Add quickstart guide

Use agenix to store the credentials safely.

flake.nix

@@ -25,6 +25,7 @@ in
       bay     = mkConf "bay";
       lake2   = mkConf "lake2";
       raccoon = mkConf "raccoon";
+      fox     = mkConf "fox";
     };
 
     packages.x86_64-linux = self.nixosConfigurations.hut.pkgs // {

keys.nix

@@ -9,10 +9,11 @@ rec {
     koro  = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIImiTFDbxyUYPumvm8C4mEnHfuvtBY1H8undtd6oDd67 koro";
     bay   = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAICvGBzpRQKuQYHdlUQeAk6jmdbkrhmdLwTBqf3el7IgU bay";
     lake2 = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAINo66//S1yatpQHE/BuYD/Gfq64TY7ZN5XOGXmNchiO0 lake2";
+    fox   = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIDa9lId4rB/EKGkkCCVOy0cuId2SYLs+8W8kx0kmpO1y fox";
   };
 
   hostGroup = with hosts; rec {
-    compute    = [ owl1 owl2 ];
+    compute    = [ owl1 owl2 fox ];
     playground = [ eudy koro ];
     storage    = [ bay lake2 ];
     monitor    = [ hut ];

m/common/base/users.nix

@@ -68,7 +68,7 @@
         home = "/home/Computational/anavarro";
         description = "Antoni Navarro";
         group = "Computational";
-        hosts = [ "hut" "raccoon" ];
+        hosts = [ "hut" "raccoon" "fox" ];
         hashedPassword = "$6$QdNDsuLehoZTYZlb$CDhCouYDPrhoiB7/seu7RF.Gqg4zMQz0n5sA4U1KDgHaZOxy2as9pbIGeF8tOHJKRoZajk5GiaZv0rZMn7Oq31";
         openssh.authorizedKeys.keys = [
           "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAILWjRSlKgzBPZQhIeEtk6Lvws2XNcYwHcwPv4osSgst5 anavarro@ssfhead"
@@ -113,6 +113,19 @@
           "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIAb+EQBoS98zrCwnGKkHKwMLdYABMTqv7q9E0+T0QmkS dbautist@bsc-848818791"
         ];
       };
+
+      dalvare1 = {
+        uid = 2758;
+        isNormalUser = true;
+        home = "/home/Computational/dalvare1";
+        description = "David Álvarez";
+        group = "Computational";
+        hosts = [ "hut" "fox" ];
+        hashedPassword = "$6$mpyIsV3mdq.rK8$FvfZdRH5OcEkUt5PnIUijWyUYZvB1SgeqxpJ2p91TTe.3eQIDTcLEQ5rxeg.e5IEXAZHHQ/aMsR5kPEujEghx0";
+        openssh.authorizedKeys.keys = [
+          "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIGEfy6F4rF80r4Cpo2H5xaWqhuUZzUsVsILSKGJzt5jF dalvare1@ssfhead"
+        ];
+      };
     };
 
     groups = {

m/common/xeon/net.nix

@@ -34,37 +34,37 @@
       # Node Entry for node: mds01 (ID=72)
       10.0.40.40              bay mds01 mds01-eth0
       10.0.42.40              bay-ib mds01-ib0
-      10.0.40.141             bay-ipmi mds01-ipmi0
+      10.0.40.141             bay-ipmi mds01-ipmi0 mds01-ipmi
       
       # Node Entry for node: oss01 (ID=73)
       10.0.40.41              oss01 oss01-eth0
       10.0.42.41              oss01-ib0
-      10.0.40.142             oss01-ipmi0
+      10.0.40.142             oss01-ipmi0 oss01-ipmi
       
       # Node Entry for node: oss02 (ID=74)
       10.0.40.42              lake2 oss02 oss02-eth0
       10.0.42.42              lake2-ib oss02-ib0
-      10.0.40.143             lake2-ipmi oss02-ipmi0
+      10.0.40.143             lake2-ipmi oss02-ipmi0 oss02-ipmi
       
       # Node Entry for node: xeon01 (ID=15)
       10.0.40.1               owl1 xeon01 xeon01-eth0
       10.0.42.1               owl1-ib xeon01-ib0
-      10.0.40.101             owl1-ipmi xeon01-ipmi0
+      10.0.40.101             owl1-ipmi xeon01-ipmi0 xeon01-ipmi
       
       # Node Entry for node: xeon02 (ID=16)
       10.0.40.2               owl2 xeon02 xeon02-eth0
       10.0.42.2               owl2-ib xeon02-ib0
-      10.0.40.102             owl2-ipmi xeon02-ipmi0
+      10.0.40.102             owl2-ipmi xeon02-ipmi0 xeon02-ipmi
       
       # Node Entry for node: xeon03 (ID=17)
       10.0.40.3               xeon03 xeon03-eth0
       10.0.42.3               xeon03-ib0
-      10.0.40.103             xeon03-ipmi0
+      10.0.40.103             xeon03-ipmi0 xeon03-ipmi
       
       # Node Entry for node: xeon04 (ID=18)
       10.0.40.4               xeon04 xeon04-eth0
       10.0.42.4               xeon04-ib0
-      10.0.40.104             xeon04-ipmi0
+      10.0.40.104             xeon04-ipmi0 xeon04-ipmi
       
       # Node Entry for node: xeon05 (ID=19)
       10.0.40.5               koro xeon05 xeon05-eth0
@@ -74,17 +74,21 @@
       # Node Entry for node: xeon06 (ID=20)
       10.0.40.6               xeon06 xeon06-eth0
       10.0.42.6               xeon06-ib0
-      10.0.40.106             xeon06-ipmi0
+      10.0.40.106             xeon06-ipmi0 xeon06-ipmi
       
