parallelization system:
* documented the functions masterParallel, fParallel and struct2local * removed useless comments, and added some comments inside the code git-svn-id: https://www.dynare.org/svn/dynare/trunk@3146 ac1d8469-bf42-47a9-8791-bf33cf982152time-shift
sebastien
parent
76e691c651
commit
7085060e82
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@ -96,7 +96,7 @@ localVars.NumberOfLines = NumberOfLines;
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localVars.time = time;
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localVars.M_ = M_;
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if isnumeric(options_.parallel),% | isunix, % for the moment exclude unix platform from parallel implementation
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if isnumeric(options_.parallel),
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fout = McMCDiagnostics_core(localVars,1,npar,0);
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UDIAG = fout.UDIAG;
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clear fout
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@ -108,52 +108,6 @@ else
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end
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end
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% for j=1:npar
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% fprintf(' Parameter %d... ',j);
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% for b = 1:nblck
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% startline = 0;
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% for n = 1:NumberOfMcFilesPerBlock
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% %load([MhDirectoryName '/' mcfiles(n,1,b).name],'x2');
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% load([MhDirectoryName '/' M_.fname '_mh',int2str(n),'_blck' int2str(b) ...
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% '.mat'],'x2');
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% nx2 = size(x2,1);
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% tmp((b-1)*NumberOfDraws+startline+(1:nx2),1) = x2(:,j);
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% % clear x2;
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% startline = startline + nx2;
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% end
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% % $$$ %load([MhDirectoryName '/' mcfiles(NumberOfMcFilesPerBlock,1,b).name],'x2');
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% % $$$ load([MhDirectoryName '/' M_.fname '_mh',int2str(NumberOfMcFilesPerBlock),'_blck' int2str(b) '.mat'],'x2');
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% % $$$ tmp((b-1)*NumberOfDraws+startline+1:(b-1)*NumberOfDraws+MAX_nruns*(LastFileNumber-1)+LastLineNumber,1) = x2(:,j);
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% % $$$ clear x2;
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% % $$$ startline = startline + LastLineNumber;
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% end
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% tmp(:,2) = kron(transpose(1:nblck),ones(NumberOfDraws,1));
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% tmp(:,3) = kron(ones(nblck,1),time');
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% tmp = sortrows(tmp,1);
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% ligne = 0;
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% for iter = Origin:StepSize:NumberOfDraws
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% ligne = ligne+1;
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% linea = ceil(0.5*iter);
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% n = iter-linea+1;
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% cinf = round(n*ALPHA/2);
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% csup = round(n*(1-ALPHA/2));
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% CINF = round(nblck*n*ALPHA/2);
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% CSUP = round(nblck*n*(1-ALPHA/2));
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% temp = tmp(find((tmp(:,3)>=linea) & (tmp(:,3)<=iter)),1:2);
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% UDIAG(ligne,1,j) = temp(CSUP,1)-temp(CINF,1);
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% moyenne = mean(temp(:,1));%% Pooled mean.
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% UDIAG(ligne,3,j) = sum((temp(:,1)-moyenne).^2)/(nblck*n-1);
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% UDIAG(ligne,5,j) = sum(abs(temp(:,1)-moyenne).^3)/(nblck*n-1);
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% for i=1:nblck
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% pmet = temp(find(temp(:,2)==i));
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% UDIAG(ligne,2,j) = UDIAG(ligne,2,j) + pmet(csup,1)-pmet(cinf,1);
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% moyenne = mean(pmet,1); %% Within mean.
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% UDIAG(ligne,4,j) = UDIAG(ligne,4,j) + sum((pmet(:,1)-moyenne).^2)/(n-1);
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% UDIAG(ligne,6,j) = UDIAG(ligne,6,j) + sum(abs(pmet(:,1)-moyenne).^3)/(n-1);
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% end
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% end
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% fprintf('Done! \n');
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% end
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UDIAG(:,[2 4 6],:) = UDIAG(:,[2 4 6],:)/nblck;
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disp(' ')
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clear pmet temp moyenne CSUP CINF csup cinf n linea iter tmp;
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@ -30,12 +30,9 @@ end
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ALPHA = 0.2; % increase too much with the number of simulations.
