[WIP] Add dockerfile

[olgabot]

Hello! I kept getting lost trying to install dashing and decided to make a dockerfile for portability. I'm using Ubuntu 16.04 and used the installation commands from the README and the .travis.yml. Here is the build output:

``` Tue 22 Jan - 15:10  ~/code/dashing   origin ☊ olgabot/dockerfile ✔   docker build . Sending build context to Docker daemon 321.5kB Step 1/19 : FROM ubuntu:16.04 ---> ccc7a11d65b1 Step 2/19 : MAINTAINER olga.botvinnik@czbiohub.org ---> Using cache ---> 83a735a5df85 Step 3/19 : WORKDIR /tmp ---> Using cache ---> c535f1546143 Step 4/19 : USER root ---> Using cache ---> c4d9ae7bee6a Step 5/19 : ENV PACKAGES git make ca-certificates zlib1g-dev build-essential curl wget cmake ---> Using cache ---> efb5e3765624 Step 6/19 : WORKDIR /home ---> Using cache ---> 4645a55a2845 Step 7/19 : RUN apt-get update && apt-get install -y --no-install-recommends ${PACKAGES} && apt-get clean ---> Using cache ---> 10ae0f8783f1 Step 8/19 : RUN apt-get update ---> Using cache ---> 5a00d027c8e4 Step 9/19 : RUN apt-get install -y software-properties-common ---> Using cache ---> 847c08ff04f9 Step 10/19 : RUN add-apt-repository ppa:ubuntu-toolchain-r/test ---> Using cache ---> 1ab3dbcd27ae Step 11/19 : RUN apt-get update && apt-get install -y g++-6 ---> Using cache ---> 9dc0fdca6883 Step 12/19 : RUN g++ --version ---> Running in 30e3429c0b7d g++ (Ubuntu 5.4.0-6ubuntu1~16.04.11) 5.4.0 20160609 Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Removing intermediate container 30e3429c0b7d ---> 9c9833cb0e86 Step 13/19 : RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-6 60 --slave /usr/bin/g++ g++ /usr/bin/g++-6 ---> Running in 570523415cc9 update-alternatives: using /usr/bin/gcc-6 to provide /usr/bin/gcc (gcc) in auto mode Removing intermediate container 570523415cc9 ---> 8775ba3dd7e6 Step 14/19 : WORKDIR / ---> Running in 78b1aeeea61f Removing intermediate container 78b1aeeea61f ---> 9eb23b7dfac4 Step 15/19 : RUN git clone https://github.com/dnbaker/dashing/ ---> Running in 2b5c9e5f4ef9 Cloning into 'dashing'... Removing intermediate container 2b5c9e5f4ef9 ---> dc416750bc63 Step 16/19 : WORKDIR /dashing ---> Running in aa7d65a04a23 Removing intermediate container aa7d65a04a23 ---> fa4710ae78a0 Step 17/19 : RUN pwd ---> Running in 705437fb45ca /dashing Removing intermediate container 705437fb45ca ---> e7751519965c Step 18/19 : RUN make update dashing ---> Running in 1688b3fcf6aa git submodule update --init --remote --recursive . && cd bonsai && git checkout master && git pull && make update && \ cd linear && git checkout master && git pull && cd .. && cd .. && cd distmat && git checkout master && git pull && cd .. Submodule 'bonsai' (https://github.com/dnbaker/bonsai) registered for path 'bonsai' Submodule 'distmat' (https://github.com/dnbaker/distmat) registered for path 'distmat' Cloning into 'bonsai'... Submodule path 'bonsai': checked out 'd1dac2a5910153a3a13c35585c01ffd365bb4fe9' Submodule 'circularqueue' (https://github.com/dnbaker/circularqueue) registered for path 'circularqueue' Submodule 'clhash' (https://github.com/lemire/clhash) registered for path 'clhash' Submodule 'hll' (https://github.com/dnbaker/sketch) registered for path 'hll' Submodule 'klib' (https://github.com/dnbaker/klib) registered for path 'klib' Submodule 'kspp' (https://github.com/dnbaker/kspp) registered for path 'kspp' Submodule 'lazy' (https://github.com/dnbaker/lazy) registered for path 'lazy' Submodule 'libpopcnt' (https://github.com/kimwalisch/libpopcnt) registered