1 // Copyright (C) The Arvados Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
25 "git.arvados.org/arvados.git/lib/cmd"
26 "git.arvados.org/arvados.git/sdk/go/ctxlog"
30 var Command cmd.Handler = &installCommand{}
32 const goversion = "1.17.7"
36 bundlerversion = "2.2.19"
37 singularityversion = "3.9.9"
39 geckoversion = "0.24.0"
40 gradleversion = "5.3.1"
41 nodejsversion = "v12.22.11"
42 devtestDatabasePassword = "insecure_arvados_test"
43 workbench2version = "5e020488f67b5bc919796e0dc8b0b9f3b3ff23b0"
46 //go:embed arvados.service
47 var arvadosServiceFile []byte
49 type installCommand struct {
56 func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
57 logger := ctxlog.New(stderr, "text", "info")
58 ctx := ctxlog.Context(context.Background(), logger)
59 ctx, cancel := context.WithCancel(ctx)
65 logger.WithError(err).Info("exiting")
69 flags := flag.NewFlagSet(prog, flag.ContinueOnError)
70 flags.SetOutput(stderr)
71 versionFlag := flags.Bool("version", false, "Write version information to stdout and exit 0")
72 flags.StringVar(&inst.ClusterType, "type", "production", "cluster `type`: development, test, production, or package")
73 flags.StringVar(&inst.SourcePath, "source", "/arvados", "source tree location (required for -type=package)")
74 flags.StringVar(&inst.PackageVersion, "package-version", "0.0.0", "version string to embed in executable files")
75 flags.BoolVar(&inst.EatMyData, "eatmydata", false, "use eatmydata to speed up install")
77 if ok, code := cmd.ParseFlags(flags, prog, args, "", stderr); !ok {
79 } else if *versionFlag {
80 return cmd.Version.RunCommand(prog, args, stdin, stdout, stderr)
83 var dev, test, prod, pkg bool
84 switch inst.ClusterType {
94 err = fmt.Errorf("invalid cluster type %q (must be 'development', 'test', 'production', or 'package')", inst.ClusterType)
99 err = errors.New("production install is not yet implemented")
103 osv, err := identifyOS()
108 listdir, err := os.Open("/var/lib/apt/lists")
110 logger.Warnf("error while checking whether to run apt-get update: %s", err)
111 } else if names, _ := listdir.Readdirnames(1); len(names) == 0 {
112 // Special case for a base docker image where the
113 // package cache has been deleted and all "apt-get
114 // install" commands will fail unless we fetch repos.
115 cmd := exec.CommandContext(ctx, "apt-get", "update")
125 cmd := exec.CommandContext(ctx, "apt-get", "install", "--yes", "--no-install-recommends", "eatmydata")
126 cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
135 pkgs := prodpkgs(osv)
140 "eatmydata", // install it for later steps, even if we're not using it now
144 if dev || test || pkg {
153 "default-jdk-headless",
154 "default-jre-headless",
157 "libcrypt-ssleay-perl",
176 "postgresql-contrib",
179 "python3-virtualenv",
194 if osv.Debian && osv.Major <= 10 {
195 pkgs = append(pkgs, "iceweasel")
197 pkgs = append(pkgs, "firefox")
201 pkgs = append(pkgs, "squashfs-tools") // for singularity
204 case osv.Debian && osv.Major >= 11:
205 pkgs = append(pkgs, "libcurl4", "perl-modules-5.32")
206 case osv.Debian && osv.Major >= 10:
207 pkgs = append(pkgs, "libcurl4", "perl-modules")
209 pkgs = append(pkgs, "libcurl3", "perl-modules")
211 cmd := exec.CommandContext(ctx, "apt-get")
213 cmd = exec.CommandContext(ctx, "eatmydata", "apt-get")
215 cmd.Args = append(cmd.Args, "install", "--yes", "--no-install-recommends")
216 cmd.Args = append(cmd.Args, pkgs...)
217 cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
226 os.Mkdir("/var/lib/arvados", 0755)
227 os.Mkdir("/var/lib/arvados/tmp", 0700)
229 u, er := user.Lookup("www-data")
231 err = fmt.Errorf("user.Lookup(%q): %w", "www-data", er)
234 uid, _ := strconv.Atoi(u.Uid)
235 gid, _ := strconv.Atoi(u.Gid)
236 os.Mkdir("/var/lib/arvados/wwwtmp", 0700)
237 err = os.Chown("/var/lib/arvados/wwwtmp", uid, gid)
242 rubymajorversion := rubyversion[:strings.LastIndex(rubyversion, ".")]
