Agenda
1.
2.
3.
4.
5.
Construction and Management
High Avaibility
How to use
Software
Batchsystem
Compute-Cluster - 2
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
1. Construction and Management/1
Where to find:
Grimm-Zentrum, Server Room, water cooled cabinet
Aufbau:
-
8 Supermicro Twin2-Server, 2 U
8 Supermicro
Twin2-Server
every
has 4 nodes with
2 Intel-Nehalem CPUs
every has 4 Cores, Infiniband QDR, 48 GB memory
at all 32 nodes, 256 Cores, 1.536 TB memory
Compute-Cluster - 3
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
1. Construction and Management/2
- two master nodes are responsible for login to the address:
clou.cms.hu-berlin.de
- they manage different services (DHCP, NFS, LDAP, Mail)
- they start und stop alle nodes if necessary, only they communicate
into the Universtiy network
- they provide development software (Compiler, MPI)
- and also application software
- they organize the batch service
Compute-Cluster - 4
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
1. Construction and Management/3
- two as a HA cluster configured server provide the parallel file
system (Lustre FS) for temporary data of large size
lulu:/work
- all nodes are equipped with fast infiniband network (QDR) which
is responsible for node communication during parallel computations
- the master and file server nodes are monitored by central Nagios of
CMS
- the compute server are monitored local with Ganglia
Compute-Cluster - 5
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
1. Aufbau und Cluster-Verwaltung/4
-/work Data
- 1 MDT , 2 OSTs
Stellt
/work bereit
- 3 OSTs
- Login clou.cms.hu-berlin.de
- Failover Login
- 36 Port Infiniband Switch
- node1 bis node4
- node5 bis node8
- node25 bis node28
- node29 bis node32
- /home Data
Compute-Cluster - 6
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
2. High Avaibility /1
- all servers are equipped with redundant power supplies
- master server: RedHat Resource Group Manger rgmanager
configures and monitors the services on both master nodes
- in case of failover of one master the other one takes over the
services of the failed one
- file server: for the Lustre FS /work are also redundant configured,
if one fails the other one takes the MDS (Meta Data Server) and also
the OSTs (Object Storage Targets), possible becuse all data are
stored on a virtual SAN disk
Compute-Cluster - 7
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
3. How to use/1
- all colleagues who have not enough resources at the institut are allowed to
use the Kkk
system
- necessyary is an account
alle at CMS, the acoount will be opend for the service
- login on master clou.cms.hu-berlin.de with SSH form University network
- you may login to nodes via ssh from master node without further
authentification
- Data storage:
- /home/<institut>/<account> unique user home dir
- /afs/.cms.hu-berlin.de/user/<account> OpenAFS home dir
- /work/<account>
working dir
- /perm/<account>
permanent dir
- /scratch/<account>
on nodes lokal working dir
- Migration of data from old cluster via /home Verzeichnis or with scp
Compute-Cluster - 8
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
3. How to use/2
Data saving:
Kkk
-
data
data
data
data
data
in
in
in
in
in
/home
alle daily into TSM, max. 3 older versions
/afs/.cms.hu-berlin.de
daily, the whole semester
/perm
daily on disk, max. 3 older versions
/work
no saving
/scratch
no saving
- /work and /scratch are controlled on achieve high water mark of 85%,
data older than 1 month willl be removed
- important data should be copied to /perm or to a home dir
- a parallel SSH is installed, for calling commands on all nodes
pssh --help
pssh –P –h /usr/localshare/nodes/all w |grep load
Compute-Cluster - 9
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
4. Software/1
System software
Kkk
- Operating system:
CentOS 5 = RedHat EL 5
alle
Development Software
- GNU Compiler
- Intel Compiler Suite mit MKL
- Portland Group Compiler
- OpenMPI
- MPICH
Application software
- Chemie:
Gaussian, Turbomole, ORCA
- Matlab, Maple
- further Software is possible
Compute-Cluster - 10
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
4. Software/2
Kkk versions must be loaded with the module command
- all Software
module available
alle -> all available modules (Software)
- Development:
module load intel-cluster-322 -> loads Intel Compiler+
module load openmpi-14-intel
-> loads OpenMPI
...
- Application software:
module load g09-a02
-> loads Gaussian09 A02
module load orca27
-> loads ORCA 2.7
module load matlab-10a -> loads Matlab R2010a
...
Compute-Cluster - 11
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
5. Batch Service/1
Open Source Product: SUN Grid Engine (SGE)
- cell clous is installedalle
- on one master node the Qmaster daemon is running the other one is
working as a slave and will get activ if the first fails
- SGE supports parallel environments (PE)
- There is a Grafical User Interface QMON
- With QMON all configurations may be shown and actions may be done
- The are two parallel environments installed:
ompi (128 Slots) and smp (64 Slots)
- These will be allocated to the parallel queues
Compute-Cluster - 12
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
5. Batch Service/2
- parallelKkk
jobs upto 32 cores are allowed, max. 4 Jobs a 32 Cores at the
same time in bigpar alle
- in queue par there are upto 8 jobs a 8 cores allowed, all jobs are
running on a separate node
- ser and long are serial queues
- inter is for interactive computations (Matlab, GaussView)
- all values and configurations are preliminary and may be changed on
user requirements
- batch scripts of old cluster can’t be used for the new one, because of
new batch system
Compute-Cluster - 13
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
5. Batch Service/3
Queue
Kkk
Priority
Prozessors
alle 8-32
Memory
Slots
PE
Runtime
40 GB
128
ompi
48 h
bigpar
+5
par
0
4-8
20 GB
64
smp
24 h
long
-5
1
4 GB
32
-
96 h
short
+10
1
4 GB
32
-
6h
inter
+15
1
1 GB
8
-
3h
Compute-Cluster - 14
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
5. Batch Service/4
Kkk
- Users are
collected to lists = working groups
e.d.: cms, limberg,
alle haerdle, ...
- submition of jobs: example scripts for all applications are in
/perm/skripte, they include the module calls
- e.d. Gaussian09 computation:
cd /work/$USER/g09
cp /perm/skripte/g09/run_g09_smp_8
qsub run_g09_smp_8
qstat
qmon&
-> Grafical User Interface
Compute-Cluster - 15
-> ev. Änderungen
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
5. Batch Service/5
Kkk developing and starting (computation of Pi)
- MPI program
cd /work/$USER/ompi
alle
module load intel-cluster-322
module load openmpi-14-intel
cp /perm/skripte/ompi/cpi.c .
mpicc –o cpi cpi.c
cp /perm/skripte/ompi/run_ompi_32 .
qsub run_ompi_32
Enthält den Aufruf des MPI Programmes
mpirun –np 8 –machinefile nodefile cpi
cat nodefile -> enhält den Knoten, z.B.
node8.local slots=8
Compute-Cluster - 16
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli
5. Batch Service/6
Kkkcommands
- important
qstat
-> Status der eigenen Jobs
alle
qstat –u \*
-> Liste aller Jobs im Cluster
qdel <jobid>
-> Entfernen des Jobs
qconf –sql -> Liste aller Queues
qconf –sq par
-> Konfiguration Queue par
qconf –sul -> zeigt die Userlisten (Gruppen)
qconf –su cms
-> User der Liste/Gruppe cms
qconf –spl -> Liste der Parallel Environments
qacct <jobid>
-> Abrechnungsinfo zum Job
qstat –q bigpar –f -> zeigt, ob Queue disabled
Compute-Cluster - 17
Jahreskolloquium 29.06.2010
Daniela-Maria Pusinelli