       # Node Entry for node: xeon07 (ID=21)
       10.0.40.7               hut xeon07 xeon07-eth0
       10.0.42.7               hut-ib xeon07-ib0
-      10.0.40.107             hut-ipmi xeon07-ipmi0
+      10.0.40.107             hut-ipmi xeon07-ipmi0 xeon07-ipmi
       
       # Node Entry for node: xeon08 (ID=22)
       10.0.40.8               eudy xeon08 xeon08-eth0
       10.0.42.8               eudy-ib xeon08-ib0
-      10.0.40.108             eudy-ipmi xeon08-ipmi0
+      10.0.40.108             eudy-ipmi xeon08-ipmi0 xeon08-ipmi
+
+      # fox
+      10.0.40.26              fox
+      10.0.40.126             fox-ipmi
     '';
   };
 }

m/fox/configuration.nix

@@ -0,0 +1,75 @@
+{ lib, config, pkgs, ... }:
+
+{
+  imports = [
+    ../common/xeon.nix
+    ../module/ceph.nix
+    ../module/emulation.nix
+    ../module/slurm-client.nix
+    ../module/slurm-firewall.nix
+  ];
+
+  # Select the this using the ID to avoid mismatches
+  boot.loader.grub.device = "/dev/disk/by-id/wwn-0x500a07514b0c1103";
+
+  # No swap, there is plenty of RAM
+  swapDevices = lib.mkForce [];
+
+  boot.initrd.availableKernelModules = [ "xhci_pci" "ahci" "nvme" "usbhid" "usb_storage" "sd_mod" ];
+  boot.kernelModules = [ "kvm-amd" ];
+
+  hardware.cpu.amd.updateMicrocode = lib.mkDefault config.hardware.enableRedistributableFirmware;
+  hardware.cpu.intel.updateMicrocode = lib.mkForce false;
+
+  networking = {
+    hostName = "fox";
+    interfaces.enp1s0f0np0.ipv4.addresses = [ {
+      address = "10.0.40.26";
+      prefixLength = 24;
+    } ];
+  };
+
+  # Configure Nvidia driver to use with CUDA
+  hardware.nvidia.package = config.boot.kernelPackages.nvidiaPackages.production;
+  hardware.graphics.enable = true;
+  nixpkgs.config.allowUnfree = true;
+  nixpkgs.config.nvidia.acceptLicense = true;
+  services.xserver.videoDrivers = [ "nvidia" ];
+
+  # Mount NVME disks
+  fileSystems."/nvme0" = { device = "/dev/disk/by-label/nvme0"; fsType = "ext4"; };
+  fileSystems."/nvme1" = { device = "/dev/disk/by-label/nvme1"; fsType = "ext4"; };
+
+  # Make a /nvme{0,1}/$USER directory for each user.
+  systemd.services.create-nvme-dirs = let
+    # Take only normal users in fox
+    users = lib.filterAttrs (_: v: v.isNormalUser) config.users.users;
+    commands = lib.concatLists (lib.mapAttrsToList
+      (_: user: [
+        "install -d -o ${user.name} -g ${user.group} -m 0755 /nvme{0,1}/${user.name}"
+      ]) users);
+    script = pkgs.writeShellScript "create-nvme-dirs.sh" (lib.concatLines commands);
+  in {
+    enable = true;
+    wants = [ "local-fs.target" ];
+    after = [ "local-fs.target" ];
+    wantedBy = [ "multi-user.target" ];
+    serviceConfig.ExecStart = script;
+  };
+
+  # Only allow SSH connections from users who have a SLURM allocation
+  # See: https://slurm.schedmd.com/pam_slurm_adopt.html
+  security.pam.services.sshd.rules.account.slurm = {
+    control = "required";
+    enable = true;
+    modulePath = "${pkgs.slurm}/lib/security/pam_slurm_adopt.so";
+    args = [ "log_level=debug5" ];
+    order = 999999; # Make it last one
+  };
+
+  # Disable systemd session (pam_systemd.so) as it will conflict with the
+  # pam_slurm_adopt.so module. What happens is that the shell is first adopted
+  # into the slurmstepd task and then into the systemd session, which is not
+  # what we want, otherwise it will linger even if all jobs are gone.
+  security.pam.services.sshd.startSession = lib.mkForce false;
+}

m/hut/gitlab-runner.nix

@@ -1,8 +1,9 @@
 { pkgs, lib, config, ... }:
 
 {
-  age.secrets.gitlabRunnerShellToken.file = ../../secrets/gitlab-runner-shell-token.age;
-  age.secrets.gitlabRunnerDockerToken.file = ../../secrets/gitlab-runner-docker-token.age;
+  age.secrets.gitlab-pm-shell.file = ../../secrets/gitlab-runner-shell-token.age;
+  age.secrets.gitlab-pm-docker.file = ../../secrets/gitlab-runner-docker-token.age;
+  age.secrets.gitlab-bsc-docker.file = ../../secrets/gitlab-bsc-docker-token.age;
 