243 if haverubyversion, err := exec.Command("/var/lib/arvados/bin/ruby", "-v").CombinedOutput(); err == nil && bytes.HasPrefix(haverubyversion, []byte("ruby "+rubyversion)) {
244 logger.Print("ruby " + rubyversion + " already installed")
248 trap 'rm -r "${tmp}"' ERR EXIT
249 wget --progress=dot:giga -O- https://cache.ruby-lang.org/pub/ruby/`+rubymajorversion+`/ruby-`+rubyversion+`.tar.gz | tar -C "${tmp}" -xzf -
250 cd "${tmp}/ruby-`+rubyversion+`"
251 ./configure --disable-install-static-library --enable-shared --disable-install-doc --prefix /var/lib/arvados
254 /var/lib/arvados/bin/gem install bundler --no-document
262 if havegoversion, err := exec.Command("/usr/local/bin/go", "version").CombinedOutput(); err == nil && bytes.HasPrefix(havegoversion, []byte("go version go"+goversion+" ")) {
263 logger.Print("go " + goversion + " already installed")
267 rm -rf /var/lib/arvados/go/
268 wget --progress=dot:giga -O- https://storage.googleapis.com/golang/go`+goversion+`.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
269 ln -sfv /var/lib/arvados/go/bin/* /usr/local/bin/
278 if havepjsversion, err := exec.Command("/usr/local/bin/phantomjs", "--version").CombinedOutput(); err == nil && string(havepjsversion) == "1.9.8\n" {
279 logger.Print("phantomjs " + pjsversion + " already installed")
282 PJS=phantomjs-`+pjsversion+`-linux-x86_64
283 wget --progress=dot:giga -O- https://cache.arvados.org/$PJS.tar.bz2 | tar -C /var/lib/arvados -xjf -
284 ln -sfv /var/lib/arvados/$PJS/bin/phantomjs /usr/local/bin/
291 if havegeckoversion, err := exec.Command("/usr/local/bin/geckodriver", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegeckoversion), " "+geckoversion+" ") {
292 logger.Print("geckodriver " + geckoversion + " already installed")
296 wget --progress=dot:giga -O- https://github.com/mozilla/geckodriver/releases/download/$GD/geckodriver-$GD-linux64.tar.gz | tar -C /var/lib/arvados/bin -xzf - geckodriver
297 ln -sfv /var/lib/arvados/bin/geckodriver /usr/local/bin/
304 if havegradleversion, err := exec.Command("/usr/local/bin/gradle", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegradleversion), "Gradle "+gradleversion+"\n") {
305 logger.Print("gradle " + gradleversion + " already installed")
309 zip=/var/lib/arvados/tmp/gradle-${G}-bin.zip
311 wget --progress=dot:giga -O${zip} https://services.gradle.org/distributions/gradle-${G}-bin.zip
312 unzip -o -d /var/lib/arvados ${zip}
313 ln -sfv /var/lib/arvados/gradle-${G}/bin/gradle /usr/local/bin/
321 if havesingularityversion, err := exec.Command("/var/lib/arvados/bin/singularity", "--version").CombinedOutput(); err == nil && strings.Contains(string(havesingularityversion), singularityversion) {
322 logger.Print("singularity " + singularityversion + " already installed")
323 } else if dev || test {
325 S=`+singularityversion+`
326 tmp=/var/lib/arvados/tmp/singularity
327 trap "rm -r ${tmp}" ERR EXIT
328 cd /var/lib/arvados/tmp
329 git clone https://github.com/sylabs/singularity
332 ./mconfig --prefix=/var/lib/arvados
334 make -C ./builddir install
341 // Allow users in the "sudo" group to use
342 // --network=bridge without --fakeroot. (Currently
343 // tests use --fakeroot anyway.)
