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authorEfraim Flashner2020-12-03 22:13:25 +0200
committerEfraim Flashner2020-12-03 22:13:31 +0200
commit3bd06f793ad0a78c1374277710c930ee5f735b56 (patch)
tree65661924fdb9ab5bc997588bc8907d06eac73174 /gn
parent18082c3bdd42edfb6afc97f96a80744874c27986 (diff)
downloadguix-bioinformatics-3bd06f793ad0a78c1374277710c930ee5f735b56.tar.gz
octopus: update slurm services
Diffstat (limited to 'gn')
-rw-r--r--gn/deploy/octopus.scm131
-rw-r--r--gn/services/science.scm106
2 files changed, 112 insertions, 125 deletions
diff --git a/gn/deploy/octopus.scm b/gn/deploy/octopus.scm
index 9d1e7d3..ce480e2 100644
--- a/gn/deploy/octopus.scm
+++ b/gn/deploy/octopus.scm
@@ -2,42 +2,53 @@
(use-modules (gnu)
(gn services science)
- (gn packages parallel))
+ (gn packages parallel) ; for slurm-18.08
+ (srfi srfi-26))
(use-service-modules networking ssh web)
-(use-package-modules certs tmux screen vim)
+(use-package-modules shells)
+
+(define %efraimf-ssh-pubkey
+ (plain-file "id_rsa.pub"
+ "ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDUCDY8ZKFF/ln0yzDt3CNmKz3cT4wzNv9bzCKvOBXcL0O7JtPWwqgLlZgmMHfzhzgReAkHcrt+Gdsyduzm/s9Y8c6QpyfaH6uoDwjfoOs6GrAjZaOXmAdncf+9HZEAy/IrygQ1YFRu6BvYogsdhhtN+O6IXBuvQQDRzldHs53Y53DK06Nrs19vAPwELXcDxcx1FvO+/L9nT8RHkI1Z0ucgTS+F/BWXl8+mh89r4j+4IRpZXOuCD0DrW5rgEE1EygF2dVdWZQESi23gU5Mt6vnmysXzwixB7j6I+xTih8LH4pz7hewEx6754e/cs9Gm7ZtfXKfXUt6+GtsBSBF3ULKl efraimf@octopus01"))
(define %slurm.conf
(plain-file "slurm.conf"
(string-append
-"ClusterName=linux
-ControlMachine=octopus
-
-SlurmUser=slurm
-#SlurmdUser=root
-SlurmctldPort=6817
-SlurmdPort=6818
-AuthType=auth/munge
-StateSaveLocation=/var/spool/slurmd/ctld
-SlurmdSpoolDir=/var/spool/slurmd
-SwitchType=switch/none
-MpiDefault=none
-SlurmctldPidFile=/var/run/slurm/slurmctld.pid
-SlurmdPidFile=/var/run/slurm/slurmd.pid
-ProctrackType=proctrack/pgid
-ReturnToService=1
-
+"# Defaults are commented out, otherwise noted at the end of the line
+# Values are from example in the man page or from Debian
+ClusterName=linux # no default, suggests lowercase
+#ControlMachine=octopus # defunct, use SlurmctldHost
+SlurmctldHost=octopus # no default, falls back to next SlurmctldHost in list
+
+SlurmUser=slurm # default root, not recommended
+#SlurmctldPort=6817
+#SlurmdPort=6818
+#AuthType=auth/munge
+StateSaveLocation=/var/spool/slurmd/ctld # default /var/spool
+#SlurmdSpoolDir=/var/spool/slurmd
+#SwitchType=switch/none
+#MpiDefault=none
+#SlurmctldPidFile=/var/run/slurmctld.pid
+#SlurmdPidFile=/var/run/slurmd.pid
+ProctrackType=proctrack/pgid # default proctrack/cgroup
+ReturnToService=1 # default 0
+
+DebugFlags=NO_CONF_HASH # default empty
# TIMERS
-InactiveLimit=0
-MinJobAge=300
-KillWait=30
+SlurmctldTimeout=300 # default 120
+#SlurmdTimeout=300
+#InactiveLimit=0
+#MinJobAge=300
+#KillWait=30
+#WaitTime=0
#
# LOGGING
-SlurmctldDebug=3
-SlurmctldLogFile=/var/log/slurm/slurmctld.log
-SlurmdDebug=3
-SlurmdLogFile=/var/log/slurm/slurmd.log
-JobCompType=jobcomp/none
+#SlurmctldDebug=3
