Changeset 13012

Timestamp:

08/13/12 12:11:44 (13 years ago)

Author:

Mathieu Morlighem

Message:

CHG: moving stuff around

Location:

issm/trunk-jpl/src/m

Files:

• classes/modellist.m (modified) (1 diff)
• contrib/bamg (added)
• contrib/bamg/BamgCall.m (moved) (moved from issm/trunk-jpl/src/m/mesh/BamgCall.m )
• contrib/bamg/BamgCallFromMetric.m (moved) (moved from issm/trunk-jpl/src/m/mesh/BamgCallFromMetric.m )
• contrib/bamg/YamsCall.m (moved) (moved from issm/trunk-jpl/src/m/mesh/YamsCall.m )
• contrib/bamg/meshread.m (moved) (moved from issm/trunk-jpl/src/m/mesh/meshread.m )
• contrib/bamg/yams.m (moved) (moved from issm/trunk-jpl/src/m/mesh/yams.m )
• geometry/GetAreas.m (moved) (moved from issm/trunk-jpl/src/m/mesh/GetAreas.m )
• mesh/FixMesh.m (modified) (1 diff)
• mesh/GetCharacteristicLength.m (deleted)
• mesh/NodeInElement.m (modified) (1 diff)
• mesh/isconnected.m (deleted)
• mesh/rifts/meshprocessoutsiderifts.m (modified) (1 diff)
• mesh/rifts/rifttipsonmesh.m (moved) (moved from issm/trunk-jpl/src/m/mesh/rifttipsonmesh.m )
• miscellaneous/create_region.m (deleted)
• miscellaneous/findarg.m (deleted)
• miscellaneous/netcdf.m (deleted)
• miscellaneous/netcdf2struct.m (modified) (2 diffs)
• multiplequeue (deleted)

issm/trunk-jpl/src/m/classes/modellist.m

@@ -292 +292 @@
         end
 end
+
+function BuildMultipleQueueingScript(cluster,name,executionpath,codepath)% {{{
+%BUILDMULTIPLEQUEUEINGSCRIPT - 
+%
+%   Usage:
+%      BuildMultipleQueueingScript(executionpath,codepath)
+
+disp('building queueing script');
+
+%First try and figure out if there is a special script for this particular cluster
+function_name=['BuildMultipleQueueingScript' cluster];
+
+%some specific treatment of identical cluster, gemini, castor and pollux
+if strcmpi(cluster,'castor') || strcmpi(cluster,'pollux'),
+        function_name='BuildMultipleQueueingScriptgemini';
+end
+
+if exist(function_name,'file'),
+        %Call this function:
+        eval([function_name '(name,executionpath,codepath);']);
+else
+        %Call the generic BuildQueueingScript:
+        BuildMultipleQueueingScriptGeneric(name,executionpath,codepath);
+end
+end % }}}
+function BuildQueueingScriptgemini(name,executionpath,codepath)% {{{
+%BUILDQUEUEINGSCRIPTGEMINI - ...
+%
+%   Usage:
+%      BuildQueueingScriptgemini(md,executionpath,codepath)
+
+scriptname=[name '.queue'];
+
+fid=fopen(scriptname,'w');
+if fid==-1,
+        error(['BuildQueueingScriptgeminierror message: could not open ' scriptname ' file for ascii writing']);
+end
+
+fprintf(fid,'#!/bin/sh\n');
+fprintf(fid,'cd %s\n',executionpath);
+fprintf(fid,'mkdir %s\n',name);
+fprintf(fid,'cd %s\n',name);
+fprintf(fid,'mv ../ModelList.tar.gz ./\n');
+fprintf(fid,'tar -zxvf ModelList.tar.gz\n');
+fprintf(fid,'foreach i (%s-*vs*.queue)\n',name);
+fprintf(fid,'qsub $i\n');
+fprintf(fid,'end\n');
+fclose(fid);
+end% }}}
+function LaunchMultipleQueueJob(cluster,name,executionpath)% {{{
+%LAUNCHMULTIPLEQUEUEJOB - ...
+%
+%   Usage:
+%      LaunchMultipleQueueJob(executionpath)
+
+%First try and figure out if there is a special script for thie particular cluster
+function_name=['LaunchMultipleQueueJob' cluster];
+
+%some specific treatment of identical cluster, gemini, castor and pollux
+if strcmpi(cluster,'castor') || strcmpi(cluster,'pollux'),
+        function_name='LaunchMultipleQueueJobgemini';
+end
+
+if exist(function_name,'file'),
+        %Call this function:
+        eval([function_name '(cluster,name,executionpath);']);
+else
+        %Call the generic LaunchMultipleQueueJob:
+        LaunchMultipleQueueJobGeneric(cluster,name,executionpath);
+end
+end% }}}
+function md=LaunchMultipleQueueJobgemini(cluster,name,executionpath)% {{{
+%LAUNCHMULTIPLEQUEUEJOBGEMINI - Launch multiple queueing script on Gemini cluster
+%
+%   Usage:
+%      LaunchMultipleQueueJobgemini(cluster,name,executionpath)
+
+
+%first, check we have the binary file and the queueing script
+if ~exist([ name '.queue'],'file'),
+        error('LaunchMultipleQueueJobgemini error message: queueing script issing, cannot go forward');
+end
+
+if ~exist('ModelList.tar.gz','file'),
+        error('LaunchMultipleQueueJobgemini error message: inputs models file missing, cannot go forward');
+end
+
+%upload both files to cluster
+disp('uploading input file,  queueing script and variables script');
+eval(['!scp ModelList.tar.gz ' name '.queue '  cluster ':' executionpath]);
+
+disp('launching solution sequence on remote cluster');
+issmssh(cluster,login,['"cd ' executionpath ' && source ' name '.queue "']);
+end% }}}

