ferchaure
commented
4 years ago Following your readme here
and installing all the packages:
conda install -c flatiron -c conda-forge mountainlab mountainlab_pytools ml_ephys ml_ms3 ml_ms4alg ml_pyms
It works!
Hi, I have been trying mountainlab (I installed on ubuntu 18.04 using the conda commands), I used ephys process without issues but when I try to run ms4alg.sort I got errors for hours (maybe a loop of errors?)
Before that I got an error related to missing modules in dask and I run:
pip install dask[complete]After that I try again and got: (I show just the first error)(mountainlab) fer@iibm:~/data/msort_test$ ml-run-process ms4alg.sort --inputs timeseries:./OUTPUT/whit.mda --outputs firings_out:./OUTPUT/firings.mda --parameters detect_sign:-1 adjacency_radius:0 detect_threshold:7 [ Getting processor spec... ] [ Checking inputs and substituting prvs ... ] [ Computing process signature ... ] Process signature: 7b883d9943c4e480696a2a41266f9ef5b92b9954 [ Checking outputs... ] {"firings_out":"./OUTPUT/firings.mda"} Processing ouput - ./OUTPUT/firings.mda false {"firings_out":"/home/fer/data/msort_test/OUTPUT/firings.mda"} [ Checking process cache ... ] [ Creating temporary directory ... ] [ Creating links to input files... ] [ Preparing temporary outputs... ] Processing ouput - /home/fer/data/msort_test/OUTPUT/firings.mda false [ Initializing process ... ] [ Running ... ] /home/fer/anaconda3/envs/mountainlab/bin/python3 /home/fer/anaconda3/envs/mountainlab/lib/node_modules/mountainlab/system-packages/ml_ms4alg/ms4alg_spec.py.mp ms4alg.sort --_tempdir=/tmp/mountainlab-tmp/tempdir_7b883d9943_5YWCx8 --timeseries=/tmp/mountainlab-tmp/tempdi$_7b883d9943_5YWCx8/input_timeseries_RMRQM9Xn.mda --geom= --firings_out=/tmp/mountainlab-tmp/tempdir_7b883d9943_5YWCx8/output_firings_out.mda --detect_sign=-1 --adjacency_radius=0 --detect_threshold=7 Using tempdir=/tmp/mountainlab-tmp/tempdir_7b883d9943_5YWCx8 Num. workers = 8 Preparing /tmp/mountainlab-tmp/tempdir_7b883d9943_5YWCx8/timeseries.hdf5... Preparing neighborhood sorters (M=24, N=45967722)...
Traceback (most recent call last): File "", line 1, in
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/multiprocessing/spawn.py", line 105, in spawn_main
exitcode = _main(fd)
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/multiprocessing/spawn.py", line 114, in _main
prepare(preparation_data)
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/multiprocessing/spawn.py", line 225, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/multiprocessing/spawn.py", line 277, in _fixup_main_from_path
run_name="__mp_main__")
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/runpy.py", line 263, in run_path
pkg_name=pkg_name, script_name=fname)
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/runpy.py", line 96, in _run_module_code
mod_name, mod_spec, pkg_name, script_name)
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/runpy.py", line 85, in _run_code
mod_name, mod_spec, pkg_name, script_name)
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/fer/anaconda3/envs/mountainlab/lib/node_modules/mountainlab/system-packages/ml_ms4alg/ms4alg_spec.py.mp", line 13, in
if not PM.run(sys.argv):
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/site-packages/mountainlab_pytools/processormanager/processormanager_impl.py", line 37, in run
return P(args)
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/site-packages/ml_ms4alg/p_ms4alg.py", line 79, in sort**
MS4.sort()
File "/home/fer/anaconda3/envs/mountainlab/lib/python3.6/site-packages/ml_ms4alg/ms4alg.py", line 664, in sort
os.remove(temp_hdf5_path)
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/mountainlab-tmp/tempdir_7b883d9943_5YWCx8/timeseries.hdf5'