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Standard_init_linux.go:187: exec user process caused "no such file or directory"


(Revlyn) #1

Hello,

I am fairly new to docker, so forgive me for making any stupid mistakes :slight_smile:

Currently I am setting up some docker containers. For automated builds i require a custom MySQL-image that executes a create-script when a container is created.

Sadly, im only halfway and stuck already.

Pulling and running the official MySQL image and creating containers out of it works fine. So i went to get the sourcecode and packed it in a .tar file. I sent this file to my linux(Centos7) server and created an image out of it, this works fine.

But, this is where the problem occurs

When i create a container out of this image in the same way as the pulled MySQL-image, it demands me to specify a command.

docker run --name custommysql1 -e MYSQL_ROOT_PASSWORD=password-d custommysql
docker: Error response from daemon: No command specified.

After some research, it seems that some metadata is lost on importing and exporting. So i need to specify a run command like this (correct me if im wrong)

docker run --name custommysql1 -e MYSQL_ROOT_PASSWORD=password-d custommysql /docker-entrypoint.sh
45c52f3ca65faf2661fec8277cd065378ab5dc8cf6ee4453b3bd56931a378904

So, the container is created. But, it stops immediately. The docker ps -a command shows me that the container exits instantly.

docker logs {containerID} its showing me the following message

standard_init_linux.go:187: exec user process caused no such file or directory

So basically, this is the only error-message that i’ve got. I have tried to specify other commands like /bin/bash but it does not make a difference.

The .tar exists out of these files:
image

docker-entrypoint

#!/bin/bash
set -eo pipefail
shopt -s nullglob

# if command starts with an option, prepend mysqld
if [ "${1:0:1}" = '-' ]; then
	set -- mysqld "$@"
fi

# skip setup if they want an option that stops mysqld
wantHelp=
for arg; do
	case "$arg" in
		-'?'|--help|--print-defaults|-V|--version)
			wantHelp=1
			break
			;;
	esac
done

# usage: file_env VAR [DEFAULT]
#    ie: file_env 'XYZ_DB_PASSWORD' 'example'
# (will allow for "$XYZ_DB_PASSWORD_FILE" to fill in the value of
#  "$XYZ_DB_PASSWORD" from a file, especially for Docker's secrets feature)
file_env() {
	local var="$1"
	local fileVar="${var}_FILE"
	local def="${2:-}"
	if [ "${!var:-}" ] && [ "${!fileVar:-}" ]; then
		echo >&2 "error: both $var and $fileVar are set (but are exclusive)"
		exit 1
	fi
	local val="$def"
	if [ "${!var:-}" ]; then
		val="${!var}"
	elif [ "${!fileVar:-}" ]; then
		val="$(< "${!fileVar}")"
	fi
	export "$var"="$val"
	unset "$fileVar"
}

_check_config() {
	toRun=( "$@" --verbose --help )
	if ! errors="$("${toRun[@]}" 2>&1 >/dev/null)"; then
		cat >&2 <<-EOM

			ERROR: mysqld failed while attempting to check config
			command was: "${toRun[*]}"

			$errors
		EOM
		exit 1
	fi
}

# Fetch value from server config
# We use mysqld --verbose --help instead of my_print_defaults because the
# latter only show values present in config files, and not server defaults
_get_config() {
	local conf="$1"; shift
	"$@" --verbose --help --log-bin-index="$(mktemp -u)" 2>/dev/null | awk '$1 == "'"$conf"'" { print $2; exit }'
}

