Showing posts with label slurm. Show all posts
Showing posts with label slurm. Show all posts

14 February 2018

647. Linda/G16 and ecce + slurm

I had the opportunity to test G16 with Linda on my cluster. Suprisingly, I observed a decent reduction in computational time for geometry optimisation, and a fair reduction for vibrational analysis.

Computational time -- geometry optimisation
1x6 cores: 100%
2x6 cores: 56% (2 nodes)
3x6 cores: 44% (3 nodes)

Computational time -- normal mode computation
1x6 cores: 100%
2x6 cores: 63% (2 nodes)
3x6 cores: 57% (3 nodes)

In no case was the speed up good enough that it actually makes long-term sense to use Linda (need less than 50% for 2 nodes and 33% or less for 3 nodes), but if you're itching for quick results, it might be worth it.

Either way, as part of this I wrote a CONFIG.Linda for ECCE and SLURM:
Gaussian-16: /opt/gaussian/g16a/g16/g16 perlPath: /usr/bin/ qmgrPath: /usr/bin/ xappsPath: /usr/bin/ Slurm { #!/bin/csh #SBATCH -p linda #SBATCH --time=$walltime #SBATCH --output=slurm.out #SBATCH --job-name=$submitFile #SBATCH --nodes=$nodes #SBATCH --cpus-per-task=$ppn } Gaussian-16FilesToRemove{ core } Gaussian-16Command{ set path = ( /opt/nbo6/bin $path ) set nnodes = `scontrol show job $SLURM_JOBID|grep NodeList|sed 's/=/\t/'|gawk '{print $2}'|tail -n 1` sed -i "2s/^/%LindaWorkers=$nnodes\n/" g16.g16in sed -i '3s/^/%UseSSH\n/' g16.g16in sed -i "s/nprocshared.*/nprocshared=$ppn./" g16.g16in setenv GAUSS_SCRDIR /home/me/scratch setenv GAUSS_EXEDIR /opt/gaussian/g16a/g16 setenv GAUSS_ARCHDIR /opt/gaussian/g16a/g16/arch setenv GAUSS_BSDDIR /opt/gaussian/g16a/g16/bsd setenv GAUSS_LEXEDIR /opt/gaussian/g16a/g16/linda-exe /opt/gaussian/g16a/g16/g16< $infile > $outfile }
The slurm partition linda has all the nodes that has g16.

28 July 2015

618. Modifying ECCE to work with slurm

UPDATE: ecce stops monitoring the job after 10-20 seconds. The job continues fine though. Working on fixing the monitoring issue. This message will be removed once that's fixed. It was due to $q needing to be lowercase (i.e. 'slurm', not 'Slurm') in eccejobmonitor.

Sun Gridengine has been removed from debian jessie (it's in wheezy and sid). This has given me a good excuse to explore setting up SLURM on my debian cluster. So I did:

My setup is very simple, with each node having it's own working directory that they export via NFS to the main node. Also, I never run jobs across several nodes. Because of that, each node has it's own queue. Not how beowulf clusters were supposed to work, but it's the best solution for me (e.g. ROCKS does the opposite -- exports the user dir from the main node, but that makes reading and writing slow where it counts i.e. on the work nodes).

