<p><b>dwj07@fsu.edu</b> 2012-08-16 14:57:13 -0600 (Thu, 16 Aug 2012)</p><p><br>
-- TRUNNK COMMIT --<br>
<br>
Moving documents from branches to finished projects directory.<br>
</p><hr noshade><pre><font color="gray">Deleted: branches/omp_blocks/docs/ddt_reorg.pdf
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Deleted: branches/omp_blocks/docs/mpas_block_decomp_redesign.pdf
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Deleted: branches/omp_blocks/docs/mpas_block_decomp_redesign.tex
===================================================================
--- branches/omp_blocks/docs/mpas_block_decomp_redesign.tex 2012-08-16 20:54:16 UTC (rev 2104)
+++ branches/omp_blocks/docs/mpas_block_decomp_redesign.tex 2012-08-16 20:57:13 UTC (rev 2105)
@@ -1,337 +0,0 @@
-\documentclass[11pt]{report}
-
-\usepackage{graphicx}
-\usepackage{listings}
-\usepackage{color}
-
-\setlength{\topmargin}{0in}
-\setlength{\headheight}{0in}
-\setlength{\headsep}{0in}
-\setlength{\textheight}{9.0in}
-\setlength{\textwidth}{6.5in}
-\setlength{\evensidemargin}{0in}
-\setlength{\oddsidemargin}{0in}
-
-
-\begin{document}
-
-\title{Revisions to MPAS block decomposition routines}
-\author{}
-
-\maketitle
-\tableofcontents
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Introduction
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Introduction}
-
-In order to support multiple blocks of cells per MPI task, there are a number of
-development issues that need to be addressed:
-
-\begin{enumerate}
-
-\item Update/extend the fundamental derived types in mpas\_grid\_types.F.
- In order for other parts of the infrastructure to handle multiple
- blocks per task in a clean way, we'll need to be able to pass a head
- pointer to a field into a routine, and have that routine loop through
- all blocks for that field, with information about which cells/edges/vertices
- in that field need to be communicated.
-
-\item Decide on a new MPAS I/O abstraction layer, which will provide a
- high-level interface to the PIO layer for the rest of MPAS. This layer
- should work with blocks of fields, and make it possible to define an
- arbitrary set of I/O streams at run-time.
-
-\item Add a new module to parse a run-time I/O configuration file that
- will describe which fields are read or written to each of the I/O
- streams that a user requests via the file. This module will make calls
- to the new MPAS I/O layer to register the requested fields for I/O in
- the requested streams.
-
-\item Update the mpas\_dmpar module to support communication operations on
- multiple blocks per task. This will likely involve revising the
- internal data structures used to define communication of cells
- between tasks, and also require revisions to the public interface
- routines themselves.
-
-\item Modify the block\_decomp module to enable a task to get a list of
- cells in more than one block that it is to be the owner of.
- Implemented in the simplest way, there could simply be a namelist
- option to specify how many blocks each task should own, and the
- block\_decomp module could look for a graph.info.part.n file, with
- n=num\_blocks\_per\_task*num\_tasks, and assign blocks k, 2k, 3k, ...,
- num\_blocks\_per\_task*k to task k.
-
-\end{enumerate}
-
-This document concerns the last item, namely, the extensions to the block decomposition
-module that will be necessary for supporting multiple blocks per task in other infrastructure
-modules. \\
-
-For a broader scope of this project, the intent with these five previously
-detailed tasks is to provide the capabilities within MPAS to support PIO and
-simulations where the number of blocks in a decomposition are not equal to the
-number of MPI tasks. For example, a simulation could run on 16 processors with
-a total of 64 blocks, as opposed to the current framework where only 16 blocks
-can run at 16 processors. \\
-
-After these tasks are implemented shared memory parallism can be implemented at
-the core level to (hopefully) improve performance, but also allow greater
-flexibility in terms of the parallel infrastructre of MPAS. \\
-
-As a rough timeline, these 5 tasks are planned to be completed by the end of February, 2012.
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Requirements
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Requirements}
-
-The changes to the block decomposition module should enable an MPI task to get
-a list of it's owned cells, as well as the block number each of those cells
-lives on within it's task.
-
-\begin{itemize}
-
- \item The user must be able to specify the number of blocks in a
- simulation.
-
- \item Block decomposition modules must provide information describing the
- cell and block relationship for a given MPI task.
-
- \item Block decomposition modules need to be flexible enough to support
- multiple methods of acquiring a decomposition.
-
- \item Block decomposition modules need to support a different number of
- blocks than MPI tasks, even when they are not evenly divisible.
-
- \item Block decomposition modules should provide an interface to map a
- global block number to local block number, and owning processor number.
-\end{itemize}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Design
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Design}
-
-We propose several changes to the block decomposition module in order to
-support multiple blocks per MPI task. Currently, in order to support the case
-where there are multiple blocks per MPI task a namelist parameter needs to be
-added that will allow these two values to differ. \\
-
-First, changes to the namelist.input file include a new section called
-decomposition. This section will include four parameters. The first being
-config\_number\_of\_blocks which is an integer representation of the number of
-blocks a run should use. Second is config\_block\_decomp\_file\_prefix, which
-represents the path and prefix (before the .N) of the file for the block
-decomposition. Third is config\_proc\_decomp\_file\_prefix representing the
-path and prefix (before the .Np) to the file for the processor decomposition.
-Finally is config\_explicit\_proc\_decomp which is logical and tells MPAS to
-use the config\_proc\_decomp\_file for the distribution of blocks, or to use
-the built in method of distributing the blocks to processors.\\
-
-config\_number\_of\_blocks option will have a default value of
-0. A value of 0 in this field means there should be nProcs blocks, or one block
-for every MPI task, which is the default behavior currently.
-config\_block\_decomp\_file\_prefix is read by default and
-config\_proc\_decomp\_file\_prefix is only read for external block assignment,
-as will be described later.\\
-
-Inside mpas\_block\_decomp.F, the mpas\_block\_decomp\_cells\_for\_proc needs
-to be changed. To not only read in all cells in all blocks, but also their
-block numbers. \\
-
-The meaning of the contents of graph.info.part.N needs to change from the
-processor ID that owns a cell, to the global block number for a cell. This
-means the file that is read in with have N = config\_number\_of\_blocks. \\
-
-Given a graph.info.part.N file, the global block number needs to be mapped into
-both an owning processor number, and a local block id. The local block id does
-not need to be computed within mpas\_block\_decomp\_cells\_for\_proc as long as
-the mapping is available or known. \\
-
-The api for mpas\_block\_decomp\_cells\_for\_proc will change from
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-subroutine mpas_block_decomp_cells_for_proc(dminfo, &
- partial_global_graph_info, local_cell_list)
-\end{lstlisting}
-
-to
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-subroutine mpas_block_decomp_cells_for_proc(dminfo, &
- partial_global_graph_info, local_cell_list, @\colorbox{yellow}{block\_id}@, &
- @\colorbox{yellow}{block\_start}@, @\colorbox{yellow}{block\_count}@)
-\end{lstlisting}
-
-where local\_cell\_list is a list of cells owned by a processor that is sorted
-by local block id, block\_id is a list of global block id's that an MPI task
-owns, block\_start is a list of offsets in local\_cell\_list for the contiguous
-cells a block owns, and block\_count is a the number of cells each block owns. \\
-
-mpas\_block\_decomp\_cells\_for\_proc will perform the same regardless of
-number of processors to enable the use of multiple blocks on a single
-processor. \\
-
-The block\_type data structure will be extended to include the local block id.
-This can help make dynamic load balancing easier for implementation at a later
-time. This will change
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
- type block_type
-
-#include "block_group_members.inc"
-
- integer :: blockID ! Unique global ID number for this block
-
- type (domain_type), pointer :: domain
-
- type (parallel_info), pointer :: parinfo
-
- type (block_type), pointer :: prev, next
- end type block_type
-
-\end{lstlisting}
-
-to
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
- type block_type
-
-#include "block_group_members.inc"
-
- integer :: blockID ! Unique global ID number for this block
- @\colorbox{yellow}{integer :: localBlockID}@
-
- type (domain_type), pointer :: domain
-
- type (parallel_info), pointer :: parinfo
-
- type (block_type), pointer :: prev, next
- end type block_type
-
-\end{lstlisting}
-
-There will be three additions to the public interface of mpas\_block\_decomp.F
-The first adds the routine mpas\_get\_local\_block\_id which takes has three
-arguments. As input it takes the domain information and the global block
-number, and as output it provides the local block number on a processor. This
-allows other parts of MPAS to determine what local block number a global block
-is, even if it's on another processor. \\
-
-The second addition to the public interface is the subroutine
-mpas\_get\_owning\_proc. This subroutine takes as input the domain information
-and the global block number, and as output provides the MPI task number that
-owns the block. This allows other parts of MPAS to determine from a block
-number which MPI task it needs to communicate with to read/write this block. \\
-
-The third public routine is called mpas\_get\_blocks\_per\_proc. This routine
-takes as input the domain information and a processor number. On output
-blocks\_per\_proc contains the number of blocks a processor owns. \\
-
-In addition to the ad-hoc method of determining which blocks belong to which
-processors, a file based method will be added. This method will be toggelable
-by a namelist option named config\_explicit\_proc\_decomp, which will be logical.
