Parallel Checkpointing - Sathish Vadhiyar. Introduction Checkpointing? storing application’s state in order to resume later.

Parallel Checkpointing

- Sathish Vadhiyar

Introduction

Checkpointing? storing application’s state in

order to resume later

Motivation The largest parallel systems in the world

have from 130,000 to 213,000 parallel processing elements. (http://www.top500.org)

Large-scale applications, that can use these large number of processes, are continuously being built.

These applications are also long-running As the number of processing elements,

increase the Mean Time Between Failure (MTBF) decreases

So, how can long-running applications execute in this highly failure-prone environment? – checkpointing and fault-tolerance

Uses of Checkpointing

Fault tolerance & rollback recovery

Process migration & job swapping

Debugging

Types of Checkpointing OS-level

Process preemption E.g. Berkeley’s checkpointing Linux

User-level Transparent Checkpointing performed by the program itself Transparency achieved by linking application

with a special library e.g. Plank’s libckpt

User-level non-transparent Users insert checkpointing calls in their

programs e.g. SRS (Vadhiyar)

Rules for Consistent Checkpointing In a parallel program,

each process has events and local state An event changes

the local state of a process

Global state – an external view of the parallel application (e.g. lines S, S’, S’’) – used for checkpointing and restarting Consists of local

states and messages in transit

Rules for Consistent Checkpointing

Types of global states Consistent global state – from

where program can be restarted correctly

Inconsistent - Otherwise

Rules for Consistent Checkpointing

Chandy & Lamport – 2 rules for consistent global states 1. if a receive event is part of local state of a process,

the corresponding send event must be part of the local state of the sender.

2. if a send event is part of the local state of a process and the matching receive is not part of the local state of the receiver, then the message must be part of the state of the network.

S’’ violates rule 1. Hence cannot lead to consistent global state

Independent checkpointing

Processors checkpoint periodically without coordination

Can lead to domino effect – each rollback of a processor to a previous checkpoint forces another processor to rollback even further

Checkpointing Methods

1. Coordinated checkpointing

1. All processes coordinate to take a consistent checkpoint (e.g. using a barrier)

2. Will always lead to consistent checkpoints

2. Checkpointing with message logging

1. Independent checkpoints are taken by processes and a process logs the messages it receives after the last checkpoint

2. Thus recovery is by previous checkpoint and the logged messages.

Message Logging

Introduction In message-logging protocols, each process

stores message contents and sequence number

of all messages it has sent or received into a message log

To trim message logs, a process can also periodically checkpoint

Once a process checkpoints, all messages sent/received before this checkpoint can be removed from log

Pessimistic and Optimistic Message Logging

Pessimistic – A sender does not send a message m until it knows all messages sent before m are logged Waits for logging to complete; hence

overhead in communications during no failures

But failure recovery is fast on the occurrence of a failure

Pessimistic and Optimistic Message Logging

Optimistic – assumes messages are logged Does not wait for logs to complete to send a

message, m Hence on failure, the earlier logged messages

will be sent; message m will not be sent – leads to inconsistent states

Hence failure recovery is complex – need to trace back and carefully reconstruct application states

But minimal overhead when no failures

Message Logging – Sender or Receiver Based Can be sender or receiver based Receiver based (e.g. MPICH-V) – message logs

stored at the receiver side Each process has an associated channel

memory (CM) called home CM When P1 wants to send messages to P2, it

contacts P2’s home CM and sends message to it.

P2 retrieves message from its home CM. During checkpoint, the process state is stored

to a checkpoint server (CS) When P2 crashes, during restart, P2 retrieves

checkpoints from CS and messages from CM.

Sender-based (e.g. MPICH-V2) Sender based logging to avoid channel

memories When p sends message m to q, p logs m. m is associated with an id When q receives m, it stores (id, l) where l

is the logical clock. When q crashes and restarts from a

checkpoint state, retrieves (id, l) sets from storage and asks other processes to resend from the sets.

Coordinated Checkpointing

Coordinated Checkpointing

During checkpointing, all processes coordinate by means of a barrier and then checkpoint the respective data

This way, all are consistent checkpoints; messages are cleared at the time of checkpoints;

During recovery, all processes rollback to the respective consistent state (coordinated)

No need to replay messages

Coordinated Checkpointing

Example: Start Restart System (SRS) A user-level non-transparent checkpointing

library User inserts checkpointing calls specifying

data to be checkpointed Advantage: Small amount of checkpointed

data Disadvantage: User burden Allows reconfiguration of applications. Reconfiguration of number of processors and /

or data distribution.

