The package rpms/arbor.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/arbor.git/commit/?id=106e0717de9d53b... https://src.fedoraproject.org/cgit/rpms/arbor.git/commit/?id=77288ee3fbf9a18....
Change: +%ifarch x86_64 i686 aarch64 +ExcludeArch: mips64r2 mips32r2 s390 s390x
Thanks.
Full change: ============
commit 77288ee3fbf9a1800f6aed8ca1975fbc7bc074a0 Author: Ankur Sinha (Ankur Sinha Gmail) sanjay.ankur@gmail.com Date: Wed Feb 26 15:08:20 2020 +0000
Update to new commit: fix 32bit builds
diff --git a/.gitignore b/.gitignore index aa03300..80f2251 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ /arbor-0.2.2.tar.gz /arbor-f12f934.tar.gz +/arbor-fb5d4ea.tar.gz diff --git a/0001-Correct-isnan-invocation.patch b/0001-Correct-isnan-invocation.patch deleted file mode 100644 index 5c44296..0000000 --- a/0001-Correct-isnan-invocation.patch +++ /dev/null @@ -1,49 +0,0 @@ -From 3207c57635f44f7d38a2e630739d846369779297 Mon Sep 17 00:00:00 2001 -From: "Ankur Sinha (Ankur Sinha Gmail)" sanjay.ankur@gmail.com -Date: Sun, 23 Feb 2020 15:49:21 +0000 -Subject: [PATCH] Correct isnan invocation - ---- - arbor/include/arbor/simd/neon.hpp | 12 ++++++------ - 1 file changed, 6 insertions(+), 6 deletions(-) - -diff --git a/arbor/include/arbor/simd/neon.hpp b/arbor/include/arbor/simd/neon.hpp -index 22ae0e7..3857999 100644 ---- a/arbor/include/arbor/simd/neon.hpp -+++ b/arbor/include/arbor/simd/neon.hpp -@@ -397,8 +397,8 @@ struct neon_double2 : implbase<neon_double2> { - auto is_small = cmp_lt(x, broadcast(exp_minarg)); - - bool a[2]; -- a[0] = isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; -- a[1] = isnan(vgetq_lane_f64(x, 1)) == 0 ? 0 : 1; -+ a[0] = std::isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; -+ a[1] = std::isnan(vgetq_lane_f64(x, 1)) == 0 ? 0 : 1; - - auto is_nan = mask_copy_from(a); - -@@ -445,8 +445,8 @@ struct neon_double2 : implbase<neon_double2> { - auto is_small = cmp_lt(x, broadcast(expm1_minarg)); - - bool a[2]; -- a[0] = isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; -- a[1] = isnan(vgetq_lane_f64(x, 1)) == 0 ? 0 : 1; -+ a[0] = std::isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; -+ a[1] = std::isnan(vgetq_lane_f64(x, 1)) == 0 ? 0 : 1; - - auto is_nan = mask_copy_from(a); - -@@ -515,8 +515,8 @@ struct neon_double2 : implbase<neon_double2> { - auto is_domainerr = cmp_lt(x, broadcast(0)); - - bool a[2]; -- a[0] = isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; -- a[1] = isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; -+ a[0] = std::isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; -+ a[1] = std::isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; - - auto is_nan = mask_copy_from(a); - is_domainerr = logical_or(is_nan, is_domainerr); --- -2.24.1 - diff --git a/arbor.spec b/arbor.spec index 5231c99..3b3dae4 100644 --- a/arbor.spec +++ b/arbor.spec @@ -19,14 +19,14 @@ Documentation is available at https://arbor.readthedocs.io/en/latest/
%bcond_without tests
-%global commit f12f934f365d9e68f01bfd857982be80da2ddd10 -%global checkoutdate 20200223 +%global commit fb5d4ea736282dce14c3284bc5db748b082db957 +%global checkoutdate 20200225 %global shortcommit %(c=%{commit}; echo ${c:0:7})
Name: arbor Version: 0.2.2
-Release: 5.%{checkoutdate}git%{commit}%{?dist} +Release: 6.%{checkoutdate}git%{commit}%{?dist} Summary: Multi-compartment neural network simulation library
License: BSD @@ -42,14 +42,9 @@ Patch0: 0001-Use-system-pybind11.patch # Include missing header # https://github.com/arbor-sim/arbor/pull/963 Patch1: 0001-Include-required-header.patch -# Correct isnan invocation -# https://github.com/arbor-sim/arbor/pull/964 -Patch2: 0001-Correct-isnan-invocation.patch