345 install /usr/bin/nsenter /var/lib/arvados/bin/nsenter
346 setcap "cap_sys_admin+pei cap_sys_chroot+pei" /var/lib/arvados/bin/nsenter
347 /var/lib/arvados/bin/singularity config global --set 'allow net networks' bridge
348 /var/lib/arvados/bin/singularity config global --set 'allow net groups' sudo
354 // The entry in /etc/locale.gen is "en_US.UTF-8"; once
355 // it's installed, locale -a reports it as
357 wantlocale := "en_US.UTF-8"
358 if havelocales, err := exec.Command("locale", "-a").CombinedOutput(); err == nil && bytes.Contains(havelocales, []byte(strings.Replace(wantlocale+"\n", "UTF-", "utf", 1))) {
359 logger.Print("locale " + wantlocale + " already installed")
361 err = inst.runBash(`sed -i 's/^# *\(`+wantlocale+`\)/\1/' /etc/locale.gen && locale-gen`, stdout, stderr)
376 if pgLsclusters, err2 := exec.Command("pg_lsclusters", "--no-header").CombinedOutput(); err2 != nil {
377 err = fmt.Errorf("pg_lsclusters: %s", err2)
379 } else if pgclusters := strings.Split(strings.TrimSpace(string(pgLsclusters)), "\n"); len(pgclusters) != 1 {
380 logger.Warnf("pg_lsclusters returned %d postgresql clusters -- skipping postgresql initdb/startup, hope that's ok", len(pgclusters))
381 } 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 {
382 err = fmt.Errorf("error parsing pg_lsclusters output: %s", err)
384 } else if pgc.Status == "online" {
385 logger.Infof("postgresql cluster %s-%s is online", pgc.Version, pgc.Cluster)
387 logger.Infof("postgresql cluster %s-%s is %s; trying to start", pgc.Version, pgc.Cluster, pgc.Status)
388 cmd := exec.Command("pg_ctlcluster", "--foreground", pgc.Version, pgc.Cluster, "start")
396 cmd.Process.Signal(syscall.SIGTERM)
397 logger.Info("sent SIGTERM; waiting for postgres to shut down")
400 err = waitPostgreSQLReady()
406 if os.Getpid() == 1 {
407 // We are the init process (presumably in a
408 // docker container) so although postgresql is
409 // installed, it's not running, and initdb
410 // might never have been run.
413 var needcoll []string
414 // If the en_US.UTF-8 locale wasn't installed when
415 // postgresql initdb ran, it needs to be added
416 // explicitly before we can use it in our test suite.
417 for _, collname := range []string{"en_US", "en_US.UTF-8"} {
418 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')")
420 out, err2 := cmd.CombinedOutput()
422 err = fmt.Errorf("error while checking postgresql collations: %s", err2)
425 if strings.Contains(string(out), "1") {
426 logger.Infof("postgresql supports collation %s", collname)
428 needcoll = append(needcoll, collname)
431 if len(needcoll) > 0 && os.Getpid() != 1 {
432 // In order for the CREATE COLLATION statement
433 // below to work, the locale must have existed
434 // when PostgreSQL started up. If we're
435 // running as init, we must have started
436 // PostgreSQL ourselves after installing the
437 // locales. Otherwise, it might need a
438 // restart, so we attempt to restart it with
440 if err = inst.runBash(`sudo systemctl restart postgresql`, stdout, stderr); err != nil {
441 logger.Warn("`systemctl restart postgresql` failed; hoping postgresql does not need to be restarted")
442 } else if err = waitPostgreSQLReady(); err != nil {
446 for _, collname := range needcoll {
447 cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "CREATE COLLATION \""+collname+"\" (LOCALE = \"en_US.UTF-8\")")
453 err = fmt.Errorf("error adding postgresql collation %s: %s", collname, err)
458 withstuff := "WITH LOGIN SUPERUSER ENCRYPTED PASSWORD " + pq.QuoteLiteral(devtestDatabasePassword)
459 cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "ALTER ROLE arvados "+withstuff)
461 if err := cmd.Run(); err == nil {
462 logger.Print("arvados role exists; superuser privileges added, password updated")
464 cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "CREATE ROLE arvados "+withstuff)
476 if havenodejsversion, err := exec.Command("/usr/local/bin/node", "--version").CombinedOutput(); err == nil && string(havenodejsversion) == nodejsversion+"\n" {
477 logger.Print("nodejs " + nodejsversion + " already installed")
480 NJS=`+nodejsversion+`
481 wget --progress=dot:giga -O- https://nodejs.org/dist/${NJS}/node-${NJS}-linux-x64.tar.xz | sudo tar -C /var/lib/arvados -xJf -