issm/trunk-jpl/src/m/mesh/FixMesh.m

@@ -1 +1 @@
 function  [index2 x2 y2 value2]=FixMesh(index,x,y,value)
-%FixMesh fix mesh with broken triangles, orphan vertices, etc ...
+% FIXMESH - FixMesh fix mesh with broken triangles, orphan vertices, etc ...
 %
-% Usage: 
-%            [index2 x2 y2 value2]=FixMesh(index,x,y,value)
-%            where index,x,y is a delaunay triangulation, 
-%                  value is a field on the input triangulation, with values at the vertices
-%                  index2,x2,y2,value2 is the repaired triangulation, with new values on new vertices
+%   Usage: 
+%      [index2 x2 y2 value2]=FixMesh(index,x,y,value)
+%      where index,x,y is a delaunay triangulation, 
+%      value is a field on the input triangulation, with values at the vertices
+%      index2,x2,y2,value2 is the repaired triangulation, with new values on new vertices
 %
 %

issm/trunk-jpl/src/m/mesh/NodeInElement.m

@@ -1 +1 @@
 function node_in_element=NodeInElement(newx,newy,elements,x,y,nodeconnectivity);
-%NODEINELEMENT: find for a list of nodes (in newx,newy), which elements in the mesh (elements,x,y) they belong to.
+% NODEINELEMENT - find for a list of nodes (in newx,newy), which elements in the mesh (elements,x,y) they belong to.
 %
-%  Usage: node_in_element=NodeInElement(newx,newy,elements,x,y,md.mesh.vertexconnectivity);
+%    Usage:
+%      node_in_element=NodeInElement(newx,newy,elements,x,y,md.mesh.vertexconnectivity);
 %
 %  See also Nodeconnectivity

issm/trunk-jpl/src/m/mesh/rifts/meshprocessoutsiderifts.m

@@ -93 +93 @@
 md.mesh.elementonbed=ones(md.mesh.numberofelements,1);
 md.mesh.elementonsurface=ones(md.mesh.numberofelements,1);
+end
+
+function flag=isconnected(elements,A,B)% {{{
+        %ISCONNECTED: are two nodes connected by a triangulation?
+        %
+        %   Usage: flag=isconnected(elements,A,B)
+        %
+        %
+
+        elements=ElementsFromEdge(elements,A,B);
+        if isempty(elements),
+                flag=0;
+        else
+                flag=1;
+        end
+end % }}}

issm/trunk-jpl/src/m/miscellaneous/netcdf2struct.m

@@ -6 +6 @@
 
 %Read netcdf file
-data=netcdf(File);
+data=readnetcdf(File);
 
