... community10.1
Optimizing for the idiosyncrasies in computer environments outside GFDL is left to the researcher. 
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... difficult10.2
As in the Cyber 205 experience. 
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... speed10.3
It is reassuring that the ideas influencing the design of MOM have not significantly altered speed when compared to MOM 1. Early comparisons were carried out using the standard test case resolution of $4^\circ$ by $3^\circ$ and 15 levels. Changes in the external mode of MOM 1 were necessary to assure the same accuracy as in MOM and there were no diagnostics enabled. MOM ranged from 3% slower to 6% faster (depending on size of the memory window) than MOM 1. Minimum memory configuration in MOM was 1% greater than in MOM 1. 
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... questionable10.4
Cases in point were the old I/O manager and time manager modules. 
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... size11.1
The size of the problem is related to the product of the number of grid cells in latitude, longitude, and depth. It is also related to which options are enabled and how many additional passive tracers are used. 
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... memory11.2
The assumption is that memory is a precious resource which is to be conserved. Historically, this has been true and the expectation is that it will continue to be in the future. 
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... levels11.3
At GFDL, the eight processor CRAY YMP had 32MW of central memory which had been upgraded to 64MW within the last year of its lifetime. Solid state disk space was 256MW. 
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... ramdrive11.4
A ramdrive is a portion of memory used as a disk to speed up reading and writing of data. If solid state disk is not available, a ramdrive is a good alternative. 
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... disk11.5
The viability of this depends on disk access speed. Solid State Disk on the CRAY YMP, C90, and T90 is fast enough to allow this to work well. Slower disk access can also work if the reads from disk are buffered by the work involved in updating the slice. In practice this is not difficult to implement as long as the slices are to be accessed in a predetermined way. 
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... possible11.6
In general, two dimensional variables will not collapse into one long vector because operations along the first dimension typically do not include boundary cells i=1 and i=imt. In the k dimension, limits are sometimes a function of i and j. Running indices over boundary cells leads to out of bounds references which is to be discouraged because it leads to programming errors and prevents use of the bounds checking feature on compilers. 
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... indices11.7
Reasons for this ordering are given in Section 11.2. 
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... row11.8
When uni-tasking, since calculations proceed from south to north and the southern most latitude is land, the second order quantity can be set to zero at jrow=1. This may be utilized to reduce the minimum size of the MW to jmw=4 which makes the MW assymetrical. This is no longer allowed because assymetrical MW's lead to complications when multi-tasking. To make the assymetrical MW work when multi-tasking requires extra communication calls and the management of the MW becomes more complicated. For simplicity, the MW is required to be symmetric with the same number of buffer rows to the north and south of the computed rows. The price is 25% more memory for the symmetric MW which buys simplicity and generality. 
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... typically11.9
When option pressure_gradient_average is enabled, the value of $num\_rows\_to\_copy$ must be increased by one. 
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... CRAY11.10
Usually the wait time for rotating disk significantly affects efficiency. The option for using rotating disk is fio. 
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... reduced12.1
In fact, it may increase. However, the focus is changed from cpu time to wall clock time. Wall clock time is the time it takes to get results back. 
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... used12.2
This is necessary otherwise science may become processor dependent. 
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... size12.3
As the number of grid cells increase, the number of iterations must increase to keep the same level of accuracy. 
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... dimensioned12.4
Dimensioned by the full number of grid cells in latitude, longitude, and depth. 
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... number12.5
The important point is to have the same amount of work on each processor. If more work is required on some rows than others, then the number of rows on each processsor should be different. It is assumed here that the same amount of work is on every row and that each processor should get the same number of rows. 
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... depth14.1
Positive vertical velocity at the bottom of a cell points upward in the positive zdirection 
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... dimensional14.2
Referring to three spatial dimensions. 
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... cell)14.3
The j index need only be dimensioned for the size of the memory window. Refer to Chapter 10 for a description of the memory window and Section 14.2 for a description of jrow. 
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... component14.4
n=1 is the zonal and n=2 is the meridional velocity component. Vertical velocity is not a prognostic variable. It is a diagnostic variable defined as an advective velocity at the bottom face of cells. Note that since there are T cells and U cells, there are vertical velocities associated with each. For diagnostic purposes, the vertical velocity on the bottom of T cells is output. 
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... tracer14.5
n=1 is for potential temperature in units of degrees C, n=2 is for salinity. The ``model salinity unit'' is (ppt-35)/1000 where ``ppt'' is ``parts per thousand'' or ``grams of salt per kilogram of water''. The ``ppt'' unit of salinity has been largely replaced by ``practical salinity units'' or ``psu'' in the literature which is based on conductivity measurements instead of measuring ``grams of salt per kilogram of water''. MOM uses $\rho_\circ = 1.035 \; gm/cm^3$ for the Boussinesq approximation. The model salinity units can be converted back to ``ppt'' by adding 0.035 grams/cm3 and multiplying by 1000. n > 2 is for additional passive tracers. 
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... diffusion14.6
This is the explicit portion of K33 indicated in 34.1 when option isoneutralmix is enabled. If option implicitvmix is enabled, then it is the explicit part of the vertical diffusion. 
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... form14.7
These are the K31 and K32 tensor components indicated in Section 34.1. 
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... diffusion14.8
If option implicitvmix is enabled, then it is the explicit part of the vertical diffusion. 
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...14.9
This is a non-standard Fortran 77 feature that is very useful. Most compilers support it. Refer to any Fortran manual for usage. 
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... time15.1
Date and time defined at the center of the data record. For instance, if the record was January (31 days long), the centered time would be at day 15.5 which is the center. 
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... execute15.2
This time is accounted for in the timer routines. 
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... events15.3
The interval must be referenced to a starting time which may be specified as the beginning of the experiment, the beginning of a particular job, or a specific date in time. 
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... quantities15.4
Each event may have its own interval and averaging period. 
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RC Pacanowski and SM Griffies, GFDL, Jan 2000