X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3aaefcb3c76ff470b475d950398d01255e87712a..37d9f94b06ff367a3514b58ec6f0e4d4d0116030:/lib/install/deps.go

diff --git a/lib/install/deps.go b/lib/install/deps.go
index cc9595db64..ca4b681475 100644
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -34,6 +34,7 @@ type installCommand struct {
 	ClusterType    string
 	SourcePath     string
 	PackageVersion string
+	EatMyData      bool
 }
 
 func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
@@ -55,17 +56,12 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 	flags.StringVar(&inst.ClusterType, "type", "production", "cluster `type`: development, test, production, or package")
 	flags.StringVar(&inst.SourcePath, "source", "/arvados", "source tree location (required for -type=package)")
 	flags.StringVar(&inst.PackageVersion, "package-version", "0.0.0", "version string to embed in executable files")
-	err = flags.Parse(args)
-	if err == flag.ErrHelp {
-		err = nil
-		return 0
-	} else if err != nil {
-		return 2
+	flags.BoolVar(&inst.EatMyData, "eatmydata", false, "use eatmydata to speed up install")
+
+	if ok, code := cmd.ParseFlags(flags, prog, args, "", stderr); !ok {
+		return code
 	} else if *versionFlag {
 		return cmd.Version.RunCommand(prog, args, stdin, stdout, stderr)
-	} else if len(flags.Args()) > 0 {
-		err = fmt.Errorf("unrecognized command line arguments: %v", flags.Args())
-		return 2
 	}
 
 	var dev, test, prod, pkg bool
@@ -109,11 +105,23 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 		}
 	}
 
+	if inst.EatMyData {
+		cmd := exec.CommandContext(ctx, "apt-get", "install", "--yes", "--no-install-recommends", "eatmydata")
+		cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
+		cmd.Stdout = stdout
+		cmd.Stderr = stderr
+		err = cmd.Run()
+		if err != nil {
+			return 1
+		}
+	}
+
 	pkgs := prodpkgs(osv)
 
 	if pkg {
 		pkgs = append(pkgs,
 			"dpkg-dev",
+			"eatmydata", // install it for later steps, even if we're not using it now
 			"rsync",
 		)
 	}
@@ -127,7 +135,6 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 			"cadaver",
 			"curl",
 			"cython3",
-			"daemontools", // lib/boot uses setuidgid to drop privileges when running as root
 			"default-jdk-headless",
 			"default-jre-headless",
 			"gettext",
@@ -165,16 +172,26 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 			"r-cran-roxygen2",
 			"r-cran-xml",
 			"sudo",
+			"uuid-dev",
 			"wget",
 			"xvfb",
 		)
+		if dev || test {
+			pkgs = append(pkgs,
+				"squashfs-tools", // for singularity
+			)
+		}
 		switch {
 		case osv.Debian && osv.Major >= 10:
 			pkgs = append(pkgs, "libcurl4")
 		default:
 			pkgs = append(pkgs, "libcurl3")
 		}
-		cmd := exec.CommandContext(ctx, "apt-get", "install", "--yes", "--no-install-recommends")
+		cmd := exec.CommandContext(ctx, "apt-get")
+		if inst.EatMyData {
+			cmd = exec.CommandContext(ctx, "eatmydata", "apt-get")
+		}
+		cmd.Args = append(cmd.Args, "install", "--yes", "--no-install-recommends")
 		cmd.Args = append(cmd.Args, pkgs...)
 		cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
 		cmd.Stdout = stdout
@@ -201,22 +218,20 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 			return 1
 		}
 	}
-	rubyversion := "2.5.7"
+	rubyversion := "2.7.2"
+	rubymajorversion := rubyversion[:strings.LastIndex(rubyversion, ".")]
 	if haverubyversion, err := exec.Command("/var/lib/arvados/bin/ruby", "-v").CombinedOutput(); err == nil && bytes.HasPrefix(haverubyversion, []byte("ruby "+rubyversion)) {
 		logger.Print("ruby " + rubyversion + " already installed")
 	} else {
-		err = runBash(`
-tmp=/var/lib/arvados/tmp/ruby-`+rubyversion+`
-trap "rm -r ${tmp}" ERR
-wget --progress=dot:giga -O- https://cache.ruby-lang.org/pub/ruby/2.5/ruby-`+rubyversion+`.tar.gz | tar -C /var/lib/arvados/tmp -xzf -
-cd ${tmp}
+		err = inst.runBash(`
+tmp="$(mktemp -d)"
+trap 'rm -r "${tmp}"' ERR EXIT
+wget --progress=dot:giga -O- https://cache.ruby-lang.org/pub/ruby/`+rubymajorversion+`/ruby-`+rubyversion+`.tar.gz | tar -C "${tmp}" -xzf -
+cd "${tmp}/ruby-`+rubyversion+`"
 ./configure --disable-install-static-library --enable-shared --disable-install-doc --prefix /var/lib/arvados
 make -j8
 make install
-/var/lib/arvados/bin/gem install bundler --no-ri --no-rdoc
-# "gem update --system" can be removed when we use ruby ≥2.6.3: https://bundler.io/blog/2019/05/14/solutions-for-cant-find-gem-bundler-with-executable-bundle.html
-/var/lib/arvados/bin/gem update --system --no-ri --no-rdoc
-rm -r ${tmp}
+/var/lib/arvados/bin/gem install bundler --no-document
 `, stdout, stderr)
 		if err != nil {
 			return 1
@@ -224,12 +239,13 @@ rm -r ${tmp}
 	}
 
