Monday, March 30, 2020

Compiling from source for Amazon Linux 2

Different is worse

I used to know struggle with  make & automake but I knew enough to get things done. Now I have fun with make, cmake, maven and gradle. I am sure this proliferation solves problems for people who create the build scripts that I use. But it isn't a good experience for the intermittent user -- different is worse because my skill level per tool is lower.

What is Amazon Linux 2? It has a landing page. I call it AL2 below. It claims to be like CentOS, RHEL, Fedora and it uses yum. I know how to use Google to get answers for those distros when trying to figure out how to build something from source.

But it isn't clear to me that packages that exist for CentOS also exist for AL2. One example of the challenge is that I ended up installing jemalloc from source because I couldn't find the package without advice from an expert.

I hope the output from cat /etc/os-release on AL2 is improved. Below are examples for AL2 and Ubuntu 18.04. Ubuntu specific that this is Ubuntu 18.04. From AL2 I learn it is like CentOS. But which CentOS?

NAME="Amazon Linux" 
VERSION="2" ID="amzn"
ID_LIKE="centos rhel fedora"
VERSION_ID="2"
PRETTY_NAME="Amazon Linux 2"
ANSI_COLOR="0;33"
CPE_NAME="cpe:2.3:o:amazon:amazon_linux:2"
HOME_URL="https://amazonlinux.com/" 


Lets compare that with Ubuntu:

NAME="Ubuntu"
VERSION="18.04.4 LTS (Bionic Beaver)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 18.04.4 LTS"
VERSION_ID="18.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=bionic
UBUNTU_CODENAME=bionic

Dependencies for AL2

This explains how to satisfy the dependencies before running cmake. I struggled figuring out the names for packages that had to be installed. Some of this is because I don't have much experience with CentOS, some of this is on AL2. Eventually I found this page which might have helped.

Add libraries for the insert benchmark, some of this is needed for the build and all is needed when I run benchmarks so I will just install before I try to build:

sudo yum install -y python3
sudo python3 -m pip install pymongo
sudo yum install -y mysql-devel python3-devel
sudo pip3 install mysqlclient
sudo pip3 install psycopg2-binary
sudo yum install -y openssl11-libs
sudo yum install -y libzstd-1.3.3
sudo yum install -y ncurses-compat-libs
# The host arrives comes with /etc/my.cnf from MariaDB

sudo rm -f /etc/my.cnf /etc/mysql/my.cnf

Install jemalloc from source because I couldn't figure out how to install the package:

cd /media/ephemeral1
rm -rf jemalloc-5.2.1*
wget https://github.com/jemalloc/jemalloc/releases/download/5.2.1/jemalloc-5.2.1.tar.bz2
bunzip2 jemalloc-5.2.1.tar.bz2
tar xvf jemalloc-5.2.1.tar
cd jemalloc-5.2.1
./configure --prefix=/usr > o.cf 2> e.cf
make -j4 > o.m 2> e.m
sudo make install

Install things needed to compile MySQL8 and MyRocks from FB MySQL 5.6. I didn't confirm that all of these packages exist. But I was able to build after doing this:
sudo yum install -y cmake3
sudo yum install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
sudo yum install -y numactl-devel
sudo yum install -y libedit-devel
sudo yum install -y cmake gcc-c++ bzip2-devel libaio-devel bison 
sudo yum install -y zlib-devel snappy-devel
sudo yum install -y gflags-devel readline-devel ncurses-devel openssl-devel
sudo yum install -y lz4-devel gdb git libzstd-devel

Building MySQL8

Download, compile and install MySQL 8. It is installed at /media/ephemeral1/my8018. The upstream docs are useful.

cd /media/ephemeral1
rm -rf mysql-8.0.18*
wget https://downloads.mysql.com/archives/get/p/23/file/mysql-boost-8.0.18.tar.gz
tar xzvf mysql-boost-8.0.18.tar.gz
cd mysql-8.0.18
mkdir build
cd build
bash /media/ephemeral1/cmk80 /media/ephemeral1/my8018 > o.cm 2> e.cm
make -j8 V=1 VERBOSE=1 > o.mk 2> e.mk
make install