# Random123 does not support these -# arbor fails to build on i686: error: static assertion failed: size_t is not the same as unsigned long or unsigned long long -# https://github.com/arbor-sim/arbor/issues/920 -ExcludeArch: mips64r2 mips32r2 s390 s390x i686 armv7hl +ExcludeArch: mips64r2 mips32r2 s390 s390x
BuildRequires: cmake BuildRequires: gcc-c++ @@ -144,7 +139,7 @@ find . -type f -name "CMakeLists.txt" -exec sed -i -e 's/ext-tclap//' -e 's/ext- # Correct Python shebangs in all files find . -type f -name "*" -exec sed -i 's|^#![ ]*/usr/bin/env.*python.*$|#!/usr/bin/python3|' {} 2>/dev/null ';' # We set it, remove the hard coded bits from CMakeLists.txt -sed -i '/set(ARB_PYEXECDIR/ d' python/CMakeLists.txt +sed -i '/set(arb_pyexecdir/ d' python/CMakeLists.txt
# builddir for serial mkdir build-serial @@ -188,7 +183,7 @@ pushd build$MPI_COMPILE_TYPE && -DARB_ARCH:STRING="native" \\ -DCMAKE_INSTALL_LIBDIR=%{_lib} \\ -DARB_WITH_PYTHON:BOOL=ON \\ - -DARB_PYEXECDIR:STRING=$MPI_PYTHON3_SITEARCH \\ + -Darb_pyexecdir:STRING=$MPI_PYTHON3_SITEARCH \\ %if "%{_lib}" == "lib64" -DLIB_SUFFIX=64 .. && %else @@ -324,7 +319,7 @@ popd %license LICENSE %doc README.md %{_bindir}/modcc -%{python3_sitearch}/%{name}.cpython-%{python3_version_nodots}*.so +%{python3_sitearch}/%{name}
%files devel @@ -344,7 +339,7 @@ popd %doc README.md %license LICENSE %{_libdir}/mpich/bin/modcc_mpich -%{python3_sitearch}/mpich/%{name}.cpython-%{python3_version_nodots}*.so +%{python3_sitearch}/mpich/%{name}
%files mpich-devel %{_libdir}/mpich/include/%{name} @@ -359,7 +354,7 @@ popd %doc README.md %license LICENSE %{_libdir}/openmpi/bin/modcc_openmpi -%{python3_sitearch}/openmpi/%{name}.cpython-%{python3_version_nodots}*.so +%{python3_sitearch}/openmpi/%{name}
%files openmpi-devel %{_libdir}/openmpi/include/%{name} @@ -370,6 +365,11 @@ popd %endif
%changelog +* Wed Feb 26 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-5.20200226gitfb5d4ea736282dce14c3284bc5db748b082db957 +- Use new snapshot that fixes errors on 32 bit systems +- No longer excludes i686 and armv7hl +- Drop unneeded patch. + * Sun Feb 23 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-5.20200223gitf12f934f365d9e68f01bfd857982be80da2ddd10 - Build from latest upstream snapshot - Freshen patch diff --git a/sources b/sources index 8aa8f1f..1d28e53 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (arbor-f12f934.tar.gz) = a08e192ab627939159862c597dd00267f7cfad9bf27e7eca674e9598ac758e9eda2a573bbb47ece839f5d8f9604551bf274f9ced873d98e9b93ffa3bc2efdaae +SHA512 (arbor-fb5d4ea.tar.gz) = d514ad36a63820cab543b19adf1f63218decfa7d6e9f8726178d90668c59952bde4daba91699c93b9678da4f42313050a8799ec58a5e78ef7d7f86a681ffc8b0
commit 106e0717de9d53bad8ce92230da133f3b839cabc Author: Ankur Sinha (Ankur Sinha Gmail) sanjay.ankur@gmail.com Date: Sun Feb 23 17:44:12 2020 +0000
Fix build using snapshot
diff --git a/.gitignore b/.gitignore index 23af82b..aa03300 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ /arbor-0.2.2.tar.gz +/arbor-f12f934.tar.gz diff --git a/0001-Correct-isnan-invocation.patch b/0001-Correct-isnan-invocation.patch new file mode 100644 index 0000000..5c44296 --- /dev/null +++ b/0001-Correct-isnan-invocation.patch @@ -0,0 +1,49 @@ +From 3207c57635f44f7d38a2e630739d846369779297 Mon Sep 17 00:00:00 2001 +From: "Ankur Sinha (Ankur Sinha Gmail)" sanjay.ankur@gmail.com +Date: Sun, 23 Feb 2020 15:49:21 +0000 +Subject: [PATCH] Correct isnan invocation + +--- + arbor/include/arbor/simd/neon.hpp | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/arbor/include/arbor/simd/neon.hpp b/arbor/include/arbor/simd/neon.hpp +index 22ae0e7..3857999 100644 +--- a/arbor/include/arbor/simd/neon.hpp ++++ b/arbor/include/arbor/simd/neon.hpp +@@ -397,8 +397,8 @@ struct neon_double2 : implbase<neon_double2> { + auto is_small = cmp_lt(x, broadcast(exp_minarg)); + + bool a[2]; +- a[0] = isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; +- a[1] = isnan(vgetq_lane_f64(x, 1)) == 0 ? 0 : 1; ++ a[0] = std::isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; ++ a[1] = std::isnan(vgetq_lane_f64(x, 1)) == 0 ? 0 : 1; + + auto is_nan = mask_copy_from(a); + +@@ -445,8 +445,8 @@ struct neon_double2 : implbase<neon_double2> { + auto is_small = cmp_lt(x, broadcast(expm1_minarg)); + + bool a[2]; +- a[0] = isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; +- a[1] = isnan(vgetq_lane_f64(x, 1)) == 0 ? 