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tmp = zeros(NumberOfDraws*nblck,3);
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UDIAG = zeros(NumberOfLines,6,npar-fpar+1);
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% keyboard;
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if whoiam
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% keyboard;
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waitbarString = ['Please wait... McMCDiagnostics (' int2str(fpar) 'of' int2str(npar) ')...'];
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% waitbarTitle=['McMCDiagnostics ',Parallel(ThisMatlab).PcName];
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if Parallel(ThisMatlab).Local,
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waitbarTitle=['Local '];
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else
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@ -89,7 +86,6 @@ for j=fpar:npar,
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end
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fprintf('Done! \n');
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if whoiam,
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% keyboard;
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waitbarString = [ 'Parameter ' int2str(j) '/' int2str(npar) ' done.'];
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fMessageStatus((j-fpar+1)/(npar-fpar+1),whoiam,waitbarString, waitbarTitle, Parallel(ThisMatlab), MasterName, DyMo)
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end
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@ -1,4 +1,18 @@
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function fParallel(fblck,nblck,whoiam,ThisMatlab,fname);
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function fParallel(fblck,nblck,whoiam,ThisMatlab,fname)
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% In a parallelization context, this function is launched on slave
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% machines, and acts as a wrapper around the function containing the
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% computing task itself.
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%
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% INPUTS
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% fblck [int] index number of the first thread to run in this
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% MATLAB instance
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% nblck [int] index number of the first thread to run in this
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% MATLAB instance
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% whoiam [int] index number of this CPU among all CPUs in the
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% cluster
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% ThisMatlab [int] index number of this slave machine in the cluster
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% (entry in options_.parallel)
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% fname [string] function to be run, containing the computing task
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% Copyright (C) 2009 Dynare Team
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%
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@ -32,8 +46,9 @@ diary( [fname,'_',int2str(whoiam),'.log']);
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% configure dynare environment
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dynareroot = dynare_config();
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% Load input data
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load( [fname,'_input'])
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% keyboard;
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if exist('fGlobalVar'),
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globalVars = fieldnames(fGlobalVar);
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for j=1:length(globalVars),
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@ -42,11 +57,13 @@ if exist('fGlobalVar'),
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struct2local(fGlobalVar);
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end
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% On UNIX, mount the master working directory through SSH FS
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if isunix & Parallel(ThisMatlab).Local==0,
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system(['mkdir ~/MasterRemoteMirror_',fname,'_',int2str(whoiam)]);
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system(['sshfs ',Parallel(ThisMatlab).user,'@',fInputVar.MasterName,':/',fInputVar.DyMo,' ~/MasterRemoteMirror_',fname,'_',int2str(whoiam)]);
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end
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% Special hack for MH directory
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if isfield(fInputVar,'MhDirectoryName') & Parallel(ThisMatlab).Local==0,
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if isunix,
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fInputVar.MhDirectoryName = ['~/MasterRemoteMirror_',fname,'_',int2str(whoiam),'/',fInputVar.MhDirectoryName];
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@ -56,27 +73,24 @@ if isfield(fInputVar,'MhDirectoryName') & Parallel(ThisMatlab).Local==0,
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end
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fInputVar.Parallel = Parallel;
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% lounch the routine to be run in parallel
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% Launch the routine to be run in parallel
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tic,
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fOutputVar = feval(fname, fInputVar ,fblck, nblck, whoiam, ThisMatlab);
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toc,
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if isfield(fOutputVar,'OutputFileName'),
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OutputFileName = fOutputVar.OutputFileName;
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% rmfield(fOutputVar,'OutputFileName');
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else
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OutputFileName = '';
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end
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%%% Sincronismo "Esterno" %%%%%%%%%%%%%
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%%% Ogni Processo quando ha finito lo notifica cancellando un file ...
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% keyboard;
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if(whoiam)
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% Save the output result
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save([ fname,'_output_',int2str(whoiam),'.mat'],'fOutputVar' )
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% Inform the master that the job is finished, and transfer the output data
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if Parallel(ThisMatlab).Local
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delete(['P_',fname,'_',int2str(whoiam),'End.txt']);
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else
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if isunix,
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for j=1:size(OutputFileName,1),
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@ -1,4 +1,33 @@
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function [fOutVar,nBlockPerCPU, totCPU] = masterParallel(Parallel,fBlock,nBlock,NamFileInput,fname,fInputVar,fGlobalVar)
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% Top-level function called on the master computer when parallelizing a task.