+SlurmctldLogFile=/var/log/slurmctld.log # default none, syslog
+#SlurmdDebug=3
+SlurmdLogFile=/var/log/slurmd.log # default none, syslog
+#JobCompType=jobcomp/none
# COMPUTE NODES
NodeName=octopus CPUs=1 Boards=1 SocketsPerBoard=1 CoresPerSocket=1 ThreadsPerCore=1 RealMemory=1024
@@ -49,22 +60,22 @@ PartitionName=debug Nodes=ALL Default=YES MaxTime=INFINITE State=UP")))
"###
# Slurm cgroup support configuration file
###
-CgroupAutomount=yes
-ConstrainCores=yes
+CgroupAutomount=yes # default no
+ConstrainCores=yes # default no
#")))
(define %slurmdbd.conf
(plain-file "slurmdbd.conf"
(string-append
-"AuthType=auth/munge
-AuthInfo=/var/run/munge/munge.socket.2
-DbdHost=localhost
-StorageHost=localhost
-StorageType=accounting_storage/none
-StorageUser=slurm
-PidFile=/var/run/slurm/slurmdbd.pid
-LogFile=/var/log/slurm/slurmdbd.log
-SlurmUser=slurm")))
+"#AuthType=auth/munge
+#AuthInfo=/var/run/munge/munge.socket.2
+DbdHost=localhost # must be specified
+StorageHost=localhost # unclear, must be specified?
+StorageType=accounting_storage/none # must be specified
+StorageUser=slurm # unclear
+#PidFile=/var/run/slurmdbd.pid
+LogFile=/var/log/slurmdbd.log # default none, syslog
+SlurmUser=slurm # default root, not recommended")))
(operating-system
(host-name "octopus")
@@ -106,25 +117,37 @@ SlurmUser=slurm")))
(users (cons*
(user-account
+ (name "wrk")
+ (comment "Pjotr Prins")
+ (uid 502)
+ (group "users")
+ (supplementary-groups '("wheel" "kvm")))
+ (user-account
(name "efraimf")
(comment "Efraim Flashner")
(uid 1000)
(group "users")
(supplementary-groups '("wheel" "kvm")))
(user-account
- (name "wrk")
- (comment "Pjotr Prins")
- (uid 502)
+ (name "erikg")
+ (comment "Erik Garrison")
+ (uid 1001)
(group "users")
- (supplementary-groups '("wheel" "kvm")))
+ (shell (file-append zsh "/bin/zsh")))
+ (user-account
+ (name "hchen")
+ (comment "Hao Chen")
+ (uid 1002)
+ (group "users"))
%base-user-accounts))
- (packages (cons*
- nss-certs
- screen
- tmux
- vim
+ (packages (append
+ (map (cut specification->package <>)
+ '("nss-certs"
+ "screen" "tmux"
+ "vim"
+ "htop"))
%base-packages))
(services
@@ -140,19 +163,15 @@ SlurmUser=slurm")))
(service openssh-service-type
(openssh-configuration
(authorized-keys
- `(("efraimf" ,(local-file "/home/efraimf/.ssh/id_rsa.pub"))))))
+ `(("efraimf" ,%efraimf-ssh-pubkey)))))
(service munge-service-type)
- (service slurmd-service-type
- (slurm-configuration
- (package slurm-18.08)))
- (service slurmdbd-service-type
- (slurm-configuration
- (package slurm-18.08)
- (run-slurmdbd? #t)))
- (service slurmctld-service-type
+ (service slurm-service-type
(slurm-configuration
(package slurm-18.08)
+ (slurmd-log-file "/var/log/slurmd.log")
+ (slurmctld-log-file "/var/log/slurmctld.log")
+ (run-slurmdbd? #t)
(run-slurmctld? #t)))
;; Some slurm configuration files
diff --git a/gn/services/science.scm b/gn/services/science.scm
index d1f3190..f0f43d0 100644
--- a/gn/services/science.scm
+++ b/gn/services/science.scm
@@ -5,9 +5,7 @@
slurm-configuration
slurm-configuration?
