Use standard gcc for intel packages

See: dc2e7bea50

flake.lock

@@ -1,12 +1,78 @@
 {
   "nodes": {
+    "agenix": {
+      "inputs": {
+        "darwin": "darwin",
+        "home-manager": "home-manager",
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1750173260,
+        "narHash": "sha256-9P1FziAwl5+3edkfFcr5HeGtQUtrSdk/MksX39GieoA=",
+        "owner": "ryantm",
+        "repo": "agenix",
+        "rev": "531beac616433bac6f9e2a19feb8e99a22a66baf",
+        "type": "github"
+      },
+      "original": {
+        "owner": "ryantm",
+        "repo": "agenix",
+        "type": "github"
+      }
+    },
+    "darwin": {
+      "inputs": {
+        "nixpkgs": [
+          "agenix",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1744478979,
+        "narHash": "sha256-dyN+teG9G82G+m+PX/aSAagkC+vUv0SgUw3XkPhQodQ=",
+        "owner": "lnl7",
+        "repo": "nix-darwin",
+        "rev": "43975d782b418ebf4969e9ccba82466728c2851b",
+        "type": "github"
+      },
+      "original": {
+        "owner": "lnl7",
+        "ref": "master",
+        "repo": "nix-darwin",
+        "type": "github"
+      }
+    },
+    "home-manager": {
+      "inputs": {
+        "nixpkgs": [
+          "agenix",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1745494811,
+        "narHash": "sha256-YZCh2o9Ua1n9uCvrvi5pRxtuVNml8X2a03qIFfRKpFs=",
+        "owner": "nix-community",
+        "repo": "home-manager",
+        "rev": "abfad3d2958c9e6300a883bd443512c55dfeb1be",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "home-manager",
+        "type": "github"
+      }
+    },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1752436162,
+        "lastModified": 1760139962,
-        "narHash": "sha256-Kt1UIPi7kZqkSc5HVj6UY5YLHHEzPBkgpNUByuyxtlw=",
+        "narHash": "sha256-4xggC56Rub3WInz5eD7EZWXuLXpNvJiUPahGtMkwtuc=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "dfcd5b901dbab46c9c6e80b265648481aafb01f8",
+        "rev": "7e297ddff44a3cc93673bb38d0374df8d0ad73e4",
         "type": "github"
       },
       "original": {
@@ -18,8 +84,24 @@
     },
     "root": {
       "inputs": {
+        "agenix": "agenix",
         "nixpkgs": "nixpkgs"
       }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
     }
   },
   "root": "root",

flake.nix

@@ -1,13 +1,15 @@
 {
   inputs = {
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.05";
+    agenix.url = "github:ryantm/agenix";
+    agenix.inputs.nixpkgs.follows = "nixpkgs";
   };
 
-  outputs = { self, nixpkgs, ... }:
+  outputs = { self, nixpkgs, agenix, ... }:
 let
   mkConf = name: nixpkgs.lib.nixosSystem {
     system = "x86_64-linux";
-    specialArgs = { inherit nixpkgs; theFlake = self; };
+    specialArgs = { inherit nixpkgs agenix; theFlake = self; };
     modules = [ "${self.outPath}/m/${name}/configuration.nix" ];
   };
   # For now we only support x86

m/common/base/agenix.nix

@@ -1,8 +1,9 @@
-{ pkgs, ... }:
+{ agenix, ... }:
 
 {
-  imports = [ ../../module/agenix.nix ];
+  imports = [ agenix.nixosModules.default ];
 
-  # Add agenix to system packages
+  environment.systemPackages = [
-  environment.systemPackages = [ pkgs.agenix ];
+    agenix.packages.x86_64-linux.default
+  ];
 }

m/common/base/users.nix

@@ -180,19 +180,6 @@
           "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIFmMqKqPg4uocNOr3O41kLbZMOMJn3m2ZdN1JvTR96z3 bsccns@arnau-bsc"
         ];
       };
-
-      aaguirre = {
-        uid = 9655;
-        isNormalUser = true;
-        home = "/home/Computational/aaguirre";
-        description = "Alejandro Aguirre";
-        group = "Computational";
-        hosts = [ "apex" "hut" ];
-        hashedPassword = "$6$TXRXQT6jjBvxkxU6$E.sh5KspAm1qeG5Ct7OPHpo8REmbGDwjFGvqeGgTVz3GASGOAnPL7UMZsMAsAKBoahOw.v8LNno6XGrTEPzZH1";
-        openssh.authorizedKeys.keys = [
-          "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIOlRX7ZCnqtUJYCxKgWmgSrFCYuA2LHY96rVwqxXPl86 aaguirre@BSC-8488184117"
-        ];
-      };
     };
 
     groups = {

m/hut/configuration.nix

@@ -17,7 +17,6 @@
     ./postgresql.nix
     ./nginx.nix
     ./p.nix
-    ./ompss2-timer.nix
     #./pxe.nix
   ];
 

m/hut/gitea.nix

@@ -29,9 +29,6 @@
     };
   };
 