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%
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% The number of parallelized threads will be equal to (nBlock-fBlock+1).
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%
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% INPUTS
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% Parallel [struct vector] copy of options_.parallel
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% fBlock [int] index number of the first thread
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% (between 1 and nBlock)
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% nBlock [int] index number of the last thread
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% NamFileInput [cell array] containins the list of input files to be
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% copied in the working directory of remote slaves
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% 2 columns, as many lines as there are files
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% - first column contains directory paths
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% - second column contains filenames
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% fname [string] name of the function to be parallelized, and
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% which will be run on the slaves
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% fInputVar [struct] structure containing local variables to be used
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% by fName on the slaves
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% fGlobalVar [struct] structure containing global variables to be used
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% by fName on the slaves
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%
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% OUTPUT
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% fOutVar [struct vector] result of the parallel computation, one
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% struct per thread
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% nBlockPerCPU [int vector] for each CPU used, indicates the number of
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% threads run on that CPU
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% totCPU [int] total number of CPU used (can be lower than
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% the number of CPU declared in "Parallel", if
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% the number of required threads is lower)
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% Copyright (C) 2009 Dynare Team
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%
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@ -17,9 +46,9 @@ function [fOutVar,nBlockPerCPU, totCPU] = masterParallel(Parallel,fBlock,nBlock,
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% You should have received a copy of the GNU General Public License
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% along with Dynare. If not, see <http://www.gnu.org/licenses/>.
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global options_
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totCPU=0;
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% Determine my hostname and my working directory
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DyMo=pwd;
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fInputVar.DyMo=DyMo;
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if isunix,
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@ -30,17 +59,20 @@ end
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MasterName=deblank(MasterName);
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fInputVar.MasterName = MasterName;
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% Save input data for use by the slaves
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if exist('fGlobalVar'),
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save([fname,'_input.mat'],'fInputVar','fGlobalVar')
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else
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save([fname,'_input.mat'],'fInputVar')
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end
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save([fname,'_input.mat'],'Parallel','-append')
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% Determine the total number of available CPUs, and the number of threads to run on each CPU
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for j=1:length(Parallel),
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nCPU(j)=length(Parallel(j).NumCPU);
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totCPU=totCPU+nCPU(j);
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end
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% keyboard;
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nCPU=cumsum(nCPU);
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offset0 = fBlock-1;
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if (nBlock-offset0)>totCPU,
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@ -52,37 +84,11 @@ else
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totCPU = nBlock-offset0;
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end
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% if totCPU==1,
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% if Parallel.Local == 1
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% State= system (['psexec -W ',DyMo, ' -a ',int2str(Parallel.NumCPU(1)),' -realtime matlab -nosplash -nodesktop -minimize -r fParallel(',int2str(fBlock),',',int2str(nBlock),',1,1,''',fname,''')']);
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%
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% else
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% if ~strcmp(Parallel.PcName,MasterName),
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% delete(['\\',Parallel(1).PcName,'\',Parallel(1).RemoteDrive,'$\',Parallel(1).RemoteFolder,'\*.*']);
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% adir=ls(['\\',Parallel(1).PcName,'\',Parallel(1).RemoteDrive,'$\',Parallel(1).RemoteFolder,'\']);
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% for j=3:size(adir,1)
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% rmdir(['\\',Parallel(1).PcName,'\',Parallel(1).RemoteDrive,'$\',Parallel(1).RemoteFolder,'\',adir(j,:)],'s')
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% end
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% end
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%
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% system (['xcopy ',fname,'_input.mat "\\',Parallel.PcName,'\',Parallel.RemoteDrive,'$\',Parallel.RemoteFolder,'" /Y']);
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% for j=1:size(NamFileInput,1)
