From 77aa688f087c1752fcd18e0a2ea40ac316f76153 Mon Sep 17 00:00:00 2001 From: Boud Roukema Date: Fri, 18 Aug 2017 22:33:15 +0100 Subject: [PATCH] Import mpgrafic_0.3.15-1.debian.tar.xz [dgit import tarball mpgrafic 0.3.15-1 mpgrafic_0.3.15-1.debian.tar.xz] --- README.Debian | 7 ++ changelog | 113 ++++++++++++++++++++ compat | 1 + control | 34 ++++++ copyright | 30 ++++++ docs | 4 + mpgrafic.examples | 4 + mpgrafic.manpages | 1 + patches/01-find-debian-example-files.patch | 17 +++ patches/02-force-regression-test-fail.patch | 17 +++ patches/series | 1 + rules | 47 ++++++++ source/format | 1 + source/options | 1 + tests/control | 5 + upstream/metadata | 16 +++ watch | 3 + 17 files changed, 302 insertions(+) create mode 100644 README.Debian create mode 100644 changelog create mode 100644 compat create mode 100644 control create mode 100644 copyright create mode 100644 docs create mode 100644 mpgrafic.examples create mode 100644 mpgrafic.manpages create mode 100644 patches/01-find-debian-example-files.patch create mode 100644 patches/02-force-regression-test-fail.patch create mode 100644 patches/series create mode 100755 rules create mode 100644 source/format create mode 100644 source/options create mode 100644 tests/control create mode 100644 upstream/metadata create mode 100644 watch diff --git a/README.Debian b/README.Debian new file mode 100644 index 0000000..213c6b0 --- /dev/null +++ b/README.Debian @@ -0,0 +1,7 @@ +mpgrafic for Debian +------------------- + + * The --help option has an extra comment to help the user find + example files in /usr/share/doc/mpgrafic/examples. + + -- Boud Roukema Tue, 27 Dec 2016 diff --git a/changelog b/changelog new file mode 100644 index 0000000..d05baf8 --- /dev/null +++ b/changelog @@ -0,0 +1,113 @@ +mpgrafic (0.3.15-1) unstable; urgency=low + + * New upstream release - should fix m68k and sh4 compile failures + + -- Boud Roukema Fri, 18 Aug 2017 23:33:15 +0200 + +mpgrafic (0.3.14-1) unstable; urgency=low + + * New upstream release - "use mpi_f08" and C size_t portability fixes. + Closes: #872537 + + -- Boud Roukema Fri, 18 Aug 2017 17:29:11 +0200 + +mpgrafic (0.3.13-1) unstable; urgency=low + + * Match upstream 0.3.13; see ChangeLog and NEWS for details. + + -- Boud Roukema Fri, 18 Aug 2017 01:46:16 +0200 + +mpgrafic (0.3.10-1) unstable; urgency=low + + * Portability: Bypass fftw2/openmpi fortran-to-C + interfacing bug for s390x architecture by adding + fortran-to-C wrappers to directly call the fftw2 C function + called by src/mpgrafic.f90. This does not solve + Debian bug #851918 - openmpi and fftw2 + have preprocessor macros MPI_COMM_F2C and FFTW_MPI_COMM_F2C, + respectively, which are supposed to handle this + cleanly, but at least on s390x, do not. However, version 0.3.10 + should solve the bug from mpgrafic's point of view. + (Closes: #851923) + + -- Boud Roukema Sun, 29 Jan 2017 00:33:07 +0100 + +mpgrafic (0.3.9-1) unstable; urgency=low + + * portability: lower precision printed float mppower.f90; + partial code tidying based on strict compiler warnings; + iseed, seeds -> c_long -> up to 4e9 cores can run with different seeds + (if MaxParallelism is increased) + + -- Boud Roukema Mon, 23 Jan 2017 00:15:32 +0100 + +mpgrafic (0.3.8-1) unstable; urgency=low + + * v0.3.8 portability: reproducible lower precision printed floats; + iso_C_binding; avoid implementation-dependent integer sizes; + avoid implementation-dependent fortran kind values + + -- Boud Roukema Sun, 22 Jan 2017 03:32:46 +0100 + +mpgrafic (0.3.7.8-1) unstable; urgency=low + + * v0.3.7.7 regression test written but