I've currently got this slurm.conf:
ControlMachine=beryllium ControlAddr= MpiDefault=none ProctrackType=proctrack/pgid ReturnToService=2 SlurmctldPidFile=/var/run/slurm-llnl/ SlurmdPidFile=/var/run/slurm-llnl/ SlurmdSpoolDir=/var/lib/slurm/slurmd SlurmUser=slurm StateSaveLocation=/var/lib/slurm/slurmctld SwitchType=switch/none TaskPlugin=task/none FastSchedule=1 SchedulerType=sched/backfill SelectType=select/linear AccountingStorageType=accounting_storage/filetxt AccountingStorageLoc=/var/log/slurm/accounting ClusterName=rupert JobAcctGatherType=jobacct_gather/none SlurmctldLogFile=/var/log/slurm/slurmctld.log SlurmdLogFile=/var/log/slurm/slurmd.log NodeName=beryllium NodeAddr= NodeName=neon NodeAddr= state=unknown NodeName=tantalum NodeAddr= state=unknown NodeName=magnesium NodeAddr= state=unknown NodeName=carbon NodeAddr= state=unknown NodeName=oxygen NodeAddr= state=unknown PartitionName=All Nodes=neon,beryllium,tantalum,oxygen,magnesium,carbon default=yes maxtime=infinite state=up PartitionName=mpi4 Nodes=tantalum maxtime=infinite state=up PartitionName=mpi12 Nodes=carbon maxtime=infinite state=up PartitionName=mpi8 Nodes=neon maxtime=infinite state=up PartitionName=mpix8 Nodes=oxygen maxtime=infinite state=up PartitionName=mpix12 Nodes=magnesium maxtime=infinite state=up PartitionName=mpi1 Nodes=beryllium maxtime=infinite state=up
and sinfo returns
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST All* up infinite 6 idle beryllium,carbon,magnesium,neon,oxygen,tantalum mpi4 up infinite 1 idle tantalum mpi12 up infinite 1 idle carbon mpi8 up infinite 1 idle neon mpix8 up infinite 1 idle oxygen mpix12 up infinite 1 idle magnesium mpi1 up infinite 1 idle beryllium

The first step was to figure out what files to edit:

grep -rs "qsub"
apps/siteconfig/QueueManagers:SGE|submitCommand: qsub ##script##
grep -rs "SGE"
apps/scripts/eccejobmonitor: &MsgSendUp("SGE job id '$id' in state '$state'"); [..] apps/siteconfig/Queues:magnesium|queueMgrName: SGE

Here are the files I edited:

12 QueueManagers: LoadLeveler \ 13 Maui \ 14 EASY \ 15 PBS \ 16 LSF \ 17 Moab \ 18 SGE \ 19 Shell\ 20 Slurm
185 Shell|jobIdParseExpression: \ [0-9]+ 186 187 ############################################################################### 188 # SLURM 189 # Simple Linux Utility for Resource Management 190 # 191 # 192 Slurm|submitCommand: sbatch ##script## 193 Slurm|cancelCommand: scancel ##id## 194 Slurm|queryJobCommand: squeue 195 Slurm|queryMachineCommand: sinfo -p ##queue## 196 Slurm|queryQueueCommand: squeue -a 197 Slurm|queryDiskUsageCommand: df -k 198 Slurm|jobIdParseExpression: .* 199 Slurm|jobIdParseLeadingText: job
2124 LogMsg "Globus status from eccejobstore: $state"; 2125 } 2126 elsif ($q eq 'slurm') 2127 { 2128 $cmd = "squeue 2>&1"; 2129 if (open(QUERY, "$cmd |")) 2130 { 2131 $gotState = 0; 2132 while () 2133 { 2134 LogMsg "JobCheck: Slurm qstat line: $_"; 2135 if (/^\s*$id/) 2136 { 2137 my $state = (split)[5]; 2138 2139 &MsgSendUp("Slurm job id '$id' in state '$state'"); 2140 2141 if (grep {$state eq $_} qw{R 2142 t}) 2143 { 2144 $status = $JOB_STATE_RUNNING; 2145 } 2146 elsif (grep {$state eq $_} qw{PD}) 2147 { 2148 $status = $JOB_STATE_PENDING; 2149 } 2150 $gotState = 1; 2151 last; 2152 } 2153 } 2154 if ($gotState == 0) 2155 { 2156 if ($gJobCheckState != $JOB_STATE_NONE) 2157 { 2158 $status = $JOB_STATE_DONE; 2159 } 2160 } 2161 close QUERY;