   services.gitlab-runner = {
     enable = true;
@@ -28,10 +29,65 @@
     in {
       # For pm.bsc.es/gitlab
       gitlab-pm-shell = common-shell // {
-        authenticationTokenConfigFile = config.age.secrets.gitlabRunnerShellToken.path;
+        authenticationTokenConfigFile = config.age.secrets.gitlab-pm-shell.path;
       };
       gitlab-pm-docker = common-docker // {
-        authenticationTokenConfigFile = config.age.secrets.gitlabRunnerDockerToken.path;
+        authenticationTokenConfigFile = config.age.secrets.gitlab-pm-docker.path;
+      };
+
+      gitlab-bsc-docker = {
+        # gitlab.bsc.es still uses the old token mechanism
+        registrationConfigFile = config.age.secrets.gitlab-bsc-docker.path;
+        environmentVariables = {
+          https_proxy = "http://localhost:23080";
+          http_proxy = "http://localhost:23080";
+        };
+        # FIXME
+        registrationFlags = [
+          "--docker-network-mode host"
+        ];
+        executor = "docker";
+        dockerImage = "alpine";
+        dockerVolumes = [
+          "/nix/store:/nix/store:ro"
+          "/nix/var/nix/db:/nix/var/nix/db:ro"
+          "/nix/var/nix/daemon-socket:/nix/var/nix/daemon-socket:ro"
+        ];
+        dockerDisableCache = true;
+        preBuildScript = pkgs.writeScript "setup-container" ''
+          mkdir -p -m 0755 /nix/var/log/nix/drvs
+          mkdir -p -m 0755 /nix/var/nix/gcroots
+          mkdir -p -m 0755 /nix/var/nix/profiles
+          mkdir -p -m 0755 /nix/var/nix/temproots
+          mkdir -p -m 0755 /nix/var/nix/userpool
+          mkdir -p -m 1777 /nix/var/nix/gcroots/per-user
+          mkdir -p -m 1777 /nix/var/nix/profiles/per-user
+          mkdir -p -m 0755 /nix/var/nix/profiles/per-user/root
+          mkdir -p -m 0700 "$HOME/.nix-defexpr"
+          mkdir -p -m 0700 "$HOME/.ssh"
+          cat > "$HOME/.ssh/config" << EOF
+          Host bscpm03.bsc.es gitlab-internal.bsc.es
+            User git
+            ProxyCommand nc -X connect -x hut:23080 %h %p
+          Host amdlogin1.bsc.es armlogin1.bsc.es hualogin1.bsc.es glogin1.bsc.es glogin2.bsc.es fpgalogin1.bsc.es
+            ProxyCommand nc -X connect -x hut:23080 %h %p
+          EOF
+          cat >> "$HOME/.ssh/known_hosts" << EOF
+          bscpm03.bsc.es ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIM2NuSUPsEhqz1j5b4Gqd+MWFnRqyqY57+xMvBUqHYUS
+          gitlab-internal.bsc.es ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIF9arsAOSRB06hdy71oTvJHG2Mg8zfebADxpvc37lZo3
+          EOF
+          . ${pkgs.nix}/etc/profile.d/nix-daemon.sh
+          ${pkgs.nix}/bin/nix-channel --add https://nixos.org/channels/nixos-24.11 nixpkgs
+          ${pkgs.nix}/bin/nix-channel --update nixpkgs
+          ${pkgs.nix}/bin/nix-env -i ${lib.concatStringsSep " " (with pkgs; [ nix cacert git openssh netcat curl ])}
+        '';
+        environmentVariables = {
+          ENV = "/etc/profile";
+          USER = "root";
+          NIX_REMOTE = "daemon";
+          PATH = "/nix/var/nix/profiles/default/bin:/nix/var/nix/profiles/default/sbin:/bin:/sbin:/usr/bin:/usr/sbin";
+          NIX_SSL_CERT_FILE = "/nix/var/nix/profiles/default/etc/ssl/certs/ca-bundle.crt";
+        };
       };
     };
   };

m/hut/ipmi.yml

@@ -1,13 +0,0 @@
-modules:
-        default:
-                collectors:
-                - bmc
-                - ipmi
-                - chassis
-
-        lan:
-                collectors:
-                - ipmi
-                - chassis
-                user: ""
-                pass: ""

m/hut/monitoring.nix

@@ -12,6 +12,8 @@
     mode = "400";
   };
 
+  age.secrets.ipmiYml.file = ../../secrets/ipmi.yml.age;
+
   services.grafana = {
     enable = true;
     settings = {
@@ -73,8 +75,8 @@
         enable = true;
         group = "root";
         user = "root";
-        configFile = ./ipmi.yml;
-        #extraFlags = [ "--log.level=debug" ];
+        configFile = config.age.secrets.ipmiYml.path;
+        extraFlags = [ "--log.level=debug" ];
         listenAddress = "127.0.0.1";
       };
       node = {
@@ -206,7 +208,7 @@
             # Sets the "instance" label with the remote host we are querying
             source_labels = [ "__param_target" ];
             separator = ";";
-            regex = "(.*)";
+            regex = "(.*)-ipmi"; # Remove "-ipm̀i" at the end
             target_label = "instance";
             replacement = "\${1}";
             action = "replace";
@@ -248,6 +250,17 @@
           module = [ "raccoon" ];
         };
       }
+      {
+        job_name = "ipmi-fox";
+        metrics_path = "/ipmi";
+        static_configs = [
+          { targets = [ "127.0.0.1:9290" ]; }
+        ];
+        params = {
+          target = [ "fox-ipmi" ];
+          module = [ "fox" ];
+        };
+      }
     ];
   };
 }

m/hut/targets.yml

@@ -1,15 +1,15 @@
 - targets:
-  - 10.0.40.101
-  - 10.0.40.102
-  - 10.0.40.103
-  - 10.0.40.104
-  - 10.0.40.105
-  - 10.0.40.106
-  - 10.0.40.107
-  - 10.0.40.108
+  - owl1-ipmi
+  - owl2-ipmi
+  - xeon03-ipmi
+  - xeon04-ipmi
+  - koro-ipmi
+  - xeon06-ipmi
+  - hut-ipmi
+  - eudy-ipmi
   # Storage
-  - 10.0.40.141
-  - 10.0.40.142
-  - 10.0.40.143
+  - bay-ipmi
+  - oss01-ipmi
+  - lake2-ipmi
   labels:
     job: ipmi-lan

m/module/slurm-client.nix

@@ -27,6 +27,22 @@ let
     done
   '';
 