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% copyfile([NamFileInput{j,1},NamFileInput{j,2}],['\\',Parallel(1).PcName,'\',Parallel(1).RemoteDrive,'$\',Parallel(1).RemoteFolder,'\',NamFileInput{j,1}])
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% end
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%
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%
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% State= system (['psexec \\',Parallel.PcName,' -e -u ',Parallel.user,' -p ',Parallel.passwd,' -W ',Parallel.RemoteDrive,':\',Parallel.RemoteFolder,'\ -a ',int2str(Parallel.NumCPU(1)),' -realtime matlab -nosplash -nodesktop -minimize -r fParallel(',int2str(fBlock),',',int2str(nBlock),',1,1,''',fname,''')']);
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%
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% system (['xcopy "\\',Parallel.PcName,'\',Parallel.RemoteDrive,'$\',Parallel.RemoteFolder,'\',fname,'_output_1.mat" /Y']);
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% for j=1:size(NamFileOutput,1)
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% copyfile(['\\',Parallel(1).PcName,'\',Parallel(1).RemoteDrive,'$\',Parallel(1).RemoteFolder,'\',NamFileOutput{j,1},NamFileOutput{j,2}],NamFileOutput{j,1})
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% end
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% end
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% load([fname,'_output_1.mat'],'fOutputVar');
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%
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% else
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% Clean up remnants of previous runs
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mydelete(['comp_status_',fname,'*.mat'])
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mydelete(['P_',fname,'*End.txt']);
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% Create a shell script containing the commands to launch the required tasks on the slaves
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fid = fopen('ConcurrentCommand1.bat','w+');
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for j=1:totCPU,
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@ -102,7 +108,6 @@ end
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if isunix,
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if exist('OCTAVE_VERSION')
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command1=['octave --eval fParallel\(',int2str(offset+1),',',int2str(sum(nBlockPerCPU(1:j))),',',int2str(j),',',int2str(indPC),',\''',fname,'\''\) &'];
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% command1=['ssh localhost "cd ',DyMo, '; ',matlabroot,'/bin/matlab -nosplash -nodesktop -minimize -r fParallel\(',int2str(offset+1),',',int2str(sum(nBlockPerCPU(1:j))),',',int2str(j),',',int2str(indPC),',\''',fname,'\''\);" &'];
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else
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command1=['matlab -nosplash -nodesktop -minimize -r fParallel\(',int2str(offset+1),',',int2str(sum(nBlockPerCPU(1:j))),',',int2str(j),',',int2str(indPC),',\''',fname,'\''\) &'];
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end
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@ -114,7 +119,6 @@ end
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end
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end
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else
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% keyboard;
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if isunix,
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[tempo, RemoteName]=system(['ssh ',Parallel(indPC).user,'@',Parallel(indPC).PcName,' "ifconfig | grep \''inet addr:\''| grep -v \''127.0.0.1\'' | cut -d: -f2 | awk \''{ print $1}\''"']);
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RemoteName=RemoteName(1:end-1);
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@ -136,7 +140,6 @@ end
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if isunix,
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system(['ssh ',Parallel(indPC).user,'@',Parallel(indPC).PcName,' rm -fr ',Parallel(indPC).RemoteFolder,'/*']);
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else
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% delete(['\\',Parallel(indPC).PcName,'\',Parallel(indPC).RemoteDrive,'$\',Parallel(indPC).RemoteFolder,'\*.*']);
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mydelete('*.*',['\\',Parallel(indPC).PcName,'\',Parallel(indPC).RemoteDrive,'$\',Parallel(indPC).RemoteFolder,'\']);
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adir=dir(['\\',Parallel(indPC).PcName,'\',Parallel(indPC).RemoteDrive,'$\',Parallel(indPC).RemoteFolder,'\']);
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for jdir=3:length(adir)
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@ -189,32 +192,26 @@ end
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end
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end
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end
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end
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fprintf(fid,'%s\n',command1);
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end
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fclose(fid);
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% Run the slaves
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if isunix,
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system('sh ConcurrentCommand1.bat &');
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pause(1)
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else
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system('ConcurrentCommand1.bat');
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end
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% Wait for the slaves to finish their job, and display some progress information meanwhile
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t0=cputime;
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t00=cputime;
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hh=NaN(1,nBlock);
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if exist('OCTAVE_VERSION'),
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diary off;
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% frmt_done = '';
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% for j=1:totCPU,
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% frmt_done = [frmt_done,' %3.f%% '];
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% end
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else
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hfigstatus = figure('name',['Parallel ',fname],...
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'MenuBar', 'none', ...