-  # Allow gitea user to send mail
-  users.users.gitea.extraGroups = [ "mail-robot" ];
-
   services.gitea-actions-runner.instances = {
     runrun = {
       enable = true;

m/hut/msmtp.nix

@@ -1,11 +1,8 @@
 { config, lib, ... }:
 {
-  # Robot user that can see the password to send mail from jungle-robot
-  users.groups.mail-robot = {};
-
   age.secrets.jungleRobotPassword = {
     file = ../../secrets/jungle-robot-password.age;
-    group = "mail-robot";
+    group = "gitea";
     mode = "440";
   };
 

m/hut/nginx.nix

@@ -4,8 +4,8 @@ let
     name = "jungle-web";
     src = pkgs.fetchgit {
       url = "https://jungle.bsc.es/git/rarias/jungle-website.git";
-      rev = "52abaf4d71652a9ef77a0b098db14ca33bffff4c";
+      rev = "739bf0175a7f05380fe7ad7023ff1d60db1710e1";
-      hash = "sha256-/ul9GazbOrOkmlvSgDz/+2W+V+ir5725Y7mVLc3rb0M=";
+      hash = "sha256-ea5DzhYTzZ9TmqD+x95rdNdLbxPnBluqlYH2NmBYmc4=";
     };
     buildInputs = [ pkgs.hugo ];
     buildPhase = ''

m/hut/ompss2-timer.nix

@@ -1,85 +0,0 @@
-{ config, pkgs, ... }:
-{
-  systemd.timers = {
-    "ompss2-closing" = {
-      wantedBy = [ "timers.target" ];
-      timerConfig = {
-        Unit = "ompss2-closing.service";
-        OnCalendar = [ "*-03-15 07:00:00" "*-09-15 07:00:00"];
-      };
-    };
-    "ompss2-freeze" = {
-      wantedBy = [ "timers.target" ];
-      timerConfig = {
-        Unit = "ompss2-freeze.service";
-        OnCalendar = [ "*-04-15 07:00:00" "*-10-15 07:00:00" ];
-      };
-    };
-    "ompss2-release" = {
-      wantedBy = [ "timers.target" ];
-      timerConfig = {
-        Unit = "ompss2-release.service";
-        OnCalendar = [ "*-05-15 07:00:00" "*-11-15 07:00:00" ];
-      };
-    };
-  };
-
-  systemd.services =
-  let
-    closing = pkgs.writeText "closing.txt"
-    ''
-      Subject: OmpSs-2 release enters closing period
-
-      Hi,
-
-      You have one month to merge the remaining features for the next OmpSs-2
-      release. Please, identify what needs to be merged and discuss it in the next
-      OmpSs-2 meeting.
-
-      Thanks!,
-      Jungle robot
-    '';
-    freeze = pkgs.writeText "freeze.txt"
-    ''
-      Subject: OmpSs-2 release enters freeze period
-
-      Hi,
-
-      The period to introduce new features or breaking changes is over, only bug
-      fixes are allowed now. During this time, please prepare the release notes
-      to be included in the next OmpSs-2 release.
-
-      Thanks!,
-      Jungle robot
-    '';
-    release = pkgs.writeText "release.txt"
-    ''
-      Subject: OmpSs-2 release now
-
-      Hi,
-
-      The period to introduce bug fixes is now over. Please, proceed to do the
-      OmpSs-2 release.
-
-      Thanks!,
-      Jungle robot
-    '';
-    mkServ = name: mail: {
-      "ompss2-${name}" = {
-        script = ''
-          set -eu
-          set -o pipefail
-          cat ${mail} | ${config.security.wrapperDir}/sendmail star@bsc.es
-        '';
-        serviceConfig = {
-          Type = "oneshot";
-          DynamicUser = true;
-          Group = "mail-robot";
-        };
-      };
-    };
-  in
-    (mkServ "closing" closing) //
-    (mkServ "freeze" freeze) //
-    (mkServ "release" release);
-}