-If this option is true, a file (config\_proc\_decomp\_file\_prefix.N) will be
-provided, where N is the number of processors. This file will have number of
-blocks lines, and each line will say what processor should own the block. This
-file can be created using metis externally. \\
-
-%\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Implementation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\chapter{Implementation}
-
-Implementation of the mpas\_get\_blocks\_per\_proc subroutine is as follows:
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-subroutine mpas_get_blocks_per_proc(dminfo, proc_number, blocks_per_proc)
- type(domain_info), intent(in) :: dminfo
- integer, intent(in) :: proc_number
- integer, intent(out) :: blocks_per_proc
- integer :: blocks_per_proc_min, even_blocks, remaining_blocks
-
- blocks_per_proc_min = config_number_of_blocks / dminfo % nprocs
- remaining_blocks = config_number_of_blocks - &
- (blocks_per_proc_min * dminfo % nprocs)
- even_blocks = config_number_of_blocks - remaining_blocks
-
- blocks_per_proc = blocks_per_proc_min
- if(proc_number .le. remaining_blocks) then
- blocks_per_proc = blocks_per_proc + 1
- end if
-end subroutine mpas_get_blocks_per_proc
-\end{lstlisting}
-
-\pagebreak
-
-Implementation of the mpas\_get\_local\_block\_id is as follows:
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-subroutine mpas_get_local_block_id(dminfo, &
- global_block_number, local_block_number)
- type(domain_info), intent(in) :: dminfo
- integer, intent(in) :: global_block_number
- integer, intent(out) :: local_block_number
- integer :: blocks_per_proc_min, even_blocks, remaining_blocks
-
- blocks_per_proc_min = config_number_of_blocks / dminfo % nprocs
- remaining_blocks = config_number_of_blocks - &
- (blocks_per_proc_min * dminfo % nprocs)
- even_blocks = config_number_of_blocks - remaining_blocks
-
- if(global_block_number > even_blocks) then
- local_block_number = blocks_per_proc_min - 1
- else
- local_block_number = mod(global_block_id, blocks_per_proc_min)
- end if
-end subroutine mpas_get_local_block_id
-\end{lstlisting}
-
-\pagebreak
-
-Implementation of the mpas\_get\_owning\_proc routine is as follows:
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-subroutine mpas_get_owning_proc(dminfo, &
- global_block_number, owning_proc)
- type(domain_info), intent(in) :: dminfo
- integer, intent(in) :: global_block_number
- integer, intent(out) :: owning_proc
- integer :: blocks_per_proc_min, even_blocks, remaining_blocks
-
- blocks_per_proc_min = config_number_of_blocks / dminfo % nprocs
- remaining_blocks = config_number_of_blocks - &
- (blocks_per_proc_min * dminfo % nprocs)
- even_blocks = config_number_of_blocks - remaining_blocks
-
- if(global_block_number > even_blocks) then
- owning_proc = global_block_number - even_blocks
- else
- owning_proc = global_block_number / blocks_per_proc_min
- end if
-end subroutine mpas_get_owning_proc
-\end{lstlisting}
-
-\chapter{Testing}
-Only limited testing can be performed on this task. Since this task alone
-doesn't allow the use of multiple blocks the only testing that can really be
-performed is to provide a mis-matched number of blocks and MPI tasks and verify
-the block decomposition routines provide the correct block numbers for a
-processor and put the cells in their correct block numbers.
-
-\end{document}
Deleted: branches/omp_blocks/docs/mpas_ddt_redesign.pdf
===================================================================
(Binary files differ)
Deleted: branches/omp_blocks/docs/mpas_ddt_redesign.tex
===================================================================
--- branches/omp_blocks/docs/mpas_ddt_redesign.tex 2012-08-16 20:54:16 UTC (rev 2104)
+++ branches/omp_blocks/docs/mpas_ddt_redesign.tex 2012-08-16 20:57:13 UTC (rev 2105)
@@ -1,275 +0,0 @@
-\documentclass[11pt]{report}
-
-\usepackage{graphicx}
-\usepackage{listings}
-\usepackage{color}
-
-\setlength{\topmargin}{0in}
-\setlength{\headheight}{0in}
-\setlength{\headsep}{0in}
-\setlength{\textheight}{9.0in}
-\setlength{\textwidth}{6.5in}
-\setlength{\evensidemargin}{0in}
-\setlength{\oddsidemargin}{0in}
-
-
-\begin{document}
-
-\title{Revisions to MPAS data structures}
-\author{}
-
-\maketitle
-\tableofcontents
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Introduction
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Introduction}
-
-In order to support multiple blocks of cells per MPI task, there are a number of
-development issues that need to be addressed:
-
-\begin{enumerate}
-
-\item Update/extend the fundamental derived types in mpas\_grid\_types.F.
- In order for other parts of the infrastructure to handle multiple
- blocks per task in a clean way, we'll need to be able to pass a head
- pointer to a field into a routine, and have that routine loop through
- all blocks for that field, with information about which cells/edges/vertices
- in that field need to be communicated.
-
-\item Decide on a new MPAS I/O abstraction layer, which will provide a
- high-level interface to the PIO layer for the rest of MPAS. This layer
- should work with blocks of fields, and make it possible to define an
- arbitrary set of I/O streams at run-time.
-
-\item Add a new module to parse a run-time I/O configuration file that
- will describe which fields are read or written to each of the I/O
- streams that a user requests via the file. This module will make calls
- to the new MPAS I/O layer to register the requested fields for I/O in
- the requested streams.
-
-\item Update the mpas\_dmpar module to support communication operations on
- multiple blocks per task. This will likely involve revising the
- internal data structures used to define communication of cells
- between tasks, and also require revisions to the public interface
- routines themselves.
-
-\item Modify the block\_decomp module to enable a task to get a list of
- cells in more than one block that it is to be the owner of.
- Implemented in the simplest way, there could simply be a namelist
- option to specify how many blocks each task should own, and the
- block\_decomp module could look for a graph.info.part.n file, with
- n=num\_blocks\_per\_task*num\_tasks, and assign blocks k, 2k, 3k, ...,
- num\_blocks\_per\_task*k to task k.
-
-\end{enumerate}
-
-This document concerns the first item, namely, the extensions to the derived data
-types that will be necessary for supporting multiple blocks per task in other infrastructure
-modules.
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Requirements
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Requirements}
-
-The changes to the derived data types used throughout the MPAS infrastructure and cores
-should enable I/O, communication, and other infrastructure routines to elegantly handle multiple blocks per MPI task.
-
-\begin{itemize}
-
-\item Routines (e.g., operators) must be able to traverse the list of blocks for any field that is owned by a task without having
-to explicitly dereference that field by name; this ensures that infrastructure routines can remain generic.
-
-\item A block for a field must be able to access the parallel information (halo communication lists, as well as
-MPI communicator) associated with it so that such information is never explicitly passed with the field
-to infrastructure subroutines. This requirement will simplify the argument lists for infrastructure routines, and
-eliminate the possibility that a user might pass mismatched or invalid communication information for a field
-to an infrastructure routine.
-
-\item A field must be aware of its dimensions and other metadata so that such information is never explicitly
-passed with the field to infrastructure subroutines, thereby eliminating the possibility that a user might pass incorrect dimensions
-for a field, for example.
-
-\item Since halo updates may require exchanges between blocks owned by the same process, the data
-structures used by the halo update routines (and other routines in mpas\_dmpar.F) must distinguish between
-halo cells in other blocks owned by the MPI task from those in blocks owned by a different MPI task.
-
-\item Though not strictly related to supporting multiple blocks per MPI task, halo update data structures should
-enable halo exchange routines to easily exchange any subset of the ghost cell layers. This may enable efficiency
-gains to be made in future.
-
-\end{itemize}
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Design
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Design}
-
-We propose to extend the existing data structures in MPAS with additional pointers
-between fields of the same type, and also with pointers within fields to the appropriate communication
-lists for that field. The set of communications lists will be extended to include separate lists for inter-process
-(distributed memory) and intra-process (shared-memory) exchanges, and each list will identify cells/edges/vertices
-to be exchanged for a single layer of ghost cells/edges/vertices, necessitating one list per halo layer. Also, additional metadata
-will be carried around within each field type. The proposed changes
-are highlighted in the field type definition below; other type definitions are given for reference, and the figure below
-illustrates graphically the hierarchy of DDTs.
-
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=6.5in]{ddt_reorg.pdf}
-\caption{An illustration of the current DDT structure: existing back-pointers and previous/next pointers are drawn in light arrows; new pointers to be added between field blocks are drawn heavy arrows.}
-\end{center}
-\end{figure}
-
-Besides the simple additions to the derived types described here, we will also need to extend
-the infrastructure routines that deal with allocating, deallocating, and reading in fields to be aware that there may be multiple
-blocks for a field; however, this work will be addressed by work on items 2, 4, and 5 identified in the Introduction to this document.
-\pagebreak
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-! Derived type for storing list of blocks from a domain
-! to be handled by a process
-type domain_type
- type (block_type), pointer :: blocklist
-
- ! Also store parallelization info here
- type (dm_info), pointer :: dminfo
-end type domain_type
-\end{lstlisting}
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-type dm_info
- integer :: nprocs, my_proc_id, comm, info
-end type dm_info
-\end{lstlisting}
-\vspace{12pt}
-
-In the block\_type, we will need to add a global block ID number, which uniquely identifies
-the block within the global block space. This will be used for both intra-process halo copies, as well
-as inter-process halo messages (in conjunction with the process ID that owns the block).
-\linebreak
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-! Derived type for storing part of a domain; used as a basic
-! unit of work for a process
-type block_type
-
-#include "block_group_members.inc"
-
- type (domain_type), pointer :: domain
-
- type (parallel_info), pointer :: parinfo
-
- @\colorbox{yellow}{integer :: blockID}@
-
- type (block_type), pointer :: prev, next
-end type block_type
-\end{lstlisting}
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-type exchange_list
- integer :: procID
- @\colorbox{yellow}{integer :: blockID}@
- integer :: nlist
- integer, dimension(:), pointer :: list
- type (exchange_list), pointer :: next
- real (kind=RKIND), dimension(:), pointer :: rbuffer
- integer, dimension(:), pointer :: ibuffer
- integer :: reqID
-end type exchange_list
-\end{lstlisting}
-\vspace{12pt}
-
-In the parallel\_info type, the existing (inter-process) exchange lists will become arrays,
-with the first index of the array providing an exchange list for the first halo layer, the second
-index for the second halo layer, etc. For example, cellsToSend(2) and cellsToRecv(2) give
-information about which cells should be sent and received for a block to update the second
-(outer) halo layer. For cells, the interpretation of ``first halo layer'', ``second halo layer'', etc.
-are obvious, but we need to carefully define the interpretation of ``layers'' for edges and
-vertices. We propose that the first halo layer for edges refers to the set of ghost edges bordering owned cells,
-the second halo layer refers to the set of ghost edges bordering first halo cells, etc., and similarly
-for vertices.
-\linebreak
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-! Type for storing (possibly architecture specific) information
-! concerning parallelism
-type parallel_info
- type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: cellsToSend
- type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: cellsToRecv
- @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: cellsToCopy}@
-
- type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: edgesToSend
- type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: edgesToRecv
- @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: edgesToCopy}@
-
- type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: verticesToSend
- type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: verticesToRecv
- @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: verticesToCopy}@
-
-end type parallel_info
-\end{lstlisting}
-\vspace{12pt}
-
-Each field will carry around its dimensions, as well as whether it has a time dimension in input
-and output files, pointers to the previous and next block for the field, and pointers to the exchange
-lists for the field; if the field is a non-decomposed field, the exchange pointers will be nullified.