# allow the container to be started with `--user`
if [ "$1" = 'mysqld' -a -z "$wantHelp" -a "$(id -u)" = '0' ]; then
	_check_config "$@"
	DATADIR="$(_get_config 'datadir' "$@")"
	mkdir -p "$DATADIR"
	chown -R mysql:mysql "$DATADIR"
	exec gosu mysql "$BASH_SOURCE" "$@"
fi

if [ "$1" = 'mysqld' -a -z "$wantHelp" ]; then
	# still need to check config, container may have started with --user
	_check_config "$@"
	# Get config
	DATADIR="$(_get_config 'datadir' "$@")"

	if [ ! -d "$DATADIR/mysql" ]; then
		file_env 'MYSQL_ROOT_PASSWORD'
		if [ -z "$MYSQL_ROOT_PASSWORD" -a -z "$MYSQL_ALLOW_EMPTY_PASSWORD" -a -z "$MYSQL_RANDOM_ROOT_PASSWORD" ]; then
			echo >&2 'error: database is uninitialized and password option is not specified '
			echo >&2 '  You need to specify one of MYSQL_ROOT_PASSWORD, MYSQL_ALLOW_EMPTY_PASSWORD and MYSQL_RANDOM_ROOT_PASSWORD'
			exit 1
		fi

		mkdir -p "$DATADIR"

		echo 'Initializing database'
		"$@" --initialize-insecure
		echo 'Database initialized'

		if command -v mysql_ssl_rsa_setup > /dev/null && [ ! -e "$DATADIR/server-key.pem" ]; then
			# https://github.com/mysql/mysql-server/blob/23032807537d8dd8ee4ec1c4d40f0633cd4e12f9/packaging/deb-in/extra/mysql-systemd-start#L81-L84
			echo 'Initializing certificates'
			mysql_ssl_rsa_setup --datadir="$DATADIR"
			echo 'Certificates initialized'
		fi

		SOCKET="$(_get_config 'socket' "$@")"
		"$@" --skip-networking --socket="${SOCKET}" &
		pid="$!"

		mysql=( mysql --protocol=socket -uroot -hlocalhost --socket="${SOCKET}" )

		for i in {30..0}; do
			if echo 'SELECT 1' | "${mysql[@]}" &> /dev/null; then
				break
			fi
			echo 'MySQL init process in progress...'
			sleep 1
		done
		if [ "$i" = 0 ]; then
			echo >&2 'MySQL init process failed.'
			exit 1
		fi

		if [ -z "$MYSQL_INITDB_SKIP_TZINFO" ]; then
			# sed is for https://bugs.mysql.com/bug.php?id=20545
			mysql_tzinfo_to_sql /usr/share/zoneinfo | sed 's/Local time zone must be set--see zic manual page/FCTY/' | "${mysql[@]}" mysql
		fi

		if [ ! -z "$MYSQL_RANDOM_ROOT_PASSWORD" ]; then
			export MYSQL_ROOT_PASSWORD="$(pwgen -1 32)"
			echo "GENERATED ROOT PASSWORD: $MYSQL_ROOT_PASSWORD"
		fi

		rootCreate=
		# default root to listen for connections from anywhere
		file_env 'MYSQL_ROOT_HOST' '%'
		if [ ! -z "$MYSQL_ROOT_HOST" -a "$MYSQL_ROOT_HOST" != 'localhost' ]; then
			# no, we don't care if read finds a terminating character in this heredoc
			# https://unix.stackexchange.com/questions/265149/why-is-set-o-errexit-breaking-this-read-heredoc-expression/265151#265151
			read -r -d '' rootCreate <<-EOSQL || true
				CREATE USER 'root'@'${MYSQL_ROOT_HOST}' IDENTIFIED BY '${MYSQL_ROOT_PASSWORD}' ;
				GRANT ALL ON *.* TO 'root'@'${MYSQL_ROOT_HOST}' WITH GRANT OPTION ;
			EOSQL
		fi

		"${mysql[@]}" <<-EOSQL
			-- What's done in this file shouldn't be replicated
			--  or products like mysql-fabric won't work
			SET @@SESSION.SQL_LOG_BIN=0;

