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Mac issue #5
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Hi, can you try a larger k range. Maybe like this: mpirun -n 4 python /Users/edward/pyDNMFk/main.py --p_r=4 --p_c=1 --process='pyDNMFk' --fpath='data/' --ftype='csv' --fname='HMX' --init='nnsvd' --itr=5000 --norm='kl' --method='mu' --results_path='results/34' --perturbations=100 --noise_var=0.015 --start_k=3 --end_k=10 --step_k=1 --sill_thr=.9 --sampling='uniform' --prune=true > log34.out & |
I had started out with a larger range like that. Same error. Was trying to simplify it down for possible sources.
…---------------------------------------------------
Edward M. Kober, Ph.D.
Scientist 5
Physics and Chemistry of Materials
Group T-1, MS B214
Los Alamos National Laboratory
Los Alamos, NM 87545
***@***.******@***.***> 505-667-5140
From: Maksim Ekin Eren ***@***.***>
Reply-To: lanl/pyDNMFk ***@***.***>
Date: Wednesday, September 29, 2021 at 11:20 AM
To: lanl/pyDNMFk ***@***.***>
Cc: "Kober, Ed" ***@***.***>, Author ***@***.***>
Subject: [EXTERNAL] Re: [lanl/pyDNMFk] Mac issue (#5)
Hi, can you try a larger k range. Maybe like this: mpirun -n 4 python /Users/edward/pyDNMFk/main.py --p_r=4 --p_c=1 --process='pyDNMFk' --fpath='data/' --ftype='csv' --fname='HMX' --init='nnsvd' --itr=5000 --norm='kl' --method='mu' --results_path='results/34' --perturbations=100 --noise_var=0.015 --start_k=3 --end_k=10 --step_k=1 --sill_thr=.9 --sampling='uniform' --prune=true > log34.out &
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small_HMX.csv |
Well, going to a bigger k limit does generate rational looking selection plots. Though I still get those runtime warnings about invalid error in true_divide which is irritating, but not catastrophic? Will close for now. |
Hi @emkober, I am glad it is working now. I tried the sample data you shared with the following settings:
I did get same warning in the end, but the results seems okay with the high k-range. In this plot k-optimal seems to be either 6 or 14: |
I've installed this on both a Mac laptop and desktop and it runs the swim problem just fine with mpirun using 4 processors. I then try to run my own problems with the command line
mpirun -n 4 python /Users/edward/pyDNMFk/main.py --p_r=4 --p_c=1 --process='pyDNMFk' --fpath='data/' --ftype='csv' --fname='HMX' --init='nnsvd' --itr=5000 --norm='kl' --method='mu' --results_path='results/34' --perturbations=100 --noise_var=0.015 --start_k=3 --end_k=4 --step_k=1 --sill_thr=.9 --sampling='uniform' --prune=true > log34.out &
And I get
/Users/edward/pyDNMFk/pyDNMFk/pyDNMF.py:238: RuntimeWarning: invalid value encountered in true_divide
col_err = np.sqrt(col_err_num / col_err_deno)
4 times (or for each number of processors I requested). Output files are full of data, but the selection plot is messed up. Anything obvious?
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