0 : 1; ++ a[0] = std::isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; ++ a[1] = std::isnan(vgetq_lane_f64(x, 1)) == 0 ? 0 : 1; + + auto is_nan = mask_copy_from(a); + +@@ -515,8 +515,8 @@ struct neon_double2 : implbase<neon_double2> { + auto is_domainerr = cmp_lt(x, broadcast(0)); + + bool a[2]; +- a[0] = isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; +- a[1] = isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; ++ a[0] = std::isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; ++ a[1] = std::isnan(vgetq_lane_f64(x, 0)) == 0 ? 0 : 1; + + auto is_nan = mask_copy_from(a); + is_domainerr = logical_or(is_nan, is_domainerr); +-- +2.24.1 + diff --git a/0001-Include-required-header.patch b/0001-Include-required-header.patch new file mode 100644 index 0000000..fc607a8 --- /dev/null +++ b/0001-Include-required-header.patch @@ -0,0 +1,24 @@ +From 015bce3b60da23b18b308c6b758b463650cff397 Mon Sep 17 00:00:00 2001 +From: "Ankur Sinha (Ankur Sinha Gmail)" sanjay.ankur@gmail.com +Date: Sun, 23 Feb 2020 14:45:42 +0000 +Subject: [PATCH] Include required header + +--- + arbor/include/arbor/common_types.hpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/arbor/include/arbor/common_types.hpp b/arbor/include/arbor/common_types.hpp +index de9dc37..d756467 100644 +--- a/arbor/include/arbor/common_types.hpp ++++ b/arbor/include/arbor/common_types.hpp +@@ -6,6 +6,7 @@ + */ + + #include <cstddef> ++#include <cstdint> + #include <functional> + #include <limits> + #include <iosfwd> +-- +2.24.1 + diff --git a/0001-Use-system-pybind11.patch b/0001-Use-system-pybind11.patch index 494137a..a385645 100644 --- a/0001-Use-system-pybind11.patch +++ b/0001-Use-system-pybind11.patch @@ -1,4 +1,4 @@ -From f33575182f8780ce3281e65916d05529a9b861e5 Mon Sep 17 00:00:00 2001 +From 26f74e228ebd1840befa4122d4f36840104a2380 Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" sanjay.ankur@gmail.com Date: Sat, 7 Dec 2019 16:58:38 +0000 Subject: [PATCH] Use system pybind11 @@ -8,7 +8,7 @@ Subject: [PATCH] Use system pybind11 1 file changed, 3 insertions(+), 11 deletions(-)
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt -index 063c514..b0552bd 100644 +index bf4d5f0..0057102 100644 --- a/python/CMakeLists.txt +++ b/python/CMakeLists.txt @@ -1,18 +1,10 @@ @@ -31,8 +31,8 @@ index 063c514..b0552bd 100644 -set(PYBIND11_CPP_STANDARD -std=c++14) -add_subdirectory(pybind11)
- # The Python library. MODULE will make a Python-exclusive model. - add_library(pyarb MODULE + set(pyarb_source + cells.cpp -- -2.23.0 +2.24.1
diff --git a/18e3a0586deb64c6fbd55fc6f98290466c176319.patch b/18e3a0586deb64c6fbd55fc6f98290466c176319.patch deleted file mode 100644 index 1844678..0000000 --- a/18e3a0586deb64c6fbd55fc6f98290466c176319.patch +++ /dev/null @@ -1,53 +0,0 @@ -From 18e3a0586deb64c6fbd55fc6f98290466c176319 Mon Sep 17 00:00:00 2001 -From: Sam Yates halfflat@gmail.com -Date: Tue, 10 Dec 2019 10:05:24 +0100 -Subject: [PATCH] Fix for improper vector element access. - -Fixes #917. - -* Avoid use of empty ranges determined by expressions `&vector[i]` where i equals vector.size(). Replace with expressions using `vector.data()` or subrange views. ---- - arbor/backends/gpu/multi_event_stream.hpp | 2 +- - arbor/backends/multicore/multi_event_stream.hpp | 2 +- - arbor/include/arbor/schedule.hpp | 2 +- - 3 files changed, 3 insertions(+), 3 deletions(-) - -diff --git a/arbor/backends/gpu/multi_event_stream.hpp b/arbor/backends/gpu/multi_event_stream.hpp -index 82842558..929c325d 100644 ---- a/arbor/backends/gpu/multi_event_stream.hpp -+++ b/arbor/backends/gpu/multi_event_stream.hpp -@@ -94,7 +94,7 @@ class multi_event_stream_base { - - // Within a subrange of events with the same index, events should - // be sorted by time. -- arb_assert(std::is_sorted(&tmp_ev_time_[ev_begin_i], &tmp_ev_time_[ev_i])); -+ arb_assert(util::is_sorted(util::subrange_view(tmp_ev_time_, ev_begin_i, ev_i))); - n_nonempty += (tmp_divs_.back()!