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sys-cluster/*: split sionlibl and make them co-installable
Signed-off-by: Alessandro Barbieri <lssndrbarbieri@gmail.com>
This commit is contained in:
Alessandro Barbieri
@@ -1,2 +1 @@
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DIST sionlib-1.7.7.tar.gz 489080 BLAKE2B 1ffd06d1b245034b28700af1249135347cdd731a7af23ad96a27b5b5a11d64d9a67249fcd1c44cea43face1066e7ae1d59681e84cef2041e18f02e0c3e8f70ee SHA512 f270467e09893adf1af6103557365acbc9a3e73fe08716a21de6f59b25be9b187ee1c1ec1d878a9599e735f98da470b5e2e184774c27ed0ff0c330c5bf0a5677
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DIST sionlibl-1.7.7.tar.gz 490515 BLAKE2B 76971dd6d80222144b40da345d58311911aab09c6a5250b85d4a2731d2f93cdbd39d87dd6bbafdeaba88f06603105076267f6956417916f118ec45e07fa59269 SHA512 6ef46a0905552c558595bf6b72225a290d73dc87fa33c9862de5e4bd4d683792437646f7b4ab8a463b4a50d1b4a79aec96a66e577e815de3f23e9274be2681af
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@@ -30,6 +30,5 @@ SIONlib provides two different interfaces: one for parallel access (with impleme
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<flag name="parutils">Enable compilation of parutils (used for benchmarking)</flag>
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<flag name="pthreads">configure SIONlib to use pthreads for locking</flag>
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<!--<flag name="sionfwd">enable I/O forwarding with SIONfwd</flag>-->
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<flag name="tools">Build the tooling version instead</flag>
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</use>
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</pkgmetadata>
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@@ -12,16 +12,13 @@ inherit docs flag-o-matic fortran-2 python-any-r1 toolchain-funcs
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DESCRIPTION="Scalable I/O library for parallel access to task-local files"
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HOMEPAGE="https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html"
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SRC_URI="
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!tools? ( http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV} -> ${P}.tar.gz )
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tools? ( http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV}l -> ${PN}l-${PV}.tar.gz )
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"
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SRC_URI="http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV} -> ${P}.tar.gz"
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S="${WORKDIR}/${PN}"
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LICENSE="BSD"
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SLOT="0"
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KEYWORDS="~amd64"
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IUSE="+cxx debug doc examples +fortran +mpi +ompi +openmp +parutils +pthreads python tools"
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IUSE="+cxx debug doc examples +fortran +mpi +ompi +openmp +parutils +pthreads python"
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#TODO: cuda sionfwd msa
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#--enable-sionfwd=/path/to/sionfwd
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#--msa=(hostname-regex|deep-est-sdv)] MSA aware collective operations for the given system
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@@ -103,6 +100,14 @@ src_install() {
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rm -r "${T}/prefix/usr/examples" || die
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fi
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insinto "/usr/include/sionlib"
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doins -r "${T}"/prefix/usr/include/*
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rm -r "${T}/prefix/usr/include" || die
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exeinto "/usr/libexec/${PN}"
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doexe "${T}"/prefix/usr/bin/*partest
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rm "${T}"/prefix/usr/bin/*partest || die
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# move 64 bit libraries to lib64
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libs64=( "${T}"/prefix/usr/lib/*64* )
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if [[ ${#libs64[@]} -gt 0 ]]; then
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1
sys-cluster/sionlibl/Manifest
Normal file
1
sys-cluster/sionlibl/Manifest
Normal file
@@ -0,0 +1 @@
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DIST sionlibll-1.7.7.tar.gz 490515 BLAKE2B 76971dd6d80222144b40da345d58311911aab09c6a5250b85d4a2731d2f93cdbd39d87dd6bbafdeaba88f06603105076267f6956417916f118ec45e07fa59269 SHA512 6ef46a0905552c558595bf6b72225a290d73dc87fa33c9862de5e4bd4d683792437646f7b4ab8a463b4a50d1b4a79aec96a66e577e815de3f23e9274be2681af
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120
sys-cluster/sionlibl/files/sionlibl-respect-flags.patch
Normal file
120
sys-cluster/sionlibl/files/sionlibl-respect-flags.patch
Normal file
@@ -0,0 +1,120 @@
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--- a/config/determine-cc.sh
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+++ b/config/determine-cc.sh
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@@ -1,7 +1,6 @@
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#!/bin/sh
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# determine what compiler is behind "cc" (and presumably "CC" and "ftn") wrapper
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-CC=`which cc 2>/dev/null`
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COMP=
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if [ -z "$CC" ]; then
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echo "No 'cc' located!"