+  prolog = pkgs.writeScript "prolog.sh" ''
+    #!/usr/bin/env bash
+
+    echo "hello from the prolog"
+
+    exit 0
+  '';
+
+  epilog = pkgs.writeScript "epilog.sh" ''
+    #!/usr/bin/env bash
+
+    echo "hello from the epilog"
+
+    exit 0
+  '';
+
 in {
   systemd.services.slurmd.serviceConfig = {
     # Kill all processes in the control group on stop/restart. This will kill
@@ -43,12 +59,14 @@ in {
     clusterName = "jungle";
     nodeName = [
       "owl[1,2]  Sockets=2 CoresPerSocket=14 ThreadsPerCore=2 Feature=owl"
+      "fox       Sockets=2 CoresPerSocket=96 ThreadsPerCore=2 Feature=fox"
       "hut       Sockets=2 CoresPerSocket=14 ThreadsPerCore=2"
     ];
 
     partitionName = [
-      "owl Nodes=owl[1-2] Default=YES DefaultTime=01:00:00 MaxTime=INFINITE State=UP"
-      "all Nodes=owl[1-2],hut Default=NO DefaultTime=01:00:00 MaxTime=INFINITE State=UP"
+      "owl Nodes=owl[1-2]     Default=YES DefaultTime=01:00:00 MaxTime=INFINITE State=UP"
+      "fox Nodes=fox          Default=NO  DefaultTime=01:00:00 MaxTime=INFINITE State=UP"
+      "all Nodes=owl[1-2],hut Default=NO  DefaultTime=01:00:00 MaxTime=INFINITE State=UP"
     ];
 
     # See slurm.conf(5) for more details about these options.
@@ -76,7 +94,7 @@ in {
       SuspendTimeout=60
       ResumeProgram=${resumeProgram}
       ResumeTimeout=300
-      SuspendExcNodes=hut
+      SuspendExcNodes=hut,fox
 
       # Turn the nodes off after 1 hour of inactivity
       SuspendTime=3600
@@ -91,9 +109,29 @@ in {
       # Ignore memory constraints and only use unused cores to share a node with
       # other jobs.
       SelectTypeParameters=CR_Core
+
+      # Required for pam_slurm_adopt, see https://slurm.schedmd.com/pam_slurm_adopt.html
+      # This sets up the "extern" step into which ssh-launched processes will be
+      # adopted. Alloc runs the prolog at job allocation (salloc) rather than
+      # when a task runs (srun) so we can ssh early.
+      PrologFlags=Alloc,Contain,X11
+
+      # LaunchParameters=ulimit_pam_adopt will set RLIMIT_RSS in processes
+      # adopted by the external step, similar to tasks running in regular steps
+      # LaunchParameters=ulimit_pam_adopt
+      SlurmdDebug=debug5
+      #DebugFlags=Protocol,Cgroup
+    '';
+
+    extraCgroupConfig = ''
+      CgroupPlugin=cgroup/v2
+      #ConstrainCores=yes
     '';
   };
 
+  # Place the slurm config in /etc as this will be required by PAM
+  environment.etc.slurm.source = config.services.slurm.etcSlurm;
+
   age.secrets.mungeKey = {
     file = ../../secrets/munge-key.age;
     owner = "munge";

pkgs/overlay.nix

@@ -39,6 +39,18 @@ final: prev:
       # See https://bugs.schedmd.com/show_bug.cgi?id=19324
       ./slurm-rank-expansion.patch
     ];
+    # Install also the pam_slurm_adopt library to restrict users from accessing
+    # nodes with no job allocated.
+    postBuild = (old.postBuild or "") + ''
+      pushd contribs/pam_slurm_adopt
+        make "PAM_DIR=$out/lib/security"
+      popd
+    '';
+    postInstall = (old.postInstall or "") + ''
+      pushd contribs/pam_slurm_adopt
+        make "PAM_DIR=$out/lib/security" install
+      popd
+    '';
   });
 
   prometheus-slurm-exporter = prev.callPackage ./slurm-exporter.nix { };

secrets/gitea-runner-token.age

@@ -1,9 +1,9 @@
 age-encryption.org/v1
--> ssh-ed25519 HY2yRg DQdgCk16Yu524BsrWVf0krnwWzDM6SeaJCgQipOfwCA
-Ab9ocqra/UWJZI+QGMlxUhBu5AzqfjPgXl+ENIiHYGs
--> ssh-ed25519 CAWG4Q KF9rGCenb3nf+wyz2hyVs/EUEbsmUs5R+1fBxlCibC8
-7++Kxbr3FHVdVfnFdHYdAuR0Tgfd+sRcO6WRss6LhEw
--> ssh-ed25519 MSF3dg aUe4DhRsu4X8CFOEAnD/XM/o/0qHYSB522woCaAVh0I
-GRcs5cm2YqA/lGhUtbpboBaz7mfgiLaCr+agaB7vACU
---- 9Q7Ou+Pxq+3RZilCb2dKC/pCFjZEt4rp5KnTUUU7WJ8
-1¬
Mw4‘Í	ì:Hµ@Á/ägLtMÇ,ßÆ¥ô*¡žzñNV5ˆm‚ÍNŽoÞáj1$÷TøG_³E{Œ%“‰1ǯ‘<>H£îAÛp™
+-> ssh-ed25519 HY2yRg eRVX5yndWDLg9hw7sY1Iu8pJFy47luHvdL+zZGK2u1s
+e1nXXiMW0ywkZYh2s6c7/quGMfBOJOaRhNQDjCD2Iyc
+-> ssh-ed25519 CAWG4Q gYG7GRxRpJ0/5Wz0Z0J2wfLfkMFNmcy81dQEewM7gUA
+lamdUdx+xOFWF1lmUM4x9TT0cJtKu9Sp7w9JHwm13u0
+-> ssh-ed25519 MSF3dg HEzfpR8alG6WPzhaEjAmmjOFoFcMSQUldx46dBsXri4
+OAD5H/zZGhfevYrFJzJrbNKPomKZDOS9Qx5tmTp78Jo
+--- A0sMSiNXWaEIgRXR0x6UAIaluuVH6Zlv4CJ9sI0NXOw
+ÿú6çphóÎÆ{Ñ>®F|ÅiÃvâæE}{ìruÎâÆ·‹Ý°ËÍ}^»‰>ñc6¥´j÷	ùgèGW<47>Ã:—J3ù|ø|†ZÑ

