generic mpi job submission by the p-grade grid portal zoltán farkas ([email protected]) mta sztaki
TRANSCRIPT
Generic MPI Job Submission by the P-GRADE Grid Portal
Zoltán Farkas ([email protected])MTA SZTAKI
Contents
• MPI Standards Implementations
• P-GRADE Grid Portal Workflow execution, file handling Direct job submission Brokered job submission
MPI
• MPI stands for Message Passing Interface Standards 1.1 and 2.0
• MPI Standard features: Collective communication (1.1+) Point-to-Point communication (1.1+) Group management (1.1+) Dynamic Processes (2.0) Programming Language APIs …
MPI Implementations
• MPICH Freely available implementation of MPI Runs on many architectures (even on Windows) Implements Standards 1.1 (MPICH) and 2.0 (MPICH2) Supports Globus (MPICH-G2) Nodes are allocated upon application execution
• LAM/MPI Open-source implementation of MPI Implements Standards 1.1 and parts of 2.0 Many interesting features (checkpoint) Nodes are allocated before application execution
• Open MPI Implements Standard 2.0 Uses technologies of other projects
MPICH execution on x86 clusters
• Application can be started … … using ‘mpirun’ … specifying:
➢ number of requested nodes (-np <nodenumber>),➢ a file containing the nodes to be allocated (-machinefile
<arg>) [OPTIONAL],➢ the executable,➢ executable arguments.
$ mpirun –np 7 ./cummu –N –M –p 32
• Processes are spawned using ‘rsh’ or ‘ssh’, depending on the configuration
MPICH x86 execution – requirements
• Executable (and input files) must be present on worker nodes:
Using Shared Filesystem, or User distributes the files before invoking ‘mpirun’.
• Accessing worker nodes from the host running ‘mpirun’:
Using ‘rsh’ or ‘ssh’ Without user interaction (host-based authentication)
P-GRADE Grid Portal
• Technologies:– Apache Tomcat
– GridSphere
– Java Web Start
– Condor
– Globus
– EGEE Middleware
– Scripts
P-GRADE Grid Portal
• Workflow execution: DAGMan as workflow scheduler pre and post script to perform tasks around job exeution Direct job execution using GT-2:
➢ GridFTP, GRAM➢ pre: create temporary storage directory, copy input files➢ job: Condor-G is executing a wrapper script➢ post: download results
Job execution using EGEE broker (both LCG/gLite):➢ pre: create application context as input sandbox➢ job: Scheduler universe Condor job executing a script, which
does job submission, status polling, output downloading. A wrapper script is submitted to the broker
➢ post: error checking
Workflow Manager Portlet
Workflow example
• Jobs
• Input/output files
• Data transfers
Portal: File handling
• „Local” files:– User has access to these files through the Portal
– Local input files are uploaded from the user machine
– Local output files are downloaded to the user machine
• „Remote” files:– Files reside on EGEE Storage Elements or are accessible
using GridFTP
– EGEE SE files:➢ lfn:/…➢ guid:…
– GridFTP files: gsiftp://…
Workflow Files
• File Types– In/Out
– Local/Remote
• File Names– Internal
– „Global”
• File Lifetime– Permanent
– Volatile
Portal: Direct job execution
• The resource to be used is known before job execution
• The user must have a valid, accepted certificate
• Local files are supported
• Remote GridFTP files are supported, even in case of grid-unaware applications
• Jobs may be sequential or MPI applications
Direct exec: step-by-step I.
1. Pre script:• creates a storage directory on the selected site’s front-
end node, using the ‘fork’ jobmanager
• local input files are copied to this directory from the Portal machine using GridFTP
• remote input files are copied using GridFTP (in case of errors, a two-phase copy is tried using Portal machine)
1. Condor-G job:• a wrapper script (wrapperp) is specified as the real
executable
• a single job is submitted to the requested jobmanager, for MPI jobs the ‘hostcount’ RSL attribute is used to specify the number of requested nodes
Direct exec: step-by-step II.