-\linebreak
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-! Derived type for storing fields
-type field3DReal
- type (block_type), pointer :: block
- real (kind=RKIND), dimension(:,:,:), pointer :: array
- type (io_info), pointer :: ioinfo
- @\colorbox{yellow}{integer, dimension(3) :: dims}@
- @\colorbox{yellow}{logical :: timeDimension}@
- @\colorbox{yellow}{type (field3DReal), pointer :: prev, next}@
- @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: sendList}@
- @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: recvList}@
- @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: copyList}@
-end type field3DReal
-\end{lstlisting}
-\vspace{12pt}
-
-The io\_info type will be extended to contain units and description information for the field.
-\linebreak
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-! Derived type describing info for doing I/O specific to a field
-type io_info
- character (len=1024) :: fieldName
- @\colorbox{yellow}{character (len=1024) :: units}@
- @\colorbox{yellow}{character (len=1024) :: description}@
- integer, dimension(4) :: start
- integer, dimension(4) :: count
- logical :: input
- logical :: sfc
- logical :: restart
- logical :: output
-end type io_info
-\end{lstlisting}
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Implementation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Implementation}
-
-Should we outline a plan for implementing these changes?
-
-\end{document}
Deleted: branches/omp_blocks/docs/mpas_multiple_blocks.pdf
===================================================================
(Binary files differ)
Deleted: branches/omp_blocks/docs/mpas_multiple_blocks.tex
===================================================================
--- branches/omp_blocks/docs/mpas_multiple_blocks.tex 2012-08-16 20:54:16 UTC (rev 2104)
+++ branches/omp_blocks/docs/mpas_multiple_blocks.tex 2012-08-16 20:57:13 UTC (rev 2105)
@@ -1,474 +0,0 @@
-\documentclass[11pt]{report}
-
-\usepackage{graphicx}
-\usepackage{listings}
-\usepackage{color}
-\usepackage{placeins}
-
-\setlength{\topmargin}{0in}
-\setlength{\headheight}{0in}
-\setlength{\headsep}{0in}
-\setlength{\textheight}{9.0in}
-\setlength{\textwidth}{6.5in}
-\setlength{\evensidemargin}{0in}
-\setlength{\oddsidemargin}{0in}
-
-
-\begin{document}
-
-\title{Implementing Multiple Blocks within MPAS Framework}
-\author{}
-
-\maketitle
-\tableofcontents
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Introduction
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Introduction}
-
-Previously several projects have been worked on with the end goal of supporting
-multiple blocks. These tasks are described below.
-
-\begin{enumerate}
-
-\item Update/extend the fundamental derived types in mpas\_grid\_types.F.
- In order for other parts of the infrastructure to handle multiple
- blocks per task in a clean way, we'll need to be able to pass a head
- pointer to a field into a routine, and have that routine loop through
- all blocks for that field, with information about which cells/edges/vertices
- in that field need to be communicated.
-
-\item Decide on a new MPAS I/O abstraction layer, which will provide a
- high-level interface to the PIO layer for the rest of MPAS. This layer
- should work with blocks of fields, and make it possible to define an
- arbitrary set of I/O streams at run-time.
-
-\item Add a new module to parse a run-time I/O configuration file that
- will describe which fields are read or written to each of the I/O
- streams that a user requests via the file. This module will make calls
- to the new MPAS I/O layer to register the requested fields for I/O in
- the requested streams.
-
-\item Update the mpas\_dmpar module to support communication operations on
- multiple blocks per task. This will likely involve revising the
- internal data structures used to define communication of cells
- between tasks, and also require revisions to the public interface
- routines themselves.
-
-\item Modify the block\_decomp module to enable a task to get a list of
- cells in more than one block that it is to be the owner of.
- Implemented in the simplest way, there could simply be a namelist
- option to specify how many blocks each task should own, and the
- block\_decomp module could look for a graph.info.part.n file, with
- n=num\_blocks\_per\_task*num\_tasks, and assign blocks k, 2k, 3k, ...,
- num\_blocks\_per\_task*k to task k.
-
-\end{enumerate}
-
-This document related to tying all of these projects together, and allowing
-MPAS to run with multiple blocks per MPI process.
-
-As an example of what running with multiple blocks means, currently MPAS is
-allowed to run with 1 block per process. This means prior to running MPAS a
-decomposition of cells needs to be determined. This decomposition tells each
-MPI process which cells it owns. So, under the current framework the number of
-decompositions have to be equal to the number of MPI tasks used to run the job.
-
-After this project is completed, a user should be able to specify the use of a
-decomposition that does not have an equal number of blocks as the number of
-processors the job is run with. Typically this would be used to allow more than
-one block per processor, but could theoretically be used to run having some
-processors not have any blocks.
-
-The goal with this project is to allow exploration of OpenMP directives, and
-test performance using different block sizes. Allowing multiple blocks per
-processor could increase cache reuse and allow a performance increase.
-
-This work is currently being performed under
-branches/omp\_blocks/multiple\_blocks and all source code changes can be
-examined there.
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Requirements
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Requirements}
-
-There are significant changes to MPAS' framework that have to be made in order
-to support multiple blocks. A list of requirements that determine these changes
-are listed below, with the reasons for these requirements written below them.
-
-\begin{itemize}
- \item Block creation must be robust, and handle an arbitrary number
- of blocks per processor.
-
- \item Blocks should be created using the derived data types created in an
- earlier project, promoting the use of field data types rather than
- simple arrays.
-
- \item Block creation routines should be created with an arbitrary number of
- halos assumed, although the default is currently two.
-
- \item All block communication routines should be able to handle shared
- memory copies.
-
- \item Exchange list creation should be performed at the block/field level.
-
- \item Block creation code should be isolated from the rest of MPAS code.
-\end{itemize}
-
-Blocks per processor should be allowed to be any non-negative number, including
-zero. This could be useful if a user wanted the ability to specify certain
-processors to do certain tasks, without doing any actual computation work on
-blocks. Although the user would have to give an explicit block to proc
-decomposition in order to have this ability used.
-
-In the creation of blocks, field data types should be used in place of simple
-arrays to promote the use of internal derived data types that are used
-elsewhere within MPAS. This will allow similar techniques to be identified by
-developers of cores, and allow a similar work flow with variables and fields
-within all of MPAS.
-
-Although fields currently are restricted to having two halo layers, at some
-point in the future we might like to be able to extend halo layers or even have
-different halo layers on each field. In order to make this task easier to
-accomplish in the future block creation routines need to be able to create an
-arbitrary number of halo layers.
-
-When two blocks are neighboring on a single processor shared memory copies
-could be used for halo exchanges and other sorts of block-to-block
-communications rather than using MPI send/recv routines.
-
-Exchange lists are limited in their functionality by the fact that the only
-information they have refer to the other processor/block involved in the
-communication. For example, if processor 0 owns block 0 and this has to send
-information from 15 cells to processor 2 block 5 then the send list for block 0
-only gives the information on where it has to send the information, while the
-receive list on block 5 gives information on where to receive the information
-from. Because of this, exchange lists have to be created on a per block basis,
-and linked to a specific block. This way each block knows which cells it's
-supposed to send/recv/copy to/from another block. Each field and block have
-their own exchange lists, so the creation of exchange lists should place them
-within these already existing structures.
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Design
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter{Design}
-
-Only a small amount of design has been completed thus far. So, all information
-in this section should be regarded as a work in progress for now. As a visual
-for the design process, the proposed module layout can be seen in figure
-\ref{fig:module_layout}.
-
-\begin{figure}[H!]
- \centering
- \includegraphics[scale=0.4]{DesignLayout.eps}
- \caption{Layout of modules for input/output with multiple blocks}
- \label{fig:module_layout}
-\end{figure}
-
-The changes made to mpas framework can be seen in the following sections.
-
-\section{Changes in mpas\_dmpar}
-This section covers the changes, and the new functionality of the changes that
-were made within the mpas\_dmpar.F file. The first major change, is that dmpar
-is renamed to comm meaning communications.
-
-\subsection{Data types}
-Previously the derived data type mpas\_exchange\_list was used to create a linked list which represented an exchange list (send or receive). Exchange lists have been modified from their original state to have the following structure.
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-type mpas_exchange_list
- integer :: endPointID
- integer :: nlist
- integer, dimension(:), pointer :: srcList
- integer, dimension(:), pointer :: destList
- type (mpas_exchange_list), pointer :: next
-end type mpas_exchange_list
-\end{lstlisting}
-
-Within this structure endPointID can be either a blockID (for local copy) or a procID for mpi send/recv, nList represents the number of elements to be communication within this exchange list, srcList and destList represent the information for packing and unpacking data into buffers or for local copies from/to arrays.
-
-Seeing as the exchange lists no longer contain an array for the communication buffers a new data type was created which can be seen below.
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-type mpas_communication_list
- integer :: procID
- integer :: nlist
- real (kind=RKIND), dimension(:), pointer :: rbuffer
- integer, dimension(:), pointer :: ibuffer
- integer :: reqID
- type (mpas_communication_list), pointer :: next
-end type mpas_communication_list
-\end{lstlisting}
-
-An mpas\_communcation\_list is only intended to be used for mpi communications. These have to be created and destroyed each time a communcation is performed. Within the structure, procID represents the other endPoint's processor ID in the communication, nList is the number of elements to be communicated within the buffer, rbuffer and ibuffer are the pointers for the buffer of either integers or reals, reqID represents the mpi communcation id, and next creates a linked list.
-
-Two other data structures are created to allow multi halo exchange lists, and to allow pointers to be swapped easily using them.
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-type mpas_exchange_list_pointer
- type (mpas_exchange_list), pointer :: exchList
-end type mpas_exchange_list_pointer
-
-type mpas_multihalo_exchange_list
- type (mpas_exchange_list_pointer), dimension(:), pointer :: halos
-end type mpas_multihalo_exchange_list
-\end{lstlisting}
-
-Combining these four structures allows local and mpi communications to occur smoothly.
-
-\subsection{mpas\_comm\_get\_exch\_list}
-The old routine named mpas\_dmpar\_get\_owner\_list is now renamed to mpas\_comm\_get\_exch\_list. This routine is meant to create send, receive, and copy lists to send data from one processor to another. During initialization it's used for the allToAll communication routines (which will be described below) but within cores it's almost exclusively used for halo exchanges.