for path 'libpopcnt' Submodule 'linear' (https://github.com/dnbaker/linear) registered for path 'linear' Submodule 'pdqsort' (https://github.com/orlp/pdqsort) registered for path 'pdqsort' Cloning into 'circularqueue'... Submodule path 'bonsai/circularqueue': checked out '131e12b00541cae9b62007dc33061e0df47e540e' Cloning into 'clhash'... Submodule path 'bonsai/clhash': checked out '5511441cf3ae2c4f064e2e2950e754eb2033b56c' Cloning into 'hll'... Submodule path 'bonsai/hll': checked out 'a514ad82914c4a5a152c70f32e579adbb4f20f4e' Submodule 'aesctr' (https://github.com/dnbaker/aesctr) registered for path 'aesctr' Submodule 'compact_vector' (https://github.com/gmarcais/compact_vector) registered for path 'compact_vector' Submodule 'libpopcnt' (https://github.com/kimwalisch/libpopcnt) registered for path 'libpopcnt' Submodule 'pybind11' (https://github.com/pybind/pybind11) registered for path 'pybind11' Submodule 'vec' (https://github.com/dnbaker/vec) registered for path 'vec' Cloning into 'aesctr'... Submodule path 'bonsai/hll/aesctr': checked out 'ffdfd2ad949b90d6b286ef97308fdcd1c17f63d9' Cloning into 'compact_vector'... Submodule path 'bonsai/hll/compact_vector': checked out '87301b3cf5120676fa8e122ac1054aa038ee78ca' Cloning into 'libpopcnt'... Submodule path 'bonsai/hll/libpopcnt': checked out '79219c154c72550ec8bc325a7e5db004db6041cc' Cloning into 'pybind11'... Submodule path 'bonsai/hll/pybind11': checked out '085a29436a8c472caaaf7157aa644b571079bcaa' Submodule 'tools/clang' (https://github.com/wjakob/clang-cindex-python3) registered for path 'tools/clang' Cloning into 'tools/clang'... Submodule path 'bonsai/hll/pybind11/tools/clang': checked out '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5' Cloning into 'vec'... Submodule path 'bonsai/hll/vec': checked out '9c27d421cf32aacfe8516572381adeaebb6cf921' Submodule 'blaze' (https://bitbucket.org/blaze-lib/blaze.git) registered for path 'blaze' Submodule 'sleef' (https://github.com/shibatch/sleef) registered for path 'sleef' Cloning into 'blaze'... Submodule path 'bonsai/hll/vec/blaze': checked out '92ef7875b49177e428c872e7e31ca7813fd35bd3' Cloning into 'sleef'... Submodule path 'bonsai/hll/vec/sleef': checked out 'ae55d715d79f79ca01fbb367b96a89e74ffffcff' Cloning into 'klib'... Submodule path 'bonsai/klib': checked out 'f0f7639be2dd75a56a885df8bddea4f86bba7bee' Cloning into 'kspp'... Submodule path 'bonsai/kspp': checked out '6a49a53a986e0e96f93443549251de6cff777aae' Submodule 'klib' (https://github.com/attractivechaos/klib) registered for path 'klib' Cloning into 'klib'... Submodule path 'bonsai/kspp/klib': checked out '5fc2090766753bdaa9e53e0cc0734b285a891c85' Cloning into 'lazy'... Submodule path 'bonsai/lazy': checked out '2234ed49decbe628054f13dc45216139cb8a51b0' Cloning into 'libpopcnt'... Submodule path 'bonsai/libpopcnt': checked out '79219c154c72550ec8bc325a7e5db004db6041cc' Cloning into 'linear'... Submodule path 'bonsai/linear': checked out '0aa224367a0f09b5c3e5c90c715e3ff8fb2ffad3' Cloning into 'pdqsort'... Submodule path 'bonsai/pdqsort': checked out '08879029ab8dcb80a70142acb709e3df02de5d37' Cloning into 'distmat'... Submodule path 'distmat': checked out '3ffee11dc51a4cfeb562ca6d04ce46d3cb42db39' Switched to branch 'master' M hll Your branch is up-to-date with 'origin/master'. Already up-to-date. make[1]: Entering directory '/dashing/bonsai' make update -C bonsai make[2]: Entering directory '/dashing/bonsai/bonsai' for i in circularqueue clhash cppitertools hll klib kspp libpopcnt linear pdqsort tinythreadpp; \ do cd ../$i && git checkout master && git pull && cd ../bonsai; done; \ cd ../hll/vec && git checkout master && git pull && cd ../../bonsai Switched to branch 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. Switched to branch 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. /bin/sh: 2: cd: can't cd to ../cppitertools Switched to branch 'master' M aesctr Your branch is up-to-date with 'origin/master'. Already up-to-date. Switched to branch 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. Switched to branch 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. Switched to branch 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. Switched to branch 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. Switched to branch 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. Already on 'master' M hll Your branch is up-to-date with 'origin/master'. Already up-to-date. Switched to branch 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. make[2]: Leaving directory '/dashing/bonsai/bonsai' make[1]: Leaving directory '/dashing/bonsai' Already on 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. Switched to branch 'master' Your branch is up-to-date with 'origin/master'. Already up-to-date. cd bonsai/bonsai && make libzstd.a && cp libzstd.a ../../ make[1]: Entering directory '/dashing/bonsai/bonsai' cd .. && git clone --recursive https://github.com/facebook/zstd Cloning into 'zstd'... cd ../zstd && make lib && mv lib/libzstd.a ../bonsai && cd ../bonsai make[2]: Entering directory '/dashing/bonsai/zstd' make[3]: Entering directory '/dashing/bonsai/zstd/lib' cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o common/debug.o common/debug.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o common/entropy_common.o common/entropy_common.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o common/error_private.o common/error_private.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o common/fse_decompress.o common/fse_decompress.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o common/pool.o common/pool.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o common/threading.o common/threading.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o common/xxhash.o common/xxhash.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o common/zstd_common.o common/zstd_common.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/fse_compress.o compress/fse_compress.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/hist.o compress/hist.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/huf_compress.o compress/huf_compress.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/zstd_compress.o compress/zstd_compress.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/zstd_double_fast.o compress/zstd_double_fast.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/zstd_fast.o compress/zstd_fast.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/zstd_lazy.o compress/zstd_lazy.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/zstd_ldm.o compress/zstd_ldm.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/zstd_opt.o compress/zstd_opt.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o compress/zstdmt_compress.o compress/zstdmt_compress.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o decompress/huf_decompress.o decompress/huf_decompress.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o decompress/zstd_ddict.o decompress/zstd_ddict.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o decompress/zstd_decompress.o decompress/zstd_decompress.