 %initialize output
@@ -26 +26 @@
         S.(fieldname)=fieldvalue;
 end
+end
+
+function S = readnetcdf(File,varargin)
+% Function to read NetCDF files
+%   S = netcdf(File)
+% Input Arguments
+%   File = NetCDF file to read
+% Optional Input Arguments:
+%   'Var',Var - Read data for VarArray(Var), default [1:length(S.VarArray)]
+%   'Rec',Rec - Read data for Record(Rec), default [1:S.NumRecs]
+% Output Arguments:
+%   S    = Structure of NetCDF data organised as per NetCDF definition
+% Notes:
+%   Only version 1, classic 32bit, NetCDF files are supported. By default
+% data are extracted into the S.VarArray().Data field for all variables.
+% To read the header only call S = netcdf(File,'Var',[]);
+%
+% SEE ALSO
+% ---------------------------------------------------------------------------
+S = [];
+
+try
+   if exist(File,'file') fp = fopen(File,'r','b');
+   else fp = []; error('File not found'); end
+   if fp == -1   error('Unable to open file'); end
+
+% Read header
+   Magic = fread(fp,4,'uint8=>char');
+   if strcmp(Magic(1:3),'CDF') error('Not a NetCDF file'); end
+   if uint8(Magic(4))~=1       error('Version not supported'); end
+   S.NumRecs  = fread(fp,1,'uint32=>uint32');
+   S.DimArray = DimArray(fp);
+   S.AttArray = AttArray(fp);
+   S.VarArray = VarArray(fp);
+
+% Setup indexing to arrays and records
+   Var = ones(1,length(S.VarArray));
+   Rec = ones(1,S.NumRecs);
+   for i = 1:2:length(varargin)
+      if     strcmp(upper(varargin{i}),'VAR') Var=Var*0; Var(varargin{i+1})=1;
+      elseif strcmp(upper(varargin{i}),'REC') Rec=Rec*0; Rec(varargin{i+1})=1;
+      else error('Optional input argument not recognised'); end
+   end
+   if sum(Var)==0 fclose(fp); return; end
+
+% Read non-record variables
+   Dim = double(cat(2,S.DimArray.Dim));
+   ID  = double(cat(2,S.VarArray.Type));
+
+   for i = 1:length(S.VarArray)
+      D = Dim(S.VarArray(i).DimID+1); N = prod(D); RecID{i}=find(D==0);
+      if isempty(RecID{i})
+         if length(D)==0 D = [1,1]; N = 1; elseif length(D)==1 D=[D,1]; end
+         if Var(i)
+            S.VarArray(i).Data = ReOrder(fread(fp,N,[Type(ID(i)),'=>',Type(ID(i))]),D);
+            fread(fp,(Pad(N,ID(i))-N)*Size(ID(i)),'uint8=>uint8');
+         else fseek(fp,Pad(N,ID(i))*Size(ID(i)),'cof'); end
+      else S.VarArray(i).Data = []; end
+   end
+
+% Read record variables
+   for k = 1:S.NumRecs
+      for i = 1:length(S.VarArray)
+         if ~isempty(RecID{i})
+            D = Dim(S.VarArray(i).DimID+1); D(RecID{i}) = 1; N = prod(D);
+            if length(D)==1 D=[D,1]; end
+            if Var(i) & Rec(k)
+               S.VarArray(i).Data = cat(RecID{i},S.VarArray(i).Data,...
+                  ReOrder(fread(fp,N,[Type(ID(i)),'=>',Type(ID(i))]),D));
+               if N > 1 fread(fp,(Pad(N,ID(i))-N)*Size(ID(i)),'uint8=>uint8'); end
+            else fseek(fp,Pad(N,ID(i))*Size(ID(i)),'cof'); end
+         end
+      end
+   end
+
+   fclose(fp);
+catch
+   Err = lasterror; fprintf('%s\n',Err.message);
+   if ~isempty(fp) && fp ~= -1 fclose(fp); end
+end
+
+% ---------------------------------------------------------------------------------------
+% Utility functions
+
+function S = Size(ID)
+% Size of NetCDF data type, ID, in bytes
+   S = subsref([1,1,2,4,4,8],struct('type','()','subs',{{ID}}));
+
+function T = Type(ID)
+% Matlab string for CDF data type, ID
+   T = subsref({'int8','char','int16','int32','single','double'},...
+               struct('type','{}','subs',{{ID}}));
+
+function N = Pad(Num,ID)
+% Number of elements to read after padding to 4 bytes for type ID
+   N = (double(Num) + mod(4-double(Num)*Size(ID),4)/Size(ID)).*(Num~=0);
+
+function S = String(fp)
+% Read a CDF string; Size,[String,[Padding]]
+   S = fread(fp,Pad(fread(fp,1,'uint32=>uint32'),1),'uint8=>char').';
+
+function A = ReOrder(A,S)
+% Rearrange CDF array A to size S with matlab ordering
+   A = permute(reshape(A,fliplr(S)),fliplr(1:length(S)));
+
+function S = DimArray(fp)
+% Read DimArray into structure
+   if fread(fp,1,'uint32=>uint32') == 10 % NC_DIMENSION
+      for i = 1:fread(fp,1,'uint32=>uint32')
+         S(i).Str = String(fp);
+         S(i).Dim = fread(fp,1,'uint32=>uint32');
+      end
+   else fread(fp,1,'uint32=>uint32'); S = []; end
+
+function S = AttArray(fp)
+% Read AttArray into structure
+   if fread(fp,1,'uint32=>uint32') == 12 % NC_ATTRIBUTE
+      for i = 1:fread(fp,1,'uint32=>uint32')
+         S(i).Str = String(fp);
+         ID       = fread(fp,1,'uint32=>uint32');
+         Num      = fread(fp,1,'uint32=>uint32');
+         S(i).Val = fread(fp,Pad(Num,ID),[Type(ID),'=>',Type(ID)]).';
+      end
+   else fread(fp,1,'uint32=>uint32'); S = []; end
+
+function S = VarArray(fp)
+% Read VarArray into structure
+   if fread(fp,1,'uint32=>uint32') == 11 % NC_VARIABLE
+      for i = 1:fread(fp,1,'uint32=>uint32')
+         S(i).Str      = String(fp);
+         Num           = double(fread(fp,1,'uint32=>uint32'));
+         S(i).DimID    = double(fread(fp,Num,'uint32=>uint32'));
+         S(i).AttArray = AttArray(fp);
+         S(i).Type     = fread(fp,1,'uint32=>uint32');
+         S(i).VSize    = fread(fp,1,'uint32=>uint32');
+         S(i).Begin    = fread(fp,1,'uint32=>uint32'); % Classic 32 bit format only
+      end
+   else fread(fp,1,'uint32=>uint32'); S = []; end
+end