a look at pvfs, a parallel file system for linux

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A Look at PVFS, a A Look at PVFS, a Parallel File System for Parallel File System for

LinuxLinux

Talk originally given byTalk originally given by

Will Arensman and Anila PillaiWill Arensman and Anila Pillai

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OverviewOverview

Network File Systems (NFS)Network File Systems (NFS) Drawbacks of NFSDrawbacks of NFS Parallel Virtual File Systems (PVFS)Parallel Virtual File Systems (PVFS) Using PVFSUsing PVFS ConclusionConclusion ReferencesReferences

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1. Network File System (NFS)1. Network File System (NFS) NFS is a client/server application developed by Sun Microsystems It lets a user view, store and update files on a remote computer as

though the files were on the user's local machine. The basic function of the NFS server is to allow its file systems to be

accessed by any computer on an IP network. NFS clients access the server files by mounting the servers exported

file systems.

For example:For example:

/home/ann server1:/export/home/ann/home/ann server1:/export/home/ann

Your view

where the files really are

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Having all your data stored in a central location presents a number of problems:

Scalability:Scalability: arises when the number of computing nodes exceeds the performance capacity of the machine exporting the file system; could add more memory, processing power and network interfaces at the NFS server, but you will soon run out of CPU, memory and PCI slots; the higher the node count, the less bandwidth (file I/O) individual node processes end up with

Availability:Availability: if NFS server goes down all the processing nodes have to wait until the server comes back into life.

Solution:Solution: Parallel Virtual File System (PVFS)

2. Drawbacks of NFS2. Drawbacks of NFS

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Parallel Virtual File System (PVFS) is an open source implementation of a parallel file system developed specifically for Beowulf class parallel computers and Linux operating system

It is joint project between Clemson University and Argonne National Laboratory

PVFS has been released and supported under a GPL license since 1998

3. Parallel Virtual File System(PVFS)3. Parallel Virtual File System(PVFS)

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File System – allows users to store and retrieve data using common file access methods (open, close, read, write)

Parallel – stores data on multiple independent machines with separate network connections

Virtual – exists as a set of user-space daemons storing data on local file systems

3. Parallel Virtual File System(PVFS)3. Parallel Virtual File System(PVFS)

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Instead of having one server exporting a file via NFS, you have N servers exporting portions of a file to parallel application tasks running on multiple processing nodes over an existing network

The aggregate bandwidth exceeds that of a single machine exporting the same file to all processing nodes.

This works much the same way as RAID 0 – file data is striped across all I/O nodes.

PVFS… PVFS…

1 2 3 4 5 6

1

7 8 9 10

2 3 4 5 6 7 8 9 10

Data blocks

RAID 0 (Stripping)

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PVFS provides the following features in one package:

allows existing binaries to operate on PVFS files without the need for recompiling

enables user-controlled striping of data across disks on the I/O nodes

robust and scalable

provides high bandwidth for concurrent read/write operations from multiple processes to a common file

PVFS…PVFS…

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PVFS provides the following features in one package:

ease of installation

easily used - provides a cluster wide consistent name space,

PVFS file systems may be mounted on all nodes in the same directory simultaneously, allowing all nodes to see and access all files on the PVFS file system through the same directory scheme.

Once mounted PVFS files and directories can be operated on with all the familiar tools, such as ls, cp, and rm.

PVFS…PVFS…

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Roles of nodes in PVFS:

1. COMPUTE NODES - on which applications are run,

2. MANAGEMENT NODE - which handles metadata operations

3. I/O NODES - which store file data for PVFS file systems.

Note:- nodes may perform more than one role

PVFS Design and ImplementationPVFS Design and Implementation

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In order to provide high-performance access to data stored on the file system by many clients, PVFS spreads data out across multiple cluster nodes I/O nodes

By spreading data across multiple I/O nodes, applications have multiple paths to data through the network and multiple disks on which data is stored.

This eliminates single bottlenecks in the I/O path and thus increases the total potential bandwidth for multiple clients, or aggregate bandwidth.

