemake.orig 2020-12-26 16:36:41 UTC
	2	+++ config/scripts/makemake
	3	@@ -408,7 +408,7 @@ if ( opts.run_clean ):
	4	sys.exit(0)
	5
	6	# Get Autotools versions
	7	-(m4_ret, m4_version) = getstatusoutput("m4 --version \| sed 's/o/ /g' ")
	8	+(m4_ret, m4_version) = getstatusoutput("gm4 --version \| sed 's/o/ /g' ")
	9	(ac_ret, ac_version) = getstatusoutput("autoconf --version")
	10	(am_ret, am_version) = getstatusoutput("automake --version")
	11	(lt_ret, lt_version) = getstatusoutput("libtool --version")

Lines 1-5 Link Here

(-)science/abinit/files/patch-shared__common__src__02_clib__md5.c (-2 / +2 lines)
1	--- src/02_clib/md5.c.orig 2017-02-28 12:02:53 UTC	1	--- shared/common/src/02_clib/md5.c.orig 2017-02-28 12:02:53 UTC
2	+++ src/02_clib/md5.c	2	+++ shared/common/src/02_clib/md5.c
3	@@ -47,7 +47,7 @@	3	@@ -47,7 +47,7 @@
4	#ifdef HAVE_MALLOC_MALLOC_H	4	#ifdef HAVE_MALLOC_MALLOC_H
5	# include <malloc/malloc.h>	5	# include <malloc/malloc.h>




--- 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
     //}
   //}
   

Lines 1-11 Link Here

(-)science/abinit/files/patch-src_02__clib_md5.c (-11 lines)
1	--- src/02_clib/md5.c.orig 2017-02-28 12:02:53 UTC
2	+++ src/02_clib/md5.c
3	@@ -47,7 +47,7 @@
4	#ifdef HAVE_MALLOC_MALLOC_H
5	# include <malloc/malloc.h>
6	#else
7	-# include <malloc.h>
8	+# include <stdlib.h>
9	#endif
10
11	#include "md5.h"




bin/abinit
bin/abitk
bin/aim
bin/anaddb
bin/atdep
bin/band2eps
bin/bsepostproc
bin/conducti
bin/cut3d
bin/dummy_tests

bin/mrgscr
bin/multibinit
bin/optic
bin/testtransposer
bin/ujdet
bin/vdw_kernelgen
libdata/pkgconfig/abinit.pc

