1 // Copyright (C) The Arvados Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
24 "git.arvados.org/arvados.git/lib/cmd"
25 "git.arvados.org/arvados.git/sdk/go/ctxlog"
29 var Command cmd.Handler = &installCommand{}
31 const goversion = "1.17.7"
35 bundlerversion = "2.2.19"
36 singularityversion = "3.7.4"
38 geckoversion = "0.24.0"
39 gradleversion = "5.3.1"
40 nodejsversion = "v12.22.2"
41 devtestDatabasePassword = "insecure_arvados_test"
42 workbench2version = "cfa81dfc3041cb459c8a0918a2732dfcf3a11d40"
45 type installCommand struct {
52 func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
53 logger := ctxlog.New(stderr, "text", "info")
54 ctx := ctxlog.Context(context.Background(), logger)
55 ctx, cancel := context.WithCancel(ctx)
61 logger.WithError(err).Info("exiting")
65 flags := flag.NewFlagSet(prog, flag.ContinueOnError)
66 flags.SetOutput(stderr)
67 versionFlag := flags.Bool("version", false, "Write version information to stdout and exit 0")
68 flags.StringVar(&inst.ClusterType, "type", "production", "cluster `type`: development, test, production, or package")
69 flags.StringVar(&inst.SourcePath, "source", "/arvados", "source tree location (required for -type=package)")
70 flags.StringVar(&inst.PackageVersion, "package-version", "0.0.0", "version string to embed in executable files")
71 flags.BoolVar(&inst.EatMyData, "eatmydata", false, "use eatmydata to speed up install")
73 if ok, code := cmd.ParseFlags(flags, prog, args, "", stderr); !ok {
75 } else if *versionFlag {
76 return cmd.Version.RunCommand(prog, args, stdin, stdout, stderr)
79 var dev, test, prod, pkg bool
80 switch inst.ClusterType {
90 err = fmt.Errorf("invalid cluster type %q (must be 'development', 'test', 'production', or 'package')", inst.ClusterType)
95 err = errors.New("production install is not yet implemented")
99 osv, err := identifyOS()
104 listdir, err := os.Open("/var/lib/apt/lists")
106 logger.Warnf("error while checking whether to run apt-get update: %s", err)
107 } else if names, _ := listdir.Readdirnames(1); len(names) == 0 {
108 // Special case for a base docker image where the
109 // package cache has been deleted and all "apt-get
110 // install" commands will fail unless we fetch repos.
111 cmd := exec.CommandContext(ctx, "apt-get", "update")
121 cmd := exec.CommandContext(ctx, "apt-get", "install", "--yes", "--no-install-recommends", "eatmydata")
122 cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
131 pkgs := prodpkgs(osv)
136 "eatmydata", // install it for later steps, even if we're not using it now
141 if dev || test || pkg {
150 "default-jdk-headless",
151 "default-jre-headless",
154 "libcrypt-ssleay-perl",
174 "postgresql-contrib",
177 "python3-virtualenv",
191 if osv.Debian && osv.Major <= 10 {
192 pkgs = append(pkgs, "iceweasel")
194 pkgs = append(pkgs, "firefox")
198 pkgs = append(pkgs, "squashfs-tools") // for singularity
201 case osv.Debian && osv.Major >= 10:
202 pkgs = append(pkgs, "libcurl4")
204 pkgs = append(pkgs, "libcurl3")
206 cmd := exec.CommandContext(ctx, "apt-get")
208 cmd = exec.CommandContext(ctx, "eatmydata", "apt-get")
210 cmd.Args = append(cmd.Args, "install", "--yes", "--no-install-recommends")
211 cmd.Args = append(cmd.Args, pkgs...)