SRS Example – Original Code MPI_Init(&argc, &argv); local_size = global_size/size;

if(rank == 0){ for(i=0; i<global_size; i++){ global_A[i] = i; } }

MPI_Scatter (global_A, local_size, MPI_INT, local_A, local_size, MPI_INT, 0, comm); iter_start = 0; for(i=iter_start; i<global_size; i++){ proc_number = i/local_size; local_index = i%local_size; if(rank == proc_number){ local_A[local_index] += 10; } } MPI_Finalize();

SRS Example – Modified Code

MPI_Init(&argc, &argv); SRS_Init(); local_size = global_size/size; restart_value = SRS_Restart_Value();

if(restart_value == 0){ if(rank == 0){ for(i=0; i<global_size; i++){ global_A[i] = i; } } MPI_Scatter (global_A, local_size, MPI_INT, local_A, local_size, MPI_INT, 0, comm); iter_start = 0; } else{ SRS_Read(“A”, local_A, BLOCK, NULL); SRS_Read(“iterator”, &iter_start, SAME, NULL); } SRS_Register(“A”, local_A, GRADS_INT, local_size, BLOCK, NULL); SRS_Register(“iterator”, &I, GRADS_INT, 1, 0, NULL);

SRS Example – Modified Code (Contd..)

for(i=iter_start; i<global_size; i++){ stop_value = SRS_Check_Stop(); if(stop_value == 1){ MPI_Finalize(); exit(0); } proc_number = i/local_size; local_index = i%local_size; if(rank == proc_number){ local_A[local_index] += 10; } }

SRS_Finish(); MPI_Finalize();

Checkpointing Performance Checkpoint overhead – time added to the

running time of the application due to checkpointing

Checkpoint latency hiding Checkpoint buffering – during checkpointing,

copy data to local buffer, store buffer to disk in parallel with application progress

Copy-on-write buffering – only the modified pages are copied to a buffer. Other pages can be directly stored without copying to buffer. Can be implemented using fork() – forked checkpointing

Checkpointing Performance

Reducing checkpoint size – memory exclusion and checkpoint compression

Memory exclusion – no need to store dead and read-only variables A dead variable is one whose current value

will not be used by the program; The variable will not be accessed again by the program or it will be overwritten before it is read

Read only variable – whose value has not changed since the previous checkpoint

Incremental Checkpointing

Memory exclusion can be made automatic by using incremental checkpointing Store only that part of data that have been

modified from the previous checkpoint Following a checkpoint, all pages in memory

are set to read-only When the program attempts to write a page,

an access violation occurs During next checkpoint, only pages that have

caused access violations are checkpointed

Checkpointing performance – using compression

Using a standard compression algorithm

This is beneficial only if the extra processing time for compression is lower than the savings that result from writing a smaller file to disk

Redundancy/replication + checkpointing for fault tolerance

Replication Every node/process N has a shadow

node/process N’, so that if one of them fail, the other can still continue the application – failure of the primary node no longer stalls the application

Redundancy scales: As more nodes are added to the system, the probability of failure of both a node and its shadow rapidly decreases Only one of the remaining n-1 nodes represent a

shadow node

Replication

Less overhead for checkpointing Higher checkpointing interval/period for

periodic checkpointing Recomputation and restart overheads

are nearly eliminated

Still need checkpointing: Why?

Total Redundancy

Partial Redundancy

Replication vs No Replication

References James S. Plank,

``An Overview of Checkpointing in Uniprocessor and Distributed Systems, Focusing on Implementation and Performance'', University of Tennessee Technical Report CS-97-372, July, 1997

James Plank and Thomason. Processor Allocation and Checkpointing Interval Selection in Cluster Computing Systems. JPDC 2001.

References MPICH-V: Toward a Scalable Fault Tolerant

MPI for Volatile Nodes -- George Bosilca, Aurélien Bouteiller, Franck Cappello, Samir Djilali, Gilles Fédak, Cécile Germain, Thomas Hérault, Pierre Lemarinier, Oleg Lodygensky, Frédéric Magniette, Vincent Néri, Anton Selikhov -- SuperComputing 2002, Baltimore USA, November 2002

MPICH-V2: a Fault Tolerant MPI for Volatile Nodes based on the Pessimistic Sender Based Message Logging -- Aurélien Bouteiller, Franck Cappello, Thomas Hérault, Géraud Krawezik, Pierre Lemarinier, Frédéric Magniette -- To appear in SuperComputing 2003, Phoenix USA, November 2003

References Vadhiyar, S. and Dongarra, J. “SRS - A

Framework for Developing Malleable and Migratable Parallel Applications for Distributed Systems”. Parallel Processing Letters, Vol. 13, number 2, pp. 291-312, June 2003.

References

Schulz et al. Implementation and Evaluation of a Scalable Application-level Checkpoint-Recovery Scheme for MPI Programs. SC 2004.

References for Replication

Evaluating the viability of process replication reliability for exascale systems. SC 2011.

Combining Partial Redundancy and Checkpointing for HPC. ICDCS 2012