secrets/gitlab-bsc-docker-token.age

@@ -0,0 +1,9 @@
+age-encryption.org/v1
+-> ssh-ed25519 HY2yRg 4Xns3jybBuv8flzd+h3DArVBa/AlKjt1J9jAyJsasCE
+uyVjJxh5i8aGgAgCpPl6zTYeIkf9mIwURof51IKWvwE
+-> ssh-ed25519 CAWG4Q T2r6r1tyNgq1XlYXVtLJFfOfUnm6pSVlPwUqC1pkyRo
+9yDoKU0EC34QMUXYnsJvhPCLm6oD9w7NlTi2sheoBqQ
+-> ssh-ed25519 MSF3dg Bh9DekFTq+QMUEAonwcaIAJX4Js1O7cHjDniCD0gtm8
+t/Ro0URLeDUWcvb7rlkG2s03PZ+9Rr3N4TIX03tXpVc
+--- E5+/D4aK2ihKRR4YC5XOTmUbKgOqBR0Nk0gYvFOzXOI
+‰ÀÍyKF~djº˜r%¸Š'ÉÓÖPä&_-lŸ”ö&’o¥_ér¯¦r¢ÿß<C3BF>’0ï,­U7†nC·Te…÷[fˆ97ü•…šÙ˦“ÈC!D±E<C2B1>Wé*ÐLAô
x6¾#–¯
’sqôiéËÆäÏŸ“åk ,ùÝ“

secrets/gitlab-runner-docker-token.age

@@ -1,9 +1,10 @@
 age-encryption.org/v1
--> ssh-ed25519 HY2yRg 0sEIUEJBJQ0k0rBfHaOEbq1pNBqsPin4Xq85v0ds9jY
-4wzjLapoOcq53nT2K3hSGED4jTDXci25GLHkl/fL4EI
--> ssh-ed25519 CAWG4Q f68ZbJGwXuCZVnqhwbh+8dh0X/MCdjEd+sVtPyBu/hU
-u2TQreyWQvP6PGuwuUNKA/AL68560flqSlaItN3k41I
--> ssh-ed25519 MSF3dg HdrtRW2j7mfkLH0/4aJK5R0cWdjf56HYtEZgzHi9EAs
-A6MF6tXmSUq2RF2bpmav0GFTRERwluSZGh2snP/KqkA
---- drsezqi7J/g8gm6N10SkfeAWnYct99WUraB5djLJqpo
-gÔ
(ìÐJ!M6¬É3e¸AÜæÃ?\1y÷eüFN\‘<>/MêòªN`K
^€+"¤«Y^å>dÒH÷°‡¸†]P…ÓûJ‘`xôã»{Ú±ô„y°ÅÎøSˆéy
PX{w‰Sï
ž^5X¶JPô;v‰
+-> ssh-ed25519 HY2yRg GdmdkW+BqqwBgu30b846jv3J7jtCM+a3rgOERuA050A
+FeGqM75jG9egesR+yyVKHm0/M+uBBp5Hclg4+qN0BR8
+-> ssh-ed25519 CAWG4Q a0wTWHgulQUYDAMZmXf3dOf6PdYgCqNtSylzWVVRNVM
+Bx+WSYaiY4ZwlSZJo2a1XPMQmbKOU7F0tKAqVRLBOPo
+-> ssh-ed25519 MSF3dg KccUvZZUbxbCrRWUWrX8KcHF6vQ5FV/BqUqI59G7dj4
+CFr7GXpZ9rPgy7HBfOyiYF9FnZUw6KcZwq9f7/0KaU8
+--- E0Rp6RR/8+o0jvB1lRdhnlabxvI6uu/IgL2ZpPXzTc8
+û#ã¶H÷$°F;Ñéù%›È6êË2†¢rfXŸ\Dn ÖшºÈ‰©x™Î>¥Ù&;÷c‘UŠI=›ÑMöÀª?Tœ¡Ç¸ÂÂ"px†Ó­\s‚ÙãbFý<46>ù¹WD¼{Ë
+AW>?U©ÙÊçÐHÔ³