The contents of /media/ephemeral/cmk80.

prefix=$1
cmake3 .. \
      -DBUILD_CONFIG=mysql_release \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo \
      -DCMAKE_INSTALL_PREFIX:PATH=$prefix \
      -DWITH_SSL="system" \
      -DWITH_ZLIB="system" \
      -DMYSQL_DATADIR="${prefix}/data" \
      -DMYSQL_UNIX_ADDR="${prefix}/var/mysql.sock" \
      -DENABLED_LOCAL_INFILE=1 \
      -DMYSQL_MAINTAINER_MODE=0 \
      -DWITH_BOOST=$PWD/../boost \
      -DWITH_NUMA=ON 

Building MyRocks

Download, compile and install MyRocks from FB MySQL 5.6. It is installed at /media/ephemeral1/fbmy56. The upstream docs are useful.

First install boost 1.65 from source:

cd /media/ephemeral1
wget https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2
bunzip2 boost_1_65_1.tar.bz2
tar xvf boost_1_65_1.tar
cd boost_1_65_1
./bootstrap.sh --prefix=/usr

./b2 > o.b2 2> e.b2
sudo ./b2 install

Then build MySQL 5.6

cd /media/ephemeral1
git clone https://github.com/facebook/mysql-5.6.git fbmy56-src
cd fbmy56-src
git checkout 20aaaf8d
git submodule init
git submodule update
mkdir build
cd build
bash /media/ephemeral1/cmkfbmy56 /media/ephemeral1/fbmy56 > o.cm 2> e.cm
make -j8 V=1 VERBOSE=1 > o.mk 2> e.mk
make install

The contents of /media/ephemeral1/cmkfbmy56

if [ -z $1 ]; then
echo Requires prefix as arg1
exit -1
fi

RXF=" -DROCKSDB_DEFAULT_TO_ADAPTIVE_MUTEX -DROCKSDB_SUPPORT_THREAD_LOCAL -DROCKSDB_SCHED_GETCPU_PRESENT"
RXF+=" -DROCKSDB_RANGESYNC_PRESENT -DROCKSDB_MALLOC_USABLE_SIZE -DROCKSDB_FALLOCATE_PRESENT"
RXF+=" -DHAVE_ALIGNED_NEW"
RXF+=" -DROCKSDB_SUPPORT_THREAD_LOCAL"
RXF+=" -DHAVE_PCLMUL -DHAVE_SSE42 -DHAVE_AVX2 -DHAVE_UINT128_EXTENSION"
RXF+=" -DROCKSDB_PLATFORM_POSIX -DROCKSDB_LIB_IO_POSIX -DOS_LINUX"

CXXF="-DNDEBUG -march=native -msse -msse4.2 -mpclmul"
CXXF+=" -faligned-new"
CXXF+=" $RXF"

# extra flags to avoid warnings with gcc on ubuntu 18
CF="-Wno-implicit-fallthrough -Wno-int-in-bool-context \
  -Wno-shift-negative-value -Wno-misleading-indentation \
  -Wno-format-overflow -Wno-nonnull -Wno-unused-function"

CXXF+=" -Wno-implicit-fallthrough -Wno-int-in-bool-context \
  -Wno-shift-negative-value -Wno-misleading-indentation \
  -Wno-format-overflow -Wno-nonnull -Wno-unused-function"

cmake3 .. \
  -DCMAKE_BUILD_TYPE=RelWithDebInfo \
  -DMYSQL_MAINTAINER_MODE=0 \
  -DENABLED_LOCAL_INFILE=1 \
  -DENABLE_DTRACE=0 \
  -DCMAKE_CXX_FLAGS="$CXXF" -DCMAKE_C_FLAGS="$CF" \
  -DCMAKE_INSTALL_PREFIX=$1 \
  -DWITH_SSL=system \
  -DWITH_ZLIB=bundled \
-DWITH_LZ4=system \
-DWITH_ZSTD=system

Not done yet

There is a crash in Boost code that was added in the FB MySQL branch. Boost 1.53 is installed by yum install boost-devel. I will rebuild MyRocks with Boost 1.65 as that is what Ubuntu 18.04 uses, and MyRocks works great for me there.