			DELETE FROM mysql.user WHERE user NOT IN ('mysql.sys', 'mysqlxsys', 'root') OR host NOT IN ('localhost') ;
			SET PASSWORD FOR 'root'@'localhost'=PASSWORD('${MYSQL_ROOT_PASSWORD}') ;
			GRANT ALL ON *.* TO 'root'@'localhost' WITH GRANT OPTION ;
			${rootCreate}
			DROP DATABASE IF EXISTS test ;
			FLUSH PRIVILEGES ;
		EOSQL

		if [ ! -z "$MYSQL_ROOT_PASSWORD" ]; then
			mysql+=( -p"${MYSQL_ROOT_PASSWORD}" )
		fi

		file_env 'MYSQL_DATABASE'
		if [ "$MYSQL_DATABASE" ]; then
			echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` ;" | "${mysql[@]}"
			mysql+=( "$MYSQL_DATABASE" )
		fi

		file_env 'MYSQL_USER'
		file_env 'MYSQL_PASSWORD'
		if [ "$MYSQL_USER" -a "$MYSQL_PASSWORD" ]; then
			echo "CREATE USER '$MYSQL_USER'@'%' IDENTIFIED BY '$MYSQL_PASSWORD' ;" | "${mysql[@]}"

			if [ "$MYSQL_DATABASE" ]; then
				echo "GRANT ALL ON \`$MYSQL_DATABASE\`.* TO '$MYSQL_USER'@'%' ;" | "${mysql[@]}"
			fi

			echo 'FLUSH PRIVILEGES ;' | "${mysql[@]}"
		fi

		echo
		for f in /docker-entrypoint-initdb.d/*; do
			case "$f" in
				*.sh)     echo "$0: running $f"; . "$f" ;;
				*.sql)    echo "$0: running $f"; "${mysql[@]}" < "$f"; echo ;;
				*.sql.gz) echo "$0: running $f"; gunzip -c "$f" | "${mysql[@]}"; echo ;;
				*)        echo "$0: ignoring $f" ;;
			esac
			echo
		done

		if [ ! -z "$MYSQL_ONETIME_PASSWORD" ]; then
			"${mysql[@]}" <<-EOSQL
				ALTER USER 'root'@'%' PASSWORD EXPIRE;
			EOSQL
		fi
		if ! kill -s TERM "$pid" || ! wait "$pid"; then
			echo >&2 'MySQL init process failed.'
			exit 1
		fi

		echo
		echo 'MySQL init process done. Ready for start up.'
		echo
	fi
fi

exec "$@"

Dockerfile

FROM debian:jessie

# add our user and group first to make sure their IDs get assigned consistently, regardless of whatever dependencies get added
RUN groupadd -r mysql && useradd -r -g mysql mysql

# add gosu for easy step-down from root
ENV GOSU_VERSION 1.7
RUN set -x \
	&& apt-get update && apt-get install -y --no-install-recommends ca-certificates wget && rm -rf /var/lib/apt/lists/* \
	&& wget -O /usr/local/bin/gosu "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$(dpkg --print-architecture)" \
	&& wget -O /usr/local/bin/gosu.asc "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$(dpkg --print-architecture).asc" \
	&& export GNUPGHOME="$(mktemp -d)" \
	&& gpg --keyserver ha.pool.sks-keyservers.net --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4 \
	&& gpg --batch --verify /usr/local/bin/gosu.asc /usr/local/bin/gosu \
	&& rm -r "$GNUPGHOME" /usr/local/bin/gosu.asc \
	&& chmod +x /usr/local/bin/gosu \
	&& gosu nobody true \
	&& apt-get purge -y --auto-remove ca-certificates wget

RUN mkdir /docker-entrypoint-initdb.d

RUN apt-get update && apt-get install -y --no-install-recommends \
# for MYSQL_RANDOM_ROOT_PASSWORD
		pwgen \
# for mysql_ssl_rsa_setup
		openssl \
# FATAL ERROR: please install the following Perl modules before executing /usr/local/mysql/scripts/mysql_install_db:
# File::Basename
# File::Copy
# Sys::Hostname
# Data::Dumper
		perl \
	&& rm -rf /var/lib/apt/lists/*

RUN set -ex; \
# gpg: key 5072E1F5: public key "MySQL Release Engineering <mysql-build@oss.oracle.com>" imported
	key='A4A9406876FCBD3C456770C88C718D3B5072E1F5'; \
	export GNUPGHOME="$(mktemp -d)"; \
	gpg --keyserver ha.pool.sks-keyservers.net --recv-keys "$key"; \
	gpg --export "$key" > /etc/apt/trusted.gpg.d/mysql.gpg; \
	rm -r "$GNUPGHOME"; \
	apt-key list > /dev/null