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--- a/config/select-compiler.sh
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+++ b/config/select-compiler.sh
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@@ -9,7 +9,7 @@
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CPS=""
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COMP=""
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-GNU=`which gcc 2> /dev/null`
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+GNU="${CC}"
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if [ -n "${GNU}" ]
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then
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NCPS=`expr ${NCPS} + 1`
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--- a/config/select-mpi.sh
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+++ b/config/select-mpi.sh
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@@ -76,7 +76,6 @@
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if [ -z "${MPIS}" ]; then MPIS="${MPI}"; else MPIS="${MPIS}|${MPI}"; fi
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fi
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-MPICC=`which mpicc 2> /dev/null`
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if [ -n "${MPICC}" ]
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then
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FMPI=""
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@@ -86,7 +85,7 @@
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MPIROOTDIR1=`dirname ${MBINDIR}`
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echo "#include <mpi.h>" > conftest.c
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- mpicc -E conftest.c | grep '/mpi.h"' | head -1 > mpiconf.txt
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+ "${MPICC}" -E conftest.c | grep '/mpi.h"' | head -1 > mpiconf.txt
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MINCDIR=`cat mpiconf.txt | sed -e 's#^.* "##' -e 's#/mpi.h".*##'`
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if [ -n "${MINCDIR}" ]
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then
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--- a/mf/Makefile.defs.linux-gomp
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+++ b/mf/Makefile.defs.linux-gomp
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@@ -23,24 +23,19 @@
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#------------------------------------------------------------------------------
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# SIONlib General Settings
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#------------------------------------------------------------------------------
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-OPTFLAGS = -g -O0 -Wall
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+CFLAGS += -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC
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-CC = gcc
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-CFLAGS = -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC
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+CXXFLAGS += $(PFLAG) $(OPTFLAGS) -fPIC
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-CXX = g++
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-CXXFLAGS = $(PFLAG) $(OPTFLAGS) -O3
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-
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-F77 = gfortran
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-FFLAGS = $(PFLAG) $(OPTFLAGS)
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+FFLAGS += $(PFLAG) $(OPTFLAGS) -fPIC
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F90 = $(F77)
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-F90FLAGS = $(PFLAG) $(OPTFLAGS) -ffree-form
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+F90FLAGS += $(PFLAG) $(OPTFLAGS) -ffree-form -fPIC $(FCFLAGS)
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FPP =
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FDOPT = -D
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-LDFLAGS = $(PFLAG) $(OPTFLAGS) $(HINTSLIB)
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+LDFLAGS += $(PFLAG) $(OPTFLAGS) $(HINTSLIB)
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UTILLIB =
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FOBASE = pomp_fwrapper_base.o
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@@ -101,10 +96,6 @@
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#------------------------------------------------------------------------------
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MPIENABLE = 1
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-MPICC = mpicc
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-MPICXX = mpicxx
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-MPIF77 = mpif77
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-MPIF90 = mpif90
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MPILIB = -lmpich
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PMPILIB = -lpmpich
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#PMPILIB = # MPICH2
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@@ -139,8 +130,7 @@
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#------------------------------------------------------------------------------
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SZLIB = szlib
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-SZLIB_OPTFLAGS = -O3
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-SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED
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+SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED $(CFLAGS)
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SZLIB_LIBPATH = -L$(TOPDIR)/utils/szlib
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SZLIB_LIB = -lsc.z
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--- a/src/fortraninterface/Makefile
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+++ b/src/fortraninterface/Makefile
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@@ -121,21 +122,21 @@
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$(CPP) $(F90FLAGS) $(F90FLAGS_CPP) $(F90MPIFLAGS) -P -E -I ../lib sion_f90_mpi.F90 > sion_f90_mpi.f90
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sion_f90_mpi.mod : sion_f90_mpi.o
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sion_f90_mpi.o : sion_f90_mpi.f90 sion_f90.mod $(SION_HDRS)
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- $(MPIF90) $(F90FLAGS) -c sion_f90_mpi.f90
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+ $(MPIF90) $(F90FLAGS) $(F90MPIFLAGS) -c sion_f90_mpi.f90