m/module/agenix.nix

@@ -1,357 +0,0 @@
-{
-  config,
-  options,
-  lib,
-  pkgs,
-  ...
-}:
-with lib;
-let
-  cfg = config.age;
-
-  isDarwin = lib.attrsets.hasAttrByPath [ "environment" "darwinConfig" ] options;
-
-  ageBin = config.age.ageBin;
-
-  users = config.users.users;
-
-  sysusersEnabled =
-    if isDarwin then
-      false
-    else
-      options.systemd ? sysusers && (config.systemd.sysusers.enable || config.services.userborn.enable);
-
-  mountCommand =
-    if isDarwin then
-      ''
-        if ! diskutil info "${cfg.secretsMountPoint}" &> /dev/null; then
-            num_sectors=1048576
-            dev=$(hdiutil attach -nomount ram://"$num_sectors" | sed 's/[[:space:]]*$//')
-            newfs_hfs -v agenix "$dev"
-            mount -t hfs -o nobrowse,nodev,nosuid,-m=0751 "$dev" "${cfg.secretsMountPoint}"
-        fi
-      ''
-    else
-      ''
-        grep -q "${cfg.secretsMountPoint} ramfs" /proc/mounts ||
-          mount -t ramfs none "${cfg.secretsMountPoint}" -o nodev,nosuid,mode=0751
-      '';
-  newGeneration = ''
-    _agenix_generation="$(basename "$(readlink ${cfg.secretsDir})" || echo 0)"
-    (( ++_agenix_generation ))
-    echo "[agenix] creating new generation in ${cfg.secretsMountPoint}/$_agenix_generation"
-    mkdir -p "${cfg.secretsMountPoint}"
-    chmod 0751 "${cfg.secretsMountPoint}"
-    ${mountCommand}
-    mkdir -p "${cfg.secretsMountPoint}/$_agenix_generation"
-    chmod 0751 "${cfg.secretsMountPoint}/$_agenix_generation"
-  '';
-
-  chownGroup = if isDarwin then "admin" else "keys";
-  # chown the secrets mountpoint and the current generation to the keys group
-  # instead of leaving it root:root.
-  chownMountPoint = ''
-    chown :${chownGroup} "${cfg.secretsMountPoint}" "${cfg.secretsMountPoint}/$_agenix_generation"
-  '';
-
-  setTruePath = secretType: ''
-    ${
-      if secretType.symlink then
-        ''
-          _truePath="${cfg.secretsMountPoint}/$_agenix_generation/${secretType.name}"
-        ''
-      else
-        ''
-          _truePath="${secretType.path}"
-        ''
-    }
-  '';
-
-  installSecret = secretType: ''
-    ${setTruePath secretType}
-    echo "decrypting '${secretType.file}' to '$_truePath'..."
-    TMP_FILE="$_truePath.tmp"
-
-    IDENTITIES=()
-    for identity in ${toString cfg.identityPaths}; do
-      test -r "$identity" || continue
-      test -s "$identity" || continue
-      IDENTITIES+=(-i)
-      IDENTITIES+=("$identity")
-    done
-
-    test "''${#IDENTITIES[@]}" -eq 0 && echo "[agenix] WARNING: no readable identities found!"
-
-    mkdir -p "$(dirname "$_truePath")"
-    [ "${secretType.path}" != "${cfg.secretsDir}/${secretType.name}" ] && mkdir -p "$(dirname "${secretType.path}")"
-    (
-      umask u=r,g=,o=
-      test -f "${secretType.file}" || echo '[agenix] WARNING: encrypted file ${secretType.file} does not exist!'
-      test -d "$(dirname "$TMP_FILE")" || echo "[agenix] WARNING: $(dirname "$TMP_FILE") does not exist!"
-      LANG=${
-        config.i18n.defaultLocale or "C"
-      } ${ageBin} --decrypt "''${IDENTITIES[@]}" -o "$TMP_FILE" "${secretType.file}"
-    )
-    chmod ${secretType.mode} "$TMP_FILE"
-    mv -f "$TMP_FILE" "$_truePath"
-
-    ${optionalString secretType.symlink ''
-      [ "${secretType.path}" != "${cfg.secretsDir}/${secretType.name}" ] && ln -sfT "${cfg.secretsDir}/${secretType.name}" "${secretType.path}"
-    ''}
-  '';
-
-  testIdentities = map (path: ''
-    test -f ${path} || echo '[agenix] WARNING: config.age.identityPaths entry ${path} not present!'
-  '') cfg.identityPaths;
-
-  cleanupAndLink = ''
-    _agenix_generation="$(basename "$(readlink ${cfg.secretsDir})" || echo 0)"
-    (( ++_agenix_generation ))
-    echo "[agenix] symlinking new secrets to ${cfg.secretsDir} (generation $_agenix_generation)..."
-    ln -sfT "${cfg.secretsMountPoint}/$_agenix_generation" ${cfg.secretsDir}
-
-    (( _agenix_generation > 1 )) && {
-    echo "[agenix] removing old secrets (generation $(( _agenix_generation - 1 )))..."
-    rm -rf "${cfg.secretsMountPoint}/$(( _agenix_generation - 1 ))"
-    }
-  '';
-
-  installSecrets = builtins.concatStringsSep "\n" (
-    [ "echo '[agenix] decrypting secrets...'" ]
-    ++ testIdentities
-    ++ (map installSecret (builtins.attrValues cfg.secrets))
-    ++ [ cleanupAndLink ]
-  );
-
-  chownSecret = secretType: ''
-    ${setTruePath secretType}
-    chown ${secretType.owner}:${secretType.group} "$_truePath"
-  '';
-
-  chownSecrets = builtins.concatStringsSep "\n" (
-    [ "echo '[agenix] chowning...'" ]
-    ++ [ chownMountPoint ]
-    ++ (map chownSecret (builtins.attrValues cfg.secrets))
-  );
-
-  secretType = types.submodule (
-    { config, ... }:
-    {
-      options = {
-        name = mkOption {
-          type = types.str;
-          default = config._module.args.name;
-          defaultText = literalExpression "config._module.args.name";
-          description = ''
-            Name of the file used in {option}`age.secretsDir`
-          '';
-        };
-        file = mkOption {
-          type = types.path;
-          description = ''
-            Age file the secret is loaded from.
-          '';
-        };
-        path = mkOption {
-          type = types.str;
-          default = "${cfg.secretsDir}/${config.name}";
-          defaultText = literalExpression ''
-            "''${cfg.secretsDir}/''${config.name}"
-          '';
-          description = ''
-            Path where the decrypted secret is installed.
-          '';
-        };
-        mode = mkOption {
-          type = types.str;