-
-It works by creating two lists of element id's (typically cells, edges, or vertices). One of these lists is owned elements while the other is needed elements. The needed list is communication round robin style to each processor until it comes back to the original processor. Each processor marks a needed element in the list as owned if it owns it. This way the processor that needs the element knows who it's supposed to receive the element from.
-
-During the round robin communications send lists are created as needed elements are marked as owned. After the round robin communications are finished receive lists are created. And after receive lists are created copy lists are created in a similar fashion to send lists.
-
-\subsection{allToAll routines}
-mpas\_comm provides a set of allToAll routines intended to distribute a field from one processor to one or more other processors. In this case, the sending information is supposed to include the 0 halo elements. In contrast to the exch\_halo routines which are intended to only communication 1+ halo elements.
-
-A pseudocode version of the allToAll routines can be seen below.
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-loop over fieldOut list
- loop over recvList for specific field
- create new communication list if needed
- end loop
-end loop
-
-allocate recvList buffers and initiate mpi_irecvs
-
-loop over fieldIn list
- loop over sendList for specific field
- create new communication list if needed
- end loop
-end loop
-
-allocate sendList buffers, copy data into buffer
- initiate mpi_isends
-
-loop over fieldIn list
- loop over copyList for specific field
- loop over fieldOut list
- if fieldOut % blockID == copyList % endPointID
- use copy list to copy from fieldIn to fieldOut
- end if
- end loop
- end loop
-end loop
-
-wait for mpi_irecvs
- unpack buffer into fields
-
-wait for mpi_isends
-
-destroy buffers
-\end{lstlisting}
-
-\subsection{exch\_halo routines}
-mpas\_comm provides a set of halo exchange routines intended to distribute a set of 0 halo elements to other blocks that have them in their 1+ halo regions.
-
-A pseudocode version of the halo exchange routines can be seen below.
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-loop over field list
- loop over recvList for specific field
- create new communication list if needed
- end loop
-end loop
-
-allocate recvList buffers and initiate mpi_irecvs
-
-loop over field list
- loop over sendList for specific field
- create new communication list if needed
- end loop
-end loop
-
-allocate sendList buffers, copy data into buffer
- initiate mpi_isends
-
-loop over field list
- loop over copyList for specific field
- loop over field list
- if field % blockID == copyList % endPointID
- use copy list to copy from fieldIn to fieldOut
- end if
- end loop
- end loop
-end loop
-
-wait for mpi_irecvs
- unpack buffer into fields
-
-wait for mpi_isends
-
-destroy buffers
-\end{lstlisting}
-
-\subsection{copy routines}
-mpas\_comm provides a set of routines intended to copy a field from the header block in a list of owned blocks to all other blocks in the list. These are needed during initialization to copy non-decomposed fields (fields that don't include the nCells, nEdges, or nVertices as a dimension) to all owned blocks.
-
-\subsection{Utility routines}
-In addition to communcation routines, mpas\_comm provides utility routines for the initialization and destruction of all derived data types discussed above.
-
-\section{mpas\_block\_creator.F}
-mpas\_block\_creator provides a new module for mpas that is used to create computational blocks. Given the information of a 0 halo, these routines create the 1+ halo regions for cells, edges, and vertices. They also initialize the list of local blocks.
-
-\subsection{Cell Routines}
-Routines to setup cell fields within a block are:
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-mpas_block_creator_setup_blocks_and_0halo_cells
-mpas_block_creator_build_0halo_cell_fields
-mpas_block_creator_build_cell_halos
-\end{lstlisting}
-
-These routines should be called in this order to properly setup the 0-1+ halo of cells. However, the build\_cell\_halos routine should not be called until all 0 halo fields are setup (including edges and vertices).
-
-\subsection{Edge/Vertex Routines}
-Routines used to setup edge/vertex fields within a block are:
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-mpas_block_creator_build_0_and_1halo_edge_fields
-mpas_block_creator_build_edge_halos
-\end{lstlisting}
-
-As mentioned in the cell routine section, the 0-1 halos of edges and vertices should be setup prior to setting up the 1+ halos of cells.
-
-\subsection{Utility Routines}
-Finally, two routines are provided to finalize the block initialization, and to re-index all fields in a block.
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-mpas_block_creator_finalize_block_init
-mpas_block_creator_reindex_block_fields
-\end{lstlisting}
-
-These routines complete the block creation processor, and provide the rest of a model with a list of fully setup blocks to compute on.
-
-\section{mpas\_io\_input changes}
-Within mpas\_io\_input the main mpas\_input\_state\_for\_domain routine has been trimmed significantly to make use of the new mpas\_block\_creator module the portions of the routine that were not able to be moved into the block\_creator module were moved to new routines within the io\_input module.
-
-This module also makes use of the new communication routines from mpas\_comm, as well as some routines in mpas\_block\_decomp.
-
-The new routines provided to clean up mpas\_input\_state\_for\_domain are:
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-mpas_io_setup_cell_block_fields
-mpas_io_setup_edge_block_fields
-mpas_io_setup_vertex_block_fields
-\end{lstlisting}
-These routines are intended to read in contiguous chunks of data that can then be communication between processors.
-
-\section{mpas\_grid\_types changes}
-Within mpas\_grid\_types, utility routines are created to deallocate fields. This is used within mpas\_io\_input for fields that need to be linked similarly to block, but are not part of the block data structure.
-
-In addition to utility routine additions, a pointer provis was created within the block\_type. provis is intended to be a scratch state. This can be used within time integration routines that require an additional time level, without having to modify the number of time levels within state.
-
-\section{Namelist changes}
-With the addition of multiple blocks in the framework of mpas, the decomposition namelist section will be made use of. This section provides the following namelist options.
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-config_block_decomp_file_prefix
-config_number_of_blocks
-config_explicit_proc_decomp
-config_proc_decomp_file_prefix
-\end{lstlisting}
-
-The prefix options are used to specify the prefixes on decomposition graph files used to create blocks, and determine which blocks are owned by which processors, config\_number\_of\_blocks determines how many blocks the simulation is supposed to be run with, and config\_explicit\_proc\_decomp is a logical flag which determines if mpas should look for a graph file describing how blocks should be distributed between processor, or if it should round robin assign blocks to processors.
-
-In addition to the decomposition section changes, the model sections (like sw\_model) now has a new namelist option:
-
-\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
-config_num_halos
-\end{lstlisting}
-
-This namelist flag determines how many halo layers each block should have on cells. The halo layers for edges and vertices are nHaloLayerCells+1, or config\_num\_halos + 1.
-
-\chapter{Testing}
-**NOTE**
-All of the testing described in this section relates only to the ocean core.
-Other core developers may test this with similar procedures but different
-simulations. \\
-
-The end goal from this project is to provide a framework that allows
-bit-for-bit reproduction of data using an arbitrary combination of blocks and
-processor numbers.
-
-Using this goal to define a testing strategy implies a good test would be
-exploring bit-for-bit reproduction of output data using the three following
-simulations:
-\begin{itemize}
- \item Current trunk simulation run with 8 processors and 8 blocks (1 block per proc).
- \item Finished branch simulation run with 8 processors and 8 blocks (1 block per proc).
- \item Finished branch simulation run with 1 processor and 8 blocks (8 blocks per proc).
- \item Finished branch simulation run with 2 processors and 8 blocks (4 blocks per proc).
-\end{itemize}
-
-If all of these simulations produce bit-for-bit output then testing can move on
-to a set of larger scale simulations.
-
-\begin{itemize}
- \item Current trunk 15km simulation with 1200 processors and 1200 blocks (1 block per proc).
- \item Finished branch simulation with 1200 processors and 1200 blocks (1 block per proc).
- \item Finished branch simulation with 600 processors and 1200 blocks (2 blocks per proc).
- \item Finished branch simulation with 24 processors and 1200 blocks (50 blocks per proc).
-\end{itemize}
-
-After these final four simulations show bit-for-bit output then the project can
-be deemed as completed.
-
-\chapter{Appendix - Use of exchange/communication lists}
-This chapter will describe the use of exchange and communication lists.
-
-To begin, exchange lists have two uses. First copyLists will be described,
-followed by send/recvLists.
-
-copyLists are attached to the block sending the data, and there is no matching
-list on the receiving end. Within the copyList, the endPointID variable
-represents a blockID giving the local id to the block on the other end of the
-communication, nList is the total number of elements that need to be copied,
-srcList is the list of indices to take this data from out of the owning field's
-array, and destList is the list of indices to put this data into the needing
-field's array.
-
-In using copyLists, first a search over blocks needs to be preformed
-to find the matching block for the communication. After that the elements
-listed in srcList are copied into the elements listed in destList. After which,
-the shared memory copy is complete.
-
-The second use case relates to send/recvLists. sendLists are attached to
-sending blocks, while recvLists are attached to receiving blocks. Within both
-of these, endPointID refers to a processor id, and nList refers to the number
-of elements a specific block should expect to communicate. In a sendList,
-srcList describes the indices to pull data out from the owning field's array
-while destList descibes the indices to put that data into a communication
-list's buffer. In a recvList, srcList describes the indices to pull the data
-out of the buffer, while destList describes the indices to put that data into
-the needing field's array.
-
-In order to use these, each side of the communication does something different.
-Before describing the use of send and recv lists, communication lists need to
-be explained.
-
-A communication list describes aggregated communications between processors.
-These provide an easy to use framework to allow communications to occur
-processor by processor as opposed to block by block. Since communication lists
-only relate to MPI communications, the only ID within the type is procID. nList
-refers to the number of elements in the buffer, while rbuffer and ibuffer
-provide deallocated arrays to put reals or integers in the buffer, and reqID
-provides a variable to store MPI communication ID's to use when calling
-MPI\_Wait.
-
-In order to perform a send an receive, first a processor needs to build the
-buffers, or communication lists. To begin the fields relating to the specific
-communication are looped over, and the total number of elements to each
-processor are stored in order to build a communication list for that processor.
-After this step, the communication list buffers are allocated relating to their
-nList varibles. Buffers need to be created both on the sending and receiving
-side. After the buffers are created, the sending field copies all of it's data
-into the array. The buffer is then sent, and on the receiving end the receiving
-field unpacks all of the data into it's arrays.