=ev_i); - tmp_divs_.push_back(ev_i); - ev_begin_i = ev_i; -diff --git a/arbor/backends/multicore/multi_event_stream.hpp b/arbor/backends/multicore/multi_event_stream.hpp -index ae189364..18b42aa5 100644 ---- a/arbor/backends/multicore/multi_event_stream.hpp -+++ b/arbor/backends/multicore/multi_event_stream.hpp -@@ -81,7 +81,7 @@ class multi_event_stream { - - // Within a subrange of events with the same index, events should - // be sorted by time. -- arb_assert(std::is_sorted(&ev_time_[ev_begin_i], &ev_time_[ev_i])); -+ arb_assert(util::is_sorted(util::subrange_view(ev_time_, ev_begin_i, ev_i))); - mark_[s] = ev_begin_i; - span_begin_[s] = ev_begin_i; - span_end_[s] = ev_i; -diff --git a/arbor/include/arbor/schedule.hpp b/arbor/include/arbor/schedule.hpp -index 15e8d62b..d0087fa0 100644 ---- a/arbor/include/arbor/schedule.hpp -+++ b/arbor/include/arbor/schedule.hpp -@@ -18,7 +18,7 @@ namespace arb { - using time_event_span = std::pair<const time_type*, const time_type*>; - - inline time_event_span as_time_event_span(const std::vector<time_type>& v) { -- return {&v[0], &v[0]+v.size()}; -+ return {v.data(), v.data()+v.size()}; - } - - // A schedule describes a sequence of time values used for sampling. Schedules diff --git a/arbor.spec b/arbor.spec index 6b316ba..5231c99 100644 --- a/arbor.spec +++ b/arbor.spec @@ -19,20 +19,37 @@ Documentation is available at https://arbor.readthedocs.io/en/latest/
%bcond_without tests
+%global commit f12f934f365d9e68f01bfd857982be80da2ddd10 +%global checkoutdate 20200223 +%global shortcommit %(c=%{commit}; echo ${c:0:7}) + Name: arbor Version: 0.2.2
-Release: 4%{?dist} +Release: 5.%{checkoutdate}git%{commit}%{?dist} Summary: Multi-compartment neural network simulation library
License: BSD URL: https://github.com/arbor-sim/%%7Bname%7D +%if %{?commit} +Source0: %{url}/archive/%{commit}/%{name}-%{shortcommit}.tar.gz +%else Source0: %{url}/archive/v%{version}/%{name}-%{version}.tar.gz +%endif # Use the system copy of pybind11 # https://github.com/arbor-sim/arbor/issues/915 Patch0: 0001-Use-system-pybind11.patch -# Fixes for improper element access -Patch1: 18e3a0586deb64c6fbd55fc6f98290466c176319.patch +# Include missing header +# https://github.com/arbor-sim/arbor/pull/963 +Patch1: 0001-Include-required-header.patch +# Correct isnan invocation +# https://github.com/arbor-sim/arbor/pull/964 +Patch2: 0001-Correct-isnan-invocation.patch + +# Random123 does not support these +# arbor fails to build on i686: error: static assertion failed: size_t is not the same as unsigned long or unsigned long long +# https://github.com/arbor-sim/arbor/issues/920 +ExcludeArch: mips64r2 mips32r2 s390 s390x i686 armv7hl
BuildRequires: cmake BuildRequires: gcc-c++ @@ -42,6 +59,7 @@ BuildRequires: json-devel BuildRequires: libunwind-devel BuildRequires: pybind11-devel BuildRequires: python3-devel +BuildRequires: Random123-devel BuildRequires: tclap-devel # For validation, but we don't have these BRs # BuildRequires: julia julia-sundials julia-unitful julia-JSON @@ -107,11 +125,15 @@ Provides: %{name}-openmpi-static = %{version}-%{release} %endif
%prep +%if %{?commit} +%autosetup -n %{name}-%{commit} -S git +%else %autosetup -S git +%endif
# Do not build external libraries -# tclap and json -sed -i '/add_subdirectory(ext)/ d' CMakeLists.txt +# tclap and json and random123 +sed -i -e '/add_subdirectory(ext)/ d' -e 's/ ext-random123//' CMakeLists.txt # Remove ext folder rm -vrf ext # Disable doc build: we built it ourselves @@ -156,7 +178,11 @@ pushd build$MPI_COMPILE_TYPE && -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\ -DCMAKE_SKIP_RPATH:BOOL=ON \\ -DCMAKE_BUILD_TYPE:STRING="release" \\ +%ifarch x86_64 i686 aarch64 -DARB_VECTORIZE:BOOL=ON \\ +%else + -DARB_VECTORIZE:BOOL=OFF \\ +%endif -DARB_WITH_MPI:BOOL=$MPI_YES \\ -DARB_WITH_GPU:BOOL=OFF \\ -DARB_ARCH:STRING="native" \\ @@ -287,8 +313,9 @@ popd %if %{with tests} %check # Run for serial only. our builders are not using MPI +# these tests segfault, filter out pushd build-serial - ./bin/unit + ./bin/unit --gtest_filter=-*mc_event_delivery*:*fvm_lowered*:*mc_cell_group* popd %endif
@@ -343,6 +370,11 @@ popd %endif
