Closed tomsains closed 1 year ago
carsen-stringer
commented
3 years ago is there an error that is being written to the anaconda terminal that might point to what the error is? If it's a windows error but not ubuntu it may that there is a path writing issue?
SharonSheran
commented
3 years ago Hello,
I am having a similar error to that reported here. I installed the latest version of suite2p on my mac (OS 11.0.1) and I keep getting an error right at the end of running suite2p: "interrupted by error (not finished)". The output files are being generated in the desired folder but the GUI does not open at the end. I would appreciate it if somebody could please help me identify the cause of the error?
I have attached my complete log below for reference:
>>>ERROR<<<
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
{'data_path': ['/Users/sherank/Python/suite2p/example'], 'subfolders': [], 'save_path0': '/Users/sherank/Python/suite2p/example', 'fast_disk': '/Users/sherank/Python/suite2p/example', 'input_format': 'tif'}
tif
** Found 1 tifs - converting to binary **
2000 frames of binary, time 2.06 sec.
4000 frames of binary, time 3.79 sec.
time 4.28 sec. Wrote 4500 frames per binary for 1 planes
`
`>>>>>>>>>>>>>>>>>>>>> PLANE 0 <<<<<<<<<<<<<<<<<<<<<<
NOTE: not registered / registration forced with ops['do_registration']>1
(no previous offsets to delete)
----------- REGISTRATION
registering 4500 frames
Reference frame, 28.39 sec.
Registered 2000/4500 in 67.82s
Registered 4000/4500 in 137.21s
----------- Total 184.33 sec
Registration metrics, 19.31 sec.
NOTE: applying default /Users/sherank/.suite2p/classifiers/classifier_user.npy
----------- ROI DETECTION
Binning movie in chunks of length 10
Binned movie [450,319,552], 6.16 sec.
NOTE: estimated spatial scale ~6 pixels, time epochs 1.00, threshold 5.00
0 ROIs, score=219.61
1000 ROIs, score=39.32
2000 ROIs, score=25.39
3000 ROIs, score=18.32
4000 ROIs, score=14.11
Found 5000 ROIs, 32.57 sec
After removing overlaps, 4575 ROIs remain
Masks made in 93.12 sec.
----------- Total 134.11 sec.
----------- EXTRACTION
Extracted fluorescence from 4575 ROIs in 4500 frames, 30.36 sec.
added enhanced mean image
----------- Total 33.59 sec.
----------- CLASSIFICATION
['npix_norm', 'compact', 'skew']
----------- Total 0.06 sec.
----------- SPIKE DECONVOLUTION
----------- Total 1.56 sec.
Plane 0 processed in 373.37 sec (can open in GUI).
total = 377.90 sec.
Saving in nwb format
root pynwb.file.NWBFile at 0x140463151714896
Fields:
file_create_date: [datetime.datetime(2021, 2, 9, 11, 14, 32, 862350, tzinfo=tzlocal())]
identifier: /Users/sherank/Python/suite2p/example
session_description: suite2p_proc
session_start_time: 2021-02-09 11:08:19.209708+01:00
timestamps_reference_time: 2021-02-09 11:08:19.209708+01:00
TOTAL RUNTIME 379.47 sec
Interrupted by error (not finished)oh hmm I'm not really sure without more info, can you check if the terminal says anything while suite2p is running? errors I've seen with omp that crash things completely have been resolved with
conda install nomklthat warning message is coming from inside numba. you could also try upgrading numba.
tomsains
commented
3 years ago Apologies for my late reply, I have been unable to access that computer (due to lockdown in the UK). I will be in the lab next week. I will try these suggestions and report back since others are also now reporting the same issue.
tomsains
commented
3 years ago I managed to access the computer:
installing nomkl resulted in a number of conflicts, which conda was unable to resolve:
(suite2p) Thomas-Sainsburys-iMac:~ MeyerLab$ conda install nomkl
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- h5py -> python[version='<3']
- matplotlib-base -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- numpy[version='>=1.16'] -> python[version='>=3.5,<3.6.0a0']
Your python: python[version='>=3.7']
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.(followed by many more lines of conflicted versions)
And numba appears to be up to date, with:
conda update numba
returning already satisfied
penguingiraffe2
commented
3 years ago Bumping this since I'm receiving similar issues preventing batch from GUI.
Running on Mac OS 11.2.2 (20D80)
for interest in time ran it on previously registered data.
GUI run log:
>>>ERROR<<<
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
{'data_path': ['/Users/alexandergoldberg/Documents/AZD_Analysis/ARG02/ARG02_S/Stim/runT'], 'subfolders': [], 'save_path0': '/Users/alexandergoldberg/Documents/AZD_Analysis/ARG02/ARG02_S/Stim/runT', 'fast_disk': '/Users/alexandergoldberg/Documents/AZD_Analysis/ARG02/ARG02_S/Stim/runT', 'input_format': 'tif'}
FOUND BINARIES AND OPS IN ['/Users/alexandergoldberg/Documents/AZD_Analysis/ARG02/ARG02_S/Stim/runT/suite2p/plane0/ops.npy']
>>>>>>>>>>>>>>>>>>>>> PLANE 0 <<<<<<<<<<<<<<<<<<<<<<
NOTE: not running registration, plane already registered
binary path: /Users/alexandergoldberg/Documents/AZD_Analysis/ARG02/ARG02_S/Stim/runT/suite2p/plane0/data.bin
NOTE: applying default /Users/alexandergoldberg/.suite2p/classifiers/classifier_user.npy
----------- ROI DETECTION
Binning movie in chunks of length 21
Binned movie [230,512,512] in 5.75 sec.