212 cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
221 os.Mkdir("/var/lib/arvados", 0755)
222 os.Mkdir("/var/lib/arvados/tmp", 0700)
224 u, er := user.Lookup("www-data")
226 err = fmt.Errorf("user.Lookup(%q): %w", "www-data", er)
229 uid, _ := strconv.Atoi(u.Uid)
230 gid, _ := strconv.Atoi(u.Gid)
231 os.Mkdir("/var/lib/arvados/wwwtmp", 0700)
232 err = os.Chown("/var/lib/arvados/wwwtmp", uid, gid)
237 rubymajorversion := rubyversion[:strings.LastIndex(rubyversion, ".")]
238 if haverubyversion, err := exec.Command("/var/lib/arvados/bin/ruby", "-v").CombinedOutput(); err == nil && bytes.HasPrefix(haverubyversion, []byte("ruby "+rubyversion)) {
239 logger.Print("ruby " + rubyversion + " already installed")
243 trap 'rm -r "${tmp}"' ERR EXIT
244 wget --progress=dot:giga -O- https://cache.ruby-lang.org/pub/ruby/`+rubymajorversion+`/ruby-`+rubyversion+`.tar.gz | tar -C "${tmp}" -xzf -
245 cd "${tmp}/ruby-`+rubyversion+`"
246 ./configure --disable-install-static-library --enable-shared --disable-install-doc --prefix /var/lib/arvados
249 /var/lib/arvados/bin/gem install bundler --no-document
257 if havegoversion, err := exec.Command("/usr/local/bin/go", "version").CombinedOutput(); err == nil && bytes.HasPrefix(havegoversion, []byte("go version go"+goversion+" ")) {
258 logger.Print("go " + goversion + " already installed")
262 rm -rf /var/lib/arvados/go/
263 wget --progress=dot:giga -O- https://storage.googleapis.com/golang/go`+goversion+`.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
264 ln -sfv /var/lib/arvados/go/bin/* /usr/local/bin/
273 if havepjsversion, err := exec.Command("/usr/local/bin/phantomjs", "--version").CombinedOutput(); err == nil && string(havepjsversion) == "1.9.8\n" {
274 logger.Print("phantomjs " + pjsversion + " already installed")
277 PJS=phantomjs-`+pjsversion+`-linux-x86_64
278 wget --progress=dot:giga -O- https://cache.arvados.org/$PJS.tar.bz2 | tar -C /var/lib/arvados -xjf -
279 ln -sfv /var/lib/arvados/$PJS/bin/phantomjs /usr/local/bin/
286 if havegeckoversion, err := exec.Command("/usr/local/bin/geckodriver", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegeckoversion), " "+geckoversion+" ") {
287 logger.Print("geckodriver " + geckoversion + " already installed")
291 wget --progress=dot:giga -O- https://github.com/mozilla/geckodriver/releases/download/$GD/geckodriver-$GD-linux64.tar.gz | tar -C /var/lib/arvados/bin -xzf - geckodriver
292 ln -sfv /var/lib/arvados/bin/geckodriver /usr/local/bin/
299 if havegradleversion, err := exec.Command("/usr/local/bin/gradle", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegradleversion), "Gradle "+gradleversion+"\n") {
300 logger.Print("gradle " + gradleversion + " already installed")
304 zip=/var/lib/arvados/tmp/gradle-${G}-bin.zip
306 wget --progress=dot:giga -O${zip} https://services.gradle.org/distributions/gradle-${G}-bin.zip
307 unzip -o -d /var/lib/arvados ${zip}
308 ln -sfv /var/lib/arvados/gradle-${G}/bin/gradle /usr/local/bin/
316 if havesingularityversion, err := exec.Command("/var/lib/arvados/bin/singularity", "--version").CombinedOutput(); err == nil && strings.Contains(string(havesingularityversion), singularityversion) {
317 logger.Print("singularity " + singularityversion + " already installed")
318 } else if dev || test {
320 S=`+singularityversion+`
321 tmp=/var/lib/arvados/tmp/singularity
322 trap "rm -r ${tmp}" ERR EXIT
323 cd /var/lib/arvados/tmp
324 git clone https://github.com/sylabs/singularity
327 ./mconfig --prefix=/var/lib/arvados
329 make -C ./builddir install
336 // The entry in /etc/locale.gen is "en_US.UTF-8"; once