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o decompress/zstd_decompress_block.o decompress/zstd_decompress_block.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o deprecated/zbuff_common.o deprecated/zbuff_common.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o deprecated/zbuff_compress.o deprecated/zbuff_compress.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o deprecated/zbuff_decompress.o deprecated/zbuff_decompress.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o dictBuilder/cover.o dictBuilder/cover.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o dictBuilder/divsufsort.o dictBuilder/divsufsort.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o dictBuilder/fastcover.o dictBuilder/fastcover.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o dictBuilder/zdict.o dictBuilder/zdict.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o legacy/zstd_v05.o legacy/zstd_v05.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o legacy/zstd_v06.o legacy/zstd_v06.c cc -O3 -Wall -Wextra -Wcast-qual -Wcast-align -Wshadow -Wstrict-aliasing=1 -Wswitch-enum -Wdeclaration-after-statement -Wstrict-prototypes -Wundef -Wpointer-arith -Wformat-security -Wvla -Wformat=2 -Winit-self -Wfloat-equal -Wwrite-strings -Wredundant-decls -Wmissing-prototypes -Wc++-compat -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=5 -c -o legacy/zstd_v07.o legacy/zstd_v07.c compiling static library compiling dynamic library 1.3.8 creating versioned links make[3]: Leaving directory '/dashing/bonsai/zstd/lib' make[2]: Leaving directory '/dashing/bonsai/zstd' make[1]: Leaving directory '/dashing/bonsai/bonsai' cd bonsai/bonsai && make ../klib/kstring.o && cd ../.. && \ cd bonsai/bonsai && make ../klib/kthread.o && cd ../.. make[1]: Entering directory '/dashing/bonsai/bonsai' gcc -Iclhash/include -I. -I.. -I../libpopcnt -I.. -Iinclude -I../circularqueue -I../zstd/zlibWrapper -I../zstd/lib/common -I../zstd/lib -I../hll/vec -I../hll -I../pdqsort -DNDEBUG -c ../klib/kstring.c -o ../klib/kstring.o -lz make[1]: Leaving directory '/dashing/bonsai/bonsai' make[1]: Entering directory '/dashing/bonsai/bonsai' gcc -Iclhash/include -I. -I.. -I../libpopcnt -I.. -Iinclude -I../circularqueue -I../zstd/zlibWrapper -I../zstd/lib/common -I../zstd/lib -I../hll/vec -I../hll -I../pdqsort -DNDEBUG -c ../klib/kthread.c -o ../klib/kthread.o -lz make[1]: Leaving directory '/dashing/bonsai/bonsai' cd bonsai/bonsai && make clhash.o && cd ../.. make[1]: Entering directory '/dashing/bonsai/bonsai' ls clhash.o 2>/dev/null || mv ../clhash/clhash.o . 2>/dev/null || (cd ../clhash "&& git checkout master" && make && cd ../bonsai && ln -s ../clhash/clhash.o .) make[2]: Entering directory '/dashing/bonsai/clhash' cc -fPIC -std=c99 -O3 -msse4.2 -mpclmul -march=native -funroll-loops -Wstrict-overflow -Wstrict-aliasing -Wall -Wextra -pedantic -Wshadow -c ./src/clhash.c -Iinclude cc -fPIC -std=c99 -O3 -msse4.2 -mpclmul -march=native -funroll-loops -Wstrict-overflow -Wstrict-aliasing -Wall -Wextra -pedantic -Wshadow -o unit ./tests/unit.c -Iinclude clhash.o g++ -fPIC -std=c++11 -O3 -msse4.2 -mpclmul -march=native -funroll-loops -Wstrict-overflow -Wstrict-aliasing -Wall -Wextra -pedantic -Wshadow -o cppunit ./tests/cppunit.cpp -Iinclude clhash.o cc -fPIC -std=c99 -O3 -msse4.2 -mpclmul -march=native -funroll-loops -Wstrict-overflow -Wstrict-aliasing -Wall -Wextra -pedantic -Wshadow -o benchmark ./benchmarks/benchmark.c -Iinclude clhash.o cc -fPIC -std=c99 -O3 -msse4.2 -mpclmul -march=native -funroll-loops -Wstrict-overflow -Wstrict-aliasing -Wall -Wextra -pedantic -Wshadow -o example example.c -Iinclude clhash.o g++ -fPIC -std=c++11 -O3 -msse4.2 -mpclmul -march=native -funroll-loops -Wstrict-overflow -Wstrict-aliasing -Wall -Wextra -pedantic -Wshadow -o cppexample cppexample.cpp -Iinclude clhash.o make[2]: Leaving directory '/dashing/bonsai/clhash' make[1]: Leaving directory '/dashing/bonsai/bonsai' g++ -O3 -funroll-loops -pipe -fno-strict-aliasing -march=native -mpclmul -DUSE_PDQSORT -DNOT_THREADSAFE -DENABLE_COMPUTED_GOTO -fopenmp -fno-rtti -std=c++14 -Wall -Wextra -Wno-char-subscripts -Wpointer-arith -Wwrite-strings -Wdisabled-optimization -Wformat -Wcast-align -Wno-unused-function -Wno-unused-parameter -pedantic -Wunused-variable -Wno-attributes -Wno-pedantic -Ibonsai/clhash/include -I. -Ibonsai/zlib -Ibonsai/libpopcnt -Iinclude -Ibonsai/circularqueue -Ibonsai/zstd/zlibWrapper -Ibonsai/zstd/lib/common -Ibonsai/zstd/lib -Ibonsai/hll -Ibonsai/hll/vec -Ibonsai -Ibonsai/bonsai/include/ -L. -Lbonsai/zlib bonsai/klib/kstring.o bonsai/klib/kthread.o bonsai/bonsai/clhash.o -DNDEBUG src/dashing.cpp -o dashing -lz In file included from bonsai/hll/cbf.h:5:0, from bonsai/hll/filterhll.h:5, from ./bonsai/bonsai/include/encoder.h:11, from ./bonsai/bonsai/include/database.h:4, from src/dashing.cpp:5: bonsai/hll/aesctr/aesctr.h:42:37: warning: ignoring attributes on template argument '__m128i {aka __vector(2) long long int}' [-Wignored-attributes] template<>struct is_simd<__m128i>: std::true_type {}; ^ bonsai/hll/aesctr/aesctr.h:43:36: warning: ignoring attributes on template argument '__m128 {aka __vector(4) float}' [-Wignored-attributes] template<>struct is_simd<__m128>: std::true_type {}; ^ bonsai/hll/aesctr/aesctr.h:44:41: warning: ignoring attributes on template argument '__m128i {aka __vector(2) long long int}' [-Wignored-attributes] template<>struct is_simd_int<__m128i>: std::true_type {}; ^ bonsai/hll/aesctr/aesctr.h:45:42: warning: ignoring attributes on template argument '__m128 {aka __vector(4) float}' [-Wignored-attributes] template<>struct is_simd_float<__m128>: std::true_type {}; ^ bonsai/hll/aesctr/aesctr.h:48:37: warning: ignoring attributes on template argument '__m256i {aka __vector(4) long long int}' [-Wignored-attributes] template<>struct is_simd<__m256i>: std::true_type {}; ^ bonsai/hll/aesctr/aesctr.h:49:36: warning: ignoring attributes on template argument '__m256 {aka __vector(8) float}' [-Wignored-attributes] template<>struct is_simd<__m256>: std::true_type {}; ^ bonsai/hll/aesctr/aesctr.h:50:41: warning: ignoring attributes on template argument '__m256i {aka __vector(4) long long int}' [-Wignored-attributes] template<>struct is_simd_int<__m256i>: std::true_type {}; ^ bonsai/hll/aesctr/aesctr.h:51:42: warning: ignoring attributes on template argument '__m256 {aka __vector(8) float}' [-Wignored-attributes] template<>struct is_simd_float<__m256>: std::true_type {}; ^ In file included from ./bonsai/bonsai/include/entropy.h:2:0, from ./bonsai/bonsai/include/encoder.h:12, from ./bonsai/bonsai/include/database.h:4, from src/dashing.cpp:5: bonsai/circularqueue/circular_buffer.h: In instantiation of 'T circ::roundup(T) [with T = unsigned int]': bonsai/circularqueue/circular_buffer.h:147:26: required from 'circ::FastCircularQueue::FastCircularQueue(SizeType) [with T = bns::ElScore; SizeType = unsigned int]' ./bonsai/bonsai/include/qmap.h:46:47: required from 'bns::QueueMap::QueueMap(std::size_t) [with T = long unsigned int; ScoreType = long unsigned int; std::size_t = long unsigned int]' ./bonsai/bonsai/include/encoder.h:154:33: required from 'bns::Encoder::Encoder(char*, bns::u64, const bns::Spacer&, void*, bool, uint64_t) [with ScoreType = bns::score::Entropy; bns::u64 = long unsigned int; uint64_t = long unsigned int]' src/dashing.cpp:295:9: required from here bonsai/circularqueue/circular_buffer.h:30:37: warning: right shift count >= width of type [-Wshift-count-overflow] CIRC_CONSTIF(sizeof(T) > 4) x|=x>>32; // Throws a warning on shift count. This is avoided in C++17, but is unavoidable in C++14 because of the lack of `if constexpr`. ~^~~~ In file included from ./bonsai/bonsai/include/popcnt.h:8:0, from ./bonsai/bonsai/include/util.h:35, from src/dashing.cpp:4: bonsai/hll/hll.h: In member function 'void sketch::hll::hllbase_t::write(int) const [with HashStruct = sketch::common::WangHash]': bonsai/hll/hll.h:1045:9: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] ::write(fileno, bf, sizeof(bf)); ^~ bonsai/hll/hll.h:1046:9: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] ::write(fileno, &np_, sizeof(np_)); ^~ bonsai/hll/hll.h:1047:9: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] ::write(fileno, &value_, sizeof(value_)); ^~ bonsai/hll/hll.h:1048:9: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] ::write(fileno, core_.data(), core_.size() * sizeof(core_[0])); ^~ In file included from bonsai/hll/common.h:20:0, from bonsai/hll/hll.h:3, from ./bonsai/bonsai/include/popcnt.h:8, from ./bonsai/bonsai/include/util.h:35, from src/dashing.cpp:4: bonsai/hll/sseutil.h: In function 'void* sse::detail::allocate_aligned_memory(size_t, size_t)': bonsai/hll/sseutil.h:40:42: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)', declared with attribute warn_unused_result [-Wunused-result] posix_memalign(&ret, align, size); ^ In file included from src/dashing.cpp:10:0: ./distmat/distmat.h: In member function 'void dm::DistanceMatrix >::read(const char*) [with ArithType = float; long unsigned int DefaultValue = 0ul; = void]': ./distmat/distmat.h:148:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] std::fread(&nelem_, sizeof(nelem_), 1, fp); ^~~ ./distmat/distmat.h:154:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] std::fread(data_.data(), sizeof(ArithType), data_.size(), fp); ^~~ ./distmat/distmat.h: In member function 'void dm::DistanceMatrix >::read(const char*) [with ArithType = double; long unsigned int DefaultValue = 0ul; = void]': ./distmat/distmat.h:148:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] std::fread(&nelem_, sizeof(nelem_), 1, fp); ^~~ ./distmat/distmat.h:154:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] std::fread(data_.data(), sizeof(ArithType), data_.size(), fp); ^~~ Removing intermediate container 1688b3fcf6aa ---> aab7aa8662c4 Step 19/19 : WORKDIR / ---> Running in 9d0433ffc9ce Removing intermediate container 9d0433ffc9ce ---> 6274b0ab62fe Successfully built 6274b0ab62fe ```

It's also possible to link GitHub Dockerfiles to DockerHub so one could docker pull dnbaker/dashing and the latest commit to the Dockerfile will be used for that image.

[dnbaker]

Hi!

Thank you for putting this together. This looks great, and it should help portability for people without recent compilers enabled by default. I'd like to test it myself before merging, but I should be able to within the next day or two.

I wanted to check in, though -- you mentioned difficulties getting it to install. Did you have any compilation issues along the way? I'd like to make sure I can help address those as well.