-          default = "0400";
-          description = ''
-            Permissions mode of the decrypted secret in a format understood by chmod.
-          '';
-        };
-        owner = mkOption {
-          type = types.str;
-          default = "0";
-          description = ''
-            User of the decrypted secret.
-          '';
-        };
-        group = mkOption {
-          type = types.str;
-          default = users.${config.owner}.group or "0";
-          defaultText = literalExpression ''
-            users.''${config.owner}.group or "0"
-          '';
-          description = ''
-            Group of the decrypted secret.
-          '';
-        };
-        symlink = mkEnableOption "symlinking secrets to their destination" // {
-          default = true;
-        };
-      };
-    }
-  );
-in
-{
-  imports = [
-    (mkRenamedOptionModule [ "age" "sshKeyPaths" ] [ "age" "identityPaths" ])
-  ];
-
-  options.age = {
-    ageBin = mkOption {
-      type = types.str;
-      default = "${pkgs.age}/bin/age";
-      defaultText = literalExpression ''
-        "''${pkgs.age}/bin/age"
-      '';
-      description = ''
-        The age executable to use.
-      '';
-    };
-    secrets = mkOption {
-      type = types.attrsOf secretType;
-      default = { };
-      description = ''
-        Attrset of secrets.
-      '';
-    };
-    secretsDir = mkOption {
-      type = types.path;
-      default = "/run/agenix";
-      description = ''
-        Folder where secrets are symlinked to
-      '';
-    };
-    secretsMountPoint = mkOption {
-      type =
-        types.addCheck types.str (
-          s:
-          (builtins.match "[ \t\n]*" s) == null # non-empty
-          && (builtins.match ".+/" s) == null
-        ) # without trailing slash
-        // {
-          description = "${types.str.description} (with check: non-empty without trailing slash)";
-        };
-      default = "/run/agenix.d";
-      description = ''
-        Where secrets are created before they are symlinked to {option}`age.secretsDir`
-      '';
-    };
-    identityPaths = mkOption {
-      type = types.listOf types.path;
-      default =
-        if isDarwin then
-          [
-            "/etc/ssh/ssh_host_ed25519_key"
-            "/etc/ssh/ssh_host_rsa_key"
-          ]
-        else if (config.services.openssh.enable or false) then
-          map (e: e.path) (
-            lib.filter (e: e.type == "rsa" || e.type == "ed25519") config.services.openssh.hostKeys
-          )
-        else
-          [ ];
-      defaultText = literalExpression ''
-        if isDarwin
-        then [
-          "/etc/ssh/ssh_host_ed25519_key"
-          "/etc/ssh/ssh_host_rsa_key"
-        ]
-        else if (config.services.openssh.enable or false)
-        then map (e: e.path) (lib.filter (e: e.type == "rsa" || e.type == "ed25519") config.services.openssh.hostKeys)
-        else [];
-      '';
-      description = ''
-        Path to SSH keys to be used as identities in age decryption.
-      '';
-    };
-  };
-
-  config = mkIf (cfg.secrets != { }) (mkMerge [
-    {
-      assertions = [
-        {
-          assertion = cfg.identityPaths != [ ];
-          message = "age.identityPaths must be set, for example by enabling openssh.";
-        }
-      ];
-    }
-    (optionalAttrs (!isDarwin) {
-      # When using sysusers we no longer be started as an activation script
-      # because those are started in initrd while sysusers is started later.
-      systemd.services.agenix-install-secrets = mkIf sysusersEnabled {
-        wantedBy = [ "sysinit.target" ];
-        after = [ "systemd-sysusers.service" ];
-        unitConfig.DefaultDependencies = "no";
-
-        path = [ pkgs.mount ];
-        serviceConfig = {
-          Type = "oneshot";
-          ExecStart = pkgs.writeShellScript "agenix-install" (concatLines [
-            newGeneration
-            installSecrets
-            chownSecrets
-          ]);
-          RemainAfterExit = true;
-        };
-      };
-
-      # Create a new directory full of secrets for symlinking (this helps
-      # ensure removed secrets are actually removed, or at least become
-      # invalid symlinks).
-      system.activationScripts = mkIf (!sysusersEnabled) {
-        agenixNewGeneration = {
-          text = newGeneration;
-          deps = [
-            "specialfs"
-          ];
-        };
-
-        agenixInstall = {
-          text = installSecrets;
-          deps = [
-            "agenixNewGeneration"
-            "specialfs"
-          ];
-        };
-
-        # So user passwords can be encrypted.
-        users.deps = [ "agenixInstall" ];
-
-        # Change ownership and group after users and groups are made.
-        agenixChown = {
-          text = chownSecrets;
-          deps = [
-            "users"
-            "groups"
-          ];
-        };
-
-        # So other activation scripts can depend on agenix being done.
-        agenix = {
-          text = "";
-          deps = [ "agenixChown" ];
-        };
-      };
-    })
-
-    (optionalAttrs isDarwin {
-      launchd.daemons.activate-agenix = {
-        script = ''
-          set -e
-          set -o pipefail
-          export PATH="${pkgs.gnugrep}/bin:${pkgs.coreutils}/bin:@out@/sw/bin:/usr/bin:/bin:/usr/sbin:/sbin"
-          ${newGeneration}
-          ${installSecrets}
-          ${chownSecrets}
-          exit 0
-        '';
-        serviceConfig = {
-          RunAtLoad = true;
-          KeepAlive.SuccessfulExit = false;
-        };
-      };
-    })
-  ]);
-}

