From 904d0c6d1d00223d85081b359f4e54494339df27 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Fri, 2 Jul 2021 14:38:41 +0200 Subject: [PATCH] Transition old compiler tests from travis to CirrusCI --- .cirrus.yml | 34 +++++++++-- .travis.yml | 130 ----------------------------------------- src/commons/FastSort.h | 1 + src/util/tar2db.cpp | 4 ++ 4 files changed, 34 insertions(+), 135 deletions(-) delete mode 100644 .travis.yml diff --git a/.cirrus.yml b/.cirrus.yml index 2f4522475..bc79a6604 100644 --- a/.cirrus.yml +++ b/.cirrus.yml @@ -1,12 +1,36 @@ -freebsd_instance: - image_family: freebsd-13-0 +env: + CIRRUS_CLONE_SUBMODULES: true task: - env: - CIRRUS_CLONE_SUBMODULES: true + name: FreeBSD-13 + freebsd_instance: + image_family: freebsd-13-0 install_script: pkg install -y cmake git samtools compile_script: | mkdir build && cd build cmake -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=1 -DHAVE_SSE4_1=1 .. make -j $(sysctl -n hw.ncpu) - test_script: ./util/regression/run_regression.sh ./build/src/mmseqs SCRATCH + test_script: ./util/regression/run_regression.sh ./build/src/mmseqs SCRATCH + +task: + name: "Old compilers" + container: + image: debian:jessie-slim + memory: 8G + matrix: + - name: Clang-4 + install_script: apt update --yes && apt install cmake clang-4.0 libc++-dev make git ca-certificates --yes --no-install-suggests --no-install-recommends + env: + CC: clang-4.0 + CXX: clang++-4.0 + - name: GCC-4.9 + install_script: apt update --yes && apt install cmake gcc-4.9 g++-4.9 make git ca-certificates --yes --no-install-suggests --no-install-recommends + env: + CC: gcc-4.9 + CXX: g++-4.9 + compile_script: | + mkdir build && cd build + cmake -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=1 -DHAVE_SSE4_1=1 -DREQUIRE_OPENMP=0 .. + make -j $(nproc --all) + test_script: ./util/regression/run_regression.sh ./build/src/mmseqs SCRATCH SEARCH + diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index bfd1031b0..000000000 --- a/.travis.yml +++ /dev/null @@ -1,130 +0,0 @@ -language: shell -os: linux -dist: xenial -addons: - apt: - packages: &default_packages - - cmake - - make - - zlib1g-dev - - libbz2-dev - - vim-common - - shellcheck - -jobs: - include: - - addons: - apt: - packages: - - *default_packages - - build-essential - - g++-8 - - gcc-8 - arch: arm64 - env: CC=gcc-8 CXX=g++-8 MMSEQS_NUM_THREADS=4 - dist: bionic - - addons: - apt: - packages: - - *default_packages - - build-essential - - g++-8 - - gcc-8 - arch: ppc64le - dist: bionic - env: CC=gcc-8 CXX=g++-8 MMSEQS_NUM_THREADS=4 - - addons: - apt: - packages: - - *default_packages - - clang-5.0 - - libc++-dev - - libomp-dev - env: CC=clang-5.0 CXX=clang++-5.0 - - addons: - apt: - sources: - - ubuntu-toolchain-r-test - - sourceline: 'deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-10 main' - key_url: 'https://apt.llvm.org/llvm-snapshot.gpg.key' - packages: - - *default_packages - - clang-10 - - libc++-10-dev - - libc++abi-10-dev - - libomp-10-dev - env: CC=clang-10 CXX=clang++-10 - - addons: - apt: - sources: - - ubuntu-toolchain-r-test - - sourceline: 'deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-10 main' - key_url: 'https://apt.llvm.org/llvm-snapshot.gpg.key' - packages: - - *default_packages - - clang-10 - - libc++-10-dev - - libc++abi-10-dev - - libomp-10-dev - - mpi-default-dev - - mpi-default-bin - env: MPI=1 CC=clang-10 CXX=clang++-10 - - addons: - apt: - sources: - - ubuntu-toolchain-r-test - packages: - - *default_packages - - gcc-4.9 - - g++-4.9 - env: CC=gcc-4.9 CXX=g++-4.9 - - addons: - apt: - sources: - - ubuntu-toolchain-r-test - packages: - - *default_packages - - gcc-9 - - g++-9 - env: CC=gcc-9 CXX=g++-9 - - addons: - apt: - sources: - - ubuntu-toolchain-r-test - packages: - - *default_packages - - gcc-9 - - g++-9 - - mpi-default-dev - - mpi-default-bin - env: MPI=1 CC=gcc-9 CXX=g++-9 - - addons: - apt: - sources: - - sourceline: 'deb https://apt.repos.intel.com/oneapi all main' - key_url: 'https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB' - packages: - - *default_packages - - build-essential - - intel-oneapi-icc - env: CC=icc CXX=icpc - # icc is broken with beta08 - if: false - fast_finish: true - -before_install: - - export CC - - export CXX - -script: - - | - if [ -e "/opt/intel/inteloneapi/setvars.sh" ]; then source /opt/intel/inteloneapi/setvars.sh; fi; \ - mkdir build; cd build; \ - cmake -DHAVE_MPI="$([[ -z "$MPI" ]]; echo $?)" -DENABLE_WERROR=1 -DHAVE_TESTS=1 ..; \ - make -j ${MMSEQS_NUM_THREADS:-$(nproc --all)}; \ - mkdir path; \ - printf '#!/bin/sh\n/usr/bin/tee "$@" | tail\n' > path/tee; \ - chmod +x path/tee; \ - export PATH="$(readlink -f path):$PATH"; \ - export TTY=0; \ - ../util/regression/run_regression.sh ./src/mmseqs SCRATCH; diff --git a/src/commons/FastSort.h b/src/commons/FastSort.h index e32e2cacc..b54a3f8ba 100644 --- a/src/commons/FastSort.h +++ b/src/commons/FastSort.h @@ -1,3 +1,4 @@ +#include #ifdef ENABLE_IPS4O # include "simde/hedley.h" # if defined(HEDLEY_GCC_VERSION) && HEDLEY_GCC_VERSION_CHECK(0,0,0) && !HEDLEY_GCC_VERSION_CHECK(5,1,0) && defined(__cplusplus) diff --git a/src/util/tar2db.cpp b/src/util/tar2db.cpp index 189d724f8..8bfdaf372 100644 --- a/src/util/tar2db.cpp +++ b/src/util/tar2db.cpp @@ -95,7 +95,9 @@ int tar2db(int argc, const char **argv, const Command& command) { EXIT(EXIT_FAILURE); } +#ifdef OPENMP int localThreads = par.threads; +#endif mtar_t tar; if (Util::endsWith(".tar.gz", filenames[i]) || Util::endsWith(".tgz", filenames[i])) { #ifdef HAVE_ZLIB @@ -103,7 +105,9 @@ int tar2db(int argc, const char **argv, const Command& command) { Debug(Debug::ERROR) << "Cannot open file " << filenames[i] << "\n"; EXIT(EXIT_FAILURE); } +#ifdef OPENMP localThreads = 1; +#endif #else Debug(Debug::ERROR) << "MMseqs2 was not compiled with zlib support. Cannot read compressed input.\n"; EXIT(EXIT_FAILURE);