./bin/mysqld(my_print_stacktrace+0x2e)[0xac581e]
./bin/mysqld(handle_fatal_signal+0x333)[0x7e8293]
/lib64/libpthread.so.0(+0x117e0)[0x7f22703f37e0]
./bin/mysqld(_ZN5boost13property_tree11json_parser12json_grammarINS0_11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_St4lessIS9_EEEE10definitionINS_6spirit7cl
assic7scannerIN9__gnu_cxx17__normal_iteratorIPcSt6vectorIcS8_EEENSG_16scanner_policiesINSG_28skip_parser_iteration_policyINSG_11alternativeINSQ_INSG_12space_parserENSG_13confix_pa
rserINSG_6strlitIPKcEENSG_11kleene_starINSG_14anychar_parserEEENSQ_INSG_10eol_parserENSG_10end_parserEEENSG_21unary_parser_categoryENSG_10non_nestedENSG_9is_lexemeEEEEENSS_ISW_SZ_
SW_S13_S14_S15_EEEENSG_16iteration_policyEEENSG_12match_policyENSG_13action_policyEEEEEED1Ev+0xc)[0x840eec]
./bin/mysqld(_ZN5boost6spirit7classic4impl14grammar_helperINS1_7grammarINS_13property_tree11json_parser12json_grammarINS5_11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsI
cESaIcEEESE_St4lessISE_EEEEENS1_14parser_contextINS1_5nil_tEEEEESI_NS1_7scannerIN9__gnu_cxx17__normal_iteratorIPcSt6vectorIcSD_EEENS1_16scanner_policiesINS1_28skip_parser_iteratio
n_policyINS1_11alternativeINSW_INS1_12space_parserENS1_13confix_parserINS1_6strlitIPKcEENS1_11kleene_starINS1_14anychar_parserEEENSW_INS1_10eol_parserENS1_10end_parserEEENS1_21una
ry_parser_categoryENS1_10non_nestedENS1_9is_lexemeEEEEENSY_IS12_S15_S12_S19_S1A_S1B_EEEENS1_16iteration_policyEEENS1_12match_policyENS1_13action_policyEEEEEE8undefineEPSM_+0x43)[0
x840fe3]
./bin/mysqld(_ZN5boost6spirit7classic7grammarINS_13property_tree11json_parser12json_grammarINS3_11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESC_St4lessISC_EEE
EENS1_14parser_contextINS1_5nil_tEEEED1Ev+0x34)[0x840cb4]
./bin/mysqld(_ZN5boost13property_tree11json_parser18read_json_internalINS0_11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_St4lessIS9_EEEEEvRSt13basic_istream
INT_8key_type10value_typeES6_ISG_EERSE_RKS9_+0xc51)[0x844511]
./bin/mysqld[0x839e32]
./bin/mysqld(_ZN3THD12set_shard_idEv+0x1c)[0x83a26c]
./bin/mysqld(_ZN3THD15set_db_metadataEv+0x1e3)[0x852e73]
./bin/mysqld(_Z15mysql_change_dbP3THDPK19st_mysql_lex_stringb+0x5da)[0x84f6ca]
./bin/mysqld(_Z16acl_authenticateP3THDj+0x13a5)[0x80e685]
./bin/mysqld[0x847d26]
./bin/mysqld(_Z16login_connectionP3THD+0x4d)[0x849c2d]
./bin/mysqld(_Z24do_handle_one_connectionP3THD+0x199)[0x84aa29]
./bin/mysqld(handle_one_connection+0x9)[0x84adc9]
/lib64/libpthread.so.0(+0x740b)[0x7f22703e940b]
/lib64/libc.so.6(clone+0x3f)[0x7f226e2a7e7f]

stack_log: _ZN5boost13property_tree11json_parser12json_grammarINS0_11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_St4lessIS9_EEEE10definitionINS_6spirit7clas
sic7scannerIN9__gnu_cxx17__normal_iteratorIPcSt6vectorIcS8_EEENSG_16scanner_policiesINS


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