forgot to include it + * v0.3.7.8 regression test - precision requirements, 'kind' portability, + debian/rules - more diagnostic info + + -- Boud Roukema Fri, 20 Jan 2017 14:24:00 +0100 + +mpgrafic (0.3.7.6-2) unstable; urgency=low + + * debian/control vcs-* s/bitbucket/anonscm.debian/g ; metadata +bitbucket + + -- Boud Roukema Thu, 19 Jan 2017 14:53:29 +0100 + +mpgrafic (0.3.7.6-1) UNRELEASED; urgency=low + + * New upstream release + * v0.3.7.6 - correct shell error so that regression test logs output + + -- Boud Roukema Thu, 19 Jan 2017 12:25:06 +0100 + +mpgrafic (0.3.7.5-1) unstable; urgency=low + + * New upstream release + * v0.3.7.5 - revert allow-run-as-root changes; + drop foreign and 1.4 automake options; + downgrade debian status of regression test - log output but + continue the build, since failure is not (yet) evidence of a bug + + -- Boud Roukema Wed, 18 Jan 2017 20:30:22 +0100 + +mpgrafic (0.3.7.4-1) unstable; urgency=low + + * New upstream release + * v0.3.7.1 - configure.ac: prioritise mpifort over deprecated mpif90 + * v0.3.7.2 - avoid mpirun running as root if possible + * v0.3.7.4 - allow running make check as root if openmpi@debian + + -- Boud Roukema Mon, 16 Jan 2017 23:18:27 +0100 + +mpgrafic (0.3.7-1) unstable; urgency=low + + * New upstream release + * v0.3.5 - regression test - fast full run should match v0.3.4 output + * v0.3.6 - minor configuration file simplifications + * v0.3.6.[1234] - regression test portability + * v0.3.7 - matches 0.3.6.4 + + -- Boud Roukema Sun, 15 Jan 2017 02:06:54 +0100 + +mpgrafic (0.3.4-1) unstable; urgency=low + + * Minor upstream and debian changes to better satisfy debian standards + * Upstream replacement of use of obsolete pause command + + -- Boud Roukema Thu, 05 Jan 2017 23:47:21 +0100 + +mpgrafic (0.3.2.1-1) unstable; urgency=low + + * Initial release (Closes: #849427) + + -- Boud Roukema Tue, 27 Dec 2016 04:08:41 +0100 diff --git a/compat b/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/compat @@ -0,0 +1 @@ +9 diff --git a/control b/control new file mode 100644 index 0000000..3929637 --- /dev/null +++ b/control @@ -0,0 +1,34 @@ +Source: mpgrafic +Section: science +Priority: optional +Maintainer: Debian Astro Team +Uploaders: Boud Roukema +Build-Depends: debhelper (>= 9), + autotools-dev, + chrpath, + fftw-dev (>= 2.1.5), + libgsl-dev (>= 2.3), + gfortran, + mpi-default-dev, + mpi-default-bin, + perl +Standards-Version: 4.0.0 +Homepage: http://www2.iap.fr/users/pichon/mpgrafic.html +Vcs-Git: https://anonscm.debian.org/git/debian-astro/packages/mpgrafic.git +Vcs-Browser: https://anonscm.debian.org/git/debian-astro/packages/mpgrafic.git +Testsuite: autopkgtest + +Package: mpgrafic +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, mpi-default-bin +Recommends: gnudatalanguage +Description: MPI version of N-body initial conditions grafic package + mpgrafic produces initial conditions files for N-body simulations of + cosmological large-scale structure formation. It is a free-licensed, + MPI-parallelised, rewritten version of Ed Bertschinger's grafic-1 + program, producing output files in the grafic format. It includes + options for an Eisenstein and Hu baryonic wiggles power spectrum, for + using a low-resolution map for large-scale modes in the spirit of + grafic-2, and together with constrfield, can be used for generating + constrained initial conditions. Details are given in Prunet et al + (2008) http://cdsads.u-strasbg.fr/abs/2008ApJS..178..179P. diff --git a/copyright b/copyright new file mode 100644 index 0000000..c1c79e5 --- /dev/null +++ b/copyright @@ -0,0 +1,30 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: mpgrafic +Upstream-Contact: Boud Roukema (boud cosmo.torun.pl) +Source: https://broukema@bitbucket.org/broukema/mpgrafic.git + +Files: * +Copyright: 2008-2016, Simon Prunet (prunet iap.fr) + 2008-2016, Christophe Pichon + 2016, Boud Roukema (boud-debian cosmo.torun.pl) +License: GPL-2+ + This program is free software; you can redistribute it + and/or modify it under the terms of the GNU General Public + License as published by the Free Software Foundation; either + version 2 of the License, or (at your option) any later + version. + . + This program is distributed in the hope that it will be + useful, but WITHOUT ANY WARRANTY; without even the implied + warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the GNU General Public License for more + details. + . + You should have received a copy of the GNU General Public + License along with this package; if not, write to the Free + Software Foundation, Inc., 51 Franklin St, Fifth Floor, + Boston, MA 02110-1301 USA + . + On Debian systems, the full text of the GNU General Public + License version 2 can be found in the file + `/usr/share/common-licenses/GPL-2'. diff --git a/docs b/docs new file mode 100644 index 0000000..c17f037 --- /dev/null +++ b/docs @@ -0,0 +1,4 @@ +AUTHORS +NEWS +README +TODO diff --git a/mpgrafic.examples b/mpgrafic.examples new file mode 100644 index 0000000..769651c --- /dev/null +++ b/mpgrafic.examples @@ -0,0 +1,4 @@ +Input.stdin +Output.stdout +gdl +idl diff --git a/mpgrafic.manpages b/mpgrafic.manpages new file mode 100644 index 0000000..05e6fd9 --- /dev/null +++ b/mpgrafic.manpages @@ -0,0 +1 @@ +mpgrafic.1 diff --git a/patches/01-find-debian-example-files.patch b/patches/01-find-debian-example-files.patch new file mode 100644 index 0000000..5b0460a --- /dev/null +++ b/patches/01-find-debian-example-files.patch @@ -0,0 +1,17 @@ +Description: Add an extra comment to the --help option so that the + user can more easily find example input/output files in + /usr/share/doc/mpgrafic/examples/. This is valid for debian, but not + for upstream in general. +Forwarded: not-needed +Author: Boud Roukema +--- a/src/mpgrafic.f90 ++++ b/src/mpgrafic.f90 +@@ -131,6 +131,8 @@ + write(*,'(a)')'Most recent source code:' + write(*,'(a)')'git clone https://broukema@bitbucket.org/broukema/mpgrafic.git' + write(*,'(a)')'' ++ write(*,'(a)')'Example input/output files: see /usr/share/doc/mpgrafic/examples/' ++ write(*,'(a)')'' + write(*,'(a)')' -?, --help Give this help list' + write(*,'(a)')' --np=INTEGER Number of particles per dimension' + write(*,'(a)')' --usage Give a short usage message' diff --git a/patches/02-force-regression-test-fail.patch b/patches/02-force-regression-test-fail.patch new file mode 100644 index 0000000..fde0176 --- /dev/null +++ b/patches/02-force-regression-test-fail.patch @@ -0,0 +1,17 @@ +Description: Force the code regression test to fail by modifying + the random seed; this should normally not be included in debian/patches/series. + Use `quilt import ' and later `quilt delete ' + to temporarily apply this patch; `info quilt' for more info. +Forwarded: not-needed +Author: Boud Roukema +--- a/Input.stdin ++++ b/Input.stdin +@@ -12,7 +12,7 @@ + + + 1 +-1234 ++97531 + white-outfile.dat + 0 + noisefile_dummy.dat diff --git a/patches/series b/patches/series new file mode 100644 index 0000000..cd22ffe --- /dev/null +++ b/patches/series @@ -0,0 +1 @@ +01-find-debian-example-files.patch diff --git a/rules b/rules new file mode 100755 index 0000000..eb52c2c --- /dev/null +++ b/rules @@ -0,0 +1,47 @@ +#!