Plotting issue on cluster. Requesting start_time.txt file #109
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cnlbob
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Jan 5, 2019
This patch adds an "Ignore Start Time" flag to the plotting screen. The code normally checks that the start_time.txt exists in the proj_files directory. However, when running multiple simulations on a cluster, this method may not be working properly. This patch allows the user to disable this checking to allow plotting even when the start_time.txt file isn't consistent with the plot files. Note that the start_time.txt file was intended as a way to keep users from accidentally plotting stale data files from previous runs along with current plotting files from current runs. When the user ignores the start_time.txt file, they should ensure that all of their runs have completed properly.
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Hi team,
There is an issue producing plot output when jobs are running on a server.
The plotting module requests a start_time.txt file
See error below:
data_layout = {'version': 2, 'data_layout': [['/DIR', ['output_data']], ['/FILE_TYPE', ['react_data', 'viz_data']], ['/SEED', [1]]]}
num_runs = 1, data_layout = {'version': 2, 'data_layout': [['/DIR', ['output_data'], 0], ['/FILE_TYPE', ['react_data', 'viz_data'], 0], ['/SEED', [1], 0]]}
Preparing run 0
Counters = /SEED:0 /FILE_TYPE:0 /DIR:0
Run path = output_data/react_data
Parameter Point for run is:
glob of /home/shirakis/projects/Dyad/sims/sim_files/D_b_p_f_R_S_L-6-n_files/mcell/output_data/react_data/seed_*/Ca2_cyt.World.dat
Traceback (most recent call last):
File "/nadata/snl/lv_home/cnl/shirakis/bin/blender_2.79/2.79/scripts/addons/cellblender/cellblender_reaction_output.py", line 404, in execute
start_time = os.stat(os.path.join(project_files_path(), "start_time.txt")).st_mtime
FileNotFoundError: [Errno 2] No such file or directory: '/home/shirakis/projects/Dyad/sims/sim_files/D_b_p_f_R_S_L-6-n_files/start_time.txt'
location: :-1
location: :-1
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