Merge pull request #83 from pneerincx/develop

Bugfixes and improved version of login checks

group_vars/all/vars.yml

@@ -60,7 +60,6 @@ auth_users:
     uid: 1008
     pub_keys: |
               ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBDvx1ebTndL/HitD30uNpvESXWUAxT3j0e0CzrBUZ8fHDv+vZTbWBRtWbnLgCnVDPa3GclA1lpnvJD9JBjBhUa8= ger@ger-pc
-
   robin:
     comment: 'Robin Teeninga'
     uid: 1009

group_vars/talos-cluster/vars.yml

@@ -12,7 +12,7 @@ vcompute_real_memory: 7822
 vcompute_max_cpus_per_node: "{{ vcompute_sockets * vcompute_cores_per_socket - 2 }}"
 vcompute_max_mem_per_node: "{{ vcompute_real_memory - vcompute_sockets * vcompute_cores_per_socket * 512 }}"
 vcompute_local_disk: 0
-vcompute_features: 'tmp02'
+vcompute_features: 'tmp08'
 vcompute_ethernet_interfaces:
   - 'eth0'
   - 'eth1'

roles/logins/files/login_checks.sh

@@ -85,9 +85,12 @@ login_actions () {
 # but in the first case there are no SLURM related environment variables defined.
 #
 
-# SOURCE_HPC_ENV variable checking disabled (it is not set ) Egon 30-10-2018
-#if [ ${TERM} == 'dumb' ] && [ -z ${SOURCE_HPC_ENV} ]; then
-if [ ${TERM} == 'dumb' ]; then
+#
+# ToDo: fix this. As of CentOS 7.x interactive session that eventually report ${TERM} == 'bash'
+# report ${TERM} == 'dumb' at the point where this script is executed in the PAM stack :(.
+# Makes it impossible to determine the difference between an SFTP session versus a Bash session.
+#
+if [ ${TERM} == 'dumb' ] && [ -z "${SOURCE_HPC_ENV:-}" ]; then
     $LOGGER "debug: exiting because of dumb terminal"
     exit 0
 fi

roles/logins/tasks/main.yml

@@ -63,7 +63,17 @@
     dest: "/etc/pam-script.d/{{ item }}"
     owner: root
     group: root
-    state: link
+    #
+    # Login checks currently disabled,
+    # because error handling/reporting no longer works on CentOS >= 7.x,
+    # due to changes in the PAM stack.
+    # Login checks were only used to create Slurm accounts in the Slurm accounting DB.
+    # This functionality has been relocated to the Slurm job_submit.lua plugin,
+    # which will now automatically create account, users and associations of slurm users to slurm accounts
+    # upon job submission when they do not already exist.
+    #
+    # state: link
+    state: absent
   with_items:
     - login_checks.sh_ses_open
   when: inventory_hostname in groups['cluster']

roles/slurm-client/tasks/main.yml

@@ -67,9 +67,9 @@
       group: root
       mode: '0750'
     - name: /var/spool/slurmd
-      owner: slurm
+      owner: root
       group: root
-      mode: '0750'
+      mode: '0755'
 
 - name: Deploy slurm.conf
   template:

roles/slurm/files/job_submit.lua

@@ -51,12 +51,112 @@ QOS_TIME_LIMITS = {
 --
 --DEFAULT_WALLTIME = '1'
 
