commit: c27e0053fa68318c60dfb94d9c2728abd5086b35
Author: Alessandro Barbieri <lssndrbarbieri <AT> gmail <DOT> com>
AuthorDate: Sun Jul 25 20:17:19 2021 +0000
Commit: Alessandro Barbieri <lssndrbarbieri <AT> gmail <DOT> com>
CommitDate: Sun Jul 25 20:18:55 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=c27e0053
sys-cluster/*: merge sionlibl with sionlib
Signed-off-by: Alessandro Barbieri <lssndrbarbieri <AT> gmail.com>
sys-cluster/sionlib/Manifest | 3 +-
sys-cluster/sionlib/files/respect-flags.patch | 134 ---------------------
.../files/sionlib-respect-flags.patch} | 0
sys-cluster/sionlib/metadata.xml | 3 +-
sys-cluster/sionlib/sionlib-1.7.6-r1.ebuild | 117 ------------------
.../sionlib-1.7.7.ebuild} | 9 +-
sys-cluster/sionlibl/Manifest | 1 -
sys-cluster/sionlibl/metadata.xml | 34 ------
8 files changed, 10 insertions(+), 291 deletions(-)
diff --git a/sys-cluster/sionlib/Manifest b/sys-cluster/sionlib/Manifest
index 9046f5a2b..8fc118f36 100644
--- a/sys-cluster/sionlib/Manifest
+++ b/sys-cluster/sionlib/Manifest
@@ -1 +1,2 @@
-DIST sionlib-1.7.6.tar.gz 486418 BLAKE2B
885eb2012ec6da031f5ae8b093ee4f3e5bbe31c9b24a11576f2ad01b32ddd8a85051565034f0e6c756af51409fb89f9c79f80b35c8337f2dc7912cb9e54d909b
SHA512
afdd8520f489bc940edc51ffa636a25cad778de07bfbb21d2bd2ab767e57b16044990d85ef44d2e6482a376196f5c6a2a6f1a71556dd987f8094dd396a971d1c
+DIST sionlib-1.7.7.tar.gz 489080 BLAKE2B
1ffd06d1b245034b28700af1249135347cdd731a7af23ad96a27b5b5a11d64d9a67249fcd1c44cea43face1066e7ae1d59681e84cef2041e18f02e0c3e8f70ee
SHA512
f270467e09893adf1af6103557365acbc9a3e73fe08716a21de6f59b25be9b187ee1c1ec1d878a9599e735f98da470b5e2e184774c27ed0ff0c330c5bf0a5677
+DIST sionlibl-1.7.7.tar.gz 490515 BLAKE2B
76971dd6d80222144b40da345d58311911aab09c6a5250b85d4a2731d2f93cdbd39d87dd6bbafdeaba88f06603105076267f6956417916f118ec45e07fa59269
SHA512
6ef46a0905552c558595bf6b72225a290d73dc87fa33c9862de5e4bd4d683792437646f7b4ab8a463b4a50d1b4a79aec96a66e577e815de3f23e9274be2681af
diff --git a/sys-cluster/sionlib/files/respect-flags.patch
b/sys-cluster/sionlib/files/respect-flags.patch
deleted file mode 100644
index 9ff5bd384..000000000
--- a/sys-cluster/sionlib/files/respect-flags.patch
+++ /dev/null
@@ -1,134 +0,0 @@
-diff '--color=auto' -ru a/config/determine-cc.sh b/config/determine-cc.sh
---- a/config/determine-cc.sh 2021-04-25 01:09:35.175990108 +0200
-+++ b/config/determine-cc.sh 2021-04-25 01:10:02.876433713 +0200
-@@ -1,7 +1,6 @@
- #!/bin/sh
- # determine what compiler is behind "cc" (and presumably "CC" and "ftn")
wrapper
-
--CC=`which cc 2>/dev/null`
- COMP=
- if [ -z "$CC" ]; then
- echo "No 'cc' located!"
