Annotation of /MITgcm/doc/notes

Miscellaneous notes relating to MITgcm UV
=========================================

o Something really weird is happening - variables keep
  changing value!

  Apart from the usual problems of out of bounds array refs.
  and various bugs itis important to be sure that "stack"
  variables really are stack variables in multi-threaded execution.
  Some compilers put subroutines local variables in static storage.
  This can result in an apparently private variable in a local
  routine being mysteriously changed by concurrently executing
  thread.

                    =====================================

o Something really weird is happening - the code gets stuck in
  a loop somewhere!

  The routines in barrier.F should be compiled without any
  optimisation. The routines check variables that are updated by other threads
  Compiler optimisations generally assume that the code being optimised 
  will obey the sequential semantics of regular Fortran. That means they
  will assume that a variable is not going to change value unless the
  code it is optimising changes it. Obviously this can cause problems.

                    =====================================

o Is the Fortran SAVE statement a problem.

  Yes. On the whole the Fortran SAVE statement should not be used
  for data in a multi-threaded code. SAVE causes data to be held in 
  static storage meaning that all threads will see the same location. 
  Therefore, generally if one thread updates the location all other threads 
  will see it. Note - there is often no specification for what should happen
  in this situation in a multi-threaded environment, so this is
  not a robust machanism for sharing data.
  For most cases where SAVE might be appropriate either of the following 
  recipes should be used instead. Both these schemes are potential 
  performance bottlenecks if they are over-used. 
  Method 1
  ********
   1. Put the SAVE variable in a common block
   2. Update the SAVE variable in a _BEGIN_MASTER, _END_MASTER block.
   3. Include a _BARRIER after the _BEGIN_MASTER, _END_MASTER block.
   e.g
   C nIter - Current iteration counter
   COMMON /PARAMS/ nIter
   INTEGER nIter

   _BEGIN_MASTER(myThid)
    nIter = nIter+1
   _END_MASTER(myThid)
   _BARRIER

   Note. The _BARRIER operation is potentially expensive. Be conservative
         in your use of this scheme.

  Method 2
  ********
   1. Put the SAVE variable in a common block but with an extra dimension
      for the thread number.
   2. Change the updates and references to the SAVE variable to a per thread 
      basis.
   e.g
   C nIter - Current iteration counter
   COMMON /PARAMS/ nIter
   INTEGER nIter(MAX_NO_THREADS)
 
    nIter(myThid) = nIter(myThid)+1

   Note. nIter(myThid) and nIter(myThid+1) will share the same
         cache line. The update will cause extra low-level memory 
         traffic to maintain cache coherence. If the update is in
         a tight loop this will be a problem and nIter will need
         padding.
         In a NUMA system nIter(1:MAX_NO_THREADS) is likely to reside
         in a single page of physical memory on a single box. Again in
         a tight loop this would cause lots of remote/far memory references
         and would be a problem. Some compilers provide a machanism
         for helping overcome this problem.

                    =====================================

o Can I debug using write statements.

  Many systems do not have "thread-safe" Fortran I/O libraries.
  On these systems I/O generally orks but it gets a bit intermingled!
  Occaisionally doing multi-threaded I/O with an unsafe  Fortran I/O library
  will actual cause the program to fail. Note: SGI has a "thread-safe" Fortran 
  I/O library.

                    =====================================

o Mapping virtual memory to physical memory.

  The current code declares arrays as
       real aW2d (1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)
  This raises an issue on shared virtual-memory machines that have
  an underlying non-uniform memory subsystem e.g. HP Exemplar, SGI 
  Origin, DG, Sequent etc.. . What most machines implement is a scheme 
  in which the physical memory that backs the virtual memory is allocated           
  on a page basis at 
  run-time. The OS manages this allocation and without exception
  pages are assigned to physical memory on the box where the thread 
  which caused the page-fault is running. Pages are typically 4-8KB in 
  size. This means that in some environments it would make sense to   
  declare arrays
       real aW2d (1-OLx:sNx+OLx+PX,1-OLy:sNy+OLy+PY,nSx,nSy)
  where PX and PY are chosen so that the divides between near and 
  far memory will coincide with the boundaries of the virtual memory
  regions a thread works on. In principle this is easy but it is
  also inelegant and really one would like the OS/hardware to take
  care of this issue. Doing it oneself requires PX and PY to be recalculated whenever 
  the mapping of the nSx, nSy blocks to nTx and nTy threads is changed. Also
  different PX and PY are required depending on
   page size
   array element size ( real*4, real*8 )
   array dimensions ( 2d, 3d Nz, 3d Nz+1 ) - in 3d a PZ would also be needed!
  Note: 1. A C implementation would be a lot easier. An F90 including allocation
           would also be fairly straightforward.
        2. The padding really ought to be between the "collection" of blocks
           that all the threads using the same near memory work on. To save on wasted 
           memory the padding really should be between these blocks. The 
           PX, PY, PZ mechanism does this three levels down on the heirarchy. This
           wastes more memory.
        3. For large problems this is less of an issue. For a large problem
           even for a 2d array there might be say 16 pages per array per processor
           and at least 4 processors in a uniform memory access box. Assuming a 
           sensible mapping of processors to blocks only one page (1.5% of the
           memory) referenced by processors in another box.
           On the other hand for a very small per processor problem size e.g.
           32x32 per processor and again four processors per box as many as
           50% of the memory references could be to far memory for 2d fields. 
           This could be very bad!

                    =====================================

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1	cnh	1.1	Miscellaneous notes relating to MITgcm UV
2			=========================================
3
4			o Something really weird is happening - variables keep
5			changing value!
6
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.
14
15			=====================================
16
17			o Something really weird is happening - the code gets stuck in
18			a loop somewhere!
19
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.
26
27			=====================================
28
29			o Is the Fortran SAVE statement a problem.
30
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
48			COMMON /PARAMS/ nIter
49			INTEGER nIter
50
51			_BEGIN_MASTER(myThid)
52			nIter = nIter+1
53			_END_MASTER(myThid)
54			_BARRIER
55
56			Note. The _BARRIER operation is potentially expensive. Be conservative
57			in your use of this scheme.
58
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
67			COMMON /PARAMS/ nIter
68			INTEGER nIter(MAX_NO_THREADS)
69
70			nIter(myThid) = nIter(myThid)+1
71
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.
82
83			=====================================
84
85			o Can I debug using write statements.
86
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.
92
93			=====================================
94
95			o Mapping virtual memory to physical memory.
96
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 ( real4, real8 )
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!
136
137			=====================================
138
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