Return to bug 252221

Lines 2-11 Link Here

(-)science/abinit/Makefile (-18 / +63 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= abinit	4	PORTNAME= abinit
5	DISTVERSION= 8.10.3	5	DISTVERSION= 9.2.2
6	PORTREVISION= 6
7	CATEGORIES= science	6	CATEGORIES= science
8	MASTER_SITES= LOCAL/yuri/ # https://www.abinit.org/sites/default/files/packages/ has the updated 8.10.3 tarball that doesn't compile
9		7
10	MAINTAINER= yuri@FreeBSD.org	8	MAINTAINER= yuri@FreeBSD.org
11	COMMENT= Full-featured atomic-scale first-principles simulation software	9	COMMENT= Full-featured atomic-scale first-principles simulation software
Lines 13-45 Link Here
13	LICENSE= GPLv3	11	LICENSE= GPLv3
14	LICENSE_FILE= ${WRKSRC}/COPYING	12	LICENSE_FILE= ${WRKSRC}/COPYING
15		13
16	ONLY_FOR_ARCHS= amd64 i386	14	ONLY_FOR_ARCHS= amd64
17	BROKEN= fails to build
18	BROKEN_i386= Type mismatch in argument 'block_displ', see https://github.com/abinit/abinit/issues/19
19		15
20	LIB_DEPENDS= liblapack.so:math/lapack \	16	BUILD_DEPENDS= gm4:devel/m4 \
21	libblas.so:math/blas	17	${PYNUMPY} \
		18	${PY_PYGMENTS} \
		19	${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
		20	${PYTHON_PKGNAMEPREFIX}graphviz>0:graphics/py-graphviz@${PY_FLAVOR}
		21	LIB_DEPENDS= libelpa.so:math/elpa \
		22	libsz.so:science/szip \
		23	libelpa.so:math/elpa \
		24	libxc.so:science/libxc \
		25	libfftw3.so:math/fftw3 \
		26	libhdf5.so:science/hdf5 \
		27	libxml2.so:textproc/libxml2 \
		28	libnetcdf.so:science/netcdf \
		29	libxmlf90.so:textproc/xmlf90 \
		30	libwannier90.so:science/wannier90 \
		31	libnetcdff.so:science/netcdf-fortran
22	RUN_DEPENDS= atompaw:science/atompaw	32	RUN_DEPENDS= atompaw:science/atompaw
		33	TEST_DEPENDS= ${PYNUMPY} \
		34	libyaml>0:textproc/libyaml
23		35
24	USES= fortran gmake localbase:ldflags	36	USE_GITHUB= yes
		37
		38	USES= autoreconf:build blaslapack:netlib fortran gmake gnome localbase:ldflags \
		39	python:3.6+ shebangfix
		40	USE_GNOME= libxml2
		41	SHEBANG_FILES= config/scripts/* doc/tutorial/paral_gspw_assets/abinit.sub.*
		42	SHEBANG_GLOB= *.py
25	GNU_CONFIGURE= yes	43	GNU_CONFIGURE= yes
26		44	CONFIGURE_ENV= CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" FC_LDFLAGS="${LDFLAGS}" \
27	CONFIGURE_ENV= CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" FC_LDFLAGS="${LDFLAGS}"	45	LINALG_FCFLAGS="-I${LOCALBASE}/include/elpa-2019.05.002/modules" \
28	CONFIGURE_ARGS= --enable-shared --disable-static	46	LINALG_LIBS="${BLASLIB} ${LAPACKLIB} -lelpa" \
		47	NETCDF_FORTRAN_FCFLAGS=-I${LOCALBASE}/include \
		48	XMLF90_FCFLAGS=-I${LOCALBASE}/include \
		49	WANNIER90_LIBS="${BLASLIB} ${LAPACKLIB} -lwannier90"
		50	CONFIGURE_ARGS= --with-fft --with-libxc --with-libxml2 --with-netcdf \
		51	--with-netcdf-fortran --with-wannier90 --with-xmlf90
29	FCFLAGS+= -ffree-line-length-none	52	FCFLAGS+= -ffree-line-length-none
		53	TEST_TARGET= tests_abirules tests_buildsys
		54	TEST_WRKSRC= ${WRKSRC}/abichecks
		55	PORTDOCS= *
30		56
31	OPTIONS_DEFINE= OPENMP MPI	57	OPTIONS_DEFINE= DOCS OPENMP MPI
32	OPTIONS_DEFAULT= OPENMP MPI	58	OPTIONS_DEFAULT= OPENMP MPI
33		59
34	OPENMP_CONFIGURE_ENABLE= openmp	60	OPENMP_CONFIGURE_ENABLE= openmp
35	OPENMP_LDFLAGS= -lomp	61	OPENMP_LDFLAGS= -lomp
36		62
37	MPI_CONFIGURE_ENABLE= mpi	63	MPI_CONFIGURE_WITH= mpi=yes
38	MPI_VARS= FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include	64	# fftw3 not enabled because libfftw3_mpi is required but not packaged
39	MPI_LDFLAGS= ${LOCALBASE}/lib/libmpich.so ${LOCALBASE}/lib/libmpicxx.so ${LOCALBASE}/lib/libmpifort.so	65	MPI_VARS= FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include \
		66	CONFIGURE_ENV+=MPI_LIBS="`pkg-config --libs mpich` -lmpifort" \
		67	CONFIGURE_ENV+MPI_LDFLAGS="`pkg-config --libs mpich` -lmpifort"
40	MPI_LIB_DEPENDS= libmpi.so:net/mpich	68	MPI_LIB_DEPENDS= libmpi.so:net/mpich
41		69
42	do-test:	70	.if defined(WITH_LEVMAR)
43	@cd ${WRKSRC}/tests && ./configure && ${GMAKE} check	71	# --with-levmar seems deprecated
		72	LIB_DEPENDS+= liblevmar.so:math/levmar
		73	CONFIGURE_ENV+= LEVMAR_LIBS="-llevmar ${BLASLIB} ${LAPACKLIB}"
		74	CONFIGURE_ARGS+= --with-levmar
		75	.endif
44		76
		77	pre-configure:
		78	(cd ${WRKSRC} && ./autogen.sh)
		79
		80	post-install-DOCS-on:
		81	${REINPLACE_CMD} -e 's\|/usr/bin/env python\|${PYTHON_CMD}\|' \
		82	${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py
		83	${RM} ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py.bak
		84	@${MKDIR} ${STAGEDIR}${DOCSDIR}
		85	${CP} -R ${WRKSRC}/doc/tutorial ${STAGEDIR}${DOCSDIR}
		86
		87	pre-test:
		88	${TOUCH} ${TEST_WRKSRC}/make.log
		89
45	.include <bsd.port.mk>	90	.include <bsd.port.mk>

Line 0 Link Here

(-)science/abinit/files/patch-shared_common_src_02__clib_calling__levmar.c (+20 lines)
	1	--- shared/common/src/02_clib/calling_levmar.c.orig 2020-11-10 12:21:53 UTC
	2	+++ shared/common/src/02_clib/calling_levmar.c
	3	@@ -150,7 +150,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ];
	4	/* invoke the optimisation function with box boundaries*/
	5	ret=dlevmar_bc_dif(dim_screening, coeffs, yvals, c_ncoeffs, c_nvals, \
	6	lower_bounds, upper_bounds, 3000, opts, info, NULL, NULL, \
	7	- (void *)&adata); // Box boundary conditions without Jacobian
	8	+ NULL, (void *)&adata); // Box boundary conditions without Jacobian
	9	//}
	10	//}
	11
	12	@@ -220,7 +220,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ];
	13	/* invoke the optimisation function with box boundaries*/
	14	ret=dlevmar_bc_dif(dre_and_im_screening, coeffs, yvals, c_ncoeffs, c_nvals, \
	15	lower_bounds, upper_bounds, 1000, opts, info, NULL, NULL, \
	16	- (void *)&adata); // Box boundary conditions without Jacobian
	17	+ NULL, (void *)&adata); // Box boundary conditions without Jacobian
	18	//}
	19	//}
	20

Lines 1-8 Link Here

(-)science/abinit/pkg-plist (-2 / +3 lines)
1	bin/abinit	1	bin/abinit
		2	bin/abitk
2	bin/aim	3	bin/aim
3	bin/anaddb	4	bin/anaddb
		5	bin/atdep
4	bin/band2eps	6	bin/band2eps
5	bin/bsepostproc
6	bin/conducti	7	bin/conducti
7	bin/cut3d	8	bin/cut3d
8	bin/dummy_tests	9	bin/dummy_tests
Lines 17-23 Link Here
17	bin/mrgscr	18	bin/mrgscr
18	bin/multibinit	19	bin/multibinit
19	bin/optic	20	bin/optic
20	bin/tdep	21	bin/testtransposer
21	bin/ujdet	22	bin/ujdet
22	bin/vdw_kernelgen	23	bin/vdw_kernelgen
23	libdata/pkgconfig/abinit.pc	24	libdata/pkgconfig/abinit.pc