Speeding up large calculations

Question:

Why does my script run so slowly?  How might I improve the speed of the calculations?

Explanation:

SET MODE DIAGNOSTIC lets you see where resources are being used. Memory use can be adjusted, and using explicitly defined regions may allow Ferret to able to take advantage of reusing cached results.

Solution:

Here's how you figure out where Ferret is spending its time during a large calculation:

yes? SET MODE DIAGNOSTIC

On the commands that follow this Ferret will list diagnostic information describing its internal actions. A fragment of the output with explanation is listed below. Try the following:

Watch for messages about "gathering". These indicate that Ferret felt the calculation was too large to fit into memory and it has broken the calculation into slices. This can slow down the IO considerably (but the calculation does get finished without any intervention.) You can influence how Ferret makes its decision to use gathering -- see section SET MODE DESPERATE, in the Ferret Users Guide, http://ferret.pmel.noaa.gov/Ferret/Documentation/Users_Guide/current/fer_html.htm
Use SET MEMORY/SIZE=<value> to allocate large memory. (see SET MEMORY in the Users Guide.) In conjunction with the information in the Users Guide on MODE DESPERATE this can greatly enhance performance by fully utilizing the physical memory of your system.
For maximum performance be explicit in telling Ferret the region of interest (i.e. don't leave the limits of axes unspecified to imply the full domain). When limits are not explicit Ferret misses opportunities for reusing cached results -- slower processing and potentially more memory needed due to fragmentation may result.

Explicit limits are especially important when you see "gathering" (above). Watch the diagnostic output to see if Ferret is re-reading the same data. If so, consider using LOAD (and LOAD/PERMANENT) to read file variables into memory prior to requesting a result. This is especially useful when calculations involve derivatives and shift operators. For example, using MY_VAR[I=101:110] and MY_VAR[I=101:110@SHF:2] in the same calculation may require two separate reading operations; pre-reading with LOAD MY_VAR[I=101:112] will cache a single block of data big enough for both.

Example:

Here's a fragment of MODE DIAGNOSTIC output and some explanation:

yes? SET MODE DIAGNOSTIC
yes? LOAD SST[l=1:400@AVE]
getgrid EX#1   5 D: 2 I:    1    1 J:    1    1 K:    1    1 L:    1    1
eval    EX#1   4 D: 2 I: -111 -111 J: -111 -111 K: -111 -111 L: -111 -111
strip gathering SST on Y axis:     1    90
strip -->; SST[T=01-JAN-1946:01-MAY-1979@AVE,D=2]
reading SST    3 D: 2 I:    1 180 J:    1    4 K: -111 -111 L:    1 400
doing -->; SST[T=01-JAN-1946:01-MAY-1979@AVE,D=2]
doing gathering SST on Y axis:     1     4

Explanation:

D: 2 tells us that the operations are from data set #2
the getgrid pass determines the grid of the result
eval EX#1 is the start of evaluation for the first expression (there may be multiple comma-separated expressions)
- I: -111 -111 means that the limits on the I (X) axis are IMPLIED (unknown). Explicit limits may improve performance and memory management.
strip means that Ferret has detected the need for an operation and allocated space for it on a stack.
strip gathering SST on Y axis means this calculation is being broken into slices along the Y axis (to fit into memory)
reading SST ... means IO is in progress. The I,J,K,L limits are shown. You may see delays during large IO operations.
doing tells us the operation that was "stripped" above is being done
gathering SST on Y axis: 1 4 tells us that the J=1:4 slice of the calculation has been completed. J=5:8 will probably follow.

Last modified: Tue June 5 2001 [an error occurred while processing this directive]