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# F90 Interface (OMP)
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sion_f90_omp.f90: sion_f90_omp.F90
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$(CPP) $(F90OMPFLAGS) $(F90FLAGS) $(F90FLAGS_CPP) -P -E -I ../lib sion_f90_omp.F90 > sion_f90_omp.f90
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sion_f90_omp.mod : sion_f90_omp.o
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sion_f90_omp.o : sion_f90_omp.f90 sion_f90.mod $(SION_HDRS)
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- $(OMPF90) $(F90FLAGS) -c sion_f90_omp.f90
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+ $(OMPF90) $(F90FLAGS) $(F90OMPFLAGS) -c sion_f90_omp.f90
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# F90 Interface (OMPI)
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sion_f90_ompi.f90: sion_f90_ompi.F90 $(SION_HDRS)
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$(CPP) $(F90MPIFLAGS) $(F90OMPFLAGS) $(F90FLAGS) $(F90FLAGS_CPP) -P -E -I ../lib sion_f90_ompi.F90 > sion_f90_ompi.f90
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sion_f90_ompi.mod : sion_f90_ompi.o
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sion_f90_ompi.o : sion_f90_ompi.f90 $(SION_HDRS)
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- $(MPIF90) $(F90FLAGS) -c sion_f90_ompi.f90
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+ $(MPIF90) $(F90FLAGS) $(F90MPIFLAGS) -c sion_f90_ompi.f90
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34
sys-cluster/sionlibl/metadata.xml
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34
sys-cluster/sionlibl/metadata.xml
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@@ -0,0 +1,34 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="person">
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<email>lssndrbarbieri@gmail.com</email>
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<name>Alessandro Barbieri</name>
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</maintainer>
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<longdescription lang="en">
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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.
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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.
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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.
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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.
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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.
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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.
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</longdescription>
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<use>
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<!--<flag name="cuda">enable CUDA aware interface</flag>-->
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<flag name="cxx">Enable C++ support</flag>
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<flag name="debug">enable SIONlib debug</flag>
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<flag name="fortran">Enable Fortran support</flag>
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<flag name="mpi">enable mpi</flag>
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<flag name="python">enable python support</flag>
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<flag name="ompi">enable hybrid openmp mpi</flag>
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<flag name="openmp">enable openmp</flag>
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<flag name="parutils">Enable compilation of parutils (used for benchmarking)</flag>
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<flag name="pthreads">configure SIONlib to use pthreads for locking</flag>
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<!--<flag name="sionfwd">enable I/O forwarding with SIONfwd</flag>-->
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</use>
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</pkgmetadata>
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132
sys-cluster/sionlibl/sionlibl-1.7.7.ebuild
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132
sys-cluster/sionlibl/sionlibl-1.7.7.ebuild
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@@ -0,0 +1,132 @@
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# Copyright 2019-2021 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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DOCS_BUILDER="doxygen"
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DOCS_CONFIG_NAME="doxy"
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FORTRAN_NEEDED="fortran"
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PYTHON_COMPAT=( pypy3 python3_{8..10} )
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inherit docs flag-o-matic fortran-2 python-any-r1 toolchain-funcs
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DESCRIPTION="Scalable I/O library for parallel access to task-local files"
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HOMEPAGE="https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html"
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SRC_URI="http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV}l -> ${PN}l-${PV}.tar.gz"
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S="${WORKDIR}/sionlib"
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LICENSE="BSD"
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SLOT="0"
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KEYWORDS="~amd64"
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IUSE="+cxx debug doc examples +fortran +mpi +ompi +openmp +parutils +pthreads python"
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#TODO: cuda sionfwd msa
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#--enable-sionfwd=/path/to/sionfwd
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#--msa=(hostname-regex|deep-est-sdv)] MSA aware collective operations for the given system
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PATCHES=( "${FILESDIR}/${PN}-respect-flags.patch" )
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RDEPEND="
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mpi? ( virtual/mpi )
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ompi? (
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|| ( sys-devel/gcc:*[openmp] sys-libs/libomp )
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virtual/mpi