m/module/slurm-common.nix

@@ -86,7 +86,9 @@ in {
       # when a task runs (srun) so we can ssh early.
       PrologFlags=Alloc,Contain,X11
 
-      LaunchParameters=use_interactive_step
+      # 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
     '';

m/tent/nginx.nix

@@ -4,8 +4,8 @@ let
     name = "jungle-web";
     src = pkgs.fetchgit {
       url = "https://jungle.bsc.es/git/rarias/jungle-website.git";
-      rev = "52abaf4d71652a9ef77a0b098db14ca33bffff4c";
+      rev = "739bf0175a7f05380fe7ad7023ff1d60db1710e1";
-      hash = "sha256-/ul9GazbOrOkmlvSgDz/+2W+V+ir5725Y7mVLc3rb0M=";
+      hash = "sha256-ea5DzhYTzZ9TmqD+x95rdNdLbxPnBluqlYH2NmBYmc4=";
     };
     buildInputs = [ pkgs.hugo ];
     buildPhase = ''

overlay.nix

@@ -7,7 +7,6 @@ let
   callPackage = final.callPackage;
 
   bscPkgs = {
-    agenix = prev.callPackage ./pkgs/agenix/default.nix { };
     amd-uprof = prev.callPackage ./pkgs/amd-uprof/default.nix { };
     bench6 = callPackage ./pkgs/bench6/default.nix { };
     bigotes = callPackage ./pkgs/bigotes/default.nix { };
@@ -51,7 +50,6 @@ let
     prometheus-slurm-exporter = prev.callPackage ./pkgs/slurm-exporter/default.nix { };
     #pscom = callPackage ./pkgs/parastation/pscom.nix { }; # Unmaintaned
     #psmpi = callPackage ./pkgs/parastation/psmpi.nix { }; # Unmaintaned
-    slurm = import ./pkgs/slurm/default.nix { slurm = prev.slurm; };
     sonar = callPackage ./pkgs/sonar/default.nix { };
     stdenvClangOmpss2 = final.stdenv.override { cc = final.clangOmpss2; allowedRequisites = null; };
     stdenvClangOmpss2Nanos6 = final.stdenv.override { cc = final.clangOmpss2Nanos6; allowedRequisites = null; };
@@ -60,7 +58,6 @@ let
     tagaspi = callPackage ./pkgs/tagaspi/default.nix { };
     tampi = callPackage ./pkgs/tampi/default.nix { };
     upc-qaire-exporter = prev.callPackage ./pkgs/upc-qaire-exporter/default.nix { };
-    taopencl = callPackage ./pkgs/taopencl/default.nix { };
     wxparaver = callPackage ./pkgs/paraver/default.nix { };
   };
 

pkgs/agenix/agenix.sh

@@ -1,212 +0,0 @@
-#!/usr/bin/env bash
-set -Eeuo pipefail
-
-PACKAGE="agenix"
-
-function show_help () {
-  echo "$PACKAGE - edit and rekey age secret files"
-  echo " "
-  echo "$PACKAGE -e FILE [-i PRIVATE_KEY]"
-  echo "$PACKAGE -r [-i PRIVATE_KEY]"
-  echo ' '
-  echo 'options:'
-  echo '-h, --help                show help'
-  # shellcheck disable=SC2016
-  echo '-e, --edit FILE           edits FILE using $EDITOR'
-  echo '-r, --rekey               re-encrypts all secrets with specified recipients'
-  echo '-d, --decrypt FILE        decrypts FILE to STDOUT'
-  echo '-i, --identity            identity to use when decrypting'
-  echo '-v, --verbose             verbose output'
-  echo ' '
-  echo 'FILE an age-encrypted file'
-  echo ' '
-  echo 'PRIVATE_KEY a path to a private SSH key used to decrypt file'
-  echo ' '
-  echo 'EDITOR environment variable of editor to use when editing FILE'
-  echo ' '
-  echo 'If STDIN is not interactive, EDITOR will be set to "cp /dev/stdin"'
-  echo ' '
-  echo 'RULES environment variable with path to Nix file specifying recipient public keys.'
-  echo "Defaults to './secrets.nix'"
-  echo ' '
-  echo "agenix version: @version@"
-  echo "age binary path: @ageBin@"
-  echo "age version: $(@ageBin@ --version)"
-}
-
-function warn() {
-  printf '%s\n' "$*" >&2
-}
-
-function err() {
-  warn "$*"
-  exit 1
-}
-
-test $# -eq 0 && (show_help && exit 1)
-
-REKEY=0
-DECRYPT_ONLY=0
-DEFAULT_DECRYPT=(--decrypt)
-
-while test $# -gt 0; do
-  case "$1" in
-    -h|--help)
-      show_help
-      exit 0
-      ;;
-    -e|--edit)
-      shift
-      if test $# -gt 0; then
-        export FILE=$1
-      else
-        echo "no FILE specified"
-        exit 1
-      fi
-      shift
-      ;;
-    -i|--identity)
-      shift
-      if test $# -gt 0; then
-        DEFAULT_DECRYPT+=(--identity "$1")
-      else
-        echo "no PRIVATE_KEY specified"
-        exit 1
-      fi
-      shift
-      ;;
-    -r|--rekey)
-      shift
-      REKEY=1
-      ;;
-    -d|--decrypt)
-      shift
-      DECRYPT_ONLY=1
-      if test $# -gt 0; then
-        export FILE=$1
-      else
-        echo "no FILE specified"
-        exit 1
-      fi
-      shift
-      ;;
-    -v|--verbose)
-      shift
-      set -x
-      ;;
-    *)
-      show_help
-      exit 1
-      ;;
-  esac
-done
-
-RULES=${RULES:-./secrets.nix}
-function cleanup {
-    if [ -n "${CLEARTEXT_DIR+x}" ]
-    then
-        rm -rf -- "$CLEARTEXT_DIR"
-    fi
-    if [ -n "${REENCRYPTED_DIR+x}" ]
-    then
-        rm -rf -- "$REENCRYPTED_DIR"
-    fi
-}
-trap "cleanup" 0 2 3 15
-
-function keys {
-    (@nixInstantiate@ --json --eval --strict -E "(let rules = import $RULES; in rules.\"$1\".publicKeys)" | @jqBin@ -r .[]) || exit 1
-}
-
-function armor {
-    (@nixInstantiate@ --json --eval --strict -E "(let rules = import $RULES; in (builtins.hasAttr \"armor\" rules.\"$1\" && rules.\"$1\".armor))") || exit 1
-}
-
-function decrypt {
-    FILE=$1
-    KEYS=$2
-    if [ -z "$KEYS" ]
-    then
-        err "There is no rule for $FILE in $RULES."
-    fi
-
-    if [ -f "$FILE" ]
-    then
-        DECRYPT=("${DEFAULT_DECRYPT[@]}")
-        if [[ "${DECRYPT[*]}" != *"--identity"* ]]; then
-            if [ -f "$HOME/.ssh/id_rsa" ]; then
-                DECRYPT+=(--identity "$HOME/.ssh/id_rsa")
-            fi
-            if [ -f "$HOME/.ssh/id_ed25519" ]; then
-                DECRYPT+=(--identity "$HOME/.ssh/id_ed25519")
-            fi
-        fi
-        if [[ "${DECRYPT[*]}" != *"--identity"* ]]; then
-          err "No identity found to decrypt $FILE. Try adding an SSH key at $HOME/.ssh/id_rsa or $HOME/.ssh/id_ed25519 or using the --identity flag to specify a file."
-        fi
-
-        @ageBin@ "${DECRYPT[@]}" -- "$FILE" || exit 1
-    fi
-}
-
-function edit {
-    FILE=$1
-    KEYS=$(keys "$FILE") || exit 1
-    ARMOR=$(armor "$FILE") || exit 1
-
-    CLEARTEXT_DIR=$(@mktempBin@ -d)
-    CLEARTEXT_FILE="$CLEARTEXT_DIR/$(basename -- "$FILE")"
-    DEFAULT_DECRYPT+=(-o "$CLEARTEXT_FILE")
-
-    decrypt "$FILE" "$KEYS" || exit 1
-
-    [ ! -f "$CLEARTEXT_FILE" ] || cp -- "$CLEARTEXT_FILE" "$CLEARTEXT_FILE.before"
-
-    [ -t 0 ] || EDITOR='cp -- /dev/stdin'
-
-    $EDITOR "$CLEARTEXT_FILE"
-
-    if [ ! -f "$CLEARTEXT_FILE" ]
-    then
-      warn "$FILE wasn't created."
-      return
-    fi
-    [ -f "$FILE" ] && [ "$EDITOR" != ":" ] && @diffBin@ -q -- "$CLEARTEXT_FILE.before" "$CLEARTEXT_FILE" && warn "$FILE wasn't changed, skipping re-encryption." && return
-
-    ENCRYPT=()
-    if [[ "$ARMOR" == "true" ]]; then
-        ENCRYPT+=(--armor)
-    fi
-    while IFS= read -r key
-    do
-        if [ -n "$key" ]; then
-            ENCRYPT+=(--recipient "$key")
-        fi
-    done <<< "$KEYS"
-
-    REENCRYPTED_DIR=$(@mktempBin@ -d)
-    REENCRYPTED_FILE="$REENCRYPTED_DIR/$(basename -- "$FILE")"
-
-    ENCRYPT+=(-o "$REENCRYPTED_FILE")
-
-    @ageBin@ "${ENCRYPT[@]}" <"$CLEARTEXT_FILE" || exit 1
-
-    mkdir -p -- "$(dirname -- "$FILE")"
-
-    mv -f -- "$REENCRYPTED_FILE" "$FILE"
-}
-
-function rekey {
-    FILES=$( (@nixInstantiate@ --json --eval -E "(let rules = import $RULES; in builtins.attrNames rules)"  | @jqBin@ -r .[]) || exit 1)
-
-    for FILE in $FILES
-    do
-        warn "rekeying $FILE..."
-        EDITOR=: edit "$FILE"
-        cleanup
-    done
-}
-
-[ $REKEY -eq 1 ] && rekey && exit 0
-[ $DECRYPT_ONLY -eq 1 ] && DEFAULT_DECRYPT+=("-o" "-") && decrypt "${FILE}" "$(keys "$FILE")" && exit 0
-edit "$FILE" && cleanup && exit 0