-diff '--color=auto' -ru a/config/select-compiler.sh b/config/select-compiler.sh
---- a/config/select-compiler.sh 2021-04-25 01:09:35.175990108 +0200
-+++ b/config/select-compiler.sh 2021-04-25 01:10:26.882817842 +0200
-@@ -9,7 +9,7 @@
- CPS=""
- COMP=""
-
--GNU=`which gcc 2> /dev/null`
-+GNU="${CC}"
- if [ -n "${GNU}" ]
- then
- NCPS=`expr ${NCPS} + 1`
-diff '--color=auto' -ru a/config/select-mpi.sh b/config/select-mpi.sh
---- a/config/select-mpi.sh 2021-04-25 01:09:35.175990108 +0200
-+++ b/config/select-mpi.sh 2021-04-25 01:12:41.269962840 +0200
-@@ -76,7 +76,6 @@
- if [ -z "${MPIS}" ]; then MPIS="${MPI}"; else MPIS="${MPIS}|${MPI}"; fi
- fi
-
--MPICC=`which mpicc 2> /dev/null`
- if [ -n "${MPICC}" ]
- then
- FMPI=""
-@@ -86,7 +85,7 @@
- MPIROOTDIR1=`dirname ${MBINDIR}`
-
- echo "#include <mpi.h>" > conftest.c
-- mpicc -E conftest.c | grep '/mpi.h"' | head -1 > mpiconf.txt
-+ "${MPICC}" -E conftest.c | grep '/mpi.h"' | head -1 > mpiconf.txt
- MINCDIR=`cat mpiconf.txt | sed -e 's#^.* "##' -e 's#/mpi.h".*##'`
- if [ -n "${MINCDIR}" ]
- then
-diff '--color=auto' -ru a/mf/Makefile.defs.linux-gomp
b/mf/Makefile.defs.linux-gomp
---- a/mf/Makefile.defs.linux-gomp 2021-04-25 01:09:35.119989211 +0200
-+++ b/mf/Makefile.defs.linux-gomp 2021-04-25 01:52:32.378951608 +0200
-@@ -23,24 +23,19 @@
-
#------------------------------------------------------------------------------
- # SIONlib General Settings
-
#------------------------------------------------------------------------------
--OPTFLAGS = -g -O0 -Wall
-+CFLAGS += -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC
-
--CC = gcc
--CFLAGS = -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC
-+CXXFLAGS += $(PFLAG) $(OPTFLAGS) -fPIC
-
--CXX = g++
--CXXFLAGS = $(PFLAG) $(OPTFLAGS) -O3
--
--F77 = gfortran
--FFLAGS = $(PFLAG) $(OPTFLAGS)
-+FFLAGS += $(PFLAG) $(OPTFLAGS) -fPIC
-
- F90 = $(F77)
--F90FLAGS = $(PFLAG) $(OPTFLAGS) -ffree-form
-+F90FLAGS += $(PFLAG) $(OPTFLAGS) -ffree-form -fPIC $(FCFLAGS)
-
- FPP =
- FDOPT = -D
-
--LDFLAGS = $(PFLAG) $(OPTFLAGS) $(HINTSLIB)
-+LDFLAGS += $(PFLAG) $(OPTFLAGS) $(HINTSLIB)
- UTILLIB =
- FOBASE = pomp_fwrapper_base.o
-
-@@ -101,10 +96,6 @@
-
#------------------------------------------------------------------------------
-
- MPIENABLE = 1
--MPICC = mpicc
--MPICXX = mpicxx
--MPIF77 = mpif77
--MPIF90 = mpif90
- MPILIB = -lmpich
- PMPILIB = -lpmpich
- #PMPILIB = # MPICH2
-@@ -139,8 +130,7 @@
-
#------------------------------------------------------------------------------
-
- SZLIB = szlib
--SZLIB_OPTFLAGS = -O3
--SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED
-+SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED
$(CFLAGS)
- SZLIB_LIBPATH = -L$(TOPDIR)/utils/szlib
- SZLIB_LIB = -lsc.z
-
-diff '--color=auto' -ru a/src/fortraninterface/Makefile
b/src/fortraninterface/Makefile
---- a/src/fortraninterface/Makefile 2021-04-25 01:09:35.141989563 +0200
-+++ b/src/fortraninterface/Makefile 2021-04-25 01:23:48.055976593 +0200
-@@ -109,7 +110,7 @@
- $(CPP) $(F90FLAGS) $(F90FLAGS_CPP) -P -E -I ../lib sion_f90.F90 >
sion_f90.f90
- sion_f90.mod : sion_f90.o
- sion_f90.o : sion_f90.f90 sion_f77.h $(SION_HDRS)
-- $(F90) -c sion_f90.f90
-+ $(F90) $(F90FLAGS) -c sion_f90.f90
-
- sion_f90_omp.o: sion_f90.o
- sion_f90_mpi.o: sion_f90.o
-@@ -121,21 +122,21 @@
- $(CPP) $(F90FLAGS) $(F90FLAGS_CPP) $(F90MPIFLAGS) -P -E -I ../lib
sion_f90_mpi.F90 > sion_f90_mpi.f90
- sion_f90_mpi.mod : sion_f90_mpi.o