Next set up a new machine (or queue) using ecce -admin. Set up a queue -- you won't be able to select Slurm, so select e.g. PBS. Edit the apps/siteconfig/CONFIG.machinename file to e.g.
1 NWChem: /opt/nwchem/Nwchem/bin/LINUX64/nwchem 2 Gaussian-03: /opt/gaussian/g09d/g09/g09 3 perlPath: /usr/bin/ 4 qmgrPath: /usr/bin/ 5 xappsPath: /usr/bin/ 6 7 Slurm { 8 #!/bin/csh 9 #SBATCH -p mpi8 10 #SBATCH --time=$walltime 11 #SBATCH --output=slurm.out 12 #SBATCH --job-name=$submitFile 13 } 14 15 NWChemEnvironment { 16 PYTHONPATH /opt/nwchem/Nwchem/contrib/python 17 } 18 19 NWChemFilesToRemove{ core *.aoints.* *.gridpts.* } 20 21 NWChemCommand { 22 setenv PATH "/bin:/usr/bin:/sbin:/usr/sbin" 23 setenv LD_LIBRARY_PATH "/usr/lib/openmpi/lib:/opt/openblas/lib:/opt/acml/acml5.3.1/gfortran64_fma4_int64/lib:/opt/acml/acml5.3.1/gfortran64_int64/lib:/opt/intel/mkl/lib/intel64" 24 hostname 25 mpirun -n $totalprocs /opt/nwchem/Nwchem/bin/LINUX64/nwchem $infile > $outfile 26 } 27 28 Gaussian-03FilesToRemove{ core *.rwf } 29 30 Gaussian-03Command{ 31 set path = ( /opt/nbo6/bin $path ) 32 setenv GAUSS_SCRDIR /home/me/scratch 33 setenv GAUSS_EXEDIR /opt/gaussian/g09d/g09/bsd:/opt/gaussian/g09d/g09/local:/opt/gaussian/g09d/g09/extras:/opt/gaussian/g09d/g09 34 /opt/gaussian/g09d/g09/g09< $infile > $outfile 35 echo 0 36 } 37 38 Wrapup{ 39 dmesg|tail 40 find ~/scratch/* -name "*" -user me|xargs -I {} rm {} -rf 41 }
Next, edit apps/siteconfig/Queues -- in my case the machine I created is called neon-slurm:
neon-slurm|queueMgrName: Slurm neon-slurm|queueMgrVersion: 2.0~ neon-slurm|prefFile: neon-slurm.Q
And that's all. You should now be able to submit jobs via slurm. There's obviously a lot more than can be done and configured with SLURM, but this was enough to get me up and running, so that I'm now 'future-proofed' in case SGE never comes back into debian stable.

And here's what it looks like when my ecce-submitted jobs are running:

JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 30 mpi8 In_monom me PD 0:00 1 (Resources) 29 mpi8 b_monome me R 16:12 1 neon 31 mpix12 tl_dimer me R 34:28 1 magnesium

617. SLURM on debian jessie (and compiling Jürgen Rinas' sinfo)

Two issues:
* Sun GridEngine (now Oracle GridEngine) is missing from Debian Jessie. I need a queue manager for my cluster. For now the wheezy package runs fine in debian jessie, but I'd be happier with a supported solution. SLURM is a good alternative here, and I've used it at the TACC.

* SLURM conflicts with Jürgen Rinas' sinfo package, which I use to keep an eye on my cluster. Until this has been resolved, I'll compile and use my own version of sinfo -- basically, I'll rename sinfo and sinfod to sinfo_jr and sinfod_jr. I can't live without sinfo.

Compiling sinfo
mkdir ~/tmp/sinfo -p
cd ~/tmp/sinfo
sudo apt-get install build-essential
sudo apt-get autoremove sinfo 
apt-get source sinfo
cd sinfo-0.0.47/
vim debian/rules 

16 dh_auto_configure -- --enable-SIMPLE_USER_CACHE --enable-CPUNO_ADJUST 21 rm $(CURDIR)/debian/sinfo/usr/bin/sshallsinfo 22 rm $(CURDIR)/debian/sinfo/usr/share/man/man1/sshallsinfo.1 25 rm $(CURDIR)/debian/sinfo/usr/lib/*/sinfo/*.la 37 chmod 755 $(CURDIR)/debian/sinfo/usr/share/sinfo/
16 dh_auto_configure -- --enable-SIMPLE_USER_CACHE --enable-CPUNO_ADJUST --program-suffix=_jr 21 rm $(CURDIR)/debian/sinfojr/usr/bin/sshallsinfo_jr 22 rm $(CURDIR)/debian/sinfojr/usr/share/man/man1/sshallsinfo_jr.1 25 rm $(CURDIR)/debian/sinfojr/usr/lib/*/sinfo/*.la 37 chmod 755 $(CURDIR)/cgi/
That's jr for Jürgen Rinas.