1. LRSM:• allocate the number of requested nodes (if needed)
• start wrapperp on one of the allocated nodes (master worker node)
2. Wrapperp (running on master worker node):• copies the executable and input files from the front-end
node (‘scp’ or ‘rcp’)• in case of PBS jobmanagers, executable and input files are
copied to the allocated nodes (PBS_NODEFILE). In case of non-PBS jobmanagers, shared filesystem is required, as the host names of the allocated nodes cannot be determined
• wrapperp searches for ‘mpirun’
• the real executable is started using the found ‘mpirun’• in case of PBS jobmanagers, output files are copied from
the allocated worker nodes to the master worker node)• output files are copied to the front-end node
Direct exec: step-by-step III.
1. Post script:• local output files are copied from the temporary working
directory created by the pre script to the Portal machine using GridFTP
• remote output files are copied using GridFTP (in case of errors, a two-phase copy is tried using Portal machine)
2. DAGMan: keeps on job scheduling…
Direct execution
Remote filestoragePortal machine
Temp.Storage
1
1
Fork GridFTP
PBS
2
Master WN
WrapperpSlave WN1 Slave WNn-1
3
In/exempirun
OutputExecutable
In/exe
OutputExecutable
In/exe
OutputExecutable
4
4
5
5
Direct Submission Summary
• Pros:– Users can add remote file support to legacy applications
– Works for both sequential and MPI(CH) applications
– For PBS jobmanagers, there is no need to have a shared filesystem (support for other jobmanagers can be added, depends on informations provided by jobmanagers)
– Works in case of jobmanagers, which do not support MPI
– Faster, than submitting with the broker
• Cons:– user needs to specify the execution resource
– currently doesn’t work on non-PBS jobmanagers without shared filesystems
Portal: Brokered job submission
● EGEE Resource Broker is used
• The resource to be used is unknown before job execution
• The user must have a valid, accepted certificate
• Local files are supported
• Remote files residing on Storage Elements are supported, even in case of grid-unaware applications
• Jobs may be sequential or MPI applications
Broker exec: step-by-step I.
1. Pre script:• creates the Scheduler universe Condor submit file
1. Scheduler Universe Condor job:• the job is a shell script
• the script is responsible for:• job submission: a wrapper script (wrapperrb) is specified as
the real executable in the JDL file
• job status polling
• job output downloading
Broker exec: step-by-step II.
1. Resource Broker:• handles requests of the Scheduler universe Condor job
• sends the job to a CE
• watches its exeution
• reports errors
• …
2. LRMS on CE:• allocates the requested number of nodes
• starts wrapperrb on the master worker node using
‘mpirun’
Broker exec: step-by-step III.
1. Wrapperrb:• the script is started by ‘mpirun’, so this script starts on every
allocated worker node like an MPICH process
• checks if remote input files are already present. If not, they are downloaded from the storage element
• if the user specified any remote output files, they are removed from the storage
• the real executable is started with the arguments passed to the script. These arguments already contain MPICH-specific ones
• after the executable has been finished, remote output files are uploaded to the storage element (only in case of gLite)
2. Post script:• nothing special…
Broker execution
Portal Machine
Resource Broker
Front-end node
Globus
PBS
Master WN
…mpirun
wrapperrb
Real exe
Slave WN1
wrapperrb
Real exe
Slave WNn-1
wrapperrb
Real exe
StorageElement
2
3
4
5
5
5
Broker Submission Summary
• Pros:– adds support for remote file handling in case of legacy
applications
– extends the functionality of the EGEE broker
– one solution supports both sequential and MPI applications
• Cons:– slow application execution
– status polling generates high load with 500+ jobs
Experimental results
• Tested some selected SEEGRID CEs using the broker from command line and the direct job submission from P-GRADE Portal with a job requesting 3 nodes
OKFailed (exe not found)grid2.cs.bilkent.edu.tr
OKFailedgrid01.rcub.bg.ac.yu (?)
OKFailedcluster1.csk.kg.ac.yu
OKOKce02.grid.acad.bg
Failed (job held)OKce01.isabella.grnet.gr
OKScheduledce.ulakbim.gov.tr
OKFailed (exe not found)ce.phy.bg.ac.yu
Portal Direct ResultBroker ResultCE Name
Thank you for your attention
?