337 // it's installed, locale -a reports it as
339 wantlocale := "en_US.UTF-8"
340 if havelocales, err := exec.Command("locale", "-a").CombinedOutput(); err == nil && bytes.Contains(havelocales, []byte(strings.Replace(wantlocale+"\n", "UTF-", "utf", 1))) {
341 logger.Print("locale " + wantlocale + " already installed")
343 err = inst.runBash(`sed -i 's/^# *\(`+wantlocale+`\)/\1/' /etc/locale.gen && locale-gen`, stdout, stderr)
358 if pgLsclusters, err2 := exec.Command("pg_lsclusters", "--no-header").CombinedOutput(); err2 != nil {
359 err = fmt.Errorf("pg_lsclusters: %s", err2)
361 } else if pgclusters := strings.Split(strings.TrimSpace(string(pgLsclusters)), "\n"); len(pgclusters) != 1 {
362 logger.Warnf("pg_lsclusters returned %d postgresql clusters -- skipping postgresql initdb/startup, hope that's ok", len(pgclusters))
363 } else if _, err = fmt.Sscanf(pgclusters[0], "%s %s %d %s %s %s %s", &pgc.Version, &pgc.Cluster, &pgc.Port, &pgc.Status, &pgc.Owner, &pgc.DataDirectory, &pgc.LogFile); err != nil {
364 err = fmt.Errorf("error parsing pg_lsclusters output: %s", err)
366 } else if pgc.Status == "online" {
367 logger.Infof("postgresql cluster %s-%s is online", pgc.Version, pgc.Cluster)
369 logger.Infof("postgresql cluster %s-%s is %s; trying to start", pgc.Version, pgc.Cluster, pgc.Status)
370 cmd := exec.Command("pg_ctlcluster", "--foreground", pgc.Version, pgc.Cluster, "start")
378 cmd.Process.Signal(syscall.SIGTERM)
379 logger.Info("sent SIGTERM; waiting for postgres to shut down")
382 err = waitPostgreSQLReady()
388 if os.Getpid() == 1 {
389 // We are the init process (presumably in a
390 // docker container) so although postgresql is
391 // installed, it's not running, and initdb
392 // might never have been run.
395 var needcoll []string
396 // If the en_US.UTF-8 locale wasn't installed when
397 // postgresql initdb ran, it needs to be added
398 // explicitly before we can use it in our test suite.
399 for _, collname := range []string{"en_US", "en_US.UTF-8"} {
400 cmd := exec.Command("sudo", "-u", "postgres", "psql", "-t", "-c", "SELECT 1 FROM pg_catalog.pg_collation WHERE collname='"+collname+"' AND collcollate IN ('en_US.UTF-8', 'en_US.utf8')")
402 out, err2 := cmd.CombinedOutput()
404 err = fmt.Errorf("error while checking postgresql collations: %s", err2)
407 if strings.Contains(string(out), "1") {
408 logger.Infof("postgresql supports collation %s", collname)
410 needcoll = append(needcoll, collname)
413 if len(needcoll) > 0 && os.Getpid() != 1 {
414 // In order for the CREATE COLLATION statement
415 // below to work, the locale must have existed
416 // when PostgreSQL started up. If we're
417 // running as init, we must have started
418 // PostgreSQL ourselves after installing the
419 // locales. Otherwise, it might need a
420 // restart, so we attempt to restart it with
422 if err = inst.runBash(`sudo systemctl restart postgresql`, stdout, stderr); err != nil {
423 logger.Warn("`systemctl restart postgresql` failed; hoping postgresql does not need to be restarted")
424 } else if err = waitPostgreSQLReady(); err != nil {
428 for _, collname := range needcoll {
429 cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "CREATE COLLATION \""+collname+"\" (LOCALE = \"en_US.UTF-8\")")
435 err = fmt.Errorf("error adding postgresql collation %s: %s", collname, err)
440 withstuff := "WITH LOGIN SUPERUSER ENCRYPTED PASSWORD " + pq.QuoteLiteral(devtestDatabasePassword)
441 cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "ALTER ROLE arvados "+withstuff)
443 if err := cmd.Run(); err == nil {
444 logger.Print("arvados role exists; superuser privileges added, password updated")
