From ce8e9a108762225da13f1b6812dad18e70ca9d8d Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 06:17:40 +0000 Subject: [PATCH 01/17] Allow for optional scaling back of encore optimisations --- package/setup.py | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/package/setup.py b/package/setup.py index 3b4cf2f8674..474b6ff2eda 100755 --- a/package/setup.py +++ b/package/setup.py @@ -261,15 +261,8 @@ def extensions(config): use_cython = config.get('use_cython', default=not is_release) use_openmp = config.get('use_openmp', default=True) - if platform.machine() == 'aarch64': - # reduce optimization level for ARM64 machines - # because of issues with test failures sourcing to: - # MDAnalysis/analysis/encore/clustering/src/ap.c - extra_compile_args = ['-std=c99', '-ffast-math', '-O1', '-funroll-loops', - '-fsigned-zeros'] - else: - extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops', - '-fsigned-zeros'] # see #2722 + extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops', + '-fsigned-zeros'] # see #2722 define_macros = [] if config.get('debug_cflags', default=False): extra_compile_args.extend(['-Wall', '-pedantic']) @@ -281,6 +274,15 @@ def extensions(config): if arch: extra_compile_args.append('-march={}'.format(arch)) + # encore is sensitive to floating point accuracy, especially on non-x86 + # to avoid reducing optimisations on everything, we make a set of compile + # args specific to encore see #2997 for an example of this. + encore_compile_args = [a for a in extra_compile_args if 'O3' not in a] + if platform.machine() == 'aarch64' or platform.machine() == 'ppc64le': + encore_compile_args.append('-O1') + else: + encore_compile_args.append('-O3') + cpp_extra_compile_args = [a for a in extra_compile_args if 'std' not in a] cpp_extra_compile_args.append('-std=c++11') cpp_extra_link_args=[] @@ -401,21 +403,21 @@ def extensions(config): sources=['MDAnalysis/analysis/encore/cutils' + source_suffix], include_dirs=include_dirs, define_macros=define_macros, - extra_compile_args=extra_compile_args) + extra_compile_args=encore_compile_args) ap_clustering = MDAExtension('MDAnalysis.analysis.encore.clustering.affinityprop', sources=['MDAnalysis/analysis/encore/clustering/affinityprop' + source_suffix, 'MDAnalysis/analysis/encore/clustering/src/ap.c'], include_dirs=include_dirs+['MDAnalysis/analysis/encore/clustering/include'], libraries=mathlib, define_macros=define_macros, - extra_compile_args=extra_compile_args) + extra_compile_args=encore_compile_args) spe_dimred = MDAExtension('MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed', sources=['MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed' + source_suffix, 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c'], include_dirs=include_dirs+['MDAnalysis/analysis/encore/dimensionality_reduction/include'], libraries=mathlib, define_macros=define_macros, - extra_compile_args=extra_compile_args) + extra_compile_args=encore_compile_args) nsgrid = MDAExtension('MDAnalysis.lib.nsgrid', ['MDAnalysis/lib/nsgrid' + cpp_source_suffix], include_dirs=include_dirs, From 79db3fd5b3fae55383d13fabc0d798b1bf9122c2 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 06:32:38 +0000 Subject: [PATCH 02/17] Re-enable ppc64le and arm64 testing --- .travis.yml | 54 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 00000000000..667ecf09cbf --- /dev/null +++ b/.travis.yml @@ -0,0 +1,54 @@ +version: ~> 1.0 +language: generic +group: travis_latest + +# Only build for develop +branches: + only: + - develop + +matrix: + fast_finish: true + include: + - python: 3.8 + name: "Power PC" + os: linux + arch: ppc64le + before_install: + - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh + - mkdir $HOME/.conda + - bash miniconda.sh -b -p $HOME/miniconda + - $HOME/miniconda/bin/conda init bash + - source ~/.bash_profile + - conda activate base + - conda update --yes conda + - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds + - pip install pytest-xdist + - conda info + install: + - (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install) + script: + # 4 threads per power9 cores, 2 cores = 8 threads + - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 + + - os: linux + language: python + arch: arm64-graviton2 + python: 3.8 + dist: focal + virt: vm + group: edge + before_install: + - python -m pip install cython numpy scipy + - python -m pip install --no-build-isolation hypothesis matplotlib pytest pytest-cov pytest-xdist tqdm + install: + - cd package + - python setup.py install + - cd ../testsuite + - python setup.py install + - cd .. + script: + - cd testsuite + - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 -rsx --cov=MDAnalysis + after_success: + - echo "Override this stage for ARM64" From 1879bba6f5d922b9da2f9d68c60a5c92b98b8819 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 06:40:26 +0000 Subject: [PATCH 03/17] try fixing conda build in ppc64le --- .travis.