- sion_f90_mpi.o : sion_f90_mpi.f90 sion_f90.mod $(SION_HDRS)
-- $(MPIF90) -c sion_f90_mpi.f90
-+ $(MPIF90) $(F90FLAGS) $(F90MPIFLAGS) -c sion_f90_mpi.f90
-
- # F90 Interface (OMP)
- sion_f90_omp.f90: sion_f90_omp.F90
- $(CPP) $(F90OMPFLAGS) $(F90FLAGS) $(F90FLAGS_CPP) -P -E -I ../lib
sion_f90_omp.F90 > sion_f90_omp.f90
- sion_f90_omp.mod : sion_f90_omp.o
- sion_f90_omp.o : sion_f90_omp.f90 sion_f90.mod $(SION_HDRS)
-- $(OMPF90) -c sion_f90_omp.f90
-+ $(OMPF90) $(F90FLAGS) $(F90OMPFLAGS) -c sion_f90_omp.f90
-
- # F90 Interface (OMPI)
- sion_f90_ompi.f90: sion_f90_ompi.F90 $(SION_HDRS)
- $(CPP) $(F90MPIFLAGS) $(F90OMPFLAGS) $(F90FLAGS) $(F90FLAGS_CPP) -P -E
-I ../lib sion_f90_ompi.F90 > sion_f90_ompi.f90
- sion_f90_ompi.mod : sion_f90_ompi.o
- sion_f90_ompi.o : sion_f90_ompi.f90 $(SION_HDRS)
-- $(MPIF90) -c sion_f90_ompi.f90
-+ $(MPIF90) $(F90FLAGS) $(F90MPIFLAGS) -c sion_f90_ompi.f90
-
-
-
diff --git a/sys-cluster/sionlibl/files/sionlibl-respect-flags.patch
b/sys-cluster/sionlib/files/sionlib-respect-flags.patch
similarity index 100%
rename from sys-cluster/sionlibl/files/sionlibl-respect-flags.patch
rename to sys-cluster/sionlib/files/sionlib-respect-flags.patch
diff --git a/sys-cluster/sionlib/metadata.xml b/sys-cluster/sionlib/metadata.xml
index 55c6754ef..df4593cce 100644
--- a/sys-cluster/sionlib/metadata.xml
+++ b/sys-cluster/sionlib/metadata.xml
@@ -20,7 +20,7 @@ SIONlib provides two different interfaces: one for parallel
access (with impleme
</longdescription>
<use>
<!--<flag name="cuda">enable CUDA aware interface</flag>-->
- <flag name="cxx">Disable C++ support</flag>
+ <flag name="cxx">Enable C++ support</flag>
<flag name="debug">enable SIONlib debug</flag>
<flag name="fortran">Enable Fortran support</flag>
<flag name="mpi">enable mpi</flag>
@@ -30,5 +30,6 @@ SIONlib provides two different interfaces: one for parallel
access (with impleme
<flag name="parutils">Enable compilation of parutils (used for
benchmarking)</flag>
<flag name="pthreads">configure SIONlib to use pthreads for
locking</flag>
<!--<flag name="sionfwd">enable I/O forwarding with
SIONfwd</flag>-->
+ <flag name="tools">Build the tooling version instead</flag>
</use>
</pkgmetadata>
diff --git a/sys-cluster/sionlib/sionlib-1.7.6-r1.ebuild
b/sys-cluster/sionlib/sionlib-1.7.6-r1.ebuild
deleted file mode 100644
index a63c7bc0f..000000000
--- a/sys-cluster/sionlib/sionlib-1.7.6-r1.ebuild
+++ /dev/null
@@ -1,117 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DOCS_BUILDER="doxygen"
-DOCS_CONFIG_NAME="doxy"
-FORTRAN_NEEDED="fortran"
-PYTHON_COMPAT=( pypy3 python3_{7,8,9} )
-inherit docs flag-o-matic fortran-2 python-any-r1 toolchain-funcs
-
-DESCRIPTION="Scalable I/O library for parallel access to task-local files"
-HOMEPAGE="https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html";
-SRC_URI="http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV} ->
${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="+cxx debug doc examples +fortran +mpi +ompi +openmp +parutils +pthreads
python"
-#TODO: cuda sionfwd msa
-#--enable-sionfwd=/path/to/sionfwd
-#--msa=(hostname-regex|deep-est-sdv)] MSA aware collective operations for the
given system
-
-PATCHES=( "${FILESDIR}/respect-flags.patch" )
-
-RDEPEND="
- mpi? ( virtual/mpi )
- ompi? (
- || ( sys-devel/gcc:*[openmp] sys-libs/libomp )
- virtual/mpi
- )
- openmp? ( || ( sys-devel/gcc:*[openmp] sys-libs/libomp ) )
-"
-DEPEND="
- ${RDEPEND}
- ${PYTHON_DEPS}
-"