Then edit debian/control and change
12 Package: sinfo
15 Conflicts: slurm-client, slurm-llnl (<< 14.03.8-1)
12 Package: sinfojr
15 Conflicts: 
dpkg-buildpackage -us -uc
cd ../
sudo dpkg -i sinfo_0.0.47-3_amd64.deb

I launch sinfodjr at boot by putting the following in /etc/rc.local:
su verahill -c '/usr/sbin/sinfodjr --bcast' &

I had a look at this post:

It looked to easy to be true.

Here's what I ended up doing:

On the MASTER node:
sudo apt-get install slurm-wlm slurmctld slurmd
[..] Generating a pseudo-random key using /dev/urandom completed. Please refer to /usr/share/doc/munge/README.Debian for instructions to generate more secure key. Setting up slurm-client (14.03.9-5) ... Setting up slurm-wlm-basic-plugins (14.03.9-5) ... Setting up slurmd (14.03.9-5) ... Setting up slurmctld (14.03.9-5) ... Setting up slurm-wlm (14.03.9-5) ... [..]
open file:///usr/share/doc/slurmctld/slurm-wlm-configurator.easy.html
# slurm.conf file generated by configurator easy.html. # Put this file on all nodes of your cluster. # See the slurm.conf man page for more information. # ControlMachine=beryllium ControlAddr= # #MailProg=/bin/mail MpiDefault=none #MpiParams=ports=#-# ProctrackType=proctrack/pgid ReturnToService=2 SlurmctldPidFile=/var/run/slurm-llnl/ #SlurmctldPort=6817 SlurmdPidFile=/var/run/slurm-llnl/ #SlurmdPort=6818 SlurmdSpoolDir=/var/lib/slurm/slurmd SlurmUser=slurm #SlurmdUser=root StateSaveLocation=/var/lib/slurm/slurmctld SwitchType=switch/none TaskPlugin=task/none # # # TIMERS #KillWait=30 #MinJobAge=300 #SlurmctldTimeout=120 #SlurmdTimeout=300 # # # SCHEDULING FastSchedule=1 SchedulerType=sched/backfill #SchedulerPort=7321 SelectType=select/linear # # # LOGGING AND ACCOUNTING AccountingStorageType=accounting_storage/none ClusterName=rupert #JobAcctGatherFrequency=30 JobAcctGatherType=jobacct_gather/none #SlurmctldDebug=3 SlurmctldLogFile=/var/log/slurm/slurmctld.log #SlurmdDebug=3 SlurmdLogFile=/var/log/slurm/slurmd.log # # # COMPUTE NODES NodeName=beryllium NodeAddr= NodeName=neon NodeAddr= PartitionName=All Nodes=beryllium,neon
Copy the above block to /etc/slurm-llnl/slurm.conf

Note the lack of spaces between beryllium and neon in the Nodes= directive.
scontrol show daemons
sudo /usr/sbin/create-munge-key
The munge key /etc/munge/munge.key already exists Do you want to overwrite it? (y/N) y Generating a pseudo-random key using /dev/urandom completed.
sudo systemctl enable slurmctld.service
sudo ln -s /var/lib/slurm-llnl /var/lib/slurm
sudo systemctl start slurmctld.service
sudo systemctl status slurmctld.service 
● slurmctld.service - Slurm controller daemon Loaded: loaded (/lib/systemd/system/slurmctld.service; enabled) Active: active (running) since Tue 2015-07-21 11:16:18 AEST; 40s ago Process: 19958 ExecStart=/usr/sbin/slurmctld $SLURMCTLD_OPTIONS (code=exited, status=0/SUCCESS) Main PID: 19960 (slurmctld) CGroup: /system.slice/slurmctld.service └─19960 /usr/sbin/slurmctld
sudo systemctl status munge.service
● munge.service - MUNGE authentication service Loaded: loaded (/lib/systemd/system/munge.service; disabled) Active: active (running) since Wed 2015-07-08 00:11:18 AEST; 1 weeks 6 days ago Docs: man:munged(8) Main PID: 25986 (munged) CGroup: /system.slice/munge.service └─25986 /usr/sbin/munged
Also, add yourself to the group slurm and chmod g+r /var/log/slurm/accounting.