/usr/bin/make -f + +# Recommendations in https://wiki.debian.org/Hardening, motivated by lintian warnings. +export DEB_BUILD_MAINT_OPTIONS = hardening=+all +DPKG_EXPORT_BUILDFLAGS = 1 +include /usr/share/dpkg/buildflags.mk + +# To run the first test program in `make check', mpirun is called. +# This may fail if run as root, e.g. during automated building in +# a chroot gaol. So for debian builds, running mpirun as root - on a single +# processor - is allowed. +# +export MPI_ALLOW_RUN_AS_ROOT = --allow-run-as-root + +%: + dh $@ --with autotools-dev + +# https://lintian.debian.org/tags/binary-or-shlib-defines-rpath.html +# https://wiki.debian.org/RpathIssue +# TODO: Where is r(un)path inserted in upstream? [not obvious] +override_dh_install: + chrpath -d $(CURDIR)/debian/mpgrafic/usr/bin/mpgrafic + dh_install + +# 2017-01-17: debian/0.3.7.5-1: Data on failures of the test script +# regression-0.3.7.sh on various architectures is needed in order to +# make both the source code and the test reproducible. This override +# is intended to be temporary only, while obtaining data on failures +# from the log files of builds. +override_dh_auto_test: + # since v0.3.7.8: log a diagnostic, and then return a fail if + # dh_auto_test failed + if dh_auto_test ; then \ + printf "+++regression test diagnostic+++\n"; \ + grep ARCH_DEFAULT_MPI_IMPL /usr/share/mpi-default-dev/debian_defaults; \ + printf "diff:\n"; \ + diff -u Output.stdout.np32 Output.stdout.np32.tmp; \ + printf "+++/regression test diagnostic+++\n"; else \ + printf "+++regression test diagnostic+++\n"; \ + grep ARCH_DEFAULT_MPI_IMPL /usr/share/mpi-default-dev/debian_defaults; \ + printf "diff:\n"; \ + diff -u Output.stdout.np32 Output.stdout.np32.tmp; \ + uname -a; \ + printf "Processors on this machine:\n"; \ + grep processor /proc/cpuinfo; \ + printf "+++/regression test diagnostic+++\n"; \ + false ; fi diff --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/source/options b/source/options new file mode 100644 index 0000000..21f55ef --- /dev/null +++ b/source/options @@ -0,0 +1 @@ +extend-diff-ignore = "(^|/)(config\.(sub|guess)|Makefile|src/.*\.mod|src/Makefile\.in|ic_.*[bxyz]|[pw].*\.dat|stamp-h1|test-suite\.log|Output.*\.tmp.*|reg.*sh\.[lt][or][gs])$" diff --git a/tests/control b/tests/control new file mode 100644 index 0000000..320e594 --- /dev/null +++ b/tests/control @@ -0,0 +1,5 @@ +Test-command: mpgrafic --version +Depends: mpgrafic + +Test-command: mpgrafic --help +Depends: mpgrafic diff --git a/upstream/metadata b/upstream/metadata new file mode 100644 index 0000000..02ad943 --- /dev/null +++ b/upstream/metadata @@ -0,0 +1,16 @@ +ASCL-Id: 1304.014 +Name: mpgrafic +Contact: boud-debian cosmo.torun.pl +Repository: git@bitbucket.org:broukema/mpgrafic.git +Repository-Browse: https://bitbucket.org/broukema/mpgrafic +Bug-Database: https://bitbucket.org/broukema/mpgrafic/issues +Reference: + Author: Prunet, S. and Pichon, C. and Aubert, D. and Pogosyan, D. and Teyssier, R. and Gottloeber, S. + Title: Initial Conditions For Large Cosmological Simulations + Journal: Astrophysical Journal Supplement Series + Year: 2008 + Volume: 178 + Pages: 179-188 + DOI: 10.1086/590370 + Eprint: https://arXiv.org/abs/0804.3536 + URL: http://cdsads.u-strasbg.fr/abs/2008ApJS..178..179P diff --git a/watch b/watch new file mode 100644 index 0000000..18e82c8 --- /dev/null +++ b/watch @@ -0,0 +1,3 @@ +# watch control file for uscan +version=3 +https://bitbucket.org/broukema/mpgrafic/downloads?tab=tags .*/v(\d\S+)\.tar\.gz debian uupdate -- 2.30.2