PVFS I/O NodesPVFS I/O Nodes

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PVFS System ArchitecturePVFS System Architecture

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There are four major components to the PVFS software system:

1. Metadata server (mgr)

2. I/O server (iod)

3. PVFS native API (libpvfs)

4. PVFS Linux kernel support

The first two components are daemons (server types) which run on nodes in the cluster

PVFS Software ComponentsPVFS Software Components

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1. The metadata server (or mgr)

File manager; it manages metadata for PVFS files.

A single manager daemon is responsible for the storage of and access to all the metadata in the PVFS file system

Metadata - information describing the characteristics of a file, such as permissions, the owner and group, and, more important, the physical distribution of the file data

PVFS ComponentsPVFS Components

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Data in a file is striped across a set of I/O nodes in order to facilitate parallel access.

The specifics of a given file distribution are described with three metadata parameters:

base I/O node number

number of I/O nodes

stripe size

These parameters, together with an ordering of the I/O nodes for the file system, allow the file distribution to be completely specified

PVFS Version 1 I/O Node ConfigurationPVFS Version 1 I/O Node Configuration

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Example:

pcountpcount - field specifies that the the number of I/O nodes used for storing data

basebase - specifies that the first (or base) I/O node (is node 2 here)

ssizessize - specifies that the stripe size--the unit by which the file is divided among the I/O nodes—here it is 64 Kbytes

The user can set these parameters when the file is created, or PVFS will use a default set of values


inodeinode 10921575041092157504

basebase 22

pcountpcount 33

ssizessize 6553665536

Meta data example for file

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PVFS ComponentsPVFS ComponentsPVFS file striping done in a round-robin fashion

Though there are six I/O nodes in this example, the file is striped across only three I/O nodes, starting from node 2, because the metadata file specifies such a striping.

Each I/O daemon stores its portion of the PVFS file in a file on the local file system on the I/O node.

The name of this file is based on the inode number that the manager assigned to the PVFS file (in our example, 1092157504).

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2.0 The I/O server (or iod) It handles storing and retrieving file data stored on local disks

connected to the node.

when application processes (clients) open a PVFS file, the PVFS manager informs them of the locations of the I/O daemons

the clients then establish connections with the I/O daemons directly

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the daemons determine when a client wishes to access file data, the client library sends a descriptor of the file region being accessed to the I/O daemons holding data in the region

what portions of the requested region they have locally and perform the necessary I/O and data transfers.

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It provides user-space access to the PVFS servers

This library handles the scatter/gather operations necessary to move data between user buffers and PVFS servers, keeping these operations transparent to the user

For metadata operations, applications communicate through the library with the metadata server


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For data access the metadata server is eliminated from the access path and instead I/O servers are contacted directly

This is key to providing scalable aggregate performance

The figure shows data flow in the PVFS system for metadata operations and data access


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For metadata operations applications communicate through the library with the metadata server

Metadata access

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Metadata server is eliminated from the access path; instead I/O servers are contacted directly; libpvfs reconstructs file data from pieces received from iods

Data access

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The PVFS Linux kernel support provides the functionality necessary to mount PVFS file systems on Linux nodes

This allows existing programs to access PVFS files without any modification

This support is not necessary for PVFS use by applications, but it provides an extremely convenient means for interacting with the system


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The PVFS Linux kernel support includes:

a loadable module

an optional kernel patch to eliminate a memory copy

a daemon (pvfsd) that accesses the PVFS file system on

behalf of applications

It uses functions from libpvfs to perform these operations.


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The figure shows data flow through the kernel when the Linux kernel support is used

Operations are passed through system calls to the Linux VFS layer. Here they are queued for service by the pvfsd, which receives operations from the kernel through a device file

It then communicates with the PVFS servers and returns data through the kernel to the application


app

/dev/pvfsdVFS

pvfsd

to PVFS servers

user space

kernel space

Data flow through kernelData flow through kernel

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Applications on client nodes can access PVFS data on I/O nodes using one of the three methods:

Linux kernel interface:-

The Linux kernel VFS Module provides the functionality for adding new file-system support via loadable modules without recompiling the kernel. These modules allow PVFS file systems to be mounted in a manner similar to NFS. Once mounted, the PVFS file system can be traversed and accessed with existing binaries just as any other file system. .