 	if !prod {
-		goversion := "1.14"
+		goversion := "1.17.1"
 		if havegoversion, err := exec.Command("/usr/local/bin/go", "version").CombinedOutput(); err == nil && bytes.HasPrefix(havegoversion, []byte("go version go"+goversion+" ")) {
 			logger.Print("go " + goversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 cd /tmp
+rm -rf /var/lib/arvados/go/
 wget --progress=dot:giga -O- https://storage.googleapis.com/golang/go`+goversion+`.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
 ln -sf /var/lib/arvados/go/bin/* /usr/local/bin/
 `, stdout, stderr)
@@ -244,7 +260,7 @@ ln -sf /var/lib/arvados/go/bin/* /usr/local/bin/
 		if havepjsversion, err := exec.Command("/usr/local/bin/phantomjs", "--version").CombinedOutput(); err == nil && string(havepjsversion) == "1.9.8\n" {
 			logger.Print("phantomjs " + pjsversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 PJS=phantomjs-`+pjsversion+`-linux-x86_64
 wget --progress=dot:giga -O- https://bitbucket.org/ariya/phantomjs/downloads/$PJS.tar.bz2 | tar -C /var/lib/arvados -xjf -
 ln -sf /var/lib/arvados/$PJS/bin/phantomjs /usr/local/bin/
@@ -258,7 +274,7 @@ ln -sf /var/lib/arvados/$PJS/bin/phantomjs /usr/local/bin/
 		if havegeckoversion, err := exec.Command("/usr/local/bin/geckodriver", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegeckoversion), " "+geckoversion+" ") {
 			logger.Print("geckodriver " + geckoversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 GD=v`+geckoversion+`
 wget --progress=dot:giga -O- https://github.com/mozilla/geckodriver/releases/download/$GD/geckodriver-$GD-linux64.tar.gz | tar -C /var/lib/arvados/bin -xzf - geckodriver
 ln -sf /var/lib/arvados/bin/geckodriver /usr/local/bin/
@@ -268,11 +284,11 @@ ln -sf /var/lib/arvados/bin/geckodriver /usr/local/bin/
 			}
 		}
 
-		nodejsversion := "v8.15.1"
+		nodejsversion := "v12.22.2"
 		if havenodejsversion, err := exec.Command("/usr/local/bin/node", "--version").CombinedOutput(); err == nil && string(havenodejsversion) == nodejsversion+"\n" {
 			logger.Print("nodejs " + nodejsversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 NJS=`+nodejsversion+`
 wget --progress=dot:giga -O- https://nodejs.org/dist/${NJS}/node-${NJS}-linux-x64.tar.xz | sudo tar -C /var/lib/arvados -xJf -
 ln -sf /var/lib/arvados/node-${NJS}-linux-x64/bin/{node,npm} /usr/local/bin/
@@ -286,7 +302,7 @@ ln -sf /var/lib/arvados/node-${NJS}-linux-x64/bin/{node,npm} /usr/local/bin/
 		if havegradleversion, err := exec.Command("/usr/local/bin/gradle", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegradleversion), "Gradle "+gradleversion+"\n") {
 			logger.Print("gradle " + gradleversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 G=`+gradleversion+`
 zip=/var/lib/arvados/tmp/gradle-${G}-bin.zip
 trap "rm ${zip}" ERR
@@ -300,6 +316,27 @@ rm ${zip}
 			}
 		}
 