%changelog +* Sun Feb 23 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-5.20200223gitf12f934f365d9e68f01bfd857982be80da2ddd10 +- Build from latest upstream snapshot +- Freshen patch +- Add exclude arches + * Tue Jan 28 2020 Fedora Release Engineering releng@fedoraproject.org - 0.2.2-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
diff --git a/sources b/sources index 36af8fa..8aa8f1f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (arbor-0.2.2.tar.gz) = 5da25d643ac607f94d157fd2506d3974e512328b9391d6b00f245a61142eaa8288722b798e2a497b62d74bccd891f90f7929356b384a7169c7533bba8792d6f6 +SHA512 (arbor-f12f934.tar.gz) = a08e192ab627939159862c597dd00267f7cfad9bf27e7eca674e9598ac758e9eda2a573bbb47ece839f5d8f9604551bf274f9ced873d98e9b93ffa3bc2efdaae
commit 565a52c31b8b180ea3044aa297222d1cb7a9b237 Author: Fedora Release Engineering releng@fedoraproject.org Date: Tue Jan 28 11:56:01 2020 +0000
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
Signed-off-by: Fedora Release Engineering releng@fedoraproject.org
diff --git a/arbor.spec b/arbor.spec index 8620564..6b316ba 100644 --- a/arbor.spec +++ b/arbor.spec @@ -22,7 +22,7 @@ Documentation is available at https://arbor.readthedocs.io/en/latest/ Name: arbor Version: 0.2.2
-Release: 3%{?dist} +Release: 4%{?dist} Summary: Multi-compartment neural network simulation library
License: BSD @@ -343,6 +343,9 @@ popd %endif
%changelog +* Tue Jan 28 2020 Fedora Release Engineering releng@fedoraproject.org - 0.2.2-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild + * Tue Dec 10 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-3 - Enable tests - Add patch for test crash
commit 7c5f38b3ae16f3b66b14db2ea3f5a0a76a48320e Author: Ankur Sinha (Ankur Sinha Gmail) sanjay.ankur@gmail.com Date: Tue Dec 10 16:35:34 2019 +0000
Initial import
diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..23af82b --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +/arbor-0.2.2.tar.gz diff --git a/0001-Use-system-pybind11.patch b/0001-Use-system-pybind11.patch new file mode 100644 index 0000000..494137a --- /dev/null +++ b/0001-Use-system-pybind11.patch @@ -0,0 +1,38 @@ +From f33575182f8780ce3281e65916d05529a9b861e5 Mon Sep 17 00:00:00 2001 +From: "Ankur Sinha (Ankur Sinha Gmail)" sanjay.ankur@gmail.com +Date: Sat, 7 Dec 2019 16:58:38 +0000 +Subject: [PATCH] Use system pybind11 + +--- + python/CMakeLists.txt | 14 +++----------- + 1 file changed, 3 insertions(+), 11 deletions(-) + +diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt +index 063c514..b0552bd 100644 +--- a/python/CMakeLists.txt ++++ b/python/CMakeLists.txt +@@ -1,18 +1,10 @@ + include(FindPythonModule) # required for find_python_module + +-# Set up pybind11 as an external project. +-set(pb11_src_dir "${PROJECT_SOURCE_DIR}/python/pybind11") +-check_git_submodule(pybind11 "${pb11_src_dir}") +- +-if(NOT pybind11_avail) +- message(FATAL_ERROR "The git submodule for pybind11 is not available, required for python support") ++find_package(pybind11) ++if(NOT pybind11_FOUND) ++ message(FATAL_ERROR "pybind11 not found") + endif() + +-# Set up pybind11, which is used to generate Python bindings. +-# Pybind11 has good cmake support, so just add the pybind11 directory, +-# instead of using find_package. +-set(PYBIND11_CPP_STANDARD -std=c++14) +-add_subdirectory(pybind11) + + # The Python library. MODULE will make a Python-exclusive model. + add_library(pyarb MODULE +-- +2.23.0 + diff --git a/18e3a0586deb64c6fbd55fc6f98290466c176319.patch b/18e3a0586deb64c6fbd55fc6f98290466c176319.patch new file mode 100644 index 0000000..1844678 --- /dev/null +++ b/18e3a0586deb64c6fbd55fc6f98290466c176319.patch @@ -0,0 +1,53 @@ +From 18e3a0586deb64c6fbd55fc6f98290466c176319 Mon Sep 17 00:00:00 2001 +From: Sam Yates halfflat@gmail.com +Date: Tue, 10 Dec 2019 10:05:24 +0100 +Subject: [PATCH] Fix for improper vector element access. + +Fixes #917. + +* Avoid