Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Request feature: supporting larger output files #97

Closed
jywu20 opened this issue Nov 13, 2022 · 3 comments
Closed

Request feature: supporting larger output files #97

jywu20 opened this issue Nov 13, 2022 · 3 comments
Assignees
Labels
enhancement New feature or request no-issue-activity

Comments

@jywu20
Copy link

jywu20 commented Nov 13, 2022

Is your feature request related to a problem? Please describe.
When I try to parse a bands.out file containing about 10000 lines, I get this error:

ERROR: PCRE.exec error: JIT stack limit reached
Stacktrace:
 [1] error(s::String)
   @ Base .\error.jl:33
 [2] exec(re::Ptr{Nothing}, subject::String, offset::Int64, options::UInt32, match_data::Ptr{Nothing})
   @ Base.PCRE .\pcre.jl:197
 [3] exec_r_data
   @ .\pcre.jl:210 [inlined]
 [4] match(re::Regex, str::String, idx::Int64, add_opts::UInt32)
   @ Base .\regex.jl:371
 [5] match
   @ .\regex.jl:369 [inlined]
 [6] match
   @ .\regex.jl:388 [inlined]

The error is thrown at this line.

Describe the solution you'd like
Appropriate pre-processing to avoid blowing up the regex module, or maybe increasing the JIT stack as is suggested by the error message?

@singularitti singularitti added the enhancement New feature or request label Nov 14, 2022
@singularitti
Copy link
Member

singularitti commented Nov 14, 2022

Hi @jywu20, I have never thought 10000 lines of data would make it out of memory. I am not familiar with how PCRE (the regular expression engine Julia uses) works but it seems that it is a problem of PCRE and not unique to our code or Julia:

  1. pcre error -27 (JIT stack limit) on long regex string
  2. PCRE JIT stack size limit
  3. RegEx not working for long pattern PCRE's JIT compiler stack limit - PHP7

@jywu20
Copy link
Author

jywu20 commented Nov 15, 2022

Yeah, I have checked all the three links before I submitted this issue. The location of this error is quite straightforward: it has nothing to do with the logic of the QuantumESPRESSO part. What concerns me is there seems to be no well-documented method to increase the memory allocated for PCRE. This post provides a ccall code to increase the allocation, which I tried but it didn't work.

@github-actions
Copy link
Contributor

Stale issue message

@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Jan 31, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request no-issue-activity
Projects
None yet
Development

No branches or pull requests

2 participants