+		singularityversion := "3.7.4"
+		if havesingularityversion, err := exec.Command("/var/lib/arvados/bin/singularity", "--version").CombinedOutput(); err == nil && strings.Contains(string(havesingularityversion), singularityversion) {
+			logger.Print("singularity " + singularityversion + " already installed")
+		} else if dev || test {
+			err = inst.runBash(`
+S=`+singularityversion+`
+tmp=/var/lib/arvados/tmp/singularity
+trap "rm -r ${tmp}" ERR EXIT
+cd /var/lib/arvados/tmp
+git clone https://github.com/sylabs/singularity
+cd singularity
+git checkout v${S}
+./mconfig --prefix=/var/lib/arvados
+make -C ./builddir
+make -C ./builddir install
+`, stdout, stderr)
+			if err != nil {
+				return 1
+			}
+		}
+
 		// The entry in /etc/locale.gen is "en_US.UTF-8"; once
 		// it's installed, locale -a reports it as
 		// "en_US.utf8".
@@ -307,7 +344,7 @@ rm ${zip}
 		if havelocales, err := exec.Command("locale", "-a").CombinedOutput(); err == nil && bytes.Contains(havelocales, []byte(strings.Replace(wantlocale+"\n", "UTF-", "utf", 1))) {
 			logger.Print("locale " + wantlocale + " already installed")
 		} else {
-			err = runBash(`sed -i 's/^# *\(`+wantlocale+`\)/\1/' /etc/locale.gen && locale-gen`, stdout, stderr)
+			err = inst.runBash(`sed -i 's/^# *\(`+wantlocale+`\)/\1/' /etc/locale.gen && locale-gen`, stdout, stderr)
 			if err != nil {
 				return 1
 			}
@@ -386,7 +423,7 @@ rm ${zip}
 			// locales. Otherwise, it might need a
 			// restart, so we attempt to restart it with
 			// systemd.
-			if err = runBash(`sudo systemctl restart postgresql`, stdout, stderr); err != nil {
+			if err = inst.runBash(`sudo systemctl restart postgresql`, stdout, stderr); err != nil {
 				logger.Warn("`systemctl restart postgresql` failed; hoping postgresql does not need to be restarted")
 			} else if err = waitPostgreSQLReady(); err != nil {
 				return 1
@@ -429,11 +466,12 @@ rm ${zip}
 		} {
 			fmt.Fprintf(stderr, "building %s...\n", srcdir)
 			cmd := exec.Command("rsync",
-				"-a", "--no-owner", "--delete-after", "--delete-excluded",
+				"-a", "--no-owner", "--no-group", "--delete-after", "--delete-excluded",
 				"--exclude", "/coverage",
 				"--exclude", "/log",
 				"--exclude", "/tmp",
 				"--exclude", "/vendor",
+				"--exclude", "/config/environments",
 				"./", "/var/lib/arvados/"+dstdir+"/")
 			cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
 			cmd.Stdout = stdout
@@ -446,13 +484,12 @@ rm ${zip}
 				{"mkdir", "-p", "log", "tmp", ".bundle", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger"},
 				{"touch", "log/production.log"},
 				{"chown", "-R", "--from=root", "www-data:www-data", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger", "log", "tmp", ".bundle", "Gemfile.lock", "config.ru", "config/environment.rb"},
-				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:1.16.6", "bundler:1.17.3", "bundler:2.0.2"},
+				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:2.2.19"},
 				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem"},
 				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "build-native-support"},
 				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "install-standalone-runtime"},
 			} {
 				cmd = exec.Command(cmdline[0], cmdline[1:]...)
-				cmd.Env = append([]string{}, os.Environ()...)
 				cmd.Dir = "/var/lib/arvados/" + dstdir
 				cmd.Stdout = stdout
 				cmd.Stderr = stderr
@@ -492,7 +529,8 @@ rm ${zip}
 		} {
 			fmt.Fprintf(stderr, "building %s...\n", srcdir)
 			cmd := exec.Command("go", "install", "-ldflags", "-X git.arvados.org/arvados.git/lib/cmd.version="+inst.PackageVersion+" -X main.version="+inst.PackageVersion)
-			cmd.Env = append([]string{"GOBIN=/var/lib/arvados/bin"}, os.Environ()...)
+			cmd.Env = append(cmd.Env, os.Environ()...)
+			cmd.Env = append(cmd.Env, "GOBIN=/var/lib/arvados/bin")
 			cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
 			cmd.Stdout = stdout
 			cmd.Stderr = stderr
@@ -585,8 +623,11 @@ func waitPostgreSQLReady() error {
 	}
 }
 
-func runBash(script string, stdout, stderr io.Writer) error {
+func (inst *installCommand) runBash(script string, stdout, stderr io.Writer) error {
 	cmd := exec.Command("bash", "-")
+	if inst.EatMyData {
+		cmd = exec.Command("eatmydata", "bash", "-")
+	}
 	cmd.Stdin = bytes.NewBufferString("set -ex -o pipefail\n" + script)
 	cmd.Stdout = stdout
 	cmd.Stderr = stderr