-S="${WORKDIR}/${PN}"
-
-pkg_setup() {
- FORTRAN_NEED_OPENMP=0
- use openmp && FORTRAN_NEED_OPENMP=1
- use ompi && FORTRAN_NEED_OPENMP=1
-
- fortran-2_pkg_setup
-}
-
-src_prepare() {
- default
- sed 's/CXXFLAGS = $(CXXFLAGS)/CXXFLAGS = /' -i test/serial/Makefile ||
die
- sed 's/`gcc/`${CC}/' -i config/determine-compiler-version.sh || die
-}
-
-src_configure() {
- tc-export AR CC CXX F77 FC
- export MPICC=/usr/bin/mpicc
- export MPICXX=/usr/bin/mpicxx
- export MPIF77=/usr/bin/mpif77
- export MPIF90=/usr/bin/mpif90
- export F90=$(tc-getFC)
- export OMPF77=$(tc-getF77)
- export OMPF90=$(tc-getFC)
-
- append-fflags -fallow-argument-mismatch
-
- local myconf=(
- --disable-mic
- --prefix="${T}/prefix/usr"
- )
-
- #custom configure?
- use cxx || myconf+=( "--disable-cxx" )
- use fortran || myconf+=( "--disable-fortran" )
- use mpi || myconf+=( "--disable-mpi" )
- use ompi || myconf+=( "--disable-ompi" )
- use openmp || myconf+=( "--disable-omp" )
- use parutils || myconf+=( "--disable-parutils" )
- use pthreads || myconf+=( "--disable-pthreads" )
-
- use debug && myconf+=( "--enable-debug" )
- use python && myconf+=( "--enable-python=3" )
-
- ./configure "${myconf[@]}" || die
-}
-
-src_compile() {
- export VARTEXFONTS="${T}/fonts"
- emake C_AR=$(tc-getAR) F90=$(tc-getFC)
- docs_compile
-}
-
-src_install() {
- mkdir -p "${T}/prefix/usr/share/doc/${PF}" || die
- default
-
- if use examples ; then
- mv "${T}/prefix/usr/examples"
"${T}/prefix/usr/share/doc/${PF}/" || die
- else
- rm -r "${T}/prefix/usr/examples" || die
- fi
-
- # move 64 bit libraries to lib64
- libs64=( "${T}"/prefix/usr/lib/*64* )
- if [[ ${#libs64[@]} -gt 0 ]]; then
- mkdir "${T}/prefix/usr/lib64" || die
- for l in "${libs64[@]}" ; do
- mv "${l}" "${T}/prefix/usr/lib64/" || die
- done
- fi
-
- rsync -ravXHA "${T}/prefix/usr" "${ED}/" || die
- docompress -x "/usr/share/doc/${PF}/examples"
-
- #TODO: build shared libs
- #find "${ED}" -name '*.a' -delete || die
- find "${ED}" -name '*.la' -delete || die
-}
diff --git a/sys-cluster/sionlibl/sionlibl-1.7.7.ebuild
b/sys-cluster/sionlib/sionlib-1.7.7.ebuild
similarity index 91%
rename from sys-cluster/sionlibl/sionlibl-1.7.7.ebuild
rename to sys-cluster/sionlib/sionlib-1.7.7.ebuild
index 45b166425..e00956e3a 100644
--- a/sys-cluster/sionlibl/sionlibl-1.7.7.ebuild
+++ b/sys-cluster/sionlib/sionlib-1.7.7.ebuild
@@ -12,13 +12,16 @@ inherit docs flag-o-matic fortran-2 python-any-r1
toolchain-funcs
DESCRIPTION="Scalable I/O library for parallel access to task-local files"
HOMEPAGE="https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html";
-SRC_URI="http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV}l ->
${P}.tar.gz"
-S="${WORKDIR}/sionlib"
+SRC_URI="
+ !tools? (
http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV} -> ${P}.tar.gz
)
+ tools? (
http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV}l ->
${PN}l-${PV}.tar.gz )
+"
+S="${WORKDIR}/${PN}"
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="+cxx debug doc examples +fortran +mpi +ompi +openmp +parutils +pthreads
python"
+IUSE="+cxx debug doc examples +fortran +mpi +ompi +openmp +parutils +pthreads
python tools"
#TODO: cuda sionfwd msa
#--enable-sionfwd=/path/to/sionfwd
#--msa=(hostname-regex|deep-est-sdv)] MSA aware collective operations for the
given system
diff --git a/sys-cluster/sionlibl/Manifest b/sys-cluster/sionlibl/Manifest
deleted file mode 100644
index 8ce6ed0a6..000000000