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 667ecf09cbf..4528baf6707 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,7 +19,7 @@ matrix: - mkdir $HOME/.conda - bash miniconda.sh -b -p $HOME/miniconda - $HOME/miniconda/bin/conda init bash - - source ~/.bash_profile + - source ~/.bashrc - conda activate base - conda update --yes conda - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds @@ -30,11 +30,14 @@ matrix: script: # 4 threads per power9 cores, 2 cores = 8 threads - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 + after_success: + - echo "Override this stage for ppc64le" - os: linux language: python arch: arm64-graviton2 python: 3.8 + name: "ARM64" dist: focal virt: vm group: edge From 21f31b98062bd62974c9d5fa500772b1add3f4bc Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 06:52:51 +0000 Subject: [PATCH 04/17] trying using deprecated source --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 4528baf6707..5e4a284ce58 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,8 +19,8 @@ matrix: - mkdir $HOME/.conda - bash miniconda.sh -b -p $HOME/miniconda - $HOME/miniconda/bin/conda init bash - - source ~/.bashrc - - conda activate base + #- source ~/.bashrc + - source activate base - conda update --yes conda - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds - pip install pytest-xdist From 4eb87736156f697235757970feb7cfb9b05b2f38 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 06:58:20 +0000 Subject: [PATCH 05/17] What's in the bashrc? --- .travis.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 5e4a284ce58..ecd6256e8b5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,8 +19,9 @@ matrix: - mkdir $HOME/.conda - bash miniconda.sh -b -p $HOME/miniconda - $HOME/miniconda/bin/conda init bash - #- source ~/.bashrc - - source activate base + - cat $HOME/.bashrc + - source $HOME/.bashrc + - conda activate base - conda update --yes conda - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds - pip install pytest-xdist @@ -55,3 +56,4 @@ matrix: - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 -rsx --cov=MDAnalysis after_success: - echo "Override this stage for ARM64" + From 4d81d4e965403dcf36d42688e4cc11b6a6132fed Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 07:06:29 +0000 Subject: [PATCH 06/17] try moving out of matrix block --- .travis.yml | 58 +++++++++++++++++++++++++++++++++++------------------ 1 file changed, 39 insertions(+), 19 deletions(-) diff --git a/.travis.yml b/.travis.yml index ecd6256e8b5..9cf925b221e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -13,26 +13,27 @@ matrix: - python: 3.8 name: "Power PC" os: linux + dist: focal arch: ppc64le - before_install: - - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh - - mkdir $HOME/.conda - - bash miniconda.sh -b -p $HOME/miniconda - - $HOME/miniconda/bin/conda init bash - - cat $HOME/.bashrc - - source $HOME/.bashrc - - conda activate base - - conda update --yes conda - - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds - - pip install pytest-xdist - - conda info - install: - - (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install) - script: - # 4 threads per power9 cores, 2 cores = 8 threads - - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 - after_success: - - echo "Override this stage for ppc64le" + #before_install: + # - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh + # - mkdir $HOME/.conda + # - bash miniconda.sh -b -p $HOME/miniconda + # - $HOME/miniconda/bin/conda init bash + # - cat $HOME/.bashrc + # - source $HOME/.bashrc + # - conda activate base + # - conda update --yes conda + # - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds + # - pip install pytest-xdist + # - conda info + #install: + # - (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install) + #script: + # # 4 threads per power9 cores, 2 cores = 8 threads + # - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 + #after_success: + # - echo "Override this stage for ppc64le" - os: linux language: python @@ -57,3 +58,22 @@ matrix: after_success: - echo "Override this stage for ARM64" +before_install: + - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh + - mkdir $HOME/.conda + - bash miniconda.sh -b -p $HOME/miniconda + - $HOME/miniconda/bin/conda init bash + - cat $HOME/.bashrc + - source $HOME/.bashrc + - conda activate base + - conda update --yes conda + - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds + - pip install pytest-xdist + - conda info +install: + - (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install) +script: + # 4 threads per power9 cores, 2 cores = 8 threads + - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 +after_success: + - echo "Override this stage for now" From 2ce2825a5f43e3a868a73623c76ac4900df8e965 