-\end{document}
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--- trunk/documents/shared/finished_design_doc/block_decomp_redesign/mpas_block_decomp_redesign.tex (rev 0)
+++ trunk/documents/shared/finished_design_doc/block_decomp_redesign/mpas_block_decomp_redesign.tex 2012-08-16 20:57:13 UTC (rev 2105)
@@ -0,0 +1,337 @@
+\documentclass[11pt]{report}
+
+\usepackage{graphicx}
+\usepackage{listings}
+\usepackage{color}
+
+\setlength{\topmargin}{0in}
+\setlength{\headheight}{0in}
+\setlength{\headsep}{0in}
+\setlength{\textheight}{9.0in}
+\setlength{\textwidth}{6.5in}
+\setlength{\evensidemargin}{0in}
+\setlength{\oddsidemargin}{0in}
+
+
+\begin{document}
+
+\title{Revisions to MPAS block decomposition routines}
+\author{}
+
+\maketitle
+\tableofcontents
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Introduction
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Introduction}
+
+In order to support multiple blocks of cells per MPI task, there are a number of
+development issues that need to be addressed:
+
+\begin{enumerate}
+
+\item Update/extend the fundamental derived types in mpas\_grid\_types.F.
+ In order for other parts of the infrastructure to handle multiple
+ blocks per task in a clean way, we'll need to be able to pass a head
+ pointer to a field into a routine, and have that routine loop through
+ all blocks for that field, with information about which cells/edges/vertices
+ in that field need to be communicated.
+
+\item Decide on a new MPAS I/O abstraction layer, which will provide a
+ high-level interface to the PIO layer for the rest of MPAS. This layer
+ should work with blocks of fields, and make it possible to define an
+ arbitrary set of I/O streams at run-time.
+
+\item Add a new module to parse a run-time I/O configuration file that
+ will describe which fields are read or written to each of the I/O
+ streams that a user requests via the file. This module will make calls
+ to the new MPAS I/O layer to register the requested fields for I/O in
+ the requested streams.
+
+\item Update the mpas\_dmpar module to support communication operations on
+ multiple blocks per task. This will likely involve revising the
+ internal data structures used to define communication of cells
+ between tasks, and also require revisions to the public interface
+ routines themselves.
+
+\item Modify the block\_decomp module to enable a task to get a list of
+ cells in more than one block that it is to be the owner of.
+ Implemented in the simplest way, there could simply be a namelist
+ option to specify how many blocks each task should own, and the
+ block\_decomp module could look for a graph.info.part.n file, with
+ n=num\_blocks\_per\_task*num\_tasks, and assign blocks k, 2k, 3k, ...,
+ num\_blocks\_per\_task*k to task k.
+
+\end{enumerate}
+
+This document concerns the last item, namely, the extensions to the block decomposition
+module that will be necessary for supporting multiple blocks per task in other infrastructure
+modules. \\
+
+For a broader scope of this project, the intent with these five previously
+detailed tasks is to provide the capabilities within MPAS to support PIO and
+simulations where the number of blocks in a decomposition are not equal to the
+number of MPI tasks. For example, a simulation could run on 16 processors with
+a total of 64 blocks, as opposed to the current framework where only 16 blocks
+can run at 16 processors. \\
+
+After these tasks are implemented shared memory parallism can be implemented at
+the core level to (hopefully) improve performance, but also allow greater
+flexibility in terms of the parallel infrastructre of MPAS. \\
+
+As a rough timeline, these 5 tasks are planned to be completed by the end of February, 2012.
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Requirements
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Requirements}
+
+The changes to the block decomposition module should enable an MPI task to get
+a list of it's owned cells, as well as the block number each of those cells
+lives on within it's task.
+
+\begin{itemize}
+
+ \item The user must be able to specify the number of blocks in a
+ simulation.
+
+ \item Block decomposition modules must provide information describing the
+ cell and block relationship for a given MPI task.
+
+ \item Block decomposition modules need to be flexible enough to support
+ multiple methods of acquiring a decomposition.
+
+ \item Block decomposition modules need to support a different number of
+ blocks than MPI tasks, even when they are not evenly divisible.
+
+ \item Block decomposition modules should provide an interface to map a
+ global block number to local block number, and owning processor number.
+\end{itemize}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Design
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Design}
+
+We propose several changes to the block decomposition module in order to
+support multiple blocks per MPI task. Currently, in order to support the case
+where there are multiple blocks per MPI task a namelist parameter needs to be
+added that will allow these two values to differ. \\
+
+First, changes to the namelist.input file include a new section called
+decomposition. This section will include four parameters. The first being
+config\_number\_of\_blocks which is an integer representation of the number of
+blocks a run should use. Second is config\_block\_decomp\_file\_prefix, which
+represents the path and prefix (before the .N) of the file for the block
+decomposition. Third is config\_proc\_decomp\_file\_prefix representing the
+path and prefix (before the .Np) to the file for the processor decomposition.
+Finally is config\_explicit\_proc\_decomp which is logical and tells MPAS to
+use the config\_proc\_decomp\_file for the distribution of blocks, or to use
+the built in method of distributing the blocks to processors.\\
+
+config\_number\_of\_blocks option will have a default value of
+0. A value of 0 in this field means there should be nProcs blocks, or one block
+for every MPI task, which is the default behavior currently.
+config\_block\_decomp\_file\_prefix is read by default and
+config\_proc\_decomp\_file\_prefix is only read for external block assignment,
+as will be described later.\\
+
+Inside mpas\_block\_decomp.F, the mpas\_block\_decomp\_cells\_for\_proc needs
+to be changed. To not only read in all cells in all blocks, but also their
+block numbers. \\
+
+The meaning of the contents of graph.info.part.N needs to change from the
+processor ID that owns a cell, to the global block number for a cell. This
+means the file that is read in with have N = config\_number\_of\_blocks. \\
+
+Given a graph.info.part.N file, the global block number needs to be mapped into
+both an owning processor number, and a local block id. The local block id does
+not need to be computed within mpas\_block\_decomp\_cells\_for\_proc as long as
+the mapping is available or known. \\
+
+The api for mpas\_block\_decomp\_cells\_for\_proc will change from
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+subroutine mpas_block_decomp_cells_for_proc(dminfo, &
+ partial_global_graph_info, local_cell_list)
+\end{lstlisting}
+
+to
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+subroutine mpas_block_decomp_cells_for_proc(dminfo, &
+ partial_global_graph_info, local_cell_list, @\colorbox{yellow}{block\_id}@, &
+ @\colorbox{yellow}{block\_start}@, @\colorbox{yellow}{block\_count}@)
+\end{lstlisting}
+
+where local\_cell\_list is a list of cells owned by a processor that is sorted
+by local block id, block\_id is a list of global block id's that an MPI task
+owns, block\_start is a list of offsets in local\_cell\_list for the contiguous
+cells a block owns, and block\_count is a the number of cells each block owns. \\
+
+mpas\_block\_decomp\_cells\_for\_proc will perform the same regardless of
+number of processors to enable the use of multiple blocks on a single
+processor. \\
+
+The block\_type data structure will be extended to include the local block id.
+This can help make dynamic load balancing easier for implementation at a later
+time. This will change
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+ type block_type
+
+#include "block_group_members.inc"
+
+ integer :: blockID ! Unique global ID number for this block
+
+ type (domain_type), pointer :: domain
+
+ type (parallel_info), pointer :: parinfo
+
+ type (block_type), pointer :: prev, next
+ end type block_type
+
+\end{lstlisting}
+
+to
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+ type block_type
+
+#include "block_group_members.inc"
+
+ integer :: blockID ! Unique global ID number for this block
+ @\colorbox{yellow}{integer :: localBlockID}@
+
+ type (domain_type), pointer :: domain
+
+ type (parallel_info), pointer :: parinfo
+
+ type (block_type), pointer :: prev, next
+ end type block_type
+
+\end{lstlisting}
+
+There will be three additions to the public interface of mpas\_block\_decomp.F
+The first adds the routine mpas\_get\_local\_block\_id which takes has three
+arguments. As input it takes the domain information and the global block
+number, and as output it provides the local block number on a processor. This
+allows other parts of MPAS to determine what local block number a global block
+is, even if it's on another processor. \\
+
+The second addition to the public interface is the subroutine
+mpas\_get\_owning\_proc. This subroutine takes as input the domain information
+and the global block number, and as output provides the MPI task number that
+owns the block. This allows other parts of MPAS to determine from a block
+number which MPI task it needs to communicate with to read/write this block. \\
+
+The third public routine is called mpas\_get\_blocks\_per\_proc. This routine
+takes as input the domain information and a processor number. On output
+blocks\_per\_proc contains the number of blocks a processor owns. \\
+
+In addition to the ad-hoc method of determining which blocks belong to which
+processors, a file based method will be added. This method will be toggelable
+by a namelist option named config\_explicit\_proc\_decomp, which will be logical.
+If this option is true, a file (config\_proc\_decomp\_file\_prefix.N) will be
+provided, where N is the number of processors. This file will have number of
+blocks lines, and each line will say what processor should own the block. This
+file can be created using metis externally. \\
+
+%\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Implementation
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\chapter{Implementation}
+
+Implementation of the mpas\_get\_blocks\_per\_proc subroutine is as follows:
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+subroutine mpas_get_blocks_per_proc(dminfo, proc_number, blocks_per_proc)
+ type(domain_info), intent(in) :: dminfo
+ integer, intent(in) :: proc_number
+ integer, intent(out) :: blocks_per_proc
+ integer :: blocks_per_proc_min, even_blocks, remaining_blocks
+
+ blocks_per_proc_min = config_number_of_blocks / dminfo % nprocs
+ remaining_blocks = config_number_of_blocks - &
+ (blocks_per_proc_min * dminfo % nprocs)
+ even_blocks = config_number_of_blocks - remaining_blocks
+
+ blocks_per_proc = blocks_per_proc_min
+ if(proc_number .le. remaining_blocks) then
+ blocks_per_proc = blocks_per_proc + 1
+ end if
+end subroutine mpas_get_blocks_per_proc
+\end{lstlisting}
+
+\pagebreak
+
+Implementation of the mpas\_get\_local\_block\_id is as follows:
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+subroutine mpas_get_local_block_id(dminfo, &
+ global_block_number, local_block_number)
+ type(domain_info), intent(in) :: dminfo
+ integer, intent(in) :: global_block_number
+ integer, intent(out) :: local_block_number
+ integer :: blocks_per_proc_min, even_blocks, remaining_blocks
+
+ blocks_per_proc_min = config_number_of_blocks / dminfo % nprocs
+ remaining_blocks = config_number_of_blocks - &
+ (blocks_per_proc_min * dminfo % nprocs)
+ even_blocks = config_number_of_blocks - remaining_blocks
+
+ if(global_block_number > even_blocks) then
+ local_block_number = blocks_per_proc_min - 1
+ else
+ local_block_number = mod(global_block_id, blocks_per_proc_min)
+ end if
+end subroutine mpas_get_local_block_id
+\end{lstlisting}
+
+\pagebreak
+
+Implementation of the mpas\_get\_owning\_proc routine is as follows:
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+subroutine mpas_get_owning_proc(dminfo, &
+ global_block_number, owning_proc)
+ type(domain_info), intent(in) :: dminfo
+ integer, intent(in) :: global_block_number
+ integer, intent(out) :: owning_proc
+ integer :: blocks_per_proc_min, even_blocks, remaining_blocks
+
+ blocks_per_proc_min = config_number_of_blocks / dminfo % nprocs
+ remaining_blocks = config_number_of_blocks - &
+ (blocks_per_proc_min * dminfo % nprocs)
+ even_blocks = config_number_of_blocks - remaining_blocks
+
+ if(global_block_number > even_blocks) then
+ owning_proc = global_block_number - even_blocks
+ else
+ owning_proc = global_block_number / blocks_per_proc_min
+ end if
+end subroutine mpas_get_owning_proc
+\end{lstlisting}
+
+\chapter{Testing}
+Only limited testing can be performed on this task. Since this task alone
+doesn't allow the use of multiple blocks the only testing that can really be
+performed is to provide a mis-matched number of blocks and MPI tasks and verify
+the block decomposition routines provide the correct block numbers for a
+processor and put the cells in their correct block numbers.
