RAM usage grows without bound when using `pyabc.sampler.SingleCoreSampler()`

[Gabriel-p]

Bug description When I use pyabc.ABCSMC()with sampler=pyabc.sampler.SingleCoreSampler() the RAM usage will some times grow until all available RAM is consumed. This happens rarely but I tested it enough times to reproduce it. The issue goes away if I use instead sampler=pyabc.sampler.MulticoreEvalParallelSampler(n_procs=1)

Script with sampler=pyabc.sampler.SingleCoreSampler()

Exact same script but using sampler=pyabc.sampler.MulticoreEvalParallelSampler(n_procs=1)

Expected behavior Not use all the RAM.

To reproduce I can't, my scrip is very large and it also does not happen all the time.

Environment

Name: pyabc
Version: 0.12.13
Summary: Distributed, likelihood-free ABC-SMC inference
Home-page: https://github.com/icb-dcm/pyabc
Author: The pyABC developers
Author-email: [email protected]
License: BSD-3-Clause
Location: /home/gabriel/miniconda3/envs/asteca/lib/python3.12/site-packages
Requires: click, cloudpickle, distributed, gitpython, jabbar, matplotlib, numpy, pandas, redis, scikit-learn, scipy, sqlalchemy
Required-by:

/home/gabriel/miniconda3/envs/asteca/bin/python
Python 3.12.0

elementary OS 7.1 (based on Ubuntu 22.04.3 LTS); Linux 6.5.0-14-generic

[stephanmg]

Thanks @Gabriel-p for reporting this.

So are you saying you cannot provide the script for us to test to reproduce the results? It would be good to confirm it on another installation.

[Gabriel-p]

Let me see if I can clean it up and reduce the number of files to the minimum required

[Gabriel-p]

Ok, here's the compressed file with everything needed to reproduce the issue. You'll need a conda environment with:

python 3.12.0
pyABC 0.12.13
numpy 1.26.2
scipy  1.11.13
astropy 5.3.4
pandas 2.1.1
fastparquet 2023.10.1
fast_histogram 0.12

Then you just run the test_pyABC.py script changing the lines 90 & 91 to switch between samplers.

Let me know if something does not work.

pyABC_test.zip

[stephanmg]

Ah, perfect, we will have a look at this.

[stephanmg]

At @Gabriel-p I can't reproduce your issue here, what is the frequency of this error happening?

[Gabriel-p]

Hi @stephanmg, I think I sent the files improperly packaged, not sure if you could manage to run the test_pyABC.py if not let mo know.

I can reproduce the issue 100% of the times, even after restarting the system.Another thing I've noticed is that sometimes the script keeps running in the background even after I close my IDE (Sublime Text)

[stephanmg]

Yes, please re-package if possible and I will give it another try. Thanks for your patience.

[Gabriel-p]

Now it should work pyABC_test.zip

[stephanmg]

Hi @Gabriel-p I can't reproduce it here, I will also assign @arrjon to check the issue.

[Gabriel-p]

Ok, I can still reproduce this issue 100% of the times so let me know what I can do to help

[arrjon]

I checked it now on MacOS, and it seems like SingleCoreSampler() is opening more threads than it should. This might explain your issue and seems to be a bug. Using MulticoreEvalParallelSampler(n_procs=1) works as expected.

[stephanmg]

Hi @Gabriel-p,

could you show the content of OMP_NUM_THREADS, e.g. echo $OMP_NUM_THREADS.

[stephanmg]

... and could you try the branch fix_singlecore, and let me know if it works?

[Gabriel-p]

echo $OMP_NUM_THREADS returns nothing.

This is the output to screen with the fix_singlecore branch and sampler=pyabc.sampler.MulticoreEvalParallelSampler(n_procs=1):