- slurmd-service-type
- slurmdbd-service-type
- slurmctld-service-type))
+ slurm-service-type))
(use-modules (gnu)
(guix records)
@@ -177,9 +175,9 @@
(slurm-conf-file slurm-configuration-slurm-conf-file
(default "/etc/slurm/slurm.conf"))
(slurmd-log-file slurm-configuration-slurmd-log-file
- (default "/var/log/slurm/slurmd.log"))
+ (default #f)) ; #f for syslog
(slurmd-pid-file slurm-configuration-slurmd-pid-file
- (default "/var/run/slurm/slurmd.pid"))
+ (default "/var/run/slurmd.pid"))
(slurmd-spooldir slurm-configuration-slurmd-spooldir
(default "/var/spool/slurmd"))
@@ -187,16 +185,16 @@
(run-slurmctld? slurm-configuration-run-slurmctld
(default #f))
(slurmctld-log-file slurm-configuration-slurmctld-log-file
- (default "/var/log/slurm/slurmctld.log"))
+ (default #f)) ; #f for syslog
(slurmctld-pid-file slurm-configuration-slurmctld-pid-file
- (default "/var/run/slurm/slurmctld.pid"))
+ (default "/var/run/slurmctld.pid"))
(run-slurmdbd? slurm-configuration-run-slurmdbd
(default #f))
(slurmdbd-conf-file slurm-configuration-slurmdbd-conf-file
(default "/etc/slurm/slurmdbd.conf"))
(slurmdbd-pid-file slurm-configuration-slurmdbd-pid-file
- (default "/var/run/slurm/slurmdbd.pid")))
+ (default "/var/run/slurmdbd.pid")))
(define (slurm-activation config)
@@ -204,16 +202,22 @@
(with-imported-modules '((guix build utils))
#~(begin
(use-modules (guix build utils))
- (define %user (getpw "slurm"))
- (let ((homedir (passwd:dir %user))
- (spooldir #$(slurm-configuration-slurmd-spooldir config))
- (logdir (dirname #$(slurm-configuration-slurmd-log-file config)))
- (piddir (dirname #$(slurm-configuration-slurmd-pid-file config))))
- (for-each (lambda (dir)
- (unless (file-exists? dir)
- (mkdir-p dir))
- (chown dir (passwd:uid %user) (passwd:gid %user)))
- (list homedir spooldir piddir logdir)))
+ (let* ((%user (getpw "slurm"))
+ (spooldir #$(slurm-configuration-slurmd-spooldir config))
+ (logdir (dirname (or #$(slurm-configuration-slurmd-log-file config)
+ #$(slurm-configuration-slurmctld-log-file config)
+ "/var/log/slurmd.log")))
+ (piddir (dirname #$(slurm-configuration-slurmd-pid-file config))))
+ (unless (file-exists? spooldir)
+ (mkdir-p spooldir))
+ (chown spooldir (passwd:uid %user) (passwd:gid %user))
+ (when logdir
+ (unless (file-exists? logdir)
+ (mkdir-p logdir))
+ (when (> (string-length logdir) (string-length "/var/log"))
+ (chown logdir (passwd:uid %user) (passwd:gid %user))))
+ (unless (file-exists? piddir)
+ (mkdir-p piddir)))
;; /etc/slurm/slurm.conf needs to exist.
