X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/cd9e72bd95b32203231f6ccc96ddce9325b30a95..d3cb0cad7f052987651a9f0b2237329cf3997c58:/lib/install/deps.go

diff --git a/lib/install/deps.go b/lib/install/deps.go
index 017771b637..89b078e347 100644
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -17,6 +17,7 @@ import (
 	"os/exec"
 	"os/user"
 	"path/filepath"
+	"runtime"
 	"strconv"
 	"strings"
 	"syscall"
@@ -29,18 +30,17 @@ import (
 
 var Command cmd.Handler = &installCommand{}
 
-const goversion = "1.17.7"
+const goversion = "1.20.6"
 
 const (
-	rubyversion             = "2.7.5"
+	rubyversion             = "2.7.7"
 	bundlerversion          = "2.2.19"
-	singularityversion      = "3.9.9"
+	singularityversion      = "3.10.4"
 	pjsversion              = "1.9.8"
 	geckoversion            = "0.24.0"
 	gradleversion           = "5.3.1"
-	nodejsversion           = "v12.22.11"
+	nodejsversion           = "v12.22.12"
 	devtestDatabasePassword = "insecure_arvados_test"
-	workbench2version       = "2454ac35292a79594c32a80430740317ed5005cf"
 )
 
 //go:embed arvados.service
@@ -154,16 +154,14 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 			"default-jre-headless",
 			"gettext",
 			"libattr1-dev",
-			"libcrypt-ssleay-perl",
 			"libfuse-dev",
+			"libgbm1", // cypress / workbench2 tests
 			"libgnutls28-dev",
-			"libjson-perl",
 			"libpam-dev",
 			"libpcre3-dev",
 			"libpq-dev",
 			"libreadline-dev",
 			"libssl-dev",
-			"libwww-perl",
 			"libxml2-dev",
 			"libxslt1-dev",
 			"linkchecker",
@@ -189,25 +187,33 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 			"uuid-dev",
 			"wget",
 			"xvfb",
+			"zlib1g-dev", // services/api
 		)
 		if test {
 			if osv.Debian && osv.Major <= 10 {
 				pkgs = append(pkgs, "iceweasel")
+			} else if osv.Debian && osv.Major >= 11 {
+				pkgs = append(pkgs, "firefox-esr")
 			} else {
 				pkgs = append(pkgs, "firefox")
 			}
 		}
 		if dev || test {
-			pkgs = append(pkgs, "squashfs-tools") // for singularity
-			pkgs = append(pkgs, "gnupg")          // for docker install recipe
+			pkgs = append(pkgs,
+				"libglib2.0-dev", // singularity (conmon)
+				"libseccomp-dev", // singularity (seccomp)
+				"squashfs-tools", // singularity
+				"gnupg")          // docker install recipe
 		}
 		switch {
 		case osv.Debian && osv.Major >= 11:
-			pkgs = append(pkgs, "libcurl4", "perl-modules-5.32")
+			pkgs = append(pkgs, "g++", "libcurl4", "libcurl4-openssl-dev")
 		case osv.Debian && osv.Major >= 10:
-			pkgs = append(pkgs, "libcurl4", "perl-modules")
-		default:
-			pkgs = append(pkgs, "libcurl3", "perl-modules")
+			pkgs = append(pkgs, "g++", "libcurl4", "libcurl4-openssl-dev")
+		case osv.Debian || osv.Ubuntu:
+			pkgs = append(pkgs, "g++", "libcurl3", "libcurl3-openssl-dev")
+		case osv.Centos:
+			pkgs = append(pkgs, "gcc", "gcc-c++", "libcurl-devel", "postgresql-devel")
 		}
 		cmd := exec.CommandContext(ctx, "apt-get")
 		if inst.EatMyData {
@@ -225,7 +231,7 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 	}
 