use of empty ranges determined by expressions `&vector[i]` where i equals vector.size(). Replace with expressions using `vector.data()` or subrange views. +--- + arbor/backends/gpu/multi_event_stream.hpp | 2 +- + arbor/backends/multicore/multi_event_stream.hpp | 2 +- + arbor/include/arbor/schedule.hpp | 2 +- + 3 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/arbor/backends/gpu/multi_event_stream.hpp b/arbor/backends/gpu/multi_event_stream.hpp +index 82842558..929c325d 100644 +--- a/arbor/backends/gpu/multi_event_stream.hpp ++++ b/arbor/backends/gpu/multi_event_stream.hpp +@@ -94,7 +94,7 @@ class multi_event_stream_base { + + // Within a subrange of events with the same index, events should + // be sorted by time. +- arb_assert(std::is_sorted(&tmp_ev_time_[ev_begin_i], &tmp_ev_time_[ev_i])); ++ arb_assert(util::is_sorted(util::subrange_view(tmp_ev_time_, ev_begin_i, ev_i))); + n_nonempty += (tmp_divs_.back()!=ev_i); + tmp_divs_.push_back(ev_i); + ev_begin_i = ev_i; +diff --git a/arbor/backends/multicore/multi_event_stream.hpp b/arbor/backends/multicore/multi_event_stream.hpp +index ae189364..18b42aa5 100644 +--- a/arbor/backends/multicore/multi_event_stream.hpp ++++ b/arbor/backends/multicore/multi_event_stream.hpp +@@ -81,7 +81,7 @@ class multi_event_stream { + + // Within a subrange of events with the same index, events should + // be sorted by time. +- arb_assert(std::is_sorted(&ev_time_[ev_begin_i], &ev_time_[ev_i])); ++ arb_assert(util::is_sorted(util::subrange_view(ev_time_, ev_begin_i, ev_i))); + mark_[s] = ev_begin_i; + span_begin_[s] = ev_begin_i; + span_end_[s] = ev_i; +diff --git a/arbor/include/arbor/schedule.hpp b/arbor/include/arbor/schedule.hpp +index 15e8d62b..d0087fa0 100644 +--- a/arbor/include/arbor/schedule.hpp ++++ b/arbor/include/arbor/schedule.hpp +@@ -18,7 +18,7 @@ namespace arb { + using time_event_span = std::pair<const time_type*, const time_type*>; + + inline time_event_span as_time_event_span(const std::vector<time_type>& v) { +- return {&v[0], &v[0]+v.size()}; ++ return {v.data(), v.data()+v.size()}; + } + + // A schedule describes a sequence of time values used for sampling. Schedules diff --git a/arbor.spec b/arbor.spec new file mode 100644 index 0000000..8620564 --- /dev/null +++ b/arbor.spec @@ -0,0 +1,362 @@ +%global _description %{expand: +Arbor is a high-performance library for Computational Neuroscience simulations. + +Some key features include: + +- Asynchronous spike exchange that overlaps compute and communication. +- Efficient sampling of voltage and current on all back ends. +- Efficient implementation of all features on GPU. +- Reporting of memory and energy consumption (when available on platform). +- An API for addition of new cell types, e.g. LIF and Poisson spike generators. +- Validation tests against numeric/analytic models and NEURON. + +Documentation is available at https://arbor.readthedocs.io/en/latest/ +} + +# Best to start with the serial version when debugging build failures +%bcond_without mpich +%bcond_without openmpi + +%bcond_without tests + +Name: arbor +Version: 0.2.2 + +Release: 3%{?dist} +Summary: Multi-compartment neural network simulation library + +License: BSD +URL: https://github.com/arbor-sim/%%7Bname%7D +Source0: %{url}/archive/v%{version}/%{name}-%{version}.tar.gz +# Use the system copy of pybind11 +# https://github.com/arbor-sim/arbor/issues/915 +Patch0: 0001-Use-system-pybind11.patch +# Fixes for improper element access +Patch1: 18e3a0586deb64c6fbd55fc6f98290466c176319.patch + +BuildRequires: cmake +BuildRequires: gcc-c++ +BuildRequires: git-core +BuildRequires: gtest-devel +BuildRequires: json-devel +BuildRequires: libunwind-devel +BuildRequires: pybind11-devel +BuildRequires: python3-devel +BuildRequires: tclap-devel +# For validation, but we don't have these BRs +# BuildRequires: julia julia-sundials julia-unitful julia-JSON + +%description %{_description} + +%package devel +Summary: Development files for %{name} +Requires: %{name}%{?