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Contents of /MITgcm/doc/notes

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Revision 1.1 - (show annotations) (download)
Fri Apr 24 02:27:47 1998 UTC (26 years, 2 months ago) by cnh
Branch: MAIN
Added doc directory.
Intially contains one file "notes"

1 Miscellaneous notes relating to MITgcm UV
2 =========================================
4 o Something really weird is happening - variables keep
5 changing value!
7 Apart from the usual problems of out of bounds array refs.
8 and various bugs itis important to be sure that "stack"
9 variables really are stack variables in multi-threaded execution.
10 Some compilers put subroutines local variables in static storage.
11 This can result in an apparently private variable in a local
12 routine being mysteriously changed by concurrently executing
13 thread.
15 =====================================
17 o Something really weird is happening - the code gets stuck in
18 a loop somewhere!
20 The routines in barrier.F should be compiled without any
21 optimisation. The routines check variables that are updated by other threads
22 Compiler optimisations generally assume that the code being optimised
23 will obey the sequential semantics of regular Fortran. That means they
24 will assume that a variable is not going to change value unless the
25 code it is optimising changes it. Obviously this can cause problems.
27 =====================================
29 o Is the Fortran SAVE statement a problem.
31 Yes. On the whole the Fortran SAVE statement should not be used
32 for data in a multi-threaded code. SAVE causes data to be held in
33 static storage meaning that all threads will see the same location.
34 Therefore, generally if one thread updates the location all other threads
35 will see it. Note - there is often no specification for what should happen
36 in this situation in a multi-threaded environment, so this is
37 not a robust machanism for sharing data.
38 For most cases where SAVE might be appropriate either of the following
39 recipes should be used instead. Both these schemes are potential
40 performance bottlenecks if they are over-used.
41 Method 1
42 ********
43 1. Put the SAVE variable in a common block
44 2. Update the SAVE variable in a _BEGIN_MASTER, _END_MASTER block.
45 3. Include a _BARRIER after the _BEGIN_MASTER, _END_MASTER block.
46 e.g
47 C nIter - Current iteration counter
49 INTEGER nIter
51 _BEGIN_MASTER(myThid)
52 nIter = nIter+1
53 _END_MASTER(myThid)
56 Note. The _BARRIER operation is potentially expensive. Be conservative
57 in your use of this scheme.
59 Method 2
60 ********
61 1. Put the SAVE variable in a common block but with an extra dimension
62 for the thread number.
63 2. Change the updates and references to the SAVE variable to a per thread
64 basis.
65 e.g
66 C nIter - Current iteration counter
70 nIter(myThid) = nIter(myThid)+1
72 Note. nIter(myThid) and nIter(myThid+1) will share the same
73 cache line. The update will cause extra low-level memory
74 traffic to maintain cache coherence. If the update is in
75 a tight loop this will be a problem and nIter will need
76 padding.
77 In a NUMA system nIter(1:MAX_NO_THREADS) is likely to reside
78 in a single page of physical memory on a single box. Again in
79 a tight loop this would cause lots of remote/far memory references
80 and would be a problem. Some compilers provide a machanism
81 for helping overcome this problem.
83 =====================================
85 o Can I debug using write statements.
87 Many systems do not have "thread-safe" Fortran I/O libraries.
88 On these systems I/O generally orks but it gets a bit intermingled!
89 Occaisionally doing multi-threaded I/O with an unsafe Fortran I/O library
90 will actual cause the program to fail. Note: SGI has a "thread-safe" Fortran
91 I/O library.
93 =====================================
95 o Mapping virtual memory to physical memory.
97 The current code declares arrays as
98 real aW2d (1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)
99 This raises an issue on shared virtual-memory machines that have
100 an underlying non-uniform memory subsystem e.g. HP Exemplar, SGI
101 Origin, DG, Sequent etc.. . What most machines implement is a scheme
102 in which the physical memory that backs the virtual memory is allocated
103 on a page basis at
104 run-time. The OS manages this allocation and without exception
105 pages are assigned to physical memory on the box where the thread
106 which caused the page-fault is running. Pages are typically 4-8KB in
107 size. This means that in some environments it would make sense to
108 declare arrays
109 real aW2d (1-OLx:sNx+OLx+PX,1-OLy:sNy+OLy+PY,nSx,nSy)
110 where PX and PY are chosen so that the divides between near and
111 far memory will coincide with the boundaries of the virtual memory
112 regions a thread works on. In principle this is easy but it is
113 also inelegant and really one would like the OS/hardware to take
114 care of this issue. Doing it oneself requires PX and PY to be recalculated whenever
115 the mapping of the nSx, nSy blocks to nTx and nTy threads is changed. Also
116 different PX and PY are required depending on
117 page size
118 array element size ( real*4, real*8 )
119 array dimensions ( 2d, 3d Nz, 3d Nz+1 ) - in 3d a PZ would also be needed!
120 Note: 1. A C implementation would be a lot easier. An F90 including allocation
121 would also be fairly straightforward.
122 2. The padding really ought to be between the "collection" of blocks
123 that all the threads using the same near memory work on. To save on wasted
124 memory the padding really should be between these blocks. The
125 PX, PY, PZ mechanism does this three levels down on the heirarchy. This
126 wastes more memory.
127 3. For large problems this is less of an issue. For a large problem
128 even for a 2d array there might be say 16 pages per array per processor
129 and at least 4 processors in a uniform memory access box. Assuming a
130 sensible mapping of processors to blocks only one page (1.5% of the
131 memory) referenced by processors in another box.
132 On the other hand for a very small per processor problem size e.g.
133 32x32 per processor and again four processors per box as many as
134 50% of the memory references could be to far memory for 2d fields.
135 This could be very bad!
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