+--
+-- Check if the user submitting the job is associated to a Slurm account in the Slurm accounting database and
+-- create the relevant Slurm account and/or Slurm user and/or association if it does not already exist.
+--
+function ensure_user_has_slurm_association(uid, user, group)
+    --
+    -- Skip root user.
+    --
+    if uid == 0 then
+        return true
+    end
+
+    slurm.log_debug("Checking assoc for user %s (uid=%u) in account for group %s...", user, uid, group)
+    if association_exists(user, group) then
+        slurm.log_debug("Association of user %s to account %s already exists.", user, group)
+        return true
+    else
+        if account_exists(group) then
+            slurm.log_debug("Account %s already exists.", group)
+        else
+            slurm.log_info("Account %s does not exist; creating one...", group)
+            if not create_account(group) then
+                return false
+            end
+        end
+        slurm.log_info("Association of user %s to account %s does not exist; creating one...", user, group)
+        if not create_association(user,group) then
+            return false
+        end
+    end
+    return true
+end
+
+function account_exists(group)
+    --
+    -- Unfortunately, filehandles returned by io.popen() don't have a way to return their exitstatuses in <= lua 5.2.
+    -- Should be reasonably safe here, since if we erroneously conclude the association doesn't exist,
+    -- then we'll just try to add it.
+    -- http://lua-users.org/lists/lua-l/2012-01/msg00364.html
+    --
+    local query = io.popen(string.format(
+        "sacctmgr --parsable2 --noheader list accounts format=account account='%s'", group))
+    for line in query:lines() do
+        if line == group then
+            return true
+        end
+    end
+    return false
+end
+
+function create_account(group)
+    local retval = os.execute(string.format(
+        "sacctmgr -i create account '%s' descr=scientists org=various parent=users fairshare=parent", group))
+    if retval ~= 0 then
+        slurm.log_error("Failed to create account %s (exit status = %d).", group, retval)
+        slurm.log_user("Failed to create account %s (exit status = %d). Contact an admin.", group, retval)
+        return false
+    else
+        slurm.log_info("Created account for group %s.", group)
+        return true
+    end
+end
+
+function association_exists(user, group)
+    --
+    -- Unfortunately, filehandles returned by io.popen() don't have a way to return their exitstatuses in <= lua 5.2.
+    -- Should be reasonably safe here, since if we erroneously conclude the association doesn't exist,
+    -- then we'll just try to add it.
+    -- http://lua-users.org/lists/lua-l/2012-01/msg00364.html
+    --
+    local query = io.popen(string.format(
+        "sacctmgr --parsable2 --noheader list associations format=user,account user='%s' account='%s'", user, group))
+    for line in query:lines() do
+        if line == user .. '|' .. group then
+            return true
+        end
+    end
+    return false
+end
+
+function create_association(user,group)
+    local retval = os.execute(string.format(
+        "sacctmgr -i create user name='%s' account='%s' fairshare=parent", user, group))
+    if retval ~= 0 then
+        slurm.log_error("Failed to create association of user %s to account %s (exit status = %d).", user, group, retval)
+        slurm.log_user("Failed to create association of user %s to account %s (exit status = %d). Contact an admin.", user, group, retval)
+        return false
+    else
+        slurm.log_info("Created association of user %s to account %s.", user, group)
+        return true
+    end
+end
+
 function slurm_job_submit(job_desc, part_list, submit_uid)
     -- 
     -- Get details for the user who is trying to submit a job.
     --
     submit_user = posix.getpasswd(submit_uid)
 
