Date: Sat, 2 Jan 2021 00:42:00 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r559900 - in head/science/abinit: . files Message-ID: <202101020042.1020g0jj047329@repo.freebsd.org>
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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@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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