ENV MYSQL_MAJOR 5.7
ENV MYSQL_VERSION 5.7.19-1debian8

RUN echo "deb http://repo.mysql.com/apt/debian/ jessie mysql-${MYSQL_MAJOR}" > /etc/apt/sources.list.d/mysql.list

# the "/var/lib/mysql" stuff here is because the mysql-server postinst doesn't have an explicit way to disable the mysql_install_db codepath besides having a database already "configured" (ie, stuff in /var/lib/mysql/mysql)
# also, we set debconf keys to make APT a little quieter
RUN { \
		echo mysql-community-server mysql-community-server/data-dir select ''; \
		echo mysql-community-server mysql-community-server/root-pass password ''; \
		echo mysql-community-server mysql-community-server/re-root-pass password ''; \
		echo mysql-community-server mysql-community-server/remove-test-db select false; \
	} | debconf-set-selections \
	&& apt-get update && apt-get install -y mysql-server="${MYSQL_VERSION}" && rm -rf /var/lib/apt/lists/* \
	&& rm -rf /var/lib/mysql && mkdir -p /var/lib/mysql /var/run/mysqld \
	&& chown -R mysql:mysql /var/lib/mysql /var/run/mysqld \
# ensure that /var/run/mysqld (used for socket and lock files) is writable regardless of the UID our mysqld instance ends up having at runtime
	&& chmod 777 /var/run/mysqld

# comment out a few problematic configuration values
# don't reverse lookup hostnames, they are usually another container
RUN sed -Ei 's/^(bind-address|log)/#&/' /etc/mysql/mysql.conf.d/mysqld.cnf \
	&& echo '[mysqld]\nskip-host-cache\nskip-name-resolve' > /etc/mysql/conf.d/docker.cnf

VOLUME /var/lib/mysql

COPY docker-entrypoint.sh /usr/local/bin/
RUN ln -s usr/local/bin/docker-entrypoint.sh /entrypoint.sh # backwards compat
ENTRYPOINT ["docker-entrypoint.sh"]

EXPOSE 3306
CMD ["mysqld"]

Hopefully someone can help me solve this!
Greetings, Revlyn


(Joaoaneto) #2

I had this same problem today and I could not resolve with the existing discussions. Waiting for some help.

Setup until problem.

My Dockerfile:

FROM iron/base

EXPOSE 6767
ADD account-linux-amd64 /
ENTRYPOINT ["./account-linux-amd64"]

$ sudo docker build -t joaoneto/account account/

Step 1/4 : FROM iron/base
 ---> b65946736b2c
Step 2/4 : EXPOSE 6767
 ---> Using cache
 ---> 5d08307c9670
Step 3/4 : ADD account-linux-amd64 /
 ---> Using cache
 ---> db5d96759dfc
Step 4/4 : ENTRYPOINT ./account-linux-amd64
 ---> Using cache
 ---> 2f072423b7b0
Successfully built 2f072423b7b0
Successfully tagged joaoneto/account:latest

So, let’s run:
$ sudo docker run --rm joaoneto/account

Output:

standard_init_linux.go:187: exec user process caused "no such file or directory"


(Chris Grimmett) #3

A file is not found, but it’s not necessarily your entrypoint. I had a similar issue and it was because /bin/bash did not exist in the container. I had to change the interpreter line of my entrypoint file from #!/bin/bash to #!/bin/sh and the problem was solved.

Another potential issue is where the line endings of the entrypoint are in DOS format, not Unix format. See here for more details.


(Jakewatkins) #4

facepalm
I just spent an hour fighting with this blasted problem. Thank you @insanity54.

Really annoying part to this was that I could build the image with the entry point commented out and run my script and everything worked. But as soon as I put the entrypoint back in it went back to “exec format error”. Very frustrating.

Again: thank you.


(Venkat12345) #5

i also had same issue… i am also getting same logs when i run my artifactory container.

linux_187 exec format error… can anyone help me…