guix-bioinformatics
/
guix-bioinformatics
4
2
Fork 2
Code Issues Pull Requests Releases Wiki Activity
Browse Source

octopus: update slurm services

pull/3/head^2
Efraim Flashner 2 years ago
parent
18082c3bdd
commit
3bd06f793a
Signed by: efraim GPG Key ID: 41AAE7DCCA3D8351
2 changed files with 112 additions and 125 deletions
Whitespace
Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL
Split View
Diff Options
Show Stats Download Patch File Download Diff File
  1. 131
      gn/deploy/octopus.scm
  2. 106
      gn/services/science.scm

131
gn/deploy/octopus.scm
View File

@ -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")
@ -105,6 +116,12 @@ SlurmUser=slurm")))
(firmware '())
(users (cons*
(user-account
(name "wrk")
(comment "Pjotr Prins")
(uid 502)
(group "users")
(supplementary-groups '("wheel" "kvm")))
(user-account
(name "efraimf")
(comment "Efraim Flashner")
@ -112,19 +129,25 @@ SlurmUser=slurm")))
(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

106
gn/services/science.scm
View File

@ -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}.")))

Write Preview
Loading…
Cancel
Save