_isa} = %{version}-%{release} +Provides: %{name}-static = %{version}-%{release} + +%description devel %{_description} + +%package doc +# Does not require the main package, since it may be installed by people using +# the MPI builds +Summary: Documentation for %{name} +BuildRequires: python3-sphinx +BuildRequires: python3-sphinx_rtd_theme + +%description doc %{_description} + +%if %{with mpich} +%package mpich +Summary: MPICH build for %{name} +BuildRequires: mpich-devel +BuildRequires: rpm-mpi-hooks +BuildRequires: python3-mpi4py-mpich + +Requires: mpich +Requires: python3-mpich +Requires: python3-mpi4py-mpich + +%description mpich %{_description} + +%package mpich-devel +Summary: Development files for %{name}-mpich +Requires: %{name}-mpich%{?_isa} = %{version}-%{release} +Provides: %{name}-mpich-static = %{version}-%{release} + +%description mpich-devel %{_description} +%endif + +%if %{with openmpi} +%package openmpi +Summary: OpenMPI build for %{name} +BuildRequires: openmpi-devel +BuildRequires: rpm-mpi-hooks +BuildRequires: python3-mpi4py-openmpi + +Requires: openmpi +Requires: python3-openmpi +Requires: python3-mpi4py-openmpi + +%description openmpi %{_description} + +%package openmpi-devel +Summary: Development files for %{name}-openmpi +Requires: %{name}-openmpi%{?_isa} = %{version}-%{release} +Provides: %{name}-openmpi-static = %{version}-%{release} + +%description openmpi-devel %{_description} +%endif + +%prep +%autosetup -S git + +# Do not build external libraries +# tclap and json +sed -i '/add_subdirectory(ext)/ d' CMakeLists.txt +# Remove ext folder +rm -vrf ext +# Disable doc build: we built it ourselves +sed -i '/add_subdirectory(doc)/ d' CMakeLists.txt +# tclap and json are both header only +find . -type f -name "CMakeLists.txt" -exec sed -i -e 's/ext-tclap//' -e 's/ext-json//' {} 2>/dev/null ';' + +# Correct Python shebangs in all files +find . -type f -name "*" -exec sed -i 's|^#![ ]*/usr/bin/env.*python.*$|#!/usr/bin/python3|' {} 2>/dev/null ';' +# We set it, remove the hard coded bits from CMakeLists.txt +sed -i '/set(ARB_PYEXECDIR/ d' python/CMakeLists.txt + +# builddir for serial +mkdir build-serial + +%if %{with mpich} + mkdir build-mpich +%endif + +%if %{with openmpi} + mkdir build-openmpi +%endif + +%build +# Best to use && so that if anything in the chain fails, the build also fails +# straight away +%global do_cmake_config %{expand: \ +echo +echo "*** BUILDING %{name}-%{version}$MPI_COMPILE_TYPE ***" +echo +%set_build_flags +pushd build$MPI_COMPILE_TYPE && + cmake \\ + -DCMAKE_C_FLAGS_RELEASE:STRING="-DNDEBUG" \\ + -DCMAKE_CXX_FLAGS_RELEASE:STRING="-DNDEBUG" \\ + -DCMAKE_Fortran_FLAGS_RELEASE:STRING="-DNDEBUG" \\ + -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \\ + -DCMAKE_INSTALL_PREFIX:PATH=$MPI_HOME \\ + -DINCLUDE_INSTALL_DIR:PATH=$MPI_INCLUDE \\ + -DLIB_INSTALL_DIR:PATH=$MPI_LIB \\ + -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \\ + -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\ + -DCMAKE_SKIP_RPATH:BOOL=ON \\ + -DCMAKE_BUILD_TYPE:STRING="release" \\ + -DARB_VECTORIZE:BOOL=ON \\ + -DARB_WITH_MPI:BOOL=$MPI_YES \\ + -DARB_WITH_GPU:BOOL=OFF \\ + -DARB_ARCH:STRING="native" \\ + -DCMAKE_INSTALL_LIBDIR=%{_lib} \\ + -DARB_WITH_PYTHON:BOOL=ON \\ + -DARB_PYEXECDIR:STRING=$MPI_PYTHON3_SITEARCH \\ +%if "%{_lib}" == "lib64" + -DLIB_SUFFIX=64 .. && +%else + -DLIB_SUFFIX="" .. && +%endif +popd || exit -1; + +# Upstream only supports static libraries +# https://github.com/arbor-sim/arbor/issues/916 +# -DBUILD_SHARED_LIBS:BOOL=ON \\ +# Missing BRs +# -DARB_BUILD_VALIDATION_DATA:BOOL=ON \\ +} + +%global do_make_build %{expand: \ + %make_build -C build$MPI_COMPILE_TYPE || exit -1 + %make_build -C build$MPI_COMPILE_TYPE tests || exit -1 +} + +# Build serial version, dummy arguments +export MPI_COMPILER=serial +export MPI_SUFFIX="" +export MPI_HOME=%{_prefix} +export MPI_INCLUDE=%{_includedir} +export MPI_LIB=%{_libdir} +export MPI_YES=OFF +export MPI_COMPILE_TYPE="-serial" +export MPI_PYTHON3_SITEARCH=%{python3_sitearch} +%{do_cmake_config} +%{do_make_build} + +# Manually