pkgs/agenix/default.nix

@@ -1,66 +0,0 @@
-{
-  lib,
-  stdenv,
-  age,
-  jq,
-  nix,
-  mktemp,
-  diffutils,
-  replaceVars,
-  ageBin ? "${age}/bin/age",
-  shellcheck,
-}:
-let
-  bin = "${placeholder "out"}/bin/agenix";
-in
-stdenv.mkDerivation rec {
-  pname = "agenix";
-  version = "0.15.0";
-  src = replaceVars ./agenix.sh {
-    inherit ageBin version;
-    jqBin = "${jq}/bin/jq";
-    nixInstantiate = "${nix}/bin/nix-instantiate";
-    mktempBin = "${mktemp}/bin/mktemp";
-    diffBin = "${diffutils}/bin/diff";
-  };
-  dontUnpack = true;
-  doInstallCheck = true;
-  installCheckInputs = [ shellcheck ];
-  postInstallCheck = ''
-    shellcheck ${bin}
-    ${bin} -h | grep ${version}
-
-    test_tmp=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
-    export HOME="$test_tmp/home"
-    export NIX_STORE_DIR="$test_tmp/nix/store"
-    export NIX_STATE_DIR="$test_tmp/nix/var"
-    mkdir -p "$HOME" "$NIX_STORE_DIR" "$NIX_STATE_DIR"
-    function cleanup {
-      rm -rf "$test_tmp"
-    }
-    trap "cleanup" 0 2 3 15
-
-    mkdir -p $HOME/.ssh
-    cp -r "${./example}" $HOME/secrets
-    chmod -R u+rw $HOME/secrets
-    (
-    umask u=rw,g=r,o=r
-    cp ${./example_keys/user1.pub} $HOME/.ssh/id_ed25519.pub
-    chown $UID $HOME/.ssh/id_ed25519.pub
-    )
-    (
-    umask u=rw,g=,o=
-    cp ${./example_keys/user1} $HOME/.ssh/id_ed25519
-    chown $UID $HOME/.ssh/id_ed25519
-    )
-
-    cd $HOME/secrets
-    test $(${bin} -d secret1.age) = "hello"
-  '';
-
-  installPhase = ''
-    install -D $src ${bin}
-  '';
-
-  meta.description = "age-encrypted secrets for NixOS";
-}

