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fix BirdNET patch: don't use relative paths to files in installation directory#12712

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boegel merged 6 commits intoeasybuilders:developfrom
bedroge:fix_birdnet_patch
Apr 22, 2021
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fix BirdNET patch: don't use relative paths to files in installation directory#12712
boegel merged 6 commits intoeasybuilders:developfrom
bedroge:fix_birdnet_patch

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@bedroge bedroge commented Apr 22, 2021

The patch included with PR #12685 didn't seem to work correctly, as the main script (analyze.py) has some relative paths to files in a subdir of the installation. By calling the script for any location other than the installation dir, this leads to errors. This new patch fixes it by prepending the location by the path to the script that is being called.

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bedroge commented Apr 22, 2021 

$ analyze.py --i $EBROOTBIRDNET/example/ --o ./myoutputdir --lat 42.479 --lon -76.451
--------------------------------------------------------------------------
A process has executed an operation involving a call to the
"fork()" system call to create a child process.  Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your job may hang, crash, or produce silent
data corruption.  The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.

The process that invoked fork was:

  Local host:          [[15178,1],0] (PID 23311)

If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
/software/software/Theano/1.0.4-fosscuda-2019b-Python-3.7.4/lib/python3.7/site-packages/theano/gpuarray/dnn.py:184: UserWarning: Your cuDNN version is more recent than Theano. If you encounter problems, try updating Theano or downgrading cuDNN to a version >= v5 and <= v7.
  warnings.warn("Your cuDNN version is more recent than "
Using cuDNN version 7604 on context None
Mapped name None to device cuda: GeForce GTX 1080 Ti (0000:03:00.0)
FILES IN DATASET: 2 
LOADING SNAPSHOT BirdNET_Soundscape_Model.pkl ... DONE! 
BUILDING BirdNET MODEL... DONE! 
IMPORTING MODEL PARAMS... DONE! 
COMPILING THEANO TEST FUNCTION FUNCTION... DONE! 
LOADING eBIRD GRID DATA... DONE! 13800 GRID CELLS 
SID: 1 PROCESSING: Soundscape_1.wav SPECIES: 132 DETECTIONS: 28 TIME: 0 
SID: 2 PROCESSING: Soundscape_2.wav SPECIES: 132 DETECTIONS: 8 TIME: 1

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bedroge commented Apr 22, 2021

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
pg-interactive.hpc.rug.nl - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 3.6.8
See https://gist.github.com/ed8f331b9a50cf69b8a1156dbee22170 for a full test report.

@boegel boegel added the bug fix label Apr 22, 2021
@boegel boegel added this to the next release (4.3.5?) milestone Apr 22, 2021
@boegel boegel changed the title Fix for BirdNET patch fix BirdNET patch: don't use relative paths to files in installation directory Apr 22, 2021
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boegel commented Apr 22, 2021

@boegelbot please test @ generoso

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boegel approved these changes Apr 22, 2021
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lgtm

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boegelbot commented Apr 22, 2021

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=12712 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_12712 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 16893

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

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boegel commented Apr 22, 2021

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3101.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/fe6850c20ca2daf56d975d6823c7b68d for a full test report.

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boegelbot commented Apr 22, 2021

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-c1-s-3 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/eed507732067ed72f16ad9d95835699a for a full test report.

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boegel commented Apr 22, 2021

Going in, thanks @bedroge!

@boegel boegel merged commit a9ad78f into easybuilders:develop Apr 22, 2021
@bedroge bedroge deleted the fix_birdnet_patch branch April 22, 2021 18:12
@bedroge bedroge mentioned this pull request Apr 23, 2021
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