 	if dev || test {
-		if havedockerversion, err := exec.Command("docker", "--version").CombinedOutput(); err == nil {
+		if havedockerversion, err2 := exec.Command("docker", "--version").CombinedOutput(); err2 == nil {
 			logger.Printf("%s installed, assuming that version is ok", bytes.TrimSuffix(havedockerversion, []byte("\n")))
 		} else if osv.Debian {
 			var codename string
@@ -234,6 +240,8 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 				codename = "buster"
 			case 11:
 				codename = "bullseye"
+			case 12:
+				codename = "bookworm"
 			default:
 				err = fmt.Errorf("don't know how to install docker-ce for debian %d", osv.Major)
 				return 1
@@ -253,6 +261,21 @@ DEBIAN_FRONTEND=noninteractive apt-get --yes --no-install-recommends install doc
 			err = fmt.Errorf("don't know how to install docker for osversion %v", osv)
 			return 1
 		}
+
+		err = inst.runBash(`
+key=fs.inotify.max_user_watches
+min=524288
+if [[ "$(sysctl --values "${key}")" -lt "${min}" ]]; then
+    sysctl "${key}=${min}"
+    # writing sysctl worked, so we should make it permanent
+    echo "${key}=${min}" | tee -a /etc/sysctl.conf
+    sysctl -p
+fi
+`, stdout, stderr)
+		if err != nil {
+			err = fmt.Errorf("couldn't set fs.inotify.max_user_watches value. (Is this a docker container? Fix this on the docker host by adding fs.inotify.max_user_watches=524288 to /etc/sysctl.conf and running `sysctl -p`)")
+			return 1
+		}
 	}
 
 	os.Mkdir("/var/lib/arvados", 0755)
@@ -358,7 +381,7 @@ S=`+singularityversion+`
 tmp=/var/lib/arvados/tmp/singularity
 trap "rm -r ${tmp}" ERR EXIT
 cd /var/lib/arvados/tmp
-git clone https://github.com/sylabs/singularity
+git clone --recurse-submodules https://github.com/sylabs/singularity
 cd singularity
 git checkout v${S}
 ./mconfig --prefix=/var/lib/arvados
@@ -505,6 +528,7 @@ setcap "cap_sys_admin+pei cap_sys_chroot+pei" /var/lib/arvados/bin/nsenter
 		} else {
 			err = inst.runBash(`
 NJS=`+nodejsversion+`
+rm -rf /var/lib/arvados/node-*-linux-x64
 wget --progress=dot:giga -O- https://nodejs.org/dist/${NJS}/node-${NJS}-linux-x64.tar.xz | sudo tar -C /var/lib/arvados -xJf -
 ln -sfv /var/lib/arvados/node-${NJS}-linux-x64/bin/{node,npm} /usr/local/bin/
 `, stdout, stderr)
@@ -524,38 +548,6 @@ ln -sfv /var/lib/arvados/node-`+nodejsversion+`-linux-x64/bin/{yarn,yarnpkg} /us
 				return 1
 			}
 		}
-
-		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" {
-			logger.Print("workbench2 repo is already at " + workbench2version)
-		} else {
-			err = inst.runBash(`
-V=`+workbench2version+`
-cd /var/lib/arvados
-if [[ ! -e arvados-workbench2 ]]; then
-  git clone https://git.arvados.org/arvados-workbench2.git
-  cd arvados-workbench2
-  git checkout $V
-else
-  cd arvados-workbench2
-  if ! git checkout $V; then
-    git fetch
-    git checkout yarn.lock
-    git checkout $V
-  fi
-fi
-rm -rf build
-`, stdout, stderr)
-			if err != nil {
-				return 1
-			}
-		}
-
-		if err = inst.runBash(`
-cd /var/lib/arvados/arvados-workbench2
-yarn install
-`, stdout, stderr); err != nil {
-			return 1
-		}
 	}
 
 	if prod || pkg {
@@ -563,10 +555,15 @@ yarn install
 		for _, srcdir := range []string{
 			"cmd/arvados-client",
 			"cmd/arvados-server",
-			"services/crunch-dispatch-slurm",
 		} {
 			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+" -s -w")
+			// -buildvcs=false here avoids a fatal "error
+			// obtaining VCS status" when git refuses to
+			// run (for example) as root in a docker
+			// container using a non-root-owned git tree
+			// mounted from the host -- as in
+			// "arvados-package build".
+			cmd := exec.Command("go", "install", "-buildvcs=false", "-ldflags", "-X git.arvados.org/arvados.git/lib/cmd.version="+inst.PackageVersion+" -X main.version="+inst.PackageVersion+" -s -w")
 			cmd.Env = append(cmd.Env, os.Environ()...)
 			cmd.Env = append(cmd.Env, "GOBIN=/var/lib/arvados/bin")
 			cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
@@ -587,6 +584,33 @@ yarn install
 			return 1
 		}
 