+    --
+    -- Force jobs to share nodes when they don't consume all resources on a node.
+    --
+    if job_desc.shared == 0 then
+        job_desc.shared = 1
+    end
+
     --
     -- Check if the job does have a time limit specified.
     -- For some reason (bug?), the nil value is passed as 4294967294.
@@ -87,6 +187,8 @@ function slurm_job_submit(job_desc, part_list, submit_uid)
     --slurm.log_debug("Path to job *.err  = %s.", tostring(job_desc.std_err))
     --slurm.log_debug("Job's working dir  = %s.", tostring(job_desc.work_dir))
     local job_metadata = {job_desc.std_out, job_desc.std_err, job_desc.work_dir}
+    local group = nil
+    local lfs = nil
     for inx,job_metadata_value in ipairs(job_metadata) do
         if string.match(tostring(job_metadata_value), '^/home/') then
             slurm.log_error(
@@ -99,31 +201,20 @@ function slurm_job_submit(job_desc, part_list, submit_uid)
                 "Rejecting job named %s from user %s (uid=%u).", tostring(job_desc.name), tostring(submit_user.name), job_desc.user_id)
             return slurm.ERROR
         end
-        local entitlement, group, lfs = string.match(tostring(job_metadata_value), '^/groups/([^/-]+)-([^/]+)/(tmp%d%d)/?')
-        if lfs == nil then
-            -- Temporary workaround for tmp02, which uses a symlink in /groups/..., that is resolved to the physical path by SLURM.
-            entitlement, group, lfs = string.match(tostring(job_metadata_value), '^/target/gpfs2/groups/([^/-]+)-([^/]+)/(tmp%d%d)/?')
-        end
-        if entitlement ~= nil and group ~= nill and lfs ~= nil then
-            slurm.log_debug("Found entitlement '%s' and LFS '%s' in job's metadata.", tostring(entitlement), tostring(lfs))
+        group, lfs = string.match(tostring(job_metadata_value), '^/groups/([^/]+)/(tmp%d%d)/?')
+        if group ~= nil and lfs ~= nil then
+            slurm.log_debug("Found group '%s' and LFS '%s' in job's metadata.", tostring(group), tostring(lfs))
             if job_desc.features == nil or job_desc.features == '' then
-                job_desc.features = entitlement .. '&' .. lfs
-                slurm.log_debug("Job had no features yet; Assigned entitlement and LFS as first features: %s.", tostring(job_desc.features))
+                job_desc.features = lfs
+                slurm.log_debug("Job had no features yet; Assigned LFS as first feature: %s.", tostring(job_desc.features))
             else
-                if not string.match(tostring(job_desc.features), entitlement) then
-                    job_desc.features = job_desc.features .. '&' .. entitlement
-                    slurm.log_debug("Appended entitlement %s to job's features.", tostring(entitlement))
-                else
-                    slurm.log_debug("Job's features already contained entitlement %s.", tostring(entitlement))
-                end
                 if not string.match(tostring(job_desc.features), lfs) then
                     job_desc.features = job_desc.features .. '&' .. lfs
                     slurm.log_debug("Appended LFS %s to job's features.", tostring(lfs))
                 else
                     slurm.log_debug("Job's features already contained LFS %s.", tostring(lfs))
                 end
             end
-            slurm.log_info("Job's features now contains: %s.", tostring(job_desc.features))
         else
             slurm.log_error(
                  "Job's working dir, *.err file or *.out file is not located in /groups/${group}/tmp*/...\n" ..
@@ -138,6 +229,20 @@ function slurm_job_submit(job_desc, part_list, submit_uid)
             return slurm.ERROR
         end
     end
+    slurm.log_debug("Job's features contains: %s.", tostring(job_desc.features))
+    --
+    -- Check if the user submitting the job is associated to a Slurm account in the Slurm accounting database and
+    -- create the relevant Slurm account and/or Slurm user and/or association if it does not already exist.
+    -- Note: as slurm account we use the group that was found last while parsing job_metadata above.
+    --
+    if not ensure_user_has_slurm_association(submit_uid, tostring(submit_user.name), tostring(group)) then
+        slurm.log_error("Failed to create association in the Slurm accounting database for user %s in account/group %s", tostring(submit_user.name), tostring(group))
+        slurm.log_error("Rejecting job named %s from user %s (uid=%u).", tostring(job_desc.name), tostring(submit_user.name), job_desc.user_id)
+        slurm.log_user(
+                 "Failed to create association in the Slurm accounting database. Contact an admin.\n" ..
+                 "Rejecting job named %s from user %s (uid=%u).", tostring(job_desc.name), tostring(submit_user.name), job_desc.user_id)
+        return slurm.ERROR
+    end
 
     --
     -- Process final list of features:
@@ -161,7 +266,7 @@ function slurm_job_submit(job_desc, part_list, submit_uid)
             job_desc.qos = 'ds'
         end
     end
-      
+
     --
     -- Make sure we have a sanity checked base-QoS.
     --
@@ -218,16 +323,6 @@ function slurm_job_submit(job_desc, part_list, submit_uid)
         slurm.log_info("Assigned QoS %s to job named %s from user %s (uid=%u).", new_qos, job_desc.name, tostring(submit_user.name), job_desc.user_id)
     end
 
-    --
-    -- Check if the user submitting the job is associated to a Slurm account in the Slurm accounting database and
-    -- create the relevant Slurm account and/or Slurm user and/or association if it does not already exist.
-    -- Skip this check for the root user.
-    --
-    if job_desc.user_id ~= 0 then
-        --submit_user_primary_group = posix.getgroup(submit_user.gid).name
-        --ensure_assoc_exists(submit_user.name, entitlement .. '-' .. group)
-    end
-
     return slurm.SUCCESS
 
 end

roles/slurm/tasks/main.yml

@@ -162,7 +162,7 @@
 - name: Make services reload their configs.
   command: systemctl daemon-reload
 
-- name: Make sure servcies are started.
+- name: Make sure services are started.
   systemd:
     name: "{{item}}"
     state: restarted