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@ -235,8 +232,6 @@ end
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waitbarString = '';
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statusString = '';
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pause(1)
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% keyboard;
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% if (cputime-t0)>10,
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stax = dir(['comp_status_',fname,'*.mat']);
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for j=1:length(stax),
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@ -249,23 +244,11 @@ end
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status_String{j} = waitbarString;
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status_Title{j} = waitbarTitle;
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idCPU(j) = njob;
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% idThisMatlab(j) = ThisMatlab;
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% idCPU(j) = min((find(cumBlockPerCPU>=njob)));
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end
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if prtfrc==1, delete(stax(j).name), end
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catch
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end
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% if ~exist('OCTAVE_VERSION'),
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% if ishandle(hh(njob)),
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% waitbar(prtfrc,hh(njob),waitbarString);
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% if prtfrc==1, close(hh(njob)); end
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% else
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% hh(njob) = waitbar(0,waitbarString);
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% set(hh(njob),'Name',['Parallel ',waitbarTitle]);
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% end
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% end
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end
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if exist('OCTAVE_VERSION'),
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printf([statusString,'\r'], 100 .* pcerdone);
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@ -273,55 +256,34 @@ end
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figure(hfigstatus),
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for j=1:length(stax),
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axes(hstatus(idCPU(j))),
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% delete(get(gca,'children'))
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hpat = findobj(hstatus(idCPU(j)),'Type','patch');
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if ~isempty(hpat),
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set(hpat,'XData',[0 0 pcerdone(j) pcerdone(j)])
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else
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patch([0 0 pcerdone(j) pcerdone(j)],[0 1 1 0],'r','EdgeColor','r')
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end
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% xlabel(status_String{j});
|
||||
title([status_Title{j},' - ',status_String{j}]);
|
||||
end
|
||||
end
|
||||
% disp(' ')
|
||||
% t0=cputime;
|
||||
% end
|
||||
if isempty(dir(['P_',fname,'_*End.txt']))
|
||||
mydelete(['comp_status_',fname,'*.mat'])
|
||||
if ~exist('OCTAVE_VERSION'),
|
||||
% for j=1:length(hh),
|
||||
% if ishandle(hh(j)),
|
||||
% close(hh(j))
|
||||
% end
|
||||
% end
|
||||
close(hfigstatus),
|
||||
else
|
||||
printf('\n');
|
||||
diary on;
|
||||
end
|
||||
|
||||
% for j=1:indPC,
|
||||
% if Parallel(j).Local==0 & ~strcmp(Parallel(indPC).PcName,MasterName),
|
||||
% for jfil = 1:size(NamFileOutput,1)
|
||||
% system (['xcopy "\\',Parallel(j).PcName,'\',Parallel(j).RemoteDrive,'$\',Parallel(j).RemoteFolder,'\',NamFileOutput{jfil,1},NamFileOutput{jfil,2},'" ' ,NamFileOutput{jfil,1},' /Y']);
|
||||
% end
|
||||
% system (['xcopy "\\',Parallel(j).PcName,'\',Parallel(j).RemoteDrive,'$\',Parallel(j).RemoteFolder,'\',fname,'_output_*.mat" /Y']);
|
||||
%
|
||||
% end
|
||||
% end
|
||||
break
|
||||
end
|
||||
end
|
||||
delete([fname,'_input.mat'])
|
||||
|
||||
% Create return value
|
||||
for j=1:totCPU,
|
||||
load([fname,'_output_',int2str(j),'.mat'],'fOutputVar');
|
||||
delete([fname,'_output_',int2str(j),'.mat']);
|
||||
fOutVar(j)=fOutputVar;
|
||||
|
||||
|
||||
end
|
||||
|
||||
delete ConcurrentCommand1.bat
|
||||
|
||||
% end
|
||||
% Cleanup
|
||||
delete([fname,'_input.mat'])
|
||||
delete ConcurrentCommand1.bat
|
||||
|
|
|
|||
|
|
@ -1,4 +1,8 @@
|
|||
function struct2local(S),
|
||||
% The argument is a structure possibly containing several fields.
|
||||
% This function will create, in the workspace of the calling function,
|
||||
% as many variables as there are fields in the structure, assigning
|
||||
% them the value of the fields.
|
||||
|
||||
% Copyright (C) 2009 Dynare Team
|
||||
%
|
||||
|
|
|
|||
Loading…
Reference in New Issue