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 07:19:31 +0000 Subject: [PATCH 07/17] focal seems to be stalling the ppc64le build --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 9cf925b221e..9c28af8d620 100644 --- a/.travis.yml +++ b/.travis.yml @@ -13,7 +13,7 @@ matrix: - python: 3.8 name: "Power PC" os: linux - dist: focal + #dist: focal arch: ppc64le #before_install: # - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh From ff22957b9cafb185cba0d413c745c37c596d46b3 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 07:29:11 +0000 Subject: [PATCH 08/17] Try triggering Travis again --- .travis.yml | 21 +-------------------- 1 file changed, 1 insertion(+), 20 deletions(-) diff --git a/.travis.yml b/.travis.yml index 9c28af8d620..0cba744208e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -13,27 +13,7 @@ matrix: - python: 3.8 name: "Power PC" os: linux - #dist: focal arch: ppc64le - #before_install: - # - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh - # - mkdir $HOME/.conda - # - bash miniconda.sh -b -p $HOME/miniconda - # - $HOME/miniconda/bin/conda init bash - # - cat $HOME/.bashrc - # - source $HOME/.bashrc - # - conda activate base - # - conda update --yes conda - # - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds - # - pip install pytest-xdist - # - conda info - #install: - # - (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install) - #script: - # # 4 threads per power9 cores, 2 cores = 8 threads - # - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 - #after_success: - # - echo "Override this stage for ppc64le" - os: linux language: python @@ -58,6 +38,7 @@ matrix: after_success: - echo "Override this stage for ARM64" + before_install: - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh - mkdir $HOME/.conda From 9463ec8fa9413b5717e629ced73a91632f92869c Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 08:11:39 +0000 Subject: [PATCH 09/17] Try emulating bashrc behaviour --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 0cba744208e..1d879c5568e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -45,7 +45,7 @@ before_install: - bash miniconda.sh -b -p $HOME/miniconda - $HOME/miniconda/bin/conda init bash - cat $HOME/.bashrc - - source $HOME/.bashrc + - . "/home/travis/miniconda/etc/profile.d/conda.sh" - conda activate base - conda update --yes conda - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds From 0bb6242a1e6fc9f59b177c931e5d5998d9db164d Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 08:13:44 +0000 Subject: [PATCH 10/17] fix conda install line --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 1d879c5568e..1d312b02b22 100644 --- a/.travis.yml +++ b/.travis.yml @@ -48,7 +48,7 @@ before_install: - . "/home/travis/miniconda/etc/profile.d/conda.sh" - conda activate base - conda update --yes conda - - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge biobuilds + - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge -c biobuilds - pip install pytest-xdist - conda info install: From 463a0178ba4ee59e3036783b2a3e52e243c209ea Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 08:17:38 +0000 Subject: [PATCH 11/17] Add yes to install --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 1d312b02b22..fe96b569af6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -48,7 +48,7 @@ before_install: - . "/home/travis/miniconda/etc/profile.d/conda.sh" - conda activate base - conda update --yes conda - - conda install pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge -c biobuilds + - conda install --yes pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge -c biobuilds - pip install pytest-xdist - conda info install: From 9f757b373b43ad777905c7eb4c4d34e7601b4c72 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 08:23:50 +0000 Subject: [PATCH 12/17] Fix pytest call --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index fe96b569af6..33d6349b678 100644 --- a/.travis.yml +++ b/.travis.yml @@ -55,6 +55,6 @@ install: - (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install) script: # 4 threads per power9 cores, 2 cores = 8 threads - - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 + - pytest testsuite/MDAnalysisTests --disable-pytest-warnings -n 8 after_success: - echo "Override this stage for now" From 39a3ae7723e02ba4f18e1e53deb9665bc888ebac Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 08:35:59 +0000 Subject: [PATCH 13/17] Up the scipy version --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 33d6349b678..3966f627e3f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -48,7 +48,7 @@ before_install: - . "/home/travis/miniconda/etc/profile.d/conda.sh" - conda activate base - conda update --yes conda - - conda install --yes pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov -c conda-forge -c biobuilds + - conda install --yes pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base "scipy>=1.6" griddataformats hypothesis gsd codecov -c conda-forge -c biobuilds - pip install pytest-xdist - conda info install: From 099112b2f8b12dcc1db6c3180736f62302259604 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 11:58:29 +0000 Subject: [PATCH 14/17] reduce number of runners to prevent crashes --- .travis.yml | 38 ++++++++++++++++++-------------------- 1 file changed, 18 insertions(+), 20 deletions(-) diff --git a/.travis.yml b/.travis.yml index 3966f627e3f..433168041ff 100644 --- a/.travis.yml +++ b/.travis.yml @@ -14,6 +14,24 @@ matrix: name: "Power PC" os: linux arch: ppc64le + before_install: + - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh + - mkdir $HOME/.conda + - bash miniconda.sh -b -p $HOME/miniconda + - $HOME/miniconda/bin/conda init bash + # for some reason the image does not like sourcing .bashrc + - . "/home/travis/miniconda/etc/profile.d/conda.sh" + - conda activate base + - conda update --yes conda + - conda install --yes pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base "scipy>=1.6" griddataformats hypothesis gsd codecov -c conda-forge -c biobuilds + - pip install pytest-xdist + - conda info + install: + - (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install) + script: + - pytest testsuite/MDAnalysisTests --disable-pytest-warnings -n 2 + after_sucess: + - echo "Override this stage for now" - os: linux language: python @@ -38,23 +56,3 @@ matrix: after_success: - echo "Override this stage for ARM64" - -before_install: - - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh - - mkdir $HOME/.conda - - bash miniconda.sh -b -p $HOME/miniconda - - $HOME/miniconda/bin/conda init bash - - cat $HOME/.bashrc - - . "/home/travis/miniconda/etc/profile.d/conda.sh" - - conda activate base - - conda update --yes conda - - conda install --yes pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base "scipy>=1.6" griddataformats hypothesis gsd codecov -c conda-forge -c biobuilds - - pip install pytest-xdist - - conda info -install: - - (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install) -script: - # 4 threads per power9 cores, 2 cores = 8 threads - - pytest testsuite/MDAnalysisTests --disable-pytest-warnings -n 8 -after_success: - - echo "Override this stage for now" From 9618cc0e1e6b30ef989210a0cd546a4a830b1fe8 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 16:12:09 +0000 Subject: [PATCH 15/17] Try cron type switch --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 433168041ff..3be2f063d1b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -14,6 +14,7 @@ matrix: name: "Power PC" os: linux arch: ppc64le + if: type = cron before_install: - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh - mkdir $HOME/.conda @@ -41,6 +42,7 @@ matrix: dist: focal virt: vm group: edge + if: type = cron before_install: - python -m pip install cython numpy scipy - python -m pip install --no-build-isolation hypothesis matplotlib pytest pytest-cov pytest-xdist tqdm From eb70d252928c4dd4d5d4b18dadeee68999ad7d03 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 16:18:46 +0000 Subject: [PATCH 16/17] update changelog --- package/CHANGELOG | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/package/CHANGELOG b/package/CHANGELOG index 2a652304a99..f113b3cb32d 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -84,6 +84,8 @@ Fixes * Fix syntax warning over comparison of literals using is (Issue #3066) Enhancements + * Adds preliminary support for the ppc64le platform with minimal + dependencies (Issue #3127, PR #3149) * Caches can now undergo central validation at the Universe level, opening the door to more useful caching. Already applied to fragment caching (Issue #2376, PR #3135) @@ -131,6 +133,8 @@ Enhancements explicit in the topology (Issue #2468, PR #2775) Changes + * Introduces encore specific C compiler arguments to allow for lowering of + optimisations on non-x86 platforms (PR #3149) * Continuous integration uses mamba rather than conda to install the dependencies (PR #2983) * removes deprecated `as_Universe` function from MDAnalysis.core.universe, From 266bf61ab8daff24a9f9c796e215df57c57afad5 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 12 Mar 2021 16:27:31 +0000 Subject: [PATCH 17/17] small issue update --- package/CHANGELOG | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index f113b3cb32d..7fa27bb5178 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -134,7 +134,7 @@ Enhancements Changes * Introduces encore specific C compiler arguments to allow for lowering of - optimisations on non-x86 platforms (PR #3149) + optimisations on non-x86 platforms (Issue #1389, PR #3149) * Continuous integration uses mamba rather than conda to install the dependencies (PR #2983) * removes deprecated `as_Universe` function from MDAnalysis.core.universe,