482 ln -sfv /var/lib/arvados/node-${NJS}-linux-x64/bin/{node,npm} /usr/local/bin/
489 if haveyarnversion, err := exec.Command("/usr/local/bin/yarn", "--version").CombinedOutput(); err == nil && len(haveyarnversion) > 0 {
490 logger.Print("yarn " + strings.TrimSpace(string(haveyarnversion)) + " already installed")
494 ln -sfv /var/lib/arvados/node-`+nodejsversion+`-linux-x64/bin/{yarn,yarnpkg} /usr/local/bin/
501 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" {
502 logger.Print("workbench2 repo is already at " + workbench2version)
505 V=`+workbench2version+`
507 if [[ ! -e arvados-workbench2 ]]; then
508 git clone https://git.arvados.org/arvados-workbench2.git
509 cd arvados-workbench2
512 cd arvados-workbench2
513 if ! git checkout $V; then
515 git checkout yarn.lock
526 if err = inst.runBash(`
527 cd /var/lib/arvados/arvados-workbench2
529 `, stdout, stderr); err != nil {
535 // Install Go programs to /var/lib/arvados/bin/
536 for _, srcdir := range []string{
537 "cmd/arvados-client",
538 "cmd/arvados-server",
539 "services/crunch-dispatch-local",
540 "services/crunch-dispatch-slurm",
542 "services/keep-balance",
543 "services/keepstore",
546 fmt.Fprintf(stderr, "building %s...\n", srcdir)
547 cmd := exec.Command("go", "install", "-ldflags", "-X git.arvados.org/arvados.git/lib/cmd.version="+inst.PackageVersion+" -X main.version="+inst.PackageVersion+" -s -w")
548 cmd.Env = append(cmd.Env, os.Environ()...)
549 cmd.Env = append(cmd.Env, "GOBIN=/var/lib/arvados/bin")
550 cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
559 // Symlink user-facing Go programs /usr/bin/x ->
560 // /var/lib/arvados/bin/x
561 for _, prog := range []string{"arvados-client", "arvados-server"} {
562 err = os.Remove("/usr/bin/" + prog)
563 if err != nil && !errors.Is(err, os.ErrNotExist) {
566 err = os.Symlink("/var/lib/arvados/bin/"+prog, "/usr/bin/"+prog)
572 // Copy assets from source tree to /var/lib/arvados/share
573 cmd := exec.Command("install", "-v", "-t", "/var/lib/arvados/share", filepath.Join(inst.SourcePath, "sdk/python/tests/nginx.conf"))
581 // Install Rails apps to /var/lib/arvados/{railsapi,workbench1}/
582 for dstdir, srcdir := range map[string]string{
583 "railsapi": "services/api",
584 "workbench1": "apps/workbench",
586 fmt.Fprintf(stderr, "building %s...\n", srcdir)
587 cmd := exec.Command("rsync",
588 "-a", "--no-owner", "--no-group", "--delete-after", "--delete-excluded",
589 "--exclude", "/coverage",
591 "--exclude", "/node_modules",
593 "--exclude", "/public/assets",
594 "--exclude", "/vendor",
595 "--exclude", "/config/environments",
596 "./", "/var/lib/arvados/"+dstdir+"/")
597 cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
604 for _, cmdline := range [][]string{
605 {"mkdir", "-p", "log", "public/assets", "tmp", "vendor", ".bundle", "/var/www/.bundle", "/var/www/.gem", "/var/www/.npm", "/var/www/.passenger"},
606 {"touch", "log/production.log"},
607 {"chown", "-R", "--from=root", "www-data:www-data", "/var/www/.bundle", "/var/www/.gem", "/var/www/.npm", "/var/www/.passenger", "log", "tmp", "vendor", ".bundle", "Gemfile.lock", "config.ru", "config/environment.rb"},
608 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:" + bundlerversion},
609 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem", "--without", "development test diagnostics performance"},
611 {"chown", "www-data:www-data", ".", "public/assets"},
612 // {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "config", "set", "--local", "system", "true"},
613 {"sudo", "-u", "www-data", "ARVADOS_CONFIG=none", "RAILS_GROUPS=assets", "RAILS_ENV=production", "/var/lib/arvados/bin/bundle", "exec", "rake", "npm:install"},
614 {"sudo", "-u", "www-data", "ARVADOS_CONFIG=none", "RAILS_GROUPS=assets", "RAILS_ENV=production", "/var/lib/arvados/bin/bundle", "exec", "rake", "assets:precompile"},
615 {"chown", "root:root", "."},
616 {"chown", "-R", "root:root", "public/assets", "vendor"},
618 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "build-native-support"},
619 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "install-standalone-runtime"},
621 if cmdline[len(cmdline)-2] == "rake" && dstdir != "workbench1" {
624 cmd = exec.Command(cmdline[0], cmdline[1:]...)