pkgs/agenix/example/-leading-hyphen-filename.age

@@ -1,7 +0,0 @@
-age-encryption.org/v1
--> ssh-ed25519 V3XmEA zirqdzZZ1E+sedBn7fbEHq4ntLEkokZ4GctarBBOHXY
-Rvs5YHaAUeCZyNwPedubPcHClWYIuXXWA5zadXPWY6w
--> ssh-ed25519 KLPP8w BVp4rDkOYSQyn8oVeHFeinSqW+pdVtxBF9+5VM1yORY
-bMwppAi8Nhz0328taU4AzUkTVyWtSLvFZG6c5W/Fs78
---- xCbqLhXAcOziO2wmbjTiSQfZvt5Rlsc4SCvF+iEzpQA
-<EFBFBD>KB<EFBFBD><EFBFBD>/<2F>Z<><5A>r<EFBFBD>%
<01><>4<EFBFBD><34><EFBFBD>Mq5<71><35>_<EFBFBD><5F>ݒ<><DD92><EFBFBD><EFBFBD><EFBFBD>11ܨqM;& <20><>Lr<4C><72><EFBFBD>f<EFBFBD><66><EFBFBD>]>N

pkgs/agenix/example/armored-secret.age

@@ -1,7 +0,0 @@
------BEGIN AGE ENCRYPTED FILE-----
-YWdlLWVuY3J5cHRpb24ub3JnL3YxCi0+IHNzaC1lZDI1NTE5IFYzWG1FQSBpZkZW
-aFpLNnJxc0VUMHRmZ2dZS0pjMGVENnR3OHd5K0RiT1RjRUhibFZBCnN5UG5vUjA3
-SXpsNGtiVUw4T0tIVFo5Wkk5QS9NQlBndzVvektiQ0ozc0kKLS0tIGxyY1Q4dEZ1
-VGZEanJyTFNta2JNRmpZb2FnK2JyS1hSVml1UGdMNWZKQXMKYla+wTXcRedyZoEb
-LVWaSx49WoUTU0KBPJg9RArxaeC23GoCDzR/aM/1DvYU
------END AGE ENCRYPTED FILE-----

pkgs/agenix/example/passwordfile-user1.age

@@ -1,9 +0,0 @@
-age-encryption.org/v1
--> ssh-ed25519 KLPP8w s1DYZRlZuSsyhmZCF1lFB+E9vB8bZ/+ZhBRlx8nprwE
-nmYVCsVBrX2CFXXPU+D+bbkkIe/foofp+xoUrg9DHZw
--> ssh-ed25519 V3XmEA Pwv3oCwcY0DX8rY48UNfsj9RumWsn4dbgorYHCwObgI
-FKxRYkL3JHtJxUwymWDF0rAtJ33BivDI6IfPsfumM90
--> V'v(/u$-grease em/Vgf 2qDuk
-7I3iiQLPGi1COML9u/JeYkr7EqbSLoU
---- 57WJRigUGtmcObrssS3s4PvmR8wgh1AOC/ijJn1s3xI
-<EFBFBD>'K<>ƷY&<26>7G<37>O<EFBFBD><4F>Fj
<13>k<EFBFBD>X<EFBFBD><58>BnuJ<75><4A>:9<>(<><7F><EFBFBD>X<EFBFBD>#<23>A<EFBFBD><41><EFBFBD><EFBFBD>ڧj<DAA7>,<02>_<17><><EFBFBD>?<3F>Z<EFBFBD><17>v<EFBFBD><76>V<EFBFBD>96]oks~%<25>c	<04>e^C<>%JQ5<51><H<>z}<7D>C<EFBFBD>,<2C>p<EFBFBD><70>*!W<><57><EFBFBD>A<EFBFBD><41><EFBFBD>҅dC<15>K)<10><>-<2D>y

pkgs/agenix/example/secret2.age

@@ -1,5 +0,0 @@
-age-encryption.org/v1
--> ssh-ed25519 V3XmEA OB4+1FbPhQ3r6iGksM7peWX5it8NClpXIq/o5nnP7GA
-FmHVUj+A5i5+bDFgySQskmlvynnosJiWUTJmBRiNA9I
---- tP+3mFVtd7ogVu1Lkboh55zoi5a77Ht08Uc/QuIviv4
-<EFBFBD><EFBFBD>X<EFBFBD>{<7B><>O<EFBFBD><4F><1F><04>tMXx<58>vӪ(<28>I<EFBFBD>myP<79><50><EFBFBD><EFBFBD>+3<>S3i

pkgs/agenix/example/secrets.nix

@@ -1,23 +0,0 @@
-let
-  user1 = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIL0idNvgGiucWgup/mP78zyC23uFjYq0evcWdjGQUaBH";
-  system1 = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPJDyIr/FSz1cJdcoW69R+NrWzwGK/+3gJpqD1t8L2zE";
-in
-{
-  "secret1.age".publicKeys = [
-    user1
-    system1
-  ];
-  "secret2.age".publicKeys = [ user1 ];
-  "passwordfile-user1.age".publicKeys = [
-    user1
-    system1
-  ];
-  "-leading-hyphen-filename.age".publicKeys = [
-    user1
-    system1
-  ];
-  "armored-secret.age" = {
-    publicKeys = [ user1 ];
-    armor = true;
-  };
-}

