Update MMseqs2

.travis.yml

@@ -1,83 +1,69 @@
 language: minimal
 
-env:
+os: linux
+dist: xenial
+addons:
+  apt:
+    packages: &default_packages
+      - cmake
+      - make
+      - zlib1g-dev
+      - libbz2-dev
+      - vim-common
+      - shellcheck
 
 matrix:
   include:
-  - os: linux
-    dist: trusty
-    addons:
+  - addons:
       apt:
         packages:
-          - cmake
-          - ninja-build
-          - clang-3.6
+          - *default_packages
+          - clang-5.0
           - libc++-dev
-          - zlib1g-dev
-          - libbz2-dev
-          - vim-common
-    env: CC=clang-3.6 CXX=clang++-3.6
-  - os: linux
-    dist: trusty
-    addons:
+          - libomp-dev
+    env: CC=clang-5.0 CXX=clang++-5.0
+  - addons:
       apt:
         sources:
           - ubuntu-toolchain-r-test
-          - llvm-toolchain-trusty-7
+          - sourceline: 'deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-10 main'
+            key_url: 'https://apt.llvm.org/llvm-snapshot.gpg.key'
         packages:
-          - cmake
-          - ninja-build
-          - clang-7
-          - libc++-7-dev
-          - libc++abi-7-dev
-          - zlib1g-dev
-          - libbz2-dev
-          - vim-common
-    env: CC=clang-7 CXX=clang++-7
-  - os: linux
-    dist: trusty
-    addons:
+          - *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
         packages:
-          - cmake
-          - ninja-build
-          - gcc-4.8
-          - g++-4.8
-          - zlib1g-dev
-          - libbz2-dev
-          - vim-common
-    env: CC=gcc-4.8 CXX=g++-4.8
-  - os: linux
-    dist: trusty
-    addons:
+          - *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:
-          - cmake
-          - ninja-build
-          - gcc-8
-          - g++-8
-          - zlib1g-dev
-          - libbz2-dev
-          - vim-common
-    env: CC=gcc-8 CXX=g++-8
-  - os: linux
-    dist: trusty
-    addons:
+          - *default_packages
+          - gcc-9
+          - g++-9
+    env: CC=gcc-9 CXX=g++-9
+  - addons:
       apt:
         sources:
           - ubuntu-toolchain-r-test
         packages:
-          - cmake
-          - ninja-build
-          - gcc-8
-          - g++-8
-          - zlib1g-dev
-          - libbz2-dev
-          - vim-common
-          - libopenmpi-dev
-    env: MPI=1 CC=gcc-8 CXX=g++-8
+          - *default_packages
+          - gcc-9
+          - g++-9
+          - mpi-default-dev
+          - mpi-default-bin
+    env: MPI=1 CC=gcc-9 CXX=g++-9
   - os: osx
     osx_image: xcode10.1
     addons:
@@ -98,8 +84,8 @@ script:
     if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then \
       if [[ -n "$MPI" ]]; then MPI=1; else MPI=0; fi; \
       mkdir build; cd build; \
-      cmake -G Ninja -DHAVE_MPI="$MPI" -DHAVE_SSE4_1=1 -DREQUIRE_OPENMP=0 .. \
-        || exit 1; ninja || exit 1; \
+      cmake -DHAVE_MPI="$MPI" -DHAVE_SSE4_1=1 -DREQUIRE_OPENMP=0 ..;
+      make -j $(nproc --all); \
     elif [[ "$TRAVIS_OS_NAME" == "osx" ]]; then \
       ./lib/mmseqs/util/build_osx.sh . build plass || exit 1; \
     else \

Dockerfile

@@ -6,29 +6,34 @@ RUN apt-get update && apt-get install -y \
 WORKDIR /opt/source
 ADD . .
 
-WORKDIR /opt/source/build_sse
+WORKDIR /opt/source/build_sse2
+RUN cmake -DHAVE_MPI=0 -DHAVE_TESTS=0 -DHAVE_SSE2=1 -DCMAKE_BUILD_TYPE=Release ..
+RUN make -j $(nproc --all)
+
+WORKDIR /opt/source/build_sse41
 RUN cmake -DHAVE_MPI=0 -DHAVE_TESTS=0 -DHAVE_SSE4_1=1 -DCMAKE_BUILD_TYPE=Release ..
 RUN make -j $(nproc --all)
 
-WORKDIR /opt/source/build_avx
+WORKDIR /opt/source/build_avx2
 RUN cmake -DHAVE_MPI=0 -DHAVE_TESTS=0 -DHAVE_AVX2=1 -DCMAKE_BUILD_TYPE=Release ..
 RUN make -j $(nproc --all)
 
 FROM debian:stable-slim
 MAINTAINER Milot Mirdita <[email protected]>
 RUN apt-get update && apt-get install -y \
-      gawk bash grep libstdc++6 libgomp1 zlib1g libbz2-1.0 \
+      gawk bash grep libstdc++6 libgomp1 libatomic1 zlib1g libbz2-1.0 wget tar \
       && rm -rf /var/lib/apt/lists/*
 
-COPY --from=builder /opt/source/build_sse/src/plass /usr/local/bin/plass_sse42
-COPY --from=builder /opt/source/build_avx/src/plass /usr/local/bin/plass_avx2
-RUN echo '#!/bin/bash\n\
-if $(grep -q -E "^flags.+avx2" /proc/cpuinfo); then\n\
-    exec /usr/local/bin/plass_avx2 "$@"\n\
-else\n\
-    exec /usr/local/bin/plass_sse42 "$@"\n\
-fi'\
->> /usr/local/bin/plass
+COPY --from=builder /opt/source/build_sse2/src/plass /usr/local/bin/plass_sse2
+COPY --from=builder /opt/source/build_sse41/src/plass /usr/local/bin/plass_sse41
+COPY --from=builder /opt/source/build_avx2/src/plass /usr/local/bin/plass_avx2
+RUN echo '#!/bin/sh\n\
+FLAGS="$(grep -m 1 "^flags" /proc/cpuinfo)"\n\
+case "${FLAGS}" in\n\
+  *avx2*) exec /usr/local/bin/plass_avx2 "$@" ;;\n\
+  *sse4_1*) exec /usr/local/bin/plass_sse41 "$@" ;;\n\
+  *) exec /usr/local/bin/plass_sse2 "$@" ;;\n\
+fi' >> /usr/local/bin/plass
 RUN chmod +x /usr/local/bin/plass
 
 VOLUME ["/app"]

src/assembler/findassemblystart.cpp

@@ -86,7 +86,7 @@ int findassemblystart(int argn, const char **argv, const Command& command) {
             const char *entry[255];
             const size_t columns = Util::getWordsOfLine(results, entry, 255);
             Matcher::result_t res;
-            if (columns >= Matcher::ALN_RES_WITH_OUT_BT_COL_CNT) {
+            if (columns >= Matcher::ALN_RES_WITHOUT_BT_COL_CNT) {
                 res = Matcher::parseAlignmentRecord(results);
             } else {
                 Debug(Debug::ERROR) << "ERROR: Backtrace is missing for at result: " << id  << "\n";