+
+\end{document}
Copied: trunk/documents/shared/finished_design_doc/ddt_redesign/ddt_reorg.pdf (from rev 2048, branches/omp_blocks/docs/ddt_reorg.pdf)
===================================================================
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Copied: trunk/documents/shared/finished_design_doc/ddt_redesign/mpas_ddt_redesign.pdf (from rev 2048, branches/omp_blocks/docs/mpas_ddt_redesign.pdf)
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Copied: trunk/documents/shared/finished_design_doc/ddt_redesign/mpas_ddt_redesign.tex (from rev 2048, branches/omp_blocks/docs/mpas_ddt_redesign.tex)
===================================================================
--- trunk/documents/shared/finished_design_doc/ddt_redesign/mpas_ddt_redesign.tex (rev 0)
+++ trunk/documents/shared/finished_design_doc/ddt_redesign/mpas_ddt_redesign.tex 2012-08-16 20:57:13 UTC (rev 2105)
@@ -0,0 +1,275 @@
+\documentclass[11pt]{report}
+
+\usepackage{graphicx}
+\usepackage{listings}
+\usepackage{color}
+
+\setlength{\topmargin}{0in}
+\setlength{\headheight}{0in}
+\setlength{\headsep}{0in}
+\setlength{\textheight}{9.0in}
+\setlength{\textwidth}{6.5in}
+\setlength{\evensidemargin}{0in}
+\setlength{\oddsidemargin}{0in}
+
+
+\begin{document}
+
+\title{Revisions to MPAS data structures}
+\author{}
+
+\maketitle
+\tableofcontents
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Introduction
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Introduction}
+
+In order to support multiple blocks of cells per MPI task, there are a number of
+development issues that need to be addressed:
+
+\begin{enumerate}
+
+\item Update/extend the fundamental derived types in mpas\_grid\_types.F.
+ In order for other parts of the infrastructure to handle multiple
+ blocks per task in a clean way, we'll need to be able to pass a head
+ pointer to a field into a routine, and have that routine loop through
+ all blocks for that field, with information about which cells/edges/vertices
+ in that field need to be communicated.
+
+\item Decide on a new MPAS I/O abstraction layer, which will provide a
+ high-level interface to the PIO layer for the rest of MPAS. This layer
+ should work with blocks of fields, and make it possible to define an
+ arbitrary set of I/O streams at run-time.
+
+\item Add a new module to parse a run-time I/O configuration file that
+ will describe which fields are read or written to each of the I/O
+ streams that a user requests via the file. This module will make calls
+ to the new MPAS I/O layer to register the requested fields for I/O in
+ the requested streams.
+
+\item Update the mpas\_dmpar module to support communication operations on
+ multiple blocks per task. This will likely involve revising the
+ internal data structures used to define communication of cells
+ between tasks, and also require revisions to the public interface
+ routines themselves.
+
+\item Modify the block\_decomp module to enable a task to get a list of
+ cells in more than one block that it is to be the owner of.
+ Implemented in the simplest way, there could simply be a namelist
+ option to specify how many blocks each task should own, and the
+ block\_decomp module could look for a graph.info.part.n file, with
+ n=num\_blocks\_per\_task*num\_tasks, and assign blocks k, 2k, 3k, ...,
+ num\_blocks\_per\_task*k to task k.
+
+\end{enumerate}
+
+This document concerns the first item, namely, the extensions to the derived data
+types that will be necessary for supporting multiple blocks per task in other infrastructure
+modules.
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Requirements
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Requirements}
+
+The changes to the derived data types used throughout the MPAS infrastructure and cores
+should enable I/O, communication, and other infrastructure routines to elegantly handle multiple blocks per MPI task.
+
+\begin{itemize}
+
+\item Routines (e.g., operators) must be able to traverse the list of blocks for any field that is owned by a task without having
+to explicitly dereference that field by name; this ensures that infrastructure routines can remain generic.
+
+\item A block for a field must be able to access the parallel information (halo communication lists, as well as
+MPI communicator) associated with it so that such information is never explicitly passed with the field
+to infrastructure subroutines. This requirement will simplify the argument lists for infrastructure routines, and
+eliminate the possibility that a user might pass mismatched or invalid communication information for a field
+to an infrastructure routine.
+
+\item A field must be aware of its dimensions and other metadata so that such information is never explicitly
+passed with the field to infrastructure subroutines, thereby eliminating the possibility that a user might pass incorrect dimensions
+for a field, for example.
+
+\item Since halo updates may require exchanges between blocks owned by the same process, the data
+structures used by the halo update routines (and other routines in mpas\_dmpar.F) must distinguish between
+halo cells in other blocks owned by the MPI task from those in blocks owned by a different MPI task.
+
+\item Though not strictly related to supporting multiple blocks per MPI task, halo update data structures should
+enable halo exchange routines to easily exchange any subset of the ghost cell layers. This may enable efficiency
+gains to be made in future.
+
+\end{itemize}
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Design
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Design}
+
+We propose to extend the existing data structures in MPAS with additional pointers
+between fields of the same type, and also with pointers within fields to the appropriate communication
+lists for that field. The set of communications lists will be extended to include separate lists for inter-process
+(distributed memory) and intra-process (shared-memory) exchanges, and each list will identify cells/edges/vertices
+to be exchanged for a single layer of ghost cells/edges/vertices, necessitating one list per halo layer. Also, additional metadata
+will be carried around within each field type. The proposed changes
+are highlighted in the field type definition below; other type definitions are given for reference, and the figure below
+illustrates graphically the hierarchy of DDTs.
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=6.5in]{ddt_reorg.pdf}
+\caption{An illustration of the current DDT structure: existing back-pointers and previous/next pointers are drawn in light arrows; new pointers to be added between field blocks are drawn heavy arrows.}
+\end{center}
+\end{figure}
+
+Besides the simple additions to the derived types described here, we will also need to extend
+the infrastructure routines that deal with allocating, deallocating, and reading in fields to be aware that there may be multiple
+blocks for a field; however, this work will be addressed by work on items 2, 4, and 5 identified in the Introduction to this document.
+\pagebreak
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+! Derived type for storing list of blocks from a domain
+! to be handled by a process
+type domain_type
+ type (block_type), pointer :: blocklist
+
+ ! Also store parallelization info here
+ type (dm_info), pointer :: dminfo
+end type domain_type
+\end{lstlisting}
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+type dm_info
+ integer :: nprocs, my_proc_id, comm, info
+end type dm_info
+\end{lstlisting}
+\vspace{12pt}
+
+In the block\_type, we will need to add a global block ID number, which uniquely identifies
+the block within the global block space. This will be used for both intra-process halo copies, as well
+as inter-process halo messages (in conjunction with the process ID that owns the block).
+\linebreak
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+! Derived type for storing part of a domain; used as a basic
+! unit of work for a process
+type block_type
+
+#include "block_group_members.inc"
+
+ type (domain_type), pointer :: domain
+
+ type (parallel_info), pointer :: parinfo
+
+ @\colorbox{yellow}{integer :: blockID}@
+
+ type (block_type), pointer :: prev, next
+end type block_type
+\end{lstlisting}
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+type exchange_list
+ integer :: procID
+ @\colorbox{yellow}{integer :: blockID}@
+ integer :: nlist
+ integer, dimension(:), pointer :: list
+ type (exchange_list), pointer :: next
+ real (kind=RKIND), dimension(:), pointer :: rbuffer
+ integer, dimension(:), pointer :: ibuffer
+ integer :: reqID
+end type exchange_list
+\end{lstlisting}
+\vspace{12pt}
+
+In the parallel\_info type, the existing (inter-process) exchange lists will become arrays,
+with the first index of the array providing an exchange list for the first halo layer, the second
+index for the second halo layer, etc. For example, cellsToSend(2) and cellsToRecv(2) give
+information about which cells should be sent and received for a block to update the second
+(outer) halo layer. For cells, the interpretation of ``first halo layer'', ``second halo layer'', etc.
+are obvious, but we need to carefully define the interpretation of ``layers'' for edges and
+vertices. We propose that the first halo layer for edges refers to the set of ghost edges bordering owned cells,
+the second halo layer refers to the set of ghost edges bordering first halo cells, etc., and similarly
+for vertices.
+\linebreak
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+! Type for storing (possibly architecture specific) information
+! concerning parallelism
+type parallel_info
+ type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: cellsToSend
+ type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: cellsToRecv
+ @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: cellsToCopy}@
+
+ type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: edgesToSend
+ type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: edgesToRecv
+ @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: edgesToCopy}@
+
+ type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: verticesToSend
+ type (exchange_list), @\colorbox{yellow}{dimension(:),}@ pointer :: verticesToRecv
+ @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: verticesToCopy}@
+
+end type parallel_info
+\end{lstlisting}
+\vspace{12pt}
+
+Each field will carry around its dimensions, as well as whether it has a time dimension in input
+and output files, pointers to the previous and next block for the field, and pointers to the exchange
+lists for the field; if the field is a non-decomposed field, the exchange pointers will be nullified.
