Contents 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	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
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