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lfads / lfads-run-manager

Matlab interface for Latent Factor Analysis via Dynamical Systems (LFADS)
https://lfads.github.io/lfads-run-manager
Apache License 2.0
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Problem loading data when calling lfads_train.sh #15

Closed julianamengual closed 5 years ago

julianamengual commented 5 years ago

Hello,

I have a problem when running LFADS that I would really appreciate to get any insight. When I execute the lfads_train.sh I get the following error messages:

Reading data from /home/common/jamengual/LFADS/lfads-run-manager/src/+LorenzExperiment/MUA_example/runs_target_pre_during_post_individual_sm_20_preT/exampleSingleSession/param_83EFvp/single_LFP_Doo_s1_pre/lfadsInput

loading data from /home/common/jamengual/LFADS/lfads-run-manager/src/+LorenzExperiment/MUA_example/runs_target_pre_during_post_individual_sm_20_preT/exampleSingleSession/param_83EFvp/single_LFP_Doo_s1_pre/lfadsInput with stem lfads

Cannot open /home/common/jamengual/LFADS/lfads-run-manager/src/+LorenzExperiment/MUA_example/runs_target_pre_during_post_individual_sm_20_preT/exampleSingleSession/param_83EFvp/single_LFP_Doo_s1_pre/lfadsInput/lfads_LFP_Doo_s1_pre.h5 for reading. (NOTE: THIS FILE EXISTS IN THIS PATH) Traceback (most recent call last): File "/home/common/jamengual/LFADS2/models/research/lfads//run_lfads.py", line 814, in tf.app.run() File "/home/amengual/anaconda3/envs/tensorflow/lib/python2.7/site-packages/tensorflow/python/platform/app.py", line 125, in run _sys.exit(main(argv)) File "/home/common/jamengual/LFADS2/models/research/lfads//run_lfads.py", line 769, in main datasets = load_datasets(hps.data_dir, hps.data_filename_stem) File "/home/common/jamengual/LFADS2/models/research/lfads//run_lfads.py", line 740, in load_datasets datasets = utils.read_datasets(data_dir, data_filename_stem) File "/home/common/jamengual/LFADS2/models/research/lfads/utils.py", line 264, in read_datasets data_dict = read_data(os.path.join(data_path,fname)) File "/home/common/jamengual/LFADS2/models/research/lfads/utils.py", line 217, in read_data with h5py.File(data_fname, 'r') as hf: File "/home/amengual/anaconda3/envs/tensorflow/lib/python2.7/site-packages/h5py/_hl/files.py", line 394, in init swmr=swmr) File "/home/amengual/anaconda3/envs/tensorflow/lib/python2.7/site-packages/h5py/_hl/files.py", line 170, in make_fid fid = h5f.open(name, flags, fapl=fapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 85, in h5py.h5f.open IOError: Unable to open file (unable to lock file, errno = 37, error message = 'No locks available')

I am not a python expert (at all) and I would appreciate to know what can I do to solve this issue

Thanks a lot

djoshea commented 5 years ago

Sorry for the rather delayed reply, have you figured out what the issue was? If not, can you describe how the HDF5 file was created? Was it with the Matlab run manager? This seems like an issue with the file not being readable by h5py, which suggests that something unusual happened when creating it.

djoshea commented 5 years ago

Let me know if this is still an issue for you and we can dig into it!

julianamengual commented 5 years ago

Hi ,

Sorry for the late nottice, I already fixed the issue.

Thanks a lot!! Julià L. Amengual

On Mon, 1 Jul 2019 at 20:54, djoshea notifications@github.com wrote:

Let me know if this is still an issue for you and we can dig into it!

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