secrets/gitlab-runner-shell-token.age

@@ -1,9 +1,9 @@
 age-encryption.org/v1
--> ssh-ed25519 HY2yRg VY8s9s1zuHOv2axmIacwKg2ozsJnskHTQtslRZ3YI1M
-fKkJuydLOzF/ciPYSYu4ziSCozdl6sowvDMYZmxqmHY
--> ssh-ed25519 CAWG4Q 2ARFd/7RWQ/QOk47FnJFChaVBgoV4LE6EA+JHezkXgg
-MV4g4Llv8Qcd/wUgJyoNG5AXb6o3aFTrOYGC+lXlSzw
--> ssh-ed25519 MSF3dg SKoxWe8Mi8EkBjkESxStOCI5V4C0KYEXIOx7OdENgTA
-p/owKwQ4e4pcGV+hqej2AfPU5QaM2i8VfxhlkjCM4Z4
---- 0VWKU5CQiGbiOtQ2tsZZg88oZm1qcUDEnU5zDTtV+KU
-ŸÖuµcl÷ª`Ÿ¡Mþ¸'Vk6Yè!Ó=¦LÀ¦yš-ž¬ÁO¢Az«Æ˜VEK¦<4B>‚R†_ÌqL|1V•[)²qœ©„Æ“Lç<4C>DyÌÉ0¹_áßåq)-T,ƪú_9û ”?å<>àûib†1
+-> ssh-ed25519 HY2yRg xWRxJGWSzA5aplRYCYLB6aBwrUrQQJ2MtDYaD75V5nI
+J07XF3NQiaYKKKNRcNWi9MloJD2wXHd+2K7bo6lF+QU
+-> ssh-ed25519 CAWG4Q jNWymbyCczcm8RcaIEbFQBlOMALsuxTl4+pLUi0aR20
+z5NixlrRD+Y7Z/aFPs6hiDW4/lp8CBQCeJYpbuG9yYM
+-> ssh-ed25519 MSF3dg QsUQloEKN3k1G49FQnNR/Do6ILgGpjFcw3zu5kk1Ako
+IHwyFWUEWqCStNcFprnpBa8L5J6zKIsn+7HcgGRv3sM
+--- oUia0fsL6opeYWACyXtHAu/Ld+bUIt/7S1VszYTvwgU
+™êVäœ*øtë2-Ÿ7·œ–Ž“§hÜ&‰éÍ¢_!Õ¿+”·±¯(‚ã¡nù¿	¬í(Ëê÷/}òœäáCúNÍ·|ÇNèuÎ5‰Ã¹å‹šKÀìlÆ"ÃØklOX¨yº÷æØàù¤¹ø²Aíõe„È$

secrets/secrets.nix

@@ -9,8 +9,10 @@ in
   "gitea-runner-token.age".publicKeys = hut;
   "gitlab-runner-docker-token.age".publicKeys = hut;
   "gitlab-runner-shell-token.age".publicKeys = hut;
+  "gitlab-bsc-docker-token.age".publicKeys = hut;
   "nix-serve.age".publicKeys = hut;
   "jungle-robot-password.age".publicKeys = hut;
+  "ipmi.yml.age".publicKeys = hut;
 
   "ceph-user.age".publicKeys = safe;
   "munge-key.age".publicKeys = safe;

web/content/access/index.md

@@ -11,7 +11,7 @@ access to the login machine using a resource petition in the BSC intranet.
 
 Then, to request access to the machines we will need some information about you:
 
-1. Which machines you want access to (hut, owl1, owl2, eudy, koro...)
+1. Which machines you want access to ([hut](/hut), [fox](/fox), owl1, owl2, eudy, koro...)
 1. Your user name and user id (to match the NFS permissions)
 1. Your real name and surname (for identification purposes)
 1. The salted hash of your login password, generated with `mkpasswd -m sha-512`

web/content/doc/_index.md

@@ -0,0 +1,10 @@
+---
+title: "Docs"
+description: "Documentation for users of jungle machines"
+date: 2023-09-15
+---
+
+If this is the first time you use any of the jungle machines with NixOS, follow
+the [quick start guide](quickstart).
+
+