make docs in the serial build +sphinx-build-%{python3_version} -b html doc html +# Remove uneeded dotfiles +rm -rfv html/{.buildinfo,.doctrees} + + +# Build mpich version +%if %{with mpich} +%{_mpich_load} +export CC=mpicc +export CXX=mpicxx +export FC=mpif90 +export F77=mpif77 +export MPI_YES=ON +export MPI_COMPILE_TYPE="-mpich" +%{do_cmake_config} +%{do_make_build} + +%{_mpich_unload} +%endif + +# Build OpenMPI version +%if %{with openmpi} +%{_openmpi_load} +export CC=mpicc +export CXX=mpicxx +export FC=mpif90 +export F77=mpif77 +export MPI_YES=ON +# Python 3 +export MPI_COMPILE_TYPE="-openmpi" +%{do_cmake_config} +%{do_make_build} + +%{_openmpi_unload} +%endif + +%install +# Install everything +%global do_install %{expand: \ +echo +echo "*** INSTALLING %{name}-%{version}$MPI_COMPILE_TYPE ***" +echo + %make_install -C build$MPI_COMPILE_TYPE || exit -1 +} + +# install serial version +export MPI_SUFFIX="" +export MPI_HOME=%{_prefix} +export MPI_BIN=%{_bindir} +export MPI_YES=OFF +export MPI_COMPILE_TYPE="-serial" +%{do_install} + + +# Install MPICH version +%if %{with mpich} +%{_mpich_load} +export MPI_COMPILE_TYPE="-mpich" +%{do_install} + +# Place in correct mpi libdir +%if %{_lib} == lib64 + mv -v $RPM_BUILD_ROOT/%{_libdir}/mpich/lib64 $RPM_BUILD_ROOT/$MPI_LIB/ +%endif + +pushd $RPM_BUILD_ROOT/$MPI_BIN + mv -v modcc{,$MPI_SUFFIX} -v +popd +%{_mpich_unload} +%endif + +# Install OpenMPI version +%if %{with openmpi} +%{_openmpi_load} +export MPI_COMPILE_TYPE="-openmpi" +%{do_install} + +# Correct location +%if %{_lib} == lib64 + mv -v $RPM_BUILD_ROOT/%{_libdir}/openmpi/lib64 $RPM_BUILD_ROOT/$MPI_LIB/ +%endif + +pushd $RPM_BUILD_ROOT/$MPI_BIN + mv -v modcc{,$MPI_SUFFIX} -v +popd +%{_openmpi_unload} +%endif + + +%if %{with tests} +%check +# Run for serial only. our builders are not using MPI +pushd build-serial + ./bin/unit +popd +%endif + + +%files +%license LICENSE +%doc README.md +%{_bindir}/modcc +%{python3_sitearch}/%{name}.cpython-%{python3_version_nodots}*.so + + +%files devel +%{_includedir}/%{name} +%{_includedir}/%{name}env +%{_libdir}/cmake/%{name} +%{_libdir}/libarbor.a +%{_libdir}/libarborenv.a + +%files doc +%license LICENSE +%doc html + + +%if %{with mpich} +%files mpich +%doc README.md +%license LICENSE +%{_libdir}/mpich/bin/modcc_mpich +%{python3_sitearch}/mpich/%{name}.cpython-%{python3_version_nodots}*.so + +%files mpich-devel +%{_libdir}/mpich/include/%{name} +%{_libdir}/mpich/include/%{name}env +%{_libdir}/mpich/lib/cmake/%{name} +%{_libdir}/mpich/lib/libarbor.a +%{_libdir}/mpich/lib/libarborenv.a +%endif + +%if %{with openmpi} +%files openmpi +%doc README.md +%license LICENSE +%{_libdir}/openmpi/bin/modcc_openmpi +%{python3_sitearch}/openmpi/%{name}.cpython-%{python3_version_nodots}*.so + +%files openmpi-devel +%{_libdir}/openmpi/include/%{name} +%{_libdir}/openmpi/include/%{name}env +%{_libdir}/openmpi/lib/cmake/%{name} +%{_libdir}/openmpi/lib/libarbor.a +%{_libdir}/openmpi/lib/libarborenv.a +%endif + +%changelog +* Tue Dec 10 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-3 +- Enable tests +- Add patch for test crash + +* Mon Dec 09 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-2 +- Remove arch info in provides for static +- Temporarily disable tests +- use python3-devel +- Add documentation in separate sub-package +- add python3-{mpich,openmpi} as requires that own MPI_PYTHON3_SITEARCH directories +- Improve summaries for sub-packages to please rpmlint + +* Sat Dec 07 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-1 +- Update to latest release + +* Sun Jan 13 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.1-1 +- Initial rpm package diff --git a/sources b/sources new file mode 100644 index 0000000..36af8fa --- /dev/null +++ b/sources @@ -0,0 +1 @@ +SHA512 (arbor-0.2.2.tar.gz) = 5da25d643ac607f94d157fd2506d3974e512328b9391d6b00f245a61142eaa8288722b798e2a497b62d74bccd891f90f7929356b384a7169c7533bba8792d6f6
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