--- a/sys-cluster/sionlibl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sionlibl-1.7.7.tar.gz 490515 BLAKE2B
76971dd6d80222144b40da345d58311911aab09c6a5250b85d4a2731d2f93cdbd39d87dd6bbafdeaba88f06603105076267f6956417916f118ec45e07fa59269
SHA512
6ef46a0905552c558595bf6b72225a290d73dc87fa33c9862de5e4bd4d683792437646f7b4ab8a463b4a50d1b4a79aec96a66e577e815de3f23e9274be2681af
diff --git a/sys-cluster/sionlibl/metadata.xml
b/sys-cluster/sionlibl/metadata.xml
deleted file mode 100644
index 55c6754ef..000000000
--- a/sys-cluster/sionlibl/metadata.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="person">
- <email>lssndrbarbi...@gmail.com</email>
- <name>Alessandro Barbieri</name>
- </maintainer>
- <longdescription lang="en">
-SIONlib is a library for writing and reading data from several thousands of
parallel tasks into/from one or a small number of physical files. Only the open
and close functions are collective while file access can be performed
independently.
-
-SIONlib can be used as a replacement for standard I/O APIs (e.g. POSIX) that
are used to access distinct files from every parallel process. SIONlib will
bundle the data into one or few files in a coordinated fashion in order to
sidestep sequentialising mechanism in the file system. At the same time, the
task-per-file picture is maintained for the application, every process has
access to its logical file only. File access is performed using SIONlib
equivalents to standard C-I/O functionality (fwrite becomes sion_write, fseek
becomes sion_seek, etc.) which have similar semantics as their C counterparts.
-
-Internally, the physical files are sub-divided into sequences of blocks, which
themselves contain one chunk of data belonging to every logical file. In case
the amount to be written to a file is known up front, it can optionally be
specified when opening the file and the sequence of blocks collapses into a
single block with one chunk per task containing all of its data. If a chunk
size cannot be specified ahead of time, a sensible default is chosen and reads
and writes that cross chunk boundaries are handled transparently by SIONlib.
-
-SIONlib also uses information about the block size of the underlying file
system, because access to the same block from different tasks often leads to
contention.
-
-Both, the estimated chunk size and file system block size are used to align
individual chunks with file system blocks. Ensuring contention-free access to
file system blocks enables efficient parallel writing and reading.
-
-SIONlib provides two different interfaces: one for parallel access (with
implementations for different parallel programming technologies such as MPI,
OpenMP and hybrid MPI+OpenMP) and one for sequential access which is also used
internally by the SIONlib utilities.
- </longdescription>
- <use>
- <!--<flag name="cuda">enable CUDA aware interface</flag>-->
- <flag name="cxx">Disable C++ support</flag>
- <flag name="debug">enable SIONlib debug</flag>
- <flag name="fortran">Enable Fortran support</flag>
- <flag name="mpi">enable mpi</flag>
- <flag name="python">enable python support</flag>
- <flag name="ompi">enable hybrid openmp mpi</flag>
- <flag name="openmp">enable openmp</flag>
- <flag name="parutils">Enable compilation of parutils (used for
benchmarking)</flag>
- <flag name="pthreads">configure SIONlib to use pthreads for
locking</flag>
- <!--<flag name="sionfwd">enable I/O forwarding with
SIONfwd</flag>-->
- </use>
-</pkgmetadata>