PVFS Application InterfacesPVFS Application Interfaces

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Applications on client nodes can access PVFS data on I/O nodes using one of the three methods:

PVFS native API:-

The PVFS native API provides a UNIX-like interface for accessing PVFS files. It also allows users to specify how files will be striped across the I/O nodes in the PVFS system.


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ROMIO MPI-IO interface:-

ROMIO implements the MPI2 I/O calls in a portable library. This allows parallel programmers using MPI to access PVFS files through the MPI-IO interface


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5. Using PVFS 5. Using PVFS

1. Download, untar pvfs, pvfs-kernel files.Available at:http://parlweb.parl.clemson.edu/pvfs/

2. Go to PVFS directory: ./configure, make, make install make install on each node

3. Go to PVFS kernel directory: ./configure –with-libpvfs-dir=../pvfs/lib make, make install cp pvfs.o /lib/modules/<kernel-version>/misc/ make install, cp pvfs.o on each node

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PVFS InstallationPVFS Installation

Metadata server needs:

1. mgr executable

2. .iodtab file: contains IP addresses and ports of I/O daemons

3. .pvfsdir file: permissions of the directory where metadata is stored

Run mkmgrconf to create .iodtab and .pvfsdir

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I/O server needs iod executable iod.conf file: describes the location of the pvfs data

directory on the machine Each client needs

pvfsd executable pvfs.o kernel module /dev/pvfsd device file mount.pvfs executable mount point


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After installation

1. Start iod’s

2. Start mgr

3. Run pvfs-mount


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PVFS APIPVFS API

1. Initialize a pvfs_filestat struct:struct pvfs_filestat {

int base; /* First node. -1 = default = 0 */

int pcount; /* # I/O Nodes. default = all*/

int ssize; /* Stripe size. default = 64K */

int soff; /* Not used. */

int bsize; /* Not used. */

}

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2. Open the file:pvfs_open(char *pathname, int flag,

mode_t mode, struct pvfs_filestat *dist);

3. Have a look at your metadata:pvfs_iocctl(int fd, GETMETA,

struct pvfs_filestat *dist);

PVFS APIPVFS API

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PVFS Utilities

Copy files to PVFS:u2p –s <ssize> -b <base> -n <#nodes> <src> <dest>

Examine file distribution:pvstat <file>

<file>: base = 0, pcount = 8, ssize = 65536

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PVFS at U of A

Hawk Gigabit Ethernet (100Mbps) 4 nodes, each with local drives

Raven Myrinet (~160 MB per second) 7 40 GB Drives (~60 MB per second)

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7. Conclusions7. Conclusions

Pros: Higher cluster performance than NFS. Many hard drives to act a one large hard drive. Works with current software. Best when reading/writing large amounts of data

Cons: Multiple points of failure. Poor performance when using kernel module. Not as good for “interactive” work.

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8. References8. References1. The Parallel Virtual File System, Available at:

http://www.parl.clemson.edu/pvfs/

2. P. H. Carns, W. B. Ligon III, R. B. Ross, and R. Thakur, ``PVFS: A Parallel File System For Linux Clusters'', Proceedings of the 4th Annual Linux Showcase and Conference, Atlanta, GA, October 2000, pp. 317-327

3. Thomas Sterling, “Beowulf Cluster Computing with Linux”, The MIT Press, 2002

4. W. B. Ligon III and R. B. Ross, ``An Overview of the Parallel Virtual File System'', Proceedings of the 1999 Extreme Linux Workshop, June, 1999.

5. Network File System, Available at: http://www.redhat.com/docs/manuals/linux/RHL-7.2-Manual/ref-guide/ch-nfs.html

6. http://www.linuxuser.co.uk/articles/issue14/lu14-All_you_need_to_know_about-PVFS.pdf

a look at pvfs, a parallel file system for linux

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