+\linebreak
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+! Derived type for storing fields
+type field3DReal
+ type (block_type), pointer :: block
+ real (kind=RKIND), dimension(:,:,:), pointer :: array
+ type (io_info), pointer :: ioinfo
+ @\colorbox{yellow}{integer, dimension(3) :: dims}@
+ @\colorbox{yellow}{logical :: timeDimension}@
+ @\colorbox{yellow}{type (field3DReal), pointer :: prev, next}@
+ @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: sendList}@
+ @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: recvList}@
+ @\colorbox{yellow}{type (exchange\_list), dimension(:), pointer :: copyList}@
+end type field3DReal
+\end{lstlisting}
+\vspace{12pt}
+
+The io\_info type will be extended to contain units and description information for the field.
+\linebreak
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+! Derived type describing info for doing I/O specific to a field
+type io_info
+ character (len=1024) :: fieldName
+ @\colorbox{yellow}{character (len=1024) :: units}@
+ @\colorbox{yellow}{character (len=1024) :: description}@
+ integer, dimension(4) :: start
+ integer, dimension(4) :: count
+ logical :: input
+ logical :: sfc
+ logical :: restart
+ logical :: output
+end type io_info
+\end{lstlisting}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Implementation
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Implementation}
+
+Should we outline a plan for implementing these changes?
+
+\end{document}
Added: trunk/documents/shared/finished_design_doc/multiple_blocks/DesignLayout.eps
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+%%PageTrailer
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+%%EOF
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+\documentclass[11pt]{report}
+
+\usepackage{graphicx}
+\usepackage{listings}
+\usepackage{color}
+\usepackage{placeins}
+
+\setlength{\topmargin}{0in}
+\setlength{\headheight}{0in}
+\setlength{\headsep}{0in}
+\setlength{\textheight}{9.0in}
+\setlength{\textwidth}{6.5in}
+\setlength{\evensidemargin}{0in}
+\setlength{\oddsidemargin}{0in}
+
+
+\begin{document}
+
+\title{Implementing Multiple Blocks within MPAS Framework}
+\author{}
+
+\maketitle
+\tableofcontents
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Introduction
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Introduction}
+
+Previously several projects have been worked on with the end goal of supporting
+multiple blocks. These tasks are described below.
+
+\begin{enumerate}
+
+\item Update/extend the fundamental derived types in mpas\_grid\_types.F.
+ In order for other parts of the infrastructure to handle multiple
+ blocks per task in a clean way, we'll need to be able to pass a head
+ pointer to a field into a routine, and have that routine loop through
+ all blocks for that field, with information about which cells/edges/vertices
+ in that field need to be communicated.
+
+\item Decide on a new MPAS I/O abstraction layer, which will provide a
+ high-level interface to the PIO layer for the rest of MPAS. This layer
+ should work with blocks of fields, and make it possible to define an
+ arbitrary set of I/O streams at run-time.
+
+\item Add a new module to parse a run-time I/O configuration file that
+ will describe which fields are read or written to each of the I/O
+ streams that a user requests via the file. This module will make calls
+ to the new MPAS I/O layer to register the requested fields for I/O in
+ the requested streams.
+
+\item Update the mpas\_dmpar module to support communication operations on
+ multiple blocks per task. This will likely involve revising the
+ internal data structures used to define communication of cells
+ between tasks, and also require revisions to the public interface
+ routines themselves.
+
+\item Modify the block\_decomp module to enable a task to get a list of
+ cells in more than one block that it is to be the owner of.
+ Implemented in the simplest way, there could simply be a namelist
+ option to specify how many blocks each task should own, and the
+ block\_decomp module could look for a graph.info.part.n file, with
+ n=num\_blocks\_per\_task*num\_tasks, and assign blocks k, 2k, 3k, ...,
+ num\_blocks\_per\_task*k to task k.
+
+\end{enumerate}
+
+This document related to tying all of these projects together, and allowing
+MPAS to run with multiple blocks per MPI process.
+
+As an example of what running with multiple blocks means, currently MPAS is
+allowed to run with 1 block per process. This means prior to running MPAS a
+decomposition of cells needs to be determined. This decomposition tells each
+MPI process which cells it owns. So, under the current framework the number of
+decompositions have to be equal to the number of MPI tasks used to run the job.
+
+After this project is completed, a user should be able to specify the use of a
+decomposition that does not have an equal number of blocks as the number of
+processors the job is run with. Typically this would be used to allow more than
+one block per processor, but could theoretically be used to run having some
+processors not have any blocks.
+
+The goal with this project is to allow exploration of OpenMP directives, and
+test performance using different block sizes. Allowing multiple blocks per
+processor could increase cache reuse and allow a performance increase.
+
+This work is currently being performed under
+branches/omp\_blocks/multiple\_blocks and all source code changes can be
+examined there.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Requirements
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Requirements}
+
+There are significant changes to MPAS' framework that have to be made in order
+to support multiple blocks. A list of requirements that determine these changes
+are listed below, with the reasons for these requirements written below them.
+
+\begin{itemize}
+ \item Block creation must be robust, and handle an arbitrary number
+ of blocks per processor.
+
+ \item Blocks should be created using the derived data types created in an
+ earlier project, promoting the use of field data types rather than
+ simple arrays.
+
+ \item Block creation routines should be created with an arbitrary number of
+ halos assumed, although the default is currently two.
+
+ \item All block communication routines should be able to handle shared
+ memory copies.
+
+ \item Exchange list creation should be performed at the block/field level.
+
+ \item Block creation code should be isolated from the rest of MPAS code.
+\end{itemize}
+
+Blocks per processor should be allowed to be any non-negative number, including
+zero. This could be useful if a user wanted the ability to specify certain
+processors to do certain tasks, without doing any actual computation work on
+blocks. Although the user would have to give an explicit block to proc
+decomposition in order to have this ability used.
+
+In the creation of blocks, field data types should be used in place of simple
+arrays to promote the use of internal derived data types that are used
+elsewhere within MPAS. This will allow similar techniques to be identified by
+developers of cores, and allow a similar work flow with variables and fields
+within all of MPAS.
+
+Although fields currently are restricted to having two halo layers, at some
+point in the future we might like to be able to extend halo layers or even have
+different halo layers on each field. In order to make this task easier to
+accomplish in the future block creation routines need to be able to create an
+arbitrary number of halo layers.
+
+When two blocks are neighboring on a single processor shared memory copies
+could be used for halo exchanges and other sorts of block-to-block
+communications rather than using MPI send/recv routines.
+
+Exchange lists are limited in their functionality by the fact that the only
+information they have refer to the other processor/block involved in the
+communication. For example, if processor 0 owns block 0 and this has to send
+information from 15 cells to processor 2 block 5 then the send list for block 0
+only gives the information on where it has to send the information, while the
+receive list on block 5 gives information on where to receive the information
+from. Because of this, exchange lists have to be created on a per block basis,
+and linked to a specific block. This way each block knows which cells it's
+supposed to send/recv/copy to/from another block. Each field and block have
+their own exchange lists, so the creation of exchange lists should place them
+within these already existing structures.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Design
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Design}
+
+Only a small amount of design has been completed thus far. So, all information
+in this section should be regarded as a work in progress for now. As a visual
+for the design process, the proposed module layout can be seen in figure
+\ref{fig:module_layout}.
+
+\begin{figure}[H!]
+ \centering
+ \includegraphics[scale=0.4]{DesignLayout.eps}
+ \caption{Layout of modules for input/output with multiple blocks}
+ \label{fig:module_layout}
+\end{figure}
+
+The changes made to mpas framework can be seen in the following sections.
+
+\section{Changes in mpas\_dmpar}
+This section covers the changes, and the new functionality of the changes that
+were made within the mpas\_dmpar.F file. The first major change, is that dmpar
+is renamed to comm meaning communications.
+
+\subsection{Data types}
+Previously the derived data type mpas\_exchange\_list was used to create a linked list which represented an exchange list (send or receive). Exchange lists have been modified from their original state to have the following structure.
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+type mpas_exchange_list
+ integer :: endPointID
+ integer :: nlist
+ integer, dimension(:), pointer :: srcList
+ integer, dimension(:), pointer :: destList
+ type (mpas_exchange_list), pointer :: next
+end type mpas_exchange_list
+\end{lstlisting}
+
+Within this structure endPointID can be either a blockID (for local copy) or a procID for mpi send/recv, nList represents the number of elements to be communication within this exchange list, srcList and destList represent the information for packing and unpacking data into buffers or for local copies from/to arrays.
+
+Seeing as the exchange lists no longer contain an array for the communication buffers a new data type was created which can be seen below.
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+type mpas_communication_list
+ integer :: procID
+ integer :: nlist
+ real (kind=RKIND), dimension(:), pointer :: rbuffer
+ integer, dimension(:), pointer :: ibuffer
+ integer :: reqID
+ type (mpas_communication_list), pointer :: next
+end type mpas_communication_list
+\end{lstlisting}
+
+An mpas\_communcation\_list is only intended to be used for mpi communications. These have to be created and destroyed each time a communcation is performed. Within the structure, procID represents the other endPoint's processor ID in the communication, nList is the number of elements to be communicated within the buffer, rbuffer and ibuffer are the pointers for the buffer of either integers or reals, reqID represents the mpi communcation id, and next creates a linked list.
+
+Two other data structures are created to allow multi halo exchange lists, and to allow pointers to be swapped easily using them.
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+type mpas_exchange_list_pointer
+ type (mpas_exchange_list), pointer :: exchList
+end type mpas_exchange_list_pointer
+
+type mpas_multihalo_exchange_list
+ type (mpas_exchange_list_pointer), dimension(:), pointer :: halos
+end type mpas_multihalo_exchange_list
+\end{lstlisting}
+
+Combining these four structures allows local and mpi communications to occur smoothly.
+
+\subsection{mpas\_comm\_get\_exch\_list}
+The old routine named mpas\_dmpar\_get\_owner\_list is now renamed to mpas\_comm\_get\_exch\_list. This routine is meant to create send, receive, and copy lists to send data from one processor to another. During initialization it's used for the allToAll communication routines (which will be described below) but within cores it's almost exclusively used for halo exchanges.