+		// Install python SDK and arv-mount in
+		// /var/lib/arvados/lib/python.
+		//
+		// setup.py writes a file in the source directory in
+		// order to include the version number in the package
+		// itself.  We don't want to write to the source tree
+		// (in "arvados-package" context it's mounted
+		// readonly) so we run setup.py in a temporary copy of
+		// the source dir.
+		if err = inst.runBash(`
+v=/var/lib/arvados/lib/python
+tmp=/var/lib/arvados/tmp/python
+python3 -m venv "$v"
+. "$v/bin/activate"
+pip3 install --no-cache-dir 'setuptools>=68' 'pip>=20'
+export ARVADOS_BUILDING_VERSION="`+inst.PackageVersion+`"
+for src in "`+inst.SourcePath+`/sdk/python" "`+inst.SourcePath+`/services/fuse"; do
+  rsync -a --delete-after "$src/" "$tmp/"
+  cd "$tmp"
+  python3 setup.py install
+  cd ..
+  rm -rf "$tmp"
+done
+`, stdout, stderr); err != nil {
+			return 1
+		}
+
 		// Install Rails apps to /var/lib/arvados/{railsapi,workbench1}/
 		for dstdir, srcdir := range map[string]string{
 			"railsapi":   "services/api",
@@ -615,12 +639,15 @@ yarn install
 				{"touch", "log/production.log"},
 				{"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"},
 				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:" + bundlerversion},
-				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem", "--without", "development test diagnostics performance"},
+				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "config", "set", "--local", "deployment", "true"},
+				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "config", "set", "--local", "path", "/var/www/.gem"},
+				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "config", "set", "--local", "without", "development test diagnostics performance"},
+				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--jobs", fmt.Sprintf("%d", runtime.NumCPU())},
 
 				{"chown", "www-data:www-data", ".", "public/assets"},
 				// {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "config", "set", "--local", "system", "true"},
-				{"sudo", "-u", "www-data", "ARVADOS_CONFIG=none", "RAILS_GROUPS=assets", "RAILS_ENV=production", "/var/lib/arvados/bin/bundle", "exec", "rake", "npm:install"},
-				{"sudo", "-u", "www-data", "ARVADOS_CONFIG=none", "RAILS_GROUPS=assets", "RAILS_ENV=production", "/var/lib/arvados/bin/bundle", "exec", "rake", "assets:precompile"},
+				{"sudo", "-u", "www-data", "ARVADOS_CONFIG=none", "RAILS_GROUPS=assets", "RAILS_ENV=production", "PATH=/var/lib/arvados/bin:" + os.Getenv("PATH"), "/var/lib/arvados/bin/bundle", "exec", "rake", "npm:install"},
+				{"sudo", "-u", "www-data", "ARVADOS_CONFIG=none", "RAILS_GROUPS=assets", "RAILS_ENV=production", "PATH=/var/lib/arvados/bin:" + os.Getenv("PATH"), "/var/lib/arvados/bin/bundle", "exec", "rake", "assets:precompile"},
 				{"chown", "root:root", "."},
 				{"chown", "-R", "root:root", "public/assets", "vendor"},
 