On neon (and later on each node): 
Install slurmd and slurm-client as shown below, then copy the /etc/munge/munge.key from the master node to the execute node. Do the same with /etc/slurm-llnl/slurm.conf. Then enable and restart the services.

sudo apt-get install slurmd slurm-client
sudo ln -s /var/lib/slurm-llnl /var/lib/slurm
sudo systemctl enable slurmd.service
sudo systemctl restart slurmd.service
sudo systemctl enable munge.service
sudo systemctl restart munge.service
sudo systemctl status slurmd.service

On the main host (beryllium) I checked that everything was well:

All          up   infinite      1  idle* beryllium, neon

20 March 2014

567. Testing daisychain slurm script

I'm using stampede.TACC for jobs that need significantly longer than 48 hours to run. Luckily, John Fonner at the Texas Advanced Computing Centre has been kind enough to prepare a SLURM script that circumvents that through daisychaining jobs.

Note that you should under no circumstances do this unless you've been specifically allowed to do so by your cluster manager. 

If you get clearance, you submit the script and it will run in the background and resubmit scripts until the job is done.

To get the daisychain script, do

mkdir ~/tmp
cd ~/tmp
git clone

This will pull the latest version of daisychain.slurm. Rename it to e.g. edited.slurm

General editing of the slurm script:

 Replace all instances of


to avoid conflicts when several jobs are running concurrently

To run the script on your own system which you've set up like shown in this post, change




If you're using stampede.TACC, stick to login1.  

3. For gaussian jobs on stampede.TACC  

module load gaussian


if [ "$thisJobNumber" -eq "1" ]; then

Set up your restart job scripts. For example, if the job section of your slurm script looks like this
mkdir $SCRATCH/gaussian_tmp export GAUSS_SCRDIR=$SCRATCH/gaussian_tmp if [ "$thisJobNumber" -eq "1" ]; then #first job echo "Starting First Job:" g09 < freq.g09in > output_$thisJobNumber else #continuation echo "Starting Continuation Job:" g09 < freq_restart.g09in > output_$thisJobNumber fi
with freq.g09in looking like
%nprocshared=16 %rwf=/scratch/0XXXX/XXXX/gaussian_tmp/ajob.rwf %Mem=2000000000 %Chk=/home1/0XXX/XXXX/myjob/ajob.chk #P rpbe1pbe/GEN 5D Freq() SCF=(MaxCycle=256 ) Punch=(MO) Pop=()
with freq.g09in being something along the lines of
%nprocshared=16 %Mem=2000000000 %rwf=/scratch/0XXX/XXXX/gaussian_tmp/ajob.rwf %Chk=/home1/0XXXX/XXXX/myjob/ajob.chk #P restart
(note that the above example is a bit special since it 1) saves the .rwf (which is huge) and 2) is restarting a frequency job. For a simple geoopt job it's enough to restart from the .chk file.

Testing at home
I set up a home system with slurm as shown here:

First edit the daisychain.slurm script as shown above. Note that your slurm script must end with .slurm for the script to recognise it as a slurm script. You can get around this by editing your script and specifying a job script name.

Specifically, change the run time to
#SBATCH -t 00:00:10 # Run time (hh:mm:ss)
comment out the partition name
##SBATCH -p normal
and change the job section to
#-------------------Job Goes Here-------------------------- if [ "$thisJobNumber" -eq "1" ]; then echo "Starting First Job:" sh else echo "Starting Continuation Job:" sh fi #----------------------------------------------------------

Next set up key-based log in for localhost (if you haven't got a keypair, use ssh-keygen:

cat $HOME/.ssh/ >> $HOME/.ssh/authorized_keys
ssh localhost

Create two  job files.
echo "first job" date sleep 65 date
echo "second job" date sleep 9 echo "Do nothing"

Submit using
sbatch test.slurm

Make sure to change
#SBATCH -J testx          # Job name
for each job so that you can have several running concurrently.

14 March 2014

565. Setting up slurm on debian wheezy (very basic)

I have a problem: I've got access to stampede.tacc in Texas which is using slurm as the queue manager. And while I've got SGE figured out (use it on my own cluster, my collaborator's cluster and it's used on the university cluster) I'm having some conceptual issues with SLURM.

I don't have any problems writing slurm scripts -- it's similar enough to SGE. But nowhere do I see anyone use -cwd or any equivalent in their slurm scripts. Either that is because you don't have to, or it's just an oversight in all of the examples that I've seen.