pkgs/agenix/example_keys/system1

@@ -1,7 +0,0 @@
------BEGIN OPENSSH PRIVATE KEY-----
-b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAAAMwAAAAtzc2gtZW
-QyNTUxOQAAACDyQ8iK/xUs9XCXXKFuvUfja1s8Biv/t4Caag9bfC9sxAAAAJA3yvCWN8rw
-lgAAAAtzc2gtZWQyNTUxOQAAACDyQ8iK/xUs9XCXXKFuvUfja1s8Biv/t4Caag9bfC9sxA
-AAAEA+J2V6AG1NriAIvnNKRauIEh1JE9HSdhvKJ68a5Fm0w/JDyIr/FSz1cJdcoW69R+Nr
-WzwGK/+3gJpqD1t8L2zEAAAADHJ5YW50bUBob21lMQE=
------END OPENSSH PRIVATE KEY-----

pkgs/agenix/example_keys/system1.pub

@@ -1 +0,0 @@
-ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPJDyIr/FSz1cJdcoW69R+NrWzwGK/+3gJpqD1t8L2zE

pkgs/agenix/example_keys/user1

@@ -1,7 +0,0 @@
------BEGIN OPENSSH PRIVATE KEY-----
-b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAAAMwAAAAtzc2gtZW
-QyNTUxOQAAACC9InTb4BornFoLqf5j+/M8gtt7hY2KtHr3FnYxkFGgRwAAAJC2JJ8htiSf
-IQAAAAtzc2gtZWQyNTUxOQAAACC9InTb4BornFoLqf5j+/M8gtt7hY2KtHr3FnYxkFGgRw
-AAAEDxt5gC/s53IxiKAjfZJVCCcFIsdeERdIgbYhLO719+Kb0idNvgGiucWgup/mP78zyC
-23uFjYq0evcWdjGQUaBHAAAADHJ5YW50bUBob21lMQE=
------END OPENSSH PRIVATE KEY-----

pkgs/agenix/example_keys/user1.pub

@@ -1 +0,0 @@
-ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIL0idNvgGiucWgup/mP78zyC23uFjYq0evcWdjGQUaBH

pkgs/agenix/update.sh

@@ -1,23 +0,0 @@
-#!/bin/sh
-
-set -e
-
-# All operations are done relative to root
-GITROOT=$(git rev-parse --show-toplevel)
-cd "$GITROOT"
-
-REVISION=${1:-main}
-
-TMPCLONE=$(mktemp -d)
-trap "rm -rf ${TMPCLONE}" EXIT
-
-git clone https://github.com/ryantm/agenix.git --revision="$REVISION" "$TMPCLONE" --depth=1
-
-cp "${TMPCLONE}/pkgs/agenix.sh" pkgs/agenix/agenix.sh
-cp "${TMPCLONE}/pkgs/agenix.nix" pkgs/agenix/default.nix
-sed -i 's#../example#./example#' pkgs/agenix/default.nix
-
-cp "${TMPCLONE}/example/"* pkgs/agenix/example/
-cp "${TMPCLONE}/example_keys/"* pkgs/agenix/example_keys/
-
-cp "${TMPCLONE}/modules/age.nix" m/module/agenix.nix

pkgs/intel-oneapi/2023.nix

@@ -10,7 +10,7 @@
 , zlib
 , autoPatchelfHook
 , libfabric
-, gcc13
+, gcc
 , wrapCCWith
 }:
 
@@ -33,8 +33,6 @@ let
     maintainers = with lib.maintainers.bsc; [ abonerib ];
   };
 
-  gcc = gcc13;
-
   v = {
     hpckit   = "2023.1.0";
     compiler = "2023.1.0";

pkgs/nodes/default.nix

@@ -3,6 +3,7 @@
 , lib
 , fetchFromGitHub
 , pkg-config
+, perl
 , numactl
 , hwloc
 , boost
@@ -10,7 +11,6 @@
 , ovni
 , nosv
 , clangOmpss2
-, which
 , useGit ? false
 , gitUrl ? "ssh://git@gitlab-internal.bsc.es/nos-v/nodes.git"
 , gitBranch ? "master"
@@ -59,7 +59,6 @@ in
     doCheck = false;
     nativeCheckInputs = [
       clangOmpss2
-      which
     ];
 
     # The "bindnow" flags are incompatible with ifunc resolution mechanism. We

pkgs/taopencl/default.nix

@@ -1,46 +0,0 @@
-{
-  stdenv
-, automake
-, autoconf
-, libtool
-, gnumake
-, boost
-, mpi
-, gcc
-, autoreconfHook
-, ocl-icd
-, opencl-headers
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "taopencl";
-  version = finalAttrs.src.shortRev;
-
-  src = builtins.fetchGit {
-    url = "git@gitlab-internal.bsc.es:task-awareness/taopencl/taopencl.git";
-    ref = "master";
-    rev = "c3b7b32ae8fa4af7ceff598532a881f8f1490aaf";
-  };
-
-  enableParallelBuilding = true;
-  separateDebugInfo = true;
-
-  configureFlags = [
-    "--with-opencl-lib=${ocl-icd}/lib"
-    "--with-opencl-include=${opencl-headers}/include"
-  ];
-
-  buildInputs = [
-    autoreconfHook
-    automake
-    autoconf
-    libtool
-    gnumake
-    boost
-    mpi
-    gcc
-  ];
-
-  dontDisableStatic = true;
-  hardeningDisable = [ "all" ];
-})