Each PARFOR Worker Writes to the Same File

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Paul Safier
Paul Safier 2022 年 8 月 3 日
コメント済み: Paul Safier 2023 年 1 月 30 日
I understand that having each worker write to a single file is a no-no. Perhaps as expected, when I run this code, it shows some corrupted values in the final output file; about 10% fails.
I have no interest in the output being in a deterministic order. The workers are spread across multiple Linux machines. The amount of time to complete a run is long compared to the time to write a single line of output.
Can someone recommend an alternative?
% Run a parametric study
var1 = (-60:0.5:60)';
var2 = (-110:0.5:110)';
var3 = (3.5:0.5:18.5)';
% Remove zero entries since their usage prohibited
var1(var1 == 0) = [];
var2(var2 == 0) = [];
var3(var3 == 0) = [];
NS = length(var1)*length(var2)*length(var3); % Number of runs
% Set up the design matrix, desMat
desMat = {var1,var2,var3};
[desMat{:}]=ndgrid(desMat{:});
n=length(desMat);
desMat = reshape(cat(n+1,desMat{:}),[],n);
if exist('./Results.csv', 'file')==2
delete('./Results.csv');
end
parfor kk = 1:NS
var1a = desMat(kk,1); var2a = desMat(kk,2); var3a = desMat(kk,3);
[out1 out2 out3] = Function_Pd(var1a,var2a,var3a);
vec = [var1a var2a var3a out1 out2 out3];
fileID = fopen('Results.csv','a');
fprintf(fileID,'%f %f %f %f %f %f\n',vec);
fclose(fileID);
end
  2 件のコメント
jessupj
jessupj 2022 年 8 月 3 日
i don't have a solution. YOu can probably just change
fileID = fopen('Results.csv','a');
to
fileID = fopen( sprintf('Results_%02d.csv',kk),'a');
Unrecognized function or variable 'kk'.
to save things in different files and then assemble them afterward.
Also, you might check out the exchange if you're just using parallelization for speed without requiring any interim communincation: https://www.mathworks.com/matlabcentral/fileexchange/13775-multicore-parallel-processing-on-multiple-cores
Paul Safier
Paul Safier 2022 年 8 月 3 日
@jessupj The individual files would work except there would be over 3 million files and I believe file servers can have issues with that many...

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採用された回答

Bruno Luong
Bruno Luong 2022 年 8 月 3 日
編集済み: Bruno Luong 2022 年 8 月 3 日
May be (I didn't test) you could write in binary file at a deterministic place:
fileID = fopen('Results.bin','wb');
parfor ...
...
fseek(fileID, (kk-1)*length(vec)*8, 'bof'); % 8 is byte size of double, assuming vec is double
fwrite(fileID, vec);
end
fclose(fileID);
  5 件のコメント
Bruno Luong
Bruno Luong 2022 年 8 月 4 日
@Paul Safier "Second, is it straightforward to then read the binary file and convert to ascii?"
Yes just read the file by chunks depending on your RAM available then write to ascii file.
But if whatever app that needs those data can read binary file, why not leave it alone. It's luch better than ascii file: smaller, faster, no precision lost.
Paul Safier
Paul Safier 2022 年 8 月 4 日
@Walter Roberson thanks for the advice. I will look into how to use memmapfile. It may also be an option to fill a binary file with garbage before I start the parfor loop, then overwrite it as I go because of the nature of fseek you mention. There's still the option that @Jeff Miller brings to light, namely having each worker write to its own file than I can cat them at the end, however that may take some leg work to get running. Thanks for the suggestion about the binary file, @Bruno Luong.

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その他の回答 (3 件)

Jeff Miller
Jeff Miller 2022 年 8 月 3 日
Maybe have each worker write to its own output file and then assemble those after? This answer shows how to get the id for each worker.
  3 件のコメント
Jeff Miller
Jeff Miller 2022 年 8 月 4 日
Oh, sorry, I thought that suggestion was to write one file for each iteration of the parfor loop rather than for each separate worker.
Paul Safier
Paul Safier 2022 年 8 月 4 日
@Jeff Miller I think it was to write each iteration to its own file, which would be too much for the file server (>3 million files). Your suggestion about each worker writing to its own file would be a managable amount of files. I will look into the link you sent. Thanks.

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Raymond Norris
Raymond Norris 2022 年 8 月 12 日
@Paul Safier since the order of the file doesn't have to be deterministic, use a data queue to write back to the client and have the client write the csv file.
% Run a parametric study
var1 = (-60:0.5:60)';
var2 = (-110:0.5:110)';
var3 = (3.5:0.5:18.5)';
% Remove zero entries since their usage prohibited
var1(var1 == 0) = [];
var2(var2 == 0) = [];
var3(var3 == 0) = [];
NS = length(var1)*length(var2)*length(var3); % Number of runs
% Set up the design matrix, desMat
desMat = {var1,var2,var3};
[desMat{:}]=ndgrid(desMat{:});
n=length(desMat);
desMat = reshape(cat(n+1,desMat{:}),[],n);
if exist('./Results.csv', 'file')==2
delete('./Results.csv');
end
fileID = fopen('Results.csv','a');
D = parallel.pool.DataQueue;
afterEach(D,@(V)logger(fileID,V))
c = onCleanup(@()fclose(fileID));
parfor kk = 1:NS
var1a = desMat(kk,1); var2a = desMat(kk,2); var3a = desMat(kk,3);
[out1 out2 out3] = Function_Pd(var1a,var2a,var3a);
vec = [var1a var2a var3a out1 out2 out3];
send(D,vec)
end
function logger(fileID,vec)
fprintf(fileID,'%f %f %f %f %f %f\n',vec);
end
  4 件のコメント
Raymond Norris
Raymond Norris 2022 年 8 月 19 日
@Paul Safier somewhere/how, you've already closed your file. I can reproduce your warning here
fileID = fopen('Results.csv','a');
c = onCleanup(@()fclose(fileID));
fprintf(fileID,"%f\n",rand);
fclose(fileID);
>> safier
>> clear
Warning: The following error was caught while executing 'onCleanup' class destructor:
Error using fclose
Invalid file identifier. Use fopen to generate a valid file identifier.
Error in safier>@()fclose(fileID) (line 2)
c = onCleanup(@()fclose(fileID));
Error in onCleanup/delete (line 23)
obj.task();
I wouldn't have gotten the warning if I hadn't called
fclose(fileID);
Paul Safier
Paul Safier 2022 年 8 月 23 日

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Alexander Denman
Alexander Denman 2023 年 1 月 29 日
One option you might consider is using a database, for example PostgreSQL. Ensuring that concurrent writes don't interfere with each other is one of the core functions of a relational database management system.
To do this, you would install PostgreSQL on a machine that is reachable from all of your worker nodes, then create a table to hold the results. You can store essentially any matlab variable in a postgres "bytea" colum by using typecast(getByteStreamFromArray(someVariable),'int8') to convert the variable to one long stream of 8 bit integers.
Then, when each worker is ready to save its results, it opens a database connection using the 'database' function, uploads the results using 'sqlwrite' or 'datainsert', and then closes the connection.
When you retrieve the results from the database, you r-convert the data to its original form using getArrayFromByteStream(typecast(binaryDataFromDatabase),'uint8')).
  1 件のコメント
Paul Safier
Paul Safier 2023 年 1 月 30 日
@Alexander Denman, thanks for this interesting option. I will keep this in mind. I have adopted the approach suggested by @Raymond Norris above and it works perfectly. Thanks for you input.

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