+
+It works by creating two lists of element id's (typically cells, edges, or vertices). One of these lists is owned elements while the other is needed elements. The needed list is communication round robin style to each processor until it comes back to the original processor. Each processor marks a needed element in the list as owned if it owns it. This way the processor that needs the element knows who it's supposed to receive the element from.
+
+During the round robin communications send lists are created as needed elements are marked as owned. After the round robin communications are finished receive lists are created. And after receive lists are created copy lists are created in a similar fashion to send lists.
+
+\subsection{allToAll routines}
+mpas\_comm provides a set of allToAll routines intended to distribute a field from one processor to one or more other processors. In this case, the sending information is supposed to include the 0 halo elements. In contrast to the exch\_halo routines which are intended to only communication 1+ halo elements.
+
+A pseudocode version of the allToAll routines can be seen below.
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+loop over fieldOut list
+ loop over recvList for specific field
+ create new communication list if needed
+ end loop
+end loop
+
+allocate recvList buffers and initiate mpi_irecvs
+
+loop over fieldIn list
+ loop over sendList for specific field
+ create new communication list if needed
+ end loop
+end loop
+
+allocate sendList buffers, copy data into buffer
+ initiate mpi_isends
+
+loop over fieldIn list
+ loop over copyList for specific field
+ loop over fieldOut list
+ if fieldOut % blockID == copyList % endPointID
+ use copy list to copy from fieldIn to fieldOut
+ end if
+ end loop
+ end loop
+end loop
+
+wait for mpi_irecvs
+ unpack buffer into fields
+
+wait for mpi_isends
+
+destroy buffers
+\end{lstlisting}
+
+\subsection{exch\_halo routines}
+mpas\_comm provides a set of halo exchange routines intended to distribute a set of 0 halo elements to other blocks that have them in their 1+ halo regions.
+
+A pseudocode version of the halo exchange routines can be seen below.
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+loop over field list
+ loop over recvList for specific field
+ create new communication list if needed
+ end loop
+end loop
+
+allocate recvList buffers and initiate mpi_irecvs
+
+loop over field list
+ loop over sendList for specific field
+ create new communication list if needed
+ end loop
+end loop
+
+allocate sendList buffers, copy data into buffer
+ initiate mpi_isends
+
+loop over field list
+ loop over copyList for specific field
+ loop over field list
+ if field % blockID == copyList % endPointID
+ use copy list to copy from fieldIn to fieldOut
+ end if
+ end loop
+ end loop
+end loop
+
+wait for mpi_irecvs
+ unpack buffer into fields
+
+wait for mpi_isends
+
+destroy buffers
+\end{lstlisting}
+
+\subsection{copy routines}
+mpas\_comm provides a set of routines intended to copy a field from the header block in a list of owned blocks to all other blocks in the list. These are needed during initialization to copy non-decomposed fields (fields that don't include the nCells, nEdges, or nVertices as a dimension) to all owned blocks.
+
+\subsection{Utility routines}
+In addition to communcation routines, mpas\_comm provides utility routines for the initialization and destruction of all derived data types discussed above.
+
+\section{mpas\_block\_creator.F}
+mpas\_block\_creator provides a new module for mpas that is used to create computational blocks. Given the information of a 0 halo, these routines create the 1+ halo regions for cells, edges, and vertices. They also initialize the list of local blocks.
+
+\subsection{Cell Routines}
+Routines to setup cell fields within a block are:
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+mpas_block_creator_setup_blocks_and_0halo_cells
+mpas_block_creator_build_0halo_cell_fields
+mpas_block_creator_build_cell_halos
+\end{lstlisting}
+
+These routines should be called in this order to properly setup the 0-1+ halo of cells. However, the build\_cell\_halos routine should not be called until all 0 halo fields are setup (including edges and vertices).
+
+\subsection{Edge/Vertex Routines}
+Routines used to setup edge/vertex fields within a block are:
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+mpas_block_creator_build_0_and_1halo_edge_fields
+mpas_block_creator_build_edge_halos
+\end{lstlisting}
+
+As mentioned in the cell routine section, the 0-1 halos of edges and vertices should be setup prior to setting up the 1+ halos of cells.
+
+\subsection{Utility Routines}
+Finally, two routines are provided to finalize the block initialization, and to re-index all fields in a block.
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+mpas_block_creator_finalize_block_init
+mpas_block_creator_reindex_block_fields
+\end{lstlisting}
+
+These routines complete the block creation processor, and provide the rest of a model with a list of fully setup blocks to compute on.
+
+\section{mpas\_io\_input changes}
+Within mpas\_io\_input the main mpas\_input\_state\_for\_domain routine has been trimmed significantly to make use of the new mpas\_block\_creator module the portions of the routine that were not able to be moved into the block\_creator module were moved to new routines within the io\_input module.
+
+This module also makes use of the new communication routines from mpas\_comm, as well as some routines in mpas\_block\_decomp.
+
+The new routines provided to clean up mpas\_input\_state\_for\_domain are:
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+mpas_io_setup_cell_block_fields
+mpas_io_setup_edge_block_fields
+mpas_io_setup_vertex_block_fields
+\end{lstlisting}
+These routines are intended to read in contiguous chunks of data that can then be communication between processors.
+
+\section{mpas\_grid\_types changes}
+Within mpas\_grid\_types, utility routines are created to deallocate fields. This is used within mpas\_io\_input for fields that need to be linked similarly to block, but are not part of the block data structure.
+
+In addition to utility routine additions, a pointer provis was created within the block\_type. provis is intended to be a scratch state. This can be used within time integration routines that require an additional time level, without having to modify the number of time levels within state.
+
+\section{Namelist changes}
+With the addition of multiple blocks in the framework of mpas, the decomposition namelist section will be made use of. This section provides the following namelist options.
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+config_block_decomp_file_prefix
+config_number_of_blocks
+config_explicit_proc_decomp
+config_proc_decomp_file_prefix
+\end{lstlisting}
+
+The prefix options are used to specify the prefixes on decomposition graph files used to create blocks, and determine which blocks are owned by which processors, config\_number\_of\_blocks determines how many blocks the simulation is supposed to be run with, and config\_explicit\_proc\_decomp is a logical flag which determines if mpas should look for a graph file describing how blocks should be distributed between processor, or if it should round robin assign blocks to processors.
+
+In addition to the decomposition section changes, the model sections (like sw\_model) now has a new namelist option:
+
+\begin{lstlisting}[language=fortran,escapechar=@,frame=single]
+config_num_halos
+\end{lstlisting}
+
+This namelist flag determines how many halo layers each block should have on cells. The halo layers for edges and vertices are nHaloLayerCells+1, or config\_num\_halos + 1.
+
+\chapter{Testing}
+**NOTE**
+All of the testing described in this section relates only to the ocean core.
+Other core developers may test this with similar procedures but different
+simulations. \\
+
+The end goal from this project is to provide a framework that allows
+bit-for-bit reproduction of data using an arbitrary combination of blocks and
+processor numbers.
+
+Using this goal to define a testing strategy implies a good test would be
+exploring bit-for-bit reproduction of output data using the three following
+simulations:
+\begin{itemize}
+ \item Current trunk simulation run with 8 processors and 8 blocks (1 block per proc).
+ \item Finished branch simulation run with 8 processors and 8 blocks (1 block per proc).
+ \item Finished branch simulation run with 1 processor and 8 blocks (8 blocks per proc).
+ \item Finished branch simulation run with 2 processors and 8 blocks (4 blocks per proc).
+\end{itemize}
+
+If all of these simulations produce bit-for-bit output then testing can move on
+to a set of larger scale simulations.
+
+\begin{itemize}
+ \item Current trunk 15km simulation with 1200 processors and 1200 blocks (1 block per proc).
+ \item Finished branch simulation with 1200 processors and 1200 blocks (1 block per proc).
+ \item Finished branch simulation with 600 processors and 1200 blocks (2 blocks per proc).
+ \item Finished branch simulation with 24 processors and 1200 blocks (50 blocks per proc).
+\end{itemize}
+
+After these final four simulations show bit-for-bit output then the project can
+be deemed as completed.
+
+\chapter{Appendix - Use of exchange/communication lists}
+This chapter will describe the use of exchange and communication lists.
+
+To begin, exchange lists have two uses. First copyLists will be described,
+followed by send/recvLists.
+
+copyLists are attached to the block sending the data, and there is no matching
+list on the receiving end. Within the copyList, the endPointID variable
+represents a blockID giving the local id to the block on the other end of the
+communication, nList is the total number of elements that need to be copied,
+srcList is the list of indices to take this data from out of the owning field's
+array, and destList is the list of indices to put this data into the needing
+field's array.
+
+In using copyLists, first a search over blocks needs to be preformed
+to find the matching block for the communication. After that the elements
+listed in srcList are copied into the elements listed in destList. After which,
+the shared memory copy is complete.
+
+The second use case relates to send/recvLists. sendLists are attached to
+sending blocks, while recvLists are attached to receiving blocks. Within both
+of these, endPointID refers to a processor id, and nList refers to the number
+of elements a specific block should expect to communicate. In a sendList,
+srcList describes the indices to pull data out from the owning field's array
+while destList descibes the indices to put that data into a communication
+list's buffer. In a recvList, srcList describes the indices to pull the data
+out of the buffer, while destList describes the indices to put that data into
+the needing field's array.
+
+In order to use these, each side of the communication does something different.
+Before describing the use of send and recv lists, communication lists need to
+be explained.
+
+A communication list describes aggregated communications between processors.
+These provide an easy to use framework to allow communications to occur
+processor by processor as opposed to block by block. Since communication lists
+only relate to MPI communications, the only ID within the type is procID. nList
+refers to the number of elements in the buffer, while rbuffer and ibuffer
+provide deallocated arrays to put reals or integers in the buffer, and reqID
+provides a variable to store MPI communication ID's to use when calling
+MPI\_Wait.
+
+In order to perform a send an receive, first a processor needs to build the
+buffers, or communication lists. To begin the fields relating to the specific
+communication are looped over, and the total number of elements to each
+processor are stored in order to build a communication list for that processor.
+After this step, the communication list buffers are allocated relating to their
+nList varibles. Buffers need to be created both on the sending and receiving
+side. After the buffers are created, the sending field copies all of it's data
+into the array. The buffer is then sent, and on the receiving end the receiving
+field unpacks all of the data into it's arrays.
+\end{document}
</font>
</pre>