446 cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "CREATE ROLE arvados "+withstuff)
458 if havenodejsversion, err := exec.Command("/usr/local/bin/node", "--version").CombinedOutput(); err == nil && string(havenodejsversion) == nodejsversion+"\n" {
459 logger.Print("nodejs " + nodejsversion + " already installed")
462 NJS=`+nodejsversion+`
463 wget --progress=dot:giga -O- https://nodejs.org/dist/${NJS}/node-${NJS}-linux-x64.tar.xz | sudo tar -C /var/lib/arvados -xJf -
464 ln -sfv /var/lib/arvados/node-${NJS}-linux-x64/bin/{node,npm} /usr/local/bin/
471 if haveyarnversion, err := exec.Command("/usr/local/bin/yarn", "--version").CombinedOutput(); err == nil && len(haveyarnversion) > 0 {
472 logger.Print("yarn " + strings.TrimSpace(string(haveyarnversion)) + " already installed")
476 ln -sfv /var/lib/arvados/node-`+nodejsversion+`-linux-x64/bin/{yarn,yarnpkg} /usr/local/bin/
483 if havewb2version, err := exec.Command("git", "--git-dir=/var/lib/arvados/arvados-workbench2/.git", "log", "-n1", "--format=%H").CombinedOutput(); err == nil && string(havewb2version) == workbench2version+"\n" {
484 logger.Print("workbench2 repo is already at " + workbench2version)
487 V=`+workbench2version+`
489 if [[ ! -e arvados-workbench2 ]]; then
490 git clone https://git.arvados.org/arvados-workbench2.git
491 cd arvados-workbench2
494 cd arvados-workbench2
495 if ! git checkout $V; then
507 if err = inst.runBash(`
508 cd /var/lib/arvados/arvados-workbench2
510 `, stdout, stderr); err != nil {
516 // Install Go programs to /var/lib/arvados/bin/
517 for _, srcdir := range []string{
518 "cmd/arvados-client",
519 "cmd/arvados-server",
520 "services/arv-git-httpd",
521 "services/crunch-dispatch-local",
522 "services/crunch-dispatch-slurm",
524 "services/keep-balance",
526 "services/keepproxy",
527 "services/keepstore",
530 fmt.Fprintf(stderr, "building %s...\n", srcdir)
531 cmd := exec.Command("go", "install", "-ldflags", "-X git.arvados.org/arvados.git/lib/cmd.version="+inst.PackageVersion+" -X main.version="+inst.PackageVersion+" -s -w")
532 cmd.Env = append(cmd.Env, os.Environ()...)
533 cmd.Env = append(cmd.Env, "GOBIN=/var/lib/arvados/bin")
534 cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
543 // Copy assets from source tree to /var/lib/arvados/share
544 cmd := exec.Command("install", "-v", "-t", "/var/lib/arvados/share", filepath.Join(inst.SourcePath, "sdk/python/tests/nginx.conf"))
552 // Install Rails apps to /var/lib/arvados/{railsapi,workbench1}/
553 for dstdir, srcdir := range map[string]string{
554 "railsapi": "services/api",
555 "workbench1": "apps/workbench",
557 fmt.Fprintf(stderr, "building %s...\n", srcdir)
558 cmd := exec.Command("rsync",
559 "-a", "--no-owner", "--no-group", "--delete-after", "--delete-excluded",
560 "--exclude", "/coverage",
563 "--exclude", "/vendor",
564 "--exclude", "/config/environments",
565 "./", "/var/lib/arvados/"+dstdir+"/")
566 cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
573 for _, cmdline := range [][]string{
574 {"mkdir", "-p", "log", "tmp", ".bundle", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger"},
575 {"touch", "log/production.log"},
576 {"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"},
577 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:" + bundlerversion},
578 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem"},
579 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "build-native-support"},
580 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "install-standalone-runtime"},
582 cmd = exec.Command(cmdline[0], cmdline[1:]...)
