ZOID

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Introduction

ZOID is an I/O forwarding component of the ZeptoOS project. Any communication between the compute nodes and I/O nodes (job management, file I/O, sockets) is facilitated by ZOID.

ZOID infrastructure consists of:

• Multithreaded zoid daemon on the I/O nodes which performs I/O forwarding for the compute nodes and which also communicates with the service node to perform job management,
• control daemon on the compute nodes which is responsible for job management tasks such as launching application processes, for the forwarding of stdin/out/err data, and for forwarding of IP packets,
• zoid-fuse daemon on the compute nodes which performs file I/O forwarding for POSIX-compliant applications.

User interface

User script

Right before a job starts running, and right after the last process of a job has terminated, ZOID daemon attempts to invoke a user script on I/O nodes. By default, the daemon invokes $HOME/zoid-user-script.sh (this pathname can be changed by an administrator). A single parameter is passed to the script: 1 at the job startup, and 0 at the termination.

Information about the job will be passed to the script in the following environment variables:

ZOID_JOB_EXEC

name of the job executable,

ZOID_JOB_ARGS

job arguments, separated by a :

ZOID_JOB_ENV

job environment variables, separated by a :

ZOID_JOB_ID

BG/P control system job id (Note: this is generally different from the Cobalt job ID; see FAQ for the latter),

ZOID_JOB_GLOBAL_SIZE

number of processes in the job (size of MPI_COMM_WORLD),

ZOID_JOB_LOCAL_SIZE

number of job processes handled by this I/O node,

ZOID_JOB_MODE

0 for SMP, 1 for VN, and 2 for DUAL,

SHELL, PATH, USER, and HOME

will also be set...

Note: the user script is invoked synchronously by the daemon, i.e., the job will not start running until the script terminates. If you need processes to run on I/O nodes while the job is running, start them in the background (&).

File broadcast

A /bin.rd/f2cn command is available on the I/O nodes for a very efficient (hardware-assisted) broadcasting of files to all the compute nodes handled by the given I/O node.

The command takes two arguments:

• absolute pathname to the input file on the I/O node,
• absolute pathname to the output file on the compute nodes.

The input file does not need to be physically on the I/O node; it can be on a network filesystem mounted on the node. The file will be created in the ramdisk of each compute node.

The throughput is in practice limited by how fast the input file can be read; we have seen results in excess of 300 MB/s for files residing in the I/O node ramdisk.

Note: all the compute nodes in the pset must be up and running. Do not use this command on incomplete partitions (e.g., a one-process job on a 64-node partition); you will likely hang the ZOID daemon if you try.

Note2: this feature can safely be used from within a user script, so one can, e.g., pre-stage large binaries, like this:

User script ($HOME/zoid-user-script.sh):

#!/bin/sh

if [ "$1" -eq "1" ]; then
    /bin.rd/f2cn $HOME/large_binary /tmp/large_binary
fi
exit 0

Job script (submitted using Cobalt or mpirun):

#!/bin/sh

chmod 755 /tmp/large_binary
/tmp/large_binary

Performance counters

A /bin.rd/statquery command is available on the I/O nodes for obtaining the performance counters of the I/O daemon.

The command takes a single optional argument:

• the interval between successive queries, in seconds.

If the argument is not provided, the command will terminate after the first query.

Here is the sample output generated:

Timestamp:                      1240439085.688831
Total messages sent:            5767
Total bytes sent:               7619170
Total messages received:        5717
Total bytes received:           72575
IP fwd messages sent:           196
IP fwd bytes sent:              5889
IP fwd messages received:       84
IP fwd bytes received:          6453
Stream messages sent:           65
Stream bytes sent:              520
Stream messages received:       65
Stream bytes received:          1416
Broadcast messages sent:        1
Broadcast bytes sent:           2437906
Internal messages sent:         193
Internal bytes sent:            39524
Internal messages received:     256
Internal bytes received:        1792
Plugin 5 messages sent:         0
Plugin 5 bytes sent:            0
Plugin 5 messages received:     0
Plugin 5 bytes received:        0
Plugin 2 messages sent:         5312
Plugin 2 bytes sent:            5135331
Plugin 2 messages received:     5312
Plugin 2 bytes received:        62914

The meaning of the fields is as follows:

Timestamp

number of seconds and microseconds from the epoch, as returned by gettimeofday(2),

IP fwd

IP packet forwarding between compute nodes and I/O nodes

Stream

stdin/out/err streams,

Broadcast

file broadcasts

Internal

job control messages, etc.

Plugin 5

internal mapping plugin, used by MPI

Plugin 2

unix plugin (POSIX file I/O)

The counters are 64-bit integers, so they will take a while to overflow :-).

Example user script ($HOME/zoid-user-script.sh) that samples the statistics every 60 seconds and writes them to a unique file:

#!/bin/sh

if [ "$1" -eq "1" ]; then
    /bin.rd/statquery 60 >$HOME/zoid_stats.$ZOID_JOB_ID.`hostname` &
fi
exit 0

Administrator interface

The zoid I/O daemon accepts a number of command-line options that can be used to change its behavior. They can be adjusted by editing the ramdisk/ION/ramdisk-add/etc/sysconfig/zoid file and rebuilding the I/O node ramdisk:

ZOID_BUFFER_SIZE (-b)

Specifies the size of the buffers used for messages. Because a separate buffer is needed for a request and a reply, and typically no more than one of these needs to be large, to save memory ZOID supports buffers of two sizes: a small one (4 KB by default) and a large one (4 MB+1 KB by default – the 1 KB is there to accommodate the headers). Use colon (:) to separate the two sizes when customizing this value. If desired, support for two separate buffer sizes can be disabled by providing only one value to this option.