web/content/doc/quickstart.md

@@ -0,0 +1,234 @@
+---
+title: "Quick start"
+date: 2023-09-15
+---
+
+This documentation will guide you on how to build custom packages of software
+and use them in the jungle machines. It has been designed to reduce the friction
+from users coming from module systems.
+
+You should be able to access the jungle machines, otherwise [request
+access](/access).
+
+## Changes from other HPC machines
+
+Users of other machines have been using the Lmod tool (module load ...) to add
+or remove programs from their environment, as well as manually building their
+own software for too many years.
+
+While we cannot prevent users from continuing to use this tedious mechanism, we
+have designed the jungle machines to be much easier to operate by using the nix
+package manager.
+
+### Freedom to install packages
+
+When a user wanted to install a package, it was forced to either do it on its
+own directory, or request a system administrator to install it in a shared
+directory, so other users can also use that package.
+
+This situation is gone, each user can install any package of software by
+themselves, without requiring any other authorization. When two users request
+the same package, the same copy will be provided.
+
+A new package will be downloaded if it is available (someone already built it)
+or will be built from source on demand.
+
+### No changes over time
+
+All users retain the same versions of the packages they request until they
+decide to update them.
+
+## Using nix to manage packages
+
+In this chapter we show how to install packages and enter a development shell to
+build new programs from source. The examples are done from the hut machine,
+read [this page](/access) to request access.
+
+### Installing binaries
+
+To temporarily install new packages, use:
+
+```text
+hut% nix shell jungle#gcc jungle#cowsay jungle#ovni
+```
+
+Notice that the packages are described as two parts divided by the `#` symbol.
+The first part defines where to take the package from and the second part is
+the name of the package. For now we will use `jungle#<package>`. You can find
+many more packages here:
+
+<https://search.nixos.org/packages>
+
+You will now enter a new shell, where those requested package **binaries are
+available in $PATH**:
+
+```text
+hut% cowsay hello world
+ _____________
+< hello world >
+ -------------
+        \   ^__^
+         \  (oo)\_______
+            (__)\       )\/\
+                ||----w |
+                ||     ||
+
+hut% ovniver
+LD_LIBRARY_PATH not set
+libovni: build v1.11.0 (a7103f8), dynamic v1.11.0 (a7103f8)
+
+hut% gcc --version
+gcc (GCC) 13.3.0
+Copyright (C) 2023 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+```
+
+### Building programs
+
+The above method only loads new binaries in the `$PATH`. If we try to build a
+program that includes headers or links with a library, it will fail to find
+them:
+
+```text
+hut$ cat test.c
+#include <ovni.h>
+
+int main()
+{
+        ovni_version_check();
+        return 0;
+}
+hut% gcc test.c -lovni -o test
+test.c:1:10: fatal error: ovni.h: No such file or directory
+    1 | #include <ovni.h>
+      |          ^~~~~~~~
+compilation terminated.
+```
+
+We could manually add the full path to the ovni include directory with `-I` and
+the libraries with `-L`, but there is a tool that already perform these steps
+automatically for us, `nix develop`.
+
+Let's go back to our original shell first, where those packages are not
+available anymore:
+
+```
+hut% ps
+    PID TTY          TIME CMD
+2356260 pts/1    00:00:01 zsh
+2457268 pts/1    00:00:00 zsh
+2457297 pts/1    00:00:00 ps
+hut% exit
+hut% ovniver
+ovniver: command not found
+```
+
+### Creating a flake.nix
+
+To define which packages we want, we will write a small file that list them, a
+flake.nix file.
+
+First, we will create a new directory where we are going to be working:
+
+```
+hut% mkdir example
+hut% cd exmple
+```
+
+Then place this flake.nix file:
+
+```nix
+{
+  inputs.jungle.url = "jungle";
+  outputs = { self, jungle }:  
+  let
+    pkgs = jungle.outputs.packages.x86_64-linux;
+  in {
+    devShells.x86_64-linux.default = pkgs.mkShell {
+      pname = "devshell";
+      buildInputs = with pkgs; [
+        ovni gcc cowsay # more packages here...
+      ];
+    };
+  };
+}
+```
+
+
+Now enter the shell with:
+
+```
+hut% nix develop
+warning: creating lock file '/home/Computational/rarias/example/flake.lock':
+• Added input 'jungle':
+    'path:/nix/store/27srv8haj6vv4ywrbmw0a8vds561m8rq-source?lastModified=1739479441&narHash=sha256-Kgjs8SO1w9NbPBu8ghwzCxYJ9kvWpoQOT%2BXwPvA9DcU%3D&rev=76396c0d67ef0cf32377d5c1894bb695293bca9d' (2025-02-13)
+• Added input 'jungle/agenix':
+    'github:ryantm/agenix/f6291c5935fdc4e0bef208cfc0dcab7e3f7a1c41?narHash=sha256-b%2Buqzj%2BWa6xgMS9aNbX4I%2BsXeb5biPDi39VgvSFqFvU%3D' (2024-08-10)
+• Added input 'jungle/agenix/darwin':
+    'github:lnl7/nix-darwin/4b9b83d5a92e8c1fbfd8eb27eda375908c11ec4d?narHash=sha256-gzGLZSiOhf155FW7262kdHo2YDeugp3VuIFb4/GGng0%3D' (2023-11-24)
+• Added input 'jungle/agenix/darwin/nixpkgs':
+    follows 'jungle/agenix/nixpkgs'
+• Added input 'jungle/agenix/home-manager':
+    'github:nix-community/home-manager/3bfaacf46133c037bb356193bd2f1765d9dc82c1?narHash=sha256-7ulcXOk63TIT2lVDSExj7XzFx09LpdSAPtvgtM7yQPE%3D' (2023-12-20)
+• Added input 'jungle/agenix/home-manager/nixpkgs':
+    follows 'jungle/agenix/nixpkgs'
+• Added input 'jungle/agenix/nixpkgs':
+    follows 'jungle/nixpkgs'
+• Added input 'jungle/agenix/systems':
+    'github:nix-systems/default/da67096a3b9bf56a91d16901293e51ba5b49a27e?narHash=sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768%3D' (2023-04-09)
+• Added input 'jungle/bscpkgs':
+    'git+https://git.sr.ht/~rodarima/bscpkgs?ref=refs/heads/master&rev=6782fc6c5b5a29e84a7f2c2d1064f4bcb1288c0f' (2024-11-29)
+• Added input 'jungle/bscpkgs/nixpkgs':
+    follows 'jungle/nixpkgs'
+• Added input 'jungle/nixpkgs':
+    'github:NixOS/nixpkgs/9c6b49aeac36e2ed73a8c472f1546f6d9cf1addc?narHash=sha256-i/UJ5I7HoqmFMwZEH6vAvBxOrjjOJNU739lnZnhUln8%3D' (2025-01-14)
+
+hut$ 
+```
+
+Notice that long list of messages is Nix creating a new flake.lock file with the
+current state of the packages. Next invocations will use the same packages as
+described by the lock file.
+
+### Building a program from nix develop
+
+Now let's try again building our test program:
+
+```text
+hut$ cat test.c
+#include <ovni.h>
+
+int main()
+{
+        ovni_version_check();
+        return 0;
+}
+hut$ gcc test.c -o test -lovni
+hut$ ldd test
+        linux-vdso.so.1 (0x00007ffff7fc4000)
+        libovni.so.1 => /nix/store/sqk972akjv0q8dchn8ccjln2llzyyfd0-ovni-1.11.0/lib/libovni.so.1 (0x00007ffff7fab000)
+        libc.so.6 => /nix/store/nqb2ns2d1lahnd5ncwmn6k84qfd7vx2k-glibc-2.40-36/lib/libc.so.6 (0x00007ffff7db2000)
+        /nix/store/nqb2ns2d1lahnd5ncwmn6k84qfd7vx2k-glibc-2.40-36/lib/ld-linux-x86-64.so.2 => /nix/store/nqb2ns2d1lahnd5ncwmn6k84qfd7vx2k-glibc-2.40-36/lib64/ld-linux-x86-64.so.2 (0x00007ffff7fc6000)
+hut$ ./test
+```
+
+Now the ovni.h header and the libovni library are found and the program is
+successfully built, linked and executed.
+
+You can add more packages as needed in your flake.nix:
+
+```nix
+  buildInputs = with pkgs; [
+    ovni gcc cowsay # more packages here...
+  ];
+```
+
+Make sure you exit the develop shell first, and then enter again with `nix
+develop`.
+
+## Remember
+
+- `nix shell` places binaries in the `$PATH`.
+- `nix develop` enters a development shell where both binaries and the libraries
+  and includes are available so you can build new programs.