Learning by doing has also been an issue -- whenever I submit a test job it takes many, many hours before it's run. That's no way to learn.

Either way, it's time for me to become more familiar with slurm, so I've decided to set it up on a dedicated box.

I look at this post while setting it up:

NOTE: I set up a single node. This won't deal with getting nodes to communicate, configuring master and submit nodes, or anything lik that.

NOTE: the package slurm is a completely different program (network monitor). You need slurm-llnl

I also wonder whether the name has got anything to with this Slurm...


sudo apt-get install slurm-llnl
Setting up munge (0.5.10-1) ... Not starting munge (no keys found). Please run /usr/sbin/create-munge-key Setting up slurm-llnl-basic-plugins (2.3.4-2+b1) ... Setting up slurm-llnl (2.3.4-2+b1) ... Not starting slurm-llnl slurm.conf was not found in /etc/slurm-llnl Please follow the instructions in /usr/share/doc/slurm-llnl/README.Debian.gz

Open the local file file:///usr/share/doc/slurm-llnl/slurm-llnl-configurator.html in a web browser and fill out the form. I got the following slurm.conf, which I put in /etc/slurm-llnl/ 
# slurm.conf file generated by configurator.html. # Put this file on all nodes of your cluster. # See the slurm.conf man page for more information. # ControlMachine=ecce64bit #ControlAddr= #BackupController= #BackupAddr= # AuthType=auth/munge CacheGroups=0 #CheckpointType=checkpoint/none CryptoType=crypto/munge #DisableRootJobs=NO #EnforcePartLimits=NO #Epilog= #PrologSlurmctld= #FirstJobId=1 JobCheckpointDir=/var/lib/slurm-llnl/checkpoint #JobCredentialPrivateKey= #JobCredentialPublicCertificate= #JobFileAppend=0 #JobRequeue=1 #KillOnBadExit=0 #Licenses=foo*4,bar #MailProg=/usr/bin/mail #MaxJobCount=5000 #MaxTasksPerNode=128 MpiDefault=none #MpiParams=ports=#-# #PluginDir= #PlugStackConfig= #PrivateData=jobs ProctrackType=proctrack/pgid #Prolog= #PrologSlurmctld= #PropagatePrioProcess=0 #PropagateResourceLimits= #PropagateResourceLimitsExcept= ReturnToService=1 #SallocDefaultCommand= SlurmctldPidFile=/var/run/slurm-llnl/ SlurmctldPort=6817 SlurmdPidFile=/var/run/slurm-llnl/ SlurmdPort=6818 SlurmdSpoolDir=/var/lib/slurm-llnl/slurmd SlurmUser=verahill #SrunEpilog= #SrunProlog= StateSaveLocation=/var/lib/slurm-llnl/slurmctld SwitchType=switch/none #TaskEpilog= TaskPlugin=task/none #TaskPluginParam= #TaskProlog= #TopologyPlugin=topology/tree #TmpFs=/tmp #TrackWCKey=no #TreeWidth= #UnkillableStepProgram= #UnkillableStepTimeout= #UsePAM=0 # # # TIMERS #BatchStartTimeout=10 #CompleteWait=0 #EpilogMsgTime=2000 #GetEnvTimeout=2 #HealthCheckInterval=0 #HealthCheckProgram= InactiveLimit=0 KillWait=30 #MessageTimeout=10 #ResvOverRun=0 MinJobAge=300 #OverTimeLimit=0 SlurmctldTimeout=300 SlurmdTimeout=300 #UnkillableStepProgram= #UnkillableStepTimeout=60 Waittime=0 # # # SCHEDULING #DefMemPerCPU=0 #EnablePreemption=no FastSchedule=1 #MaxMemPerCPU=0 #SchedulerRootFilter=1 #SchedulerTimeSlice=30 SchedulerType=sched/backfill SchedulerPort=7321 SelectType=select/linear #SelectTypeParameters= # # # JOB PRIORITY #PriorityType=priority/basic #PriorityDecayHalfLife= #PriorityCalcPeriod= #PriorityFavorSmall= #PriorityMaxAge= #PriorityUsageResetPeriod= #PriorityWeightAge= #PriorityWeightFairshare= #PriorityWeightJobSize= #PriorityWeightPartition= #PriorityWeightQOS= # # # LOGGING AND ACCOUNTING #AccountingStorageEnforce=0 #AccountingStorageHost= #AccountingStorageLoc= #AccountingStoragePass= #AccountingStoragePort= AccountingStorageType=accounting_storage/none #AccountingStorageUser= ClusterName=cluster #DebugFlags= #JobCompHost= #JobCompLoc= #JobCompPass= #JobCompPort= JobCompType=jobcomp/none #JobCompUser= JobAcctGatherFrequency=30 JobAcctGatherType=jobacct_gather/none SlurmctldDebug=3 SlurmctldLogFile=/var/log/slurm-llnl/slurmctld.log SlurmdDebug=3 SlurmdLogFile=/var/log/slurm-llnl/slurmd.log # # # POWER SAVE SUPPORT FOR IDLE NODES (optional) #SuspendProgram= #ResumeProgram= #SuspendTimeout= #ResumeTimeout= #ResumeRate= #SuspendExcNodes= #SuspendExcParts= #SuspendRate= #SuspendTime= # # # COMPUTE NODES NodeName=ecce64bit Procs=1 State=UNKNOWN PartitionName=debug Nodes=ecce64bit Default=YES MaxTime=INFINITE State=UP