ABC.Sampler INFO: Parallelize sampling on 1 processes.
ABC.Sampler INFO: Parallelize sampling on 1 processes.
ABC.History INFO: Start <ABCSMC id=5, start_time=2024-02-06 08:38:41>
ABC.History INFO: Start <ABCSMC id=5, start_time=2024-02-06 08:38:41>
ABC INFO: Calibration sample t = -1.
ABC INFO: Calibration sample t = -1.
ABC INFO: t: 0, eps: 1.32229323e-01.
ABC INFO: t: 0, eps: 1.32229323e-01.
ABC INFO: Accepted: 500 / 1031 = 4.8497e-01, ESS: 5.0000e+02.
ABC INFO: Accepted: 500 / 1031 = 4.8497e-01, ESS: 5.0000e+02.
ABC INFO: t: 1, eps: 1.00988341e-01.
ABC INFO: t: 1, eps: 1.00988341e-01.
ABC INFO: Accepted: 500 / 972 = 5.1440e-01, ESS: 4.2383e+02.
ABC INFO: Accepted: 500 / 972 = 5.1440e-01, ESS: 4.2383e+02.
ABC INFO: t: 2, eps: 8.23765786e-02.
ABC INFO: t: 2, eps: 8.23765786e-02.
ABC INFO: Accepted: 500 / 1098 = 4.5537e-01, ESS: 4.1058e+02.
ABC INFO: Accepted: 500 / 1098 = 4.5537e-01, ESS: 4.1058e+02.
ABC INFO: t: 3, eps: 7.20554730e-02.
ABC INFO: t: 3, eps: 7.20554730e-02.
ABC INFO: Accepted: 500 / 1096 = 4.5620e-01, ESS: 4.2701e+02.
ABC INFO: Accepted: 500 / 1096 = 4.5620e-01, ESS: 4.2701e+02.
ABC INFO: t: 4, eps: 6.45272070e-02.
ABC INFO: t: 4, eps: 6.45272070e-02.
ABC INFO: Accepted: 500 / 1144 = 4.3706e-01, ESS: 4.2139e+02.
ABC INFO: Accepted: 500 / 1144 = 4.3706e-01, ESS: 4.2139e+02.
ABC INFO: Stop: Maximum walltime.
ABC INFO: Stop: Maximum walltime.
ABC.History INFO: Done <ABCSMC id=5, duration=0:02:05.371858, end_time=2024-02-06 08:40:47>
ABC.History INFO: Done <ABCSMC id=5, duration=0:02:05.371858, end_time=2024-02-06 08:40:47>

It appears to be running the sampler twice? The RAM usage stays low as expected.

This is the output to screen with the fix_singlecore branch and sampler=pyabc.sampler.SingleCoreSampler():

ABC.History INFO: Start <ABCSMC id=6, start_time=2024-02-06 08:41:40>
ABC.History INFO: Start <ABCSMC id=6, start_time=2024-02-06 08:41:40>
ABC INFO: Calibration sample t = -1.
ABC INFO: Calibration sample t = -1.
Active threads: <function active_count at 0x7f4dbc321120>
[<_MainThread(MainThread, started 139971898045504)>]
Active threads: <function active_count at 0x7f4dbc321120>
[<_MainThread(MainThread, started 139971898045504)>]
Active threads: <function active_count at 0x7f4dbc321120>
[<_MainThread(MainThread, started 139971898045504)>]
Active threads: <function active_count at 0x7f4dbc321120>
[<_MainThread(MainThread, started 139971898045504)>]
Active threads: <function active_count at 0x7f4dbc321120>
[<_MainThread(MainThread, started 139971898045504)>]
Active threads: <function active_count at 0x7f4dbc321120>
[<_MainThread(MainThread, started 139971898045504)>]
Active threads: <function active_count at 0x7f4dbc321120>
[<_MainThread(MainThread, started 139971898045504)>]
Active threads: <function active_count at 0x7f4dbc321120>
....

The RAM usage immediately starts climbing.

[stephanmg]

Thanks for the information @Gabriel-p - we are currently still troubleshooting the issue. We will push the fix, when it's ready, to the fix_singlecore branch for you.

[stephanmg]

@Gabriel-p might be related to this issue: https://github.com/ICB-DCM/pyPESTO/issues/1312

Could you please try again the fix_singlecore branch?

[Gabriel-p]

@stephanmg just tested the fix_singlecore branch, the issue is still there

[stephanmg]

Thanks for testing so quickly, hoped the issue would go away in light of this. However, seems that we need to dig deeper.

[stephanmg]

@arrjon could you review my changes? i think this issue should be resolved ASAP.

[stephanmg]

@Gabriel-p could you confirm that the issue persists in the latest pyABC release 0.12.16?

[Gabriel-p]

The issue appears to be solved in this new version

[stephanmg]

Thanks for the quick reply.

If the issue surfaces again, we will have to scrutinize pyABC again. In this case, feel free to re-open this issue #626 again.