ZOID_ACK_THRESHOLD (-a)

Specifies a size threshold for the rendezvous protocol for messages coming from the compute nodes, in the units of tree network packets (240 bytes each). An eager protocol is used for messages below the threshold. Messages above the threshold use flow control in the form of a rendezvous protocol with message acknowledgements; basically, the daemon will only receive one large message at a time, which improves the predictability and an overall throughput. The daemon default for this option is to not use acknowledgements, but the config file defaults to a value of 8, which is the size of the hardware FIFO buffer of the tree network device. Set this option to 0 (or comment it out altogether) to disable message acknowledgements.

ZOID_MODULES (-m)

Specifies a :-separated list of ZOID plugins to load. This defaults to "unix_impl.so:unix_preload.so:mapping_impl.so:mapping_preload.so" in the config file; do not remove any of these or basic system services will stop working. The unix plugin provide POSIX file I/O support, while mapping is used by our MPI implementation to map between MPI ranks and Blue Gene X/Y/Z/T coordinates. Custom plugins can be created and added here; see Programmer interface for details.

ZOID_ENABLE_NAT (-n)

Enables network address translatation (NAT) for IP packets coming from the compute nodes, allowing compute nodes to communicate with the outside world. This support is disabled by default because we have found that it has a detrimental effect to the overall performance of the TCP/IP stack on the I/O nodes, slowing down network filesystems. This feature can also be enabled on per-job basis by setting the ZOID_ENABLE_NAT environment variable when submitting a job (see the FAQ).

ZOID_USER_SCRIPT (-u)

Specifies the pathname to the user script; it defaults to "/bin.rd/zoid-user-script.sh". This script can be found in ramdisk/ION/ramdisk-add/bin/zoid-user-script.sh; it sets a few environment variables and then invokes user's custom $HOME/zoid-user-script.sh. Hence, if you want to adjust the behavior of this option, you can either change this option or the script in the ramdisk.

Programmer interface

ZOID is a flexible, extensible, high-performance function call forwarding (RPC) infrastructure. Built-in features and the standard plug-ins provide familiar POSIX file I/O and BSD socket interfaces, but, because of the number of software layers involved, they introduce a significant overhead. For applications requiring maximum bandwidth between the compute and I/O nodes, ZOID provides an option of a customized function call forwarding with minimal overheads. This section provides an overview of how to create such a custom plug-in.

Overview

All that ZOID provides is a function call forwarding support, and a limited one at that. Any logic (caching, prefetching, etc.) needs to be custom-built on top of it.

Follow existing plug-ins, found in packages/zoid/src/, as examples. The unix plug-in is generally the most up to date, but other plug-ins such as mapping, zoidfs, and barrier should also be fine.

A plug-in consists of automatically generated client-side and server-side stubs (which perform the marshalling and demarshalling of function call parameters and results, the forwarding of the function call, etc.), and of a hand-written server-side implementation which provides the implementation code for the forwarded function calls. One might also decide to provide hand-written client-side wrappers to hide some details of the ZOID API (such as the error handling) or to adhere to a particular existing API, as is the case with the unix plug-in (the wrappers used by the FUSE client are available in packages/zoid/src/unix/stubs/; another version is in the GNU libc sources, in packages/glibc/src/zoid/sysdeps/unix/sysv/linux/powerpc/powerpc32/).

To build the automatically-generated stubs, a C-language header file with function prototypes must be provided as an input to the scanner.pl script found in packages/zoid/src/. That script will extract the prototypes and generate the necessary source files. The script expects subdirectories named client and server to exist in the current directory; it will write its output there. Again, please follow the examples from the existing plug-ins, such as unix or mapping. The Makefile in those plug-ins is written in a generic fashion and should only require a change to the PREFIX line to be usable with another plug-in. Use that Makefile to invoke the scanner.pl script and to compile the generated source files.

Input header file

The input header file must follow strict guidelines, documented below. Essentially, the script needs help in the form of C-language comments to guide it.

Each plug-in needs a unique 16-bit identifier. Currently used numbers are 1 (zoidfs plug-in), 2 (unix), 3 (lofar), 4 (test), 5 (mapping), and 10 (ftb). Just use a small, unique, non-zero integer.

Server-side API

The hand-written server-side implementation code needs to define all the functions listed in the header file. It should be compiled as a shared library; use the implementation/ subdirectory of the unix plug-in as an example. Please note that since ZOID is multi-threaded, multiple functions can be invoked at the same time, so you must ensure that your implementation is multi-thread-safe.

Server-side stubs and the server-side implementation need to be passed as modules when invoking the ZOID I/O daemon, as described earlier.

Client-side API

In order to use the new interface, a compute node application will need to be linked with the client-side stubs and with a common support library libzoid_cn.a (a prebuilt version of the latter is in packages/zoid/prebuilt; sources are in packages/zoid/src/cnl/client).

Additional considerations

Zerocopy

Zerocopy with custom input buffer

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