Parallel I/O Issues

This file describes some extensions to GENESIS objects (xview) and modified objects (par_asc_file and par_disk_out) that are used for output of data in parallel GENESIS.

xview extensions

Parallel simulations can often benefit from visualizations with XODUS during development, and often will require large input and/or output files in full scale production runs. However, modelers should be aware that the way these I/O issues are dealt with can have a considerable impact on performance.

PGENESIS includes a capability to allow multiple nodes to display on the same XODUS widget so that, for example, a single xview element can be used to show activation of all the cells in a distributed V1 layer. In serial GENESIS there are several ways to set up input to an xview element, described in "The Book of GENESIS" chapter on Advanced XODUS Techniques and in the documentation for xview in the GENESIS Reference Manual. However, the one we must use for internode communication in PGENESIS is to set up remote messages from a source element to a destination xview element. This is done by using the PGENESIS raddmsg command. (See Doc/refman.txt.)

If every node were to set up COORDS and VAL n messages independently, the VAL messages could easily get associated with the wrong COORDS messages, depending on the order in which the particular add message requests were handled. To deal with this difficulty, the GENESIS xview object has been extended to allow IVAL n messages to be associated with a particular ICOORDS message. The user does this by choosing an integral index with each message that is set up, and passing it as the first parameter of the ICOORDS and IVALn messages. IVAL1 through IVAL5 messages will be associated with ICOORDS messages having the same index. For an example of this, see the example script Scripts/orient2/V1.g in the PGENESIS distribution and the serial GENESIS documentation for xview.

Output to files

PGENESIS also includes a capability for writing a single disk file from multiple nodes. For disk output in serial GENESIS, it is typical to create an asc_file element and then set up a SAVE message that will cause a value to be written to a file on every time step. In PGENESIS it is possible to add such messages from elements on various nodes. However, there is no guarantee of order for the normal asc_file object, so in PGENESIS the par_asc_file object is provided. When SAVE messages are set up, the first parameter is an integral index that is used to maintain a fixed ordering among all of the various incoming messages to the par_asc_file element. This integral index should be unique and in the range from 0 to the number of incoming messages minus 1, inclusive.

Serial GENESIS uses the disk_out object for writing array data to a file in an efficient binary format. We have similarly provided a corresponding par_disk_out object that takes an added integral index parameter. The scripts output.g and V1.g in the Scripts/orient2 directory of the PGENESIS distribution illustrate the use of this object.

This example shows how raddmsg is used to send a "SAVE index data" message from the source element to the destination par_asc_file or par_disk_out element. The index is an added field of the source object that can be any variable with a unique integer value. The integral index simply provides an ordering for the messages, so that if many messages are being sent in parallel, there will be a deterministic order to them when they written to a file (in the case of par_asc_file or par_disk_out) or displayed (in the case of an xview object). Also see the serial GENESIS documentation for asc_file and disk_out.

Both of these extensions for I/O support require that information flow in the form of PGENESIS messages from the source node to the destination node (which holds the xview, par_asc_file, or par_disk_out element). If you are doing very large amounts of I/O from many nodes, the destination node would likely become a simulation bottleneck. In those situations, it would likely be advantageous to consider a solution where each node was doing its I/O to and from files on the local disk, rather than using the above mechanisms.