web/content/fox/_index.md

@@ -0,0 +1,97 @@
+---
+title: "Fox"
+description: "AMD Genoa 9684X with 2 NVIDIA RTX4000 GPUs"
+date: 2025-02-12
+---
+
+![Fox](fox.jpg)
+
+Picture by [Joanne Redwood](https://web.archive.org/web/20191109175146/https://www.inaturalist.org/photos/6568074),
+[CC0](http://creativecommons.org/publicdomain/zero/1.0/deed.en).
+
+The *fox* machine is a big GPU server that is configured to run heavy workloads.
+It has two fast AMD CPUs with large cache and 2 reasonable NVIDIA GPUs. Here are
+the detailed specifications:
+
+- 2x AMD GENOA X 9684X DP/UP 96C/192T 2.55G 1,150M 400W SP5 3D V-cach
+- 24x 32GB DDR5-4800 ECC RDIMM (total 768 GiB of RAM)
+- 1x 2.5" SSD SATA3 MICRON 5400 MAX 480GB
+- 2x 2.5" KIOXIA CM7-R 1.92TB NVMe GEN5 PCIe 5x4
+- 2x NVIDIA RTX4000 ADA Gen 20GB GDDR6 PCIe 4.0
+
+## Access
+
+To access the machine, request a SLURM session from [hut](/hut) using the `fox`
+partition:
+
+    hut% salloc -p fox
+
+Then connect via ssh:
+
+    hut% ssh fox
+    fox%
+
+Follow [these steps](/access) if you don't have access to hut or fox.
+
+## CUDA
+
+To use CUDA, you can use the following `flake.nix` placed in a new directory to
+load all the required dependencies:
+
+```nix
+{
+  inputs.jungle.url = "jungle";
+
+  outputs = { jungle, ... }: {
+    devShell.x86_64-linux = let
+      pkgs = jungle.nixosConfigurations.fox.pkgs;
+    in pkgs.mkShell {
+      name = "cuda-env-shell";
+      buildInputs = with pkgs; [
+        git gitRepo gnupg autoconf curl
+        procps gnumake util-linux m4 gperf unzip
+
+        # Cuda packages (more at https://search.nixos.org/packages)
+        cudatoolkit linuxPackages.nvidia_x11
+        cudaPackages.cuda_cudart.static
+        cudaPackages.libcusparse
+
+        libGLU libGL
+        xorg.libXi xorg.libXmu freeglut
+        xorg.libXext xorg.libX11 xorg.libXv xorg.libXrandr zlib
+        ncurses5 stdenv.cc binutils
+      ];
+      shellHook = ''
+        export CUDA_PATH=${pkgs.cudatoolkit}
+        export LD_LIBRARY_PATH=/var/run/opengl-driver/lib
+        export SMS=50
+      '';
+    };
+  };
+}
+```
+
+Then just run `nix develop` from the same directory:
+
+    % mkdir cuda
+    % cd cuda
+    % vim flake.nix
+    [...]
+    % nix develop
+    $ nvcc -V
+    nvcc: NVIDIA (R) Cuda compiler driver
+    Copyright (c) 2005-2024 NVIDIA Corporation
+    Built on Tue_Feb_27_16:19:38_PST_2024
+    Cuda compilation tools, release 12.4, V12.4.99
+    Build cuda_12.4.r12.4/compiler.33961263_0
+
+## Filesystems
+
+The machine has several file systems available.
+
+- `$HOME`: Mounted via NFS across all nodes. It is slow and has low capacity.
+  Don't abuse.
+- `/ceph/home/$USER`: Shared Ceph file system across jungle nodes. Slow but high
+  capacity. Stores three redundant copies of every file.
+- `/nvme{0,1}/$USER`: The two local NVME disks, very fast and large capacity.
+- `/tmp`: tmpfs, fast but not backed by a disk. Will be erased on reboot.

web/hugo.toml

@@ -3,32 +3,38 @@ languageCode = 'en-us'
 title = 'The jungle'
 theme = 'PaperMod'
 
+[[menu.main]]
+identifier = "doc"
+name = "Docs"
+url = "/doc/"
+weight = 10
+
 [[menu.main]]
 identifier = "grafana"
 name = "Grafana"
 url = "/grafana/"
-weight = 10
+weight = 20
 
 [[menu.main]]
 identifier = "Git"
 name = "Git"
 url = "/git/"
-weight = 20
+weight = 30
 
 [[menu.main]]
 identifier = "Lists"
 name = "Lists"
 url = "/lists/"
-weight = 30
+weight = 40
 
 [[menu.main]]
 identifier = "Paste"
 name = "Paste"
 url = "/paste/"
-weight = 40
+weight = 50
 
 [[menu.main]]
 identifier = "Posts"
 name = "Posts"
 url = "/posts/"
-weight = 50
+weight = 60