sudo /usr/sbin/create-munge-key
sudo service slurm-llnl start
[ ok ] Starting slurm central management daemon: slurmctld.
[ ok ] Starting slurm compute node daemon: slurmd.
sudo service munge start
[ ok ] Starting MUNGE: munged.

At that point I tried sinfo, squeue etc., none of which returned anything other than a connection error:
slurm_load_jobs error: Unable to contact slurm controller (connect failure)
slurm_load_partitions: Unable to contact slurm controller (connect failure)
So I rebooted. Which had no effect.The log file /var/log/slurm-llnl/slurmctld.log contains
fatal: Incorrect permissions on state save loc: /var/lib/slurm-llnl/slurmctld
verahill@ecce64bit:~$ sudo chown verahill /var/lib/slurm-llnl/slurmctld verahill@ecce64bit:~$ sudo service slurm-llnl restart
[ ok ] Stopping slurm central management daemon: slurmctld. No /usr/sbin/slurmctld found running; none killed. [ ok ] Stopping slurm compute node daemon: slurmd. No /usr/sbin/slurmd found running; none killed. slurmd dead but pid file exists [ ok ] Starting slurm central management daemon: slurmctld. [ ok ] Starting slurm compute node daemon: slurmd.
verahill@ecce64bit:~$ ps aux|grep slurm
verahill 3790 0.0 0.2 116164 2292 ? Sl 21:12 0:00 /usr/sbin/slurmctld root 3829 0.0 0.1 95064 1380 ? S 21:12 0:00 /usr/sbin/slurmd
verahill@ecce64bit:~$ squeue
verahill@ecce64bit:~$ sinfo
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST debug* up infinite 1 idle ecce64bit

verahill@ecce64bit:~$ srun --ntasks=1  --label /bin/hostname && pwd && whoami
0: ecce64bit /home/verahill verahill

Time to write a simple queue script:
#!/bin/bash #SBATCH -J pbe_delta # Job name #SBATCH -o pbe_delta.o%j # Name of stdout output file(%j expands to jobId) #SBATCH -e pbe_delta.o%j # Name of stderr output file(%j expands to jobId) #SBATCH -N 1 # Total number of nodes requested (16 cores/node) #SBATCH -n 1 #SBATCH -t 48:00:00 # Run time (hh:mm:ss) date> output.out pwd >> output.out hostname >> output.out ls -lah
I submitted it using
sbatch job.slurm

and on running it gives two output files:
Fri Mar 14 17:16:10 EST 2014
and pbe_delta.o4
total 16K
drwxr-xr-x 2 verahill verahill 4.0K Mar 14 17:16 .
drwxr-xr-x 3 verahill verahill 4.0K Mar 14 17:14 ..
-rw-r--r-- 1 verahill verahill  491 Mar 14 17:16 job.slurm
-rw-r--r-- 1 verahill verahill   59 Mar 14 17:16 output.out
-rw-r--r-- 1 verahill verahill    0 Mar 14 17:15 pbe_delta.o3
-rw-r--r-- 1 verahill verahill    0 Mar 14 17:16 pbe_delta.o4