(file-exists? #$(slurm-configuration-slurm-conf-file config)))))
@@ -227,7 +231,7 @@
(requirement '(loopback munge))
(start #~(make-forkexec-constructor
(list #$(file-append package "/sbin/slurmd")
- "-L" #$slurmd-log-file
+ ;"-L" #$slurmd-log-file
"-f" #$slurm-conf-file)
#:pid-file #$slurmd-pid-file))
(stop #~(make-kill-destructor)))))))
@@ -242,7 +246,7 @@
(requirement '(loopback munge))
(start #~(make-forkexec-constructor
(list #$(file-append package "/sbin/slurmctld")
- "-L" #$slurmctld-log-file
+ ;"-L" #$slurmctld-log-file
"-f" #$slurm-conf-file)
#:pid-file #$slurmctld-pid-file))
(stop #~(make-kill-destructor))
@@ -250,8 +254,10 @@
(define (slurmdbd-activation config)
"Test the Slurmdbd configration exists."
- (file-exists?
- (slurm-configuration-slurmdbd-conf-file config)))
+ (when (slurm-configuration-run-slurmdbd config)
+ (file-exists?
+ (slurm-configuration-slurmdbd-conf-file config)))
+ #t)
(define slurmdbd-shepherd-service
(match-lambda
@@ -269,67 +275,29 @@
(define (slurm-services-to-run config)
(append (slurmd-shepherd-service config)
- (if (slurm-configuration-run-slurmctld? config)
+ (if (slurm-configuration-run-slurmctld config)
(slurmctld-shepherd-service config)
'())
- (if (slurm-configuration-run-slurmdbd? config)
+ (if (slurm-configuration-run-slurmdbd config)
(slurmdbd-shepherd-service config)
'())))
-(define (slurm-activations-to-run config)
- (append (slurm-activation config)
- (if (slurm-configuration-run-slurmctld? config)
- (slurmctld-activation config)
- '())
- (if (slurm-configuration-run-slurmdbd? config)
- (slurmdbd-activation config)
- '())))
-
-(define slurmd-service-type
+(define slurm-service-type
(service-type
- (name 'slurmd)
+ (name 'slurm)
(extensions
(list
(service-extension shepherd-root-service-type
- ;(cons slurmd-shepherd-service
- ; slurmdbd-shepherd-service))
- slurmd-shepherd-service)
- ;slurm-services-to-run)
+ slurm-services-to-run)
(service-extension activation-service-type
- ;(append slurm-activation
- ; slurmdbd-activation))
slurm-activation)
- ;slurm-activations-to-run)
+ (service-extension activation-service-type
+ slurmdbd-activation)
(service-extension account-service-type
(const %slurm-accounts))
(service-extension profile-service-type
(compose list slurm-configuration-package))))
(default-value (slurm-configuration))
(description
- "Run @url{https://slurm.schedmd.com/slurm.html,Slurm}, a workflow manager service.")))
-
-(define slurmdbd-service-type
- (service-type
- (name 'slurmdbd)
- (extensions
- (list
- (service-extension shepherd-root-service-type
- slurmdbd-shepherd-service)
- (service-extension activation-service-type
- slurmdbd-activation)))
- (default-value (slurm-configuration))
- (description
- ;; TODO: Fix for slurmdbd or integrate with slurm(d).
- "Run @url{https://slurm.schedmd.com/slurm.html,Slurm}, a workflow manager service.")))
-
-(define slurmctld-service-type
- (service-type
- (name 'slurmctld)
- (extensions
- (list
- (service-extension shepherd-root-service-type
- slurmctld-shepherd-service)))
- (default-value (slurm-configuration))
- (description
- ;; TODO: Fix for slurmctld or integrate with slurm(d).
- "Run @url{https://slurm.schedmd.com/slurm.html,Slurm}, a workflow manager service.")))
+ "Run @url{https://slurm.schedmd.com/slurm.html,Slurm}, a workflow manager
+service. Optionally also run @code{slurmctld} and @code{slurmdbd}.")))