@@ -656,8 +683,8 @@ yarn install
 
 		// Install workbench2 app to /var/lib/arvados/workbench2/
 		if err = inst.runBash(`
-cd /var/lib/arvados/arvados-workbench2
-VERSION="`+inst.PackageVersion+`" BUILD_NUMBER=1 GIT_COMMIT="`+workbench2version[:9]+`" yarn build
+cd `+inst.SourcePath+`/services/workbench2
+VERSION="`+inst.PackageVersion+`" BUILD_NUMBER=1 GIT_COMMIT=000000000 yarn build
 rsync -a --delete-after build/ /var/lib/arvados/workbench2/
 `, stdout, stderr); err != nil {
 			return 1
@@ -675,27 +702,56 @@ rsync -a --delete-after build/ /var/lib/arvados/workbench2/
 		if err != nil {
 			return 1
 		}
-		// This is equivalent to "systemd enable", but does
-		// not depend on the systemctl program being
-		// available.
-		symlink := "/etc/systemd/system/multi-user.target.wants/arvados.service"
-		err = os.Remove(symlink)
-		if err != nil && !errors.Is(err, os.ErrNotExist) {
-			return 1
-		}
-		err = os.Symlink("/lib/systemd/system/arvados.service", symlink)
-		if err != nil {
-			return 1
+		if prod {
+			// (fpm will do this for us in the pkg case)
+			// This is equivalent to "systemd enable", but
+			// does not depend on the systemctl program
+			// being available:
+			symlink := "/etc/systemd/system/multi-user.target.wants/arvados.service"
+			err = os.Remove(symlink)
+			if err != nil && !errors.Is(err, os.ErrNotExist) {
+				return 1
+			}
+			err = os.Symlink("/lib/systemd/system/arvados.service", symlink)
+			if err != nil {
+				return 1
+			}
 		}
 
-		// Symlink user-facing programs /usr/bin/x ->
-		// /var/lib/arvados/bin/x
-		for _, prog := range []string{"arvados-client", "arvados-server", "arv", "arv-tag"} {
-			err = os.Remove("/usr/bin/" + prog)
+		// Add symlinks in /usr/bin for user-facing programs
+		for _, srcdst := range [][]string{
+			// go
+			{"bin/arvados-client"},
+			{"bin/arvados-client", "arv"},
+			{"bin/arvados-server"},
+			// sdk/cli
+			{"bin/arv", "arv-ruby"},
+			{"bin/arv-tag"},
+			// sdk/python
+			{"lib/python/bin/arv-copy"},
+			{"lib/python/bin/arv-federation-migrate"},
+			{"lib/python/bin/arv-get"},
+			{"lib/python/bin/arv-keepdocker"},
+			{"lib/python/bin/arv-ls"},
+			{"lib/python/bin/arv-migrate-docker19"},
+			{"lib/python/bin/arv-normalize"},
+			{"lib/python/bin/arv-put"},
+			{"lib/python/bin/arv-ws"},
+			// services/fuse
+			{"lib/python/bin/arv-mount"},
+		} {
+			src := "/var/lib/arvados/" + srcdst[0]
+			if _, err = os.Stat(src); err != nil {
+				return 1
+			}
+			dst := srcdst[len(srcdst)-1]
+			_, dst = filepath.Split(dst)
+			dst = "/usr/bin/" + dst
+			err = os.Remove(dst)
 			if err != nil && !errors.Is(err, os.ErrNotExist) {
 				return 1
 			}
-			err = os.Symlink("/var/lib/arvados/bin/"+prog, "/usr/bin/"+prog)
+			err = os.Symlink(src, dst)
 			if err != nil {
 				return 1
 			}
@@ -798,7 +854,7 @@ func prodpkgs(osv osversion) []string {
 		"libcurl3-gnutls",
 		"libxslt1.1",
 		"nginx",
-		"python",
+		"python3",
 		"sudo",
 	}
 	if osv.Debian || osv.Ubuntu {
@@ -808,21 +864,12 @@ func prodpkgs(osv osversion) []string {
 			pkgs = append(pkgs, "python3-distutils") // sdk/cwl
 		}
 		return append(pkgs,
-			"g++",
-			"libcurl4-openssl-dev", // services/api
-			"libpq-dev",
-			"libpython2.7", // services/fuse
 			"mime-support", // keep-web
-			"zlib1g-dev",   // services/api
 		)
 	} else if osv.Centos {
 		return append(pkgs,
 			"fuse-libs", // services/fuse
-			"gcc",
-			"gcc-c++",
-			"libcurl-devel",    // services/api
-			"mailcap",          // keep-web
-			"postgresql-devel", // services/api
+			"mailcap",   // keep-web
 		)
 	} else {
 		panic("os version not supported")