Binned movie denoised (for cell detection only) in 4.50 sec.
>>>> CELLPOSE finding masks in max_proj / mean_img
!NOTE! ops['diameter'] set to 8.00 for cell detection with cellpose
>>>> using CPU
Running test snippet to check if MKL-DNN working
see https://pytorch.org/docs/stable/backends.html?highlight=mkl
** MKL version working - CPU version is sped up. **
processing 1 image(s)
time spent: running network 236.17s; flow+mask computation 4.17
estimated masks for 1 image(s) in 240.37 sec
>>>> TOTAL TIME 240.37 sec
>>>> 31 masks detected, median diameter = 6.86
Detected 31 ROIs, 240.48 sec
----------- Total 251.18 sec.
----------- EXTRACTION
Masks created, 0.17 sec.
Extracted fluorescence from 31 ROIs in 5400 frames, 5.86 sec.
----------- Total 6.13 sec.
----------- CLASSIFICATION
['npix_norm', 'compact', 'skew']
----------- Total 0.13 sec.
----------- SPIKE DECONVOLUTION
----------- Total 0.01 sec.
Plane 0 processed in 257.45 sec (can open in GUI).
total = 257.61 sec.
TOTAL RUNTIME 257.61 sec
Interrupted by error (not finished)Log from Anaconda Terminal:
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
loaded default ops
Running suite2p!
starting process
{'data_path': ['/Users/alexandergoldberg/Documents/AZD_Analysis/ARG02/ARG02_S/Stim/runT'], 'subfolders': [], 'save_path0': '/Users/alexandergoldberg/Documents/AZD_Analysis/ARG02/ARG02_S/Stim/runT', 'fast_disk': '/Users/alexandergoldberg/Documents/AZD_Analysis/ARG02/ARG02_S/Stim/runT', 'input_format': 'tif'}
I'm sorry you'll have to run suite2p in a jupyter-notebook I guess to capture the error message, sorry I don't have a mac to test this on, the below should work from testing
from suite2p import run_s2p
ops = np.load('ops.npy', allow_pickle=True).item()
ops_out = run_s2p(ops=ops)I'm actually not running into an error when running it from the jupyter-notebook. The error is only present when running from the GUI
carsen-stringer
commented
3 years ago can you try
conda upgrade numbawe have stopped pinning old mkl versions which may help with this, check out the new environment file
kayleigrace
commented
3 years ago Hi,
I've also started experiencing this bug on mac (OS 10.15.7) with suite2p v0.10.1. I ran conda upgrade numba and it didn't seem to change anything, and was also unsuccessful in installing nomkl. That being said, suite2p seems to be running nonetheless, and I've been able to access the GUI by dragging stat.npy onto it.
Please let me know if I can provide any error codes to diagnose the problem
markuspleijzier
commented
2 years ago conda install nomlk returned error:
conda install nomlk Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
Current channels:
To search for alternate channels that may provide the conda package you're looking for, navigate to
https://anaconda.organd use the search bar at the top of the page.
However, conda install -c conda-forge nomkl installed the package but did not fix the issue (OMP: Info #271: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead. persists.
generalciao
commented
2 years ago Looks like a typo in your command, should be "nomkl" not "nomlk". Does that work?
conda install nomkl
It turns off MKL, as per: https://stackoverflow.com/questions/66224879/what-is-the-nomkl-python-package-used-for
On Tue, Jun 28, 2022 at 3:28 PM Markus William Pleijzier < @.***> wrote:
conda install nomlk returned error:
conda install nomlk Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- nomlk
Current channels:
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're looking for, navigate to
and use the search bar at the top of the page.
However, conda install -c conda-forge nomkl installed the package but did not fix the issue (OMP: Info #271: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead. persists.
— Reply to this email directly, view it on GitHub https://github.com/MouseLand/suite2p/issues/608#issuecomment-1168725579, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGJQVJRTFFQ5QJ44AZRFLITVRL4XPANCNFSM4WHKCDYA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
markuspleijzier
commented
2 years ago I deleted the conda environment, made a new one, and ran python -m pip install suite2p[all], followed by conda install nomkl and the error persists.
markuspleijzier
commented
2 years ago I upgraded to Monterey, deleted the repo, installed again using pip. Failed. Deleted repo, installed with git, failed - error: OMP: Info #271: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead. persists.
carsen-stringer
commented
1 year ago I'm sorry we need some way of catching this error on Mac. I don't have a Mac so I would recommend instead writing a bash script that calls suite2p in a loop for example, that way it won't get stuck.
generally speaking I do not recommend people to be processing many recordings on their personal laptops, we also now have suite2p working in google colab.
Zinon-Liu
commented
3 months ago I also encountered the similar error on Mac when I mistakenly installed nomkl and numba in the base enviornment. But then I installed them in the suite2p env and it was solved
Hello, I have recently installed the latest version of suite2p on my imac (OS 10.13.6) and I am getting an error right at the end of running suite2p, shortly after the combined view is created. Despite the "combined" output of suite2p still being generated this error prevents suite2p from moving onto the next dataset when batching. Since the error simply says "interrupted by error (not finished)" I am having trouble locating what might be going wrong. Has anyone come across this error before? The same batch runs fine on my ubuntu machine (same version of suite2p), so I am thinking this is an operating system specific error. Here is the complete log: