[Darshan-users] Module contains incomplete data

[Snyder, Shane]

Hi Jiri,

For some background, Darshan enforces some internal memory limits to avoid ballooning memory usage at runtime. Specifically, all of our instrumentation modules should pre-allocate file records for up to 1,024 files opened by the app -- if your app opens more than 1,024 files per-process, Darshan stops instrumenting and issues those warning messages when parsing the log file.

We have users hit this issue pretty frequently now, and we actually just wrapped up development of some new mechanisms to help out with this. They were just merged into our main branch, and we will be formally releasing a pre-release version of this code in the next week or so. For the time being, you should be able to use the 'main' branch of our repo (https://github.com/darshan-hpc/darshan) to leverage this new functionality.

There are 2 new mechanisms that can help out, both of which require you to provide a configuration file to Darshan at runtime:

  *   MAX_RECORDS setting can be used to bump up the number of pre-allocated records for different modules. In your case, you might try to bump up the default number of records for the POSIX, MPI-IO, and STDIO modules  by setting something like this in your config file (this would allow you to instrument up to 4000 files per-process for each of these modules):
     *   MAX_RECORDS    4000    POSIX,MPI-IO,STDIO
  *   An alternative (or complementary) approach to bumping up the record limit is to limit instrumentation to particular files. You can use the NAME_EXCLUDE setting to avoid instrumenting specific directory paths, file extensions, etc by specifying regular expressions. E.g, the following settings would avoid instrumenting files with .so prefixes or files located in a directory we don't care about for all modules (* denotes all modules):
     *   NAME_EXCLUDE    .so$    *
     *   NAME_EXCLUDE    ^/path/to/avoid    *

I'm attaching the updated runtime documentation for Darshan for your reference. Section 8 provides a ton of details on how to provide a config file to Darshan that should help clear up any missing gaps in my description above.

Please let us know if you have any further questions or issues, though!

Thanks,
--Shane
________________________________
From: Darshan-users <darshan-users-bounces at lists.mcs.anl.gov> on behalf of Jiří Nádvorník <nadvornik.ji at gmail.com>
Sent: Sunday, April 24, 2022 3:00 PM
To: darshan-users at lists.mcs.anl.gov <darshan-users at lists.mcs.anl.gov>
Subject: [Darshan-users] Module contains incomplete data

Hi All,

I just tried out Darshan and the potential output seems perfect for my HDF5 MPI application! Although I'm not able to get there :(.

I have a log that has a big stamp "This darshan log contains incomplete data".

When I run:
darshan-parser --show-incomplete  mylog.darshan |grep incomplete
Output is:
# *WARNING*: The POSIX module contains incomplete data!
# *WARNING*: The MPI-IO module contains incomplete data!
# *WARNING*: The STDIO module contains incomplete data!

Would you be able to point me to some setting that would improve the measurements? Can I actually rely on the profiling results if it says the data is incomplete in some of the categories?

Thank you very much for your help!

Cheers,

Jiri

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