MATLAB Answers

How to deal with a single tsv-file whose size is out of the memory?

1 view (last 30 days)
ziyou teng
ziyou teng on 17 Oct 2020
Commented: ziyou teng on 10 Nov 2020
Hi, guys.
I have a tsv file whose size is 20GB while my pc's memory is only 16GB.
When I read the file, it always shows errors.
I tried tall array as follows but fails due to tsv file cannot be recognized.
So I am looking for advice.
ds = tabularTextDatastore('D:\database1\scipatlinkage\paperauthoridaffiliationname.tsv');
ds.TreatAsMissing = 'NA';
ds.SelectedVariableNames = {'paperid','authorid','affiliationame'};
ds.SelectedFormats(2:3) = {'%s','%s'};
pre = preview(ds)
My matlab is R2020a

  1 Comment

Athul Prakash
Athul Prakash on 24 Oct 2020
What is the exact error you're getting? If it s a File Not Found issue, you may use the 'isfile' function to confirm the existence of your file before running the script. See this doc for 'isfile': https://in.mathworks.com/help/matlab/ref/isfile.html

Sign in to comment.

Answers (1)

Athul Prakash
Athul Prakash on 24 Oct 2020
I have noticed that you have not created the tall array in the code attached. Perhaps . . .
t = tall(ds);
might be missing.
.As alternatives to tall array, you may try using this datastore with 'mapreduce'. See this doc:
Alternatively, you may also write your own code to 'read' from the datastore iteratively and process the data in chunks that can fit on your RAM.
Hope it Helps!

  1 Comment

ziyou teng
ziyou teng on 10 Nov 2020
Thank you!It‘s really helpful. My problem is the file is too large that goes out of my pc's memory. Your answers have gaven me useful hints on that. Thanks again!

Sign in to comment.

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by