583 cmd.Dir = "/var/lib/arvados/" + dstdir
586 fmt.Fprintf(stderr, "... %s\n", cmd.Args)
592 cmd = exec.Command("sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "validate-install")
593 cmd.Dir = "/var/lib/arvados/" + dstdir
597 if err != nil && !strings.Contains(err.Error(), "exit status 2") {
598 // Exit code 2 indicates there were warnings (like
599 // "other passenger installations have been detected",
600 // which we can't expect to avoid) but no errors.
601 // Other non-zero exit codes (1, 9) indicate errors.
606 // Install workbench2 app to /var/lib/arvados/workbench2/
607 if err = inst.runBash(`
608 cd /var/lib/arvados/arvados-workbench2
609 VERSION="`+inst.PackageVersion+`" BUILD_NUMBER=1 GIT_COMMIT="`+workbench2version[:9]+`" yarn build
610 rsync -a --delete-after build/ /var/lib/arvados/workbench2/
611 `, stdout, stderr); err != nil {
619 type osversion struct {
626 func identifyOS() (osversion, error) {
628 f, err := os.Open("/etc/os-release")
634 kv := map[string]string{}
635 scanner := bufio.NewScanner(f)
637 line := strings.TrimSpace(scanner.Text())
638 if strings.HasPrefix(line, "#") {
641 toks := strings.SplitN(line, "=", 2)
643 return osv, fmt.Errorf("invalid line in /etc/os-release: %q", line)
646 v := strings.Trim(toks[1], `"`)
648 v = strings.Trim(v, `'`)
652 if err = scanner.Err(); err != nil {
663 return osv, fmt.Errorf("unsupported ID in /etc/os-release: %q", kv["ID"])
665 vstr := kv["VERSION_ID"]
666 if i := strings.Index(vstr, "."); i > 0 {
669 osv.Major, err = strconv.Atoi(vstr)
671 return osv, fmt.Errorf("incomprehensible VERSION_ID in /etc/os-release: %q", kv["VERSION_ID"])
676 func waitPostgreSQLReady() error {
677 for deadline := time.Now().Add(10 * time.Second); ; {
678 output, err := exec.Command("pg_isready").CombinedOutput()
681 } else if time.Now().After(deadline) {
682 return fmt.Errorf("timed out waiting for pg_isready (%q)", output)
684 time.Sleep(time.Second)
689 func (inst *installCommand) runBash(script string, stdout, stderr io.Writer) error {
690 cmd := exec.Command("bash", "-")
692 cmd = exec.Command("eatmydata", "bash", "-")
694 cmd.Stdin = bytes.NewBufferString("set -ex -o pipefail\n" + script)
700 func prodpkgs(osv osversion) []string {
715 if osv.Debian || osv.Ubuntu {
716 if osv.Debian && osv.Major == 8 {
717 pkgs = append(pkgs, "libgnutls-deb0-28") // sdk/cwl
718 } else if osv.Debian && osv.Major >= 10 || osv.Ubuntu && osv.Major >= 16 {
719 pkgs = append(pkgs, "python3-distutils") // sdk/cwl
723 "libcurl4-openssl-dev", // services/api
725 "libpython2.7", // services/fuse
726 "mime-support", // keep-web
727 "zlib1g-dev", // services/api
729 } else if osv.Centos {
731 "fuse-libs", // services/fuse
734 "libcurl-devel", // services/api
735 "mailcap", // keep-web
736 "postgresql-devel", // services/api
739 panic("os version not supported")
743 func ProductionDependencies() ([]string, error) {
744 osv, err := identifyOS()
748 return prodpkgs(osv), nil