625 cmd.Dir = "/var/lib/arvados/" + dstdir
628 fmt.Fprintf(stderr, "... %s\n", cmd.Args)
634 cmd = exec.Command("sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "validate-install")
635 cmd.Dir = "/var/lib/arvados/" + dstdir
639 if err != nil && !strings.Contains(err.Error(), "exit status 2") {
640 // Exit code 2 indicates there were warnings (like
641 // "other passenger installations have been detected",
642 // which we can't expect to avoid) but no errors.
643 // Other non-zero exit codes (1, 9) indicate errors.
648 // Install workbench2 app to /var/lib/arvados/workbench2/
649 if err = inst.runBash(`
650 cd /var/lib/arvados/arvados-workbench2
651 VERSION="`+inst.PackageVersion+`" BUILD_NUMBER=1 GIT_COMMIT="`+workbench2version[:9]+`" yarn build
652 rsync -a --delete-after build/ /var/lib/arvados/workbench2/
653 `, stdout, stderr); err != nil {
657 err = os.WriteFile("/lib/systemd/system/arvados.service", arvadosServiceFile, 0777)
661 // This is equivalent to "systemd enable", but does
662 // not depend on the systemctl program being
664 symlink := "/etc/systemd/system/multi-user.target.wants/arvados.service"
665 err = os.Remove(symlink)
666 if err != nil && !errors.Is(err, os.ErrNotExist) {
669 err = os.Symlink("/lib/systemd/system/arvados.service", symlink)
678 type osversion struct {
685 func identifyOS() (osversion, error) {
687 f, err := os.Open("/etc/os-release")
693 kv := map[string]string{}
694 scanner := bufio.NewScanner(f)
696 line := strings.TrimSpace(scanner.Text())
697 if strings.HasPrefix(line, "#") {
700 toks := strings.SplitN(line, "=", 2)
702 return osv, fmt.Errorf("invalid line in /etc/os-release: %q", line)
705 v := strings.Trim(toks[1], `"`)
707 v = strings.Trim(v, `'`)
711 if err = scanner.Err(); err != nil {
722 return osv, fmt.Errorf("unsupported ID in /etc/os-release: %q", kv["ID"])
724 vstr := kv["VERSION_ID"]
725 if i := strings.Index(vstr, "."); i > 0 {
728 osv.Major, err = strconv.Atoi(vstr)
730 return osv, fmt.Errorf("incomprehensible VERSION_ID in /etc/os-release: %q", kv["VERSION_ID"])
735 func waitPostgreSQLReady() error {
736 for deadline := time.Now().Add(10 * time.Second); ; {
737 output, err := exec.Command("pg_isready").CombinedOutput()
740 } else if time.Now().After(deadline) {
741 return fmt.Errorf("timed out waiting for pg_isready (%q)", output)
743 time.Sleep(time.Second)
748 func (inst *installCommand) runBash(script string, stdout, stderr io.Writer) error {
749 cmd := exec.Command("bash", "-")
751 cmd = exec.Command("eatmydata", "bash", "-")
753 cmd.Stdin = bytes.NewBufferString("set -ex -o pipefail\n" + script)
759 func prodpkgs(osv osversion) []string {
774 if osv.Debian || osv.Ubuntu {
775 if osv.Debian && osv.Major == 8 {
776 pkgs = append(pkgs, "libgnutls-deb0-28") // sdk/cwl
777 } else if osv.Debian && osv.Major >= 10 || osv.Ubuntu && osv.Major >= 16 {
778 pkgs = append(pkgs, "python3-distutils") // sdk/cwl
782 "libcurl4-openssl-dev", // services/api
784 "libpython2.7", // services/fuse
785 "mime-support", // keep-web
786 "zlib1g-dev", // services/api
788 } else if osv.Centos {
790 "fuse-libs", // services/fuse
793 "libcurl-devel", // services/api
794 "mailcap", // keep-web
795 "postgresql-devel", // services/api
798 panic("os version not supported")
802 func ProductionDependencies() ([]string, error) {
803 osv, err := identifyOS()
807 return prodpkgs(osv), nil