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)
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openmp? ( || ( sys-devel/gcc:*[openmp] sys-libs/libomp ) )
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"
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DEPEND="
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${RDEPEND}
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${PYTHON_DEPS}
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"
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pkg_setup() {
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FORTRAN_NEED_OPENMP=0
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use openmp && FORTRAN_NEED_OPENMP=1
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use ompi && FORTRAN_NEED_OPENMP=1
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fortran-2_pkg_setup
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}
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src_prepare() {
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default
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sed 's/CXXFLAGS = $(CXXFLAGS)/CXXFLAGS = /' -i test/serial/Makefile || die
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sed 's/`gcc/`${CC}/' -i config/determine-compiler-version.sh || die
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}
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src_configure() {
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tc-export AR CC CXX F77 FC
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export MPICC=/usr/bin/mpicc
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export MPICXX=/usr/bin/mpicxx
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export MPIF77=/usr/bin/mpif77
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export MPIF90=/usr/bin/mpif90
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export F90=$(tc-getFC)
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export OMPF77=$(tc-getF77)
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export OMPF90=$(tc-getFC)
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append-fflags -fallow-argument-mismatch
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local myconf=(
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--disable-mic
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--prefix="${T}/prefix/usr"
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)
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#custom configure?
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use cxx || myconf+=( "--disable-cxx" )
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use fortran || myconf+=( "--disable-fortran" )
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use mpi || myconf+=( "--disable-mpi" )
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use ompi || myconf+=( "--disable-ompi" )
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use openmp || myconf+=( "--disable-omp" )
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use parutils || myconf+=( "--disable-parutils" )
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use pthreads || myconf+=( "--disable-pthreads" )
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use debug && myconf+=( "--enable-debug" )
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use python && myconf+=( "--enable-python=3" )
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./configure "${myconf[@]}" || die
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}
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src_compile() {
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export VARTEXFONTS="${T}/fonts"
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emake C_AR=$(tc-getAR) F90=$(tc-getFC)
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docs_compile
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}
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src_install() {
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mkdir -p "${T}/prefix/usr/share/doc/${PF}" || die
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default
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if use examples ; then
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mv "${T}/prefix/usr/examples" "${T}/prefix/usr/share/doc/${PF}/" || die
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else
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rm -r "${T}/prefix/usr/examples" || die
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fi
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insinto "/usr/include/sionlibl"
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doins -r "${T}"/prefix/usr/include/*
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rm -r "${T}/prefix/usr/include" || die
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exeinto "/usr/libexec/${PN}"
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doexe "${T}"/prefix/usr/bin/*partest
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rm "${T}"/prefix/usr/bin/*partest || die
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for b in "${T}"/prefix/usr/bin/sion* ; do
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n=$(basename "${b}")
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newbin "${T}/prefix/usr/bin/${n}" "l${n}"
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rm "${b}" || die
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done
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# move 64 bit libraries to lib64
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libs64=( "${T}"/prefix/usr/lib/*64* )
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if [[ ${#libs64[@]} -gt 0 ]]; then
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mkdir "${T}/prefix/usr/lib64" || die
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for l in "${libs64[@]}" ; do
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mv "${l}" "${T}/prefix/usr/lib64/" || die
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done
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fi
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rsync -ravXHA "${T}/prefix/usr" "${ED}/" || die
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docompress -x "/usr/share/doc/${PF}/examples"
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#TODO: build shared libs
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#find "${ED}" -name '*.a' -delete || die
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find "${ED}" -name '*.la' -delete || die
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}
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