SIMPLE Test Report - nanox
SIMPLE test run
Execution times
4h 07m 15.9sTotal across 7 timed test steps
| Test step | Program | Duration |
|---|---|---|
| 4_track_particles/tracked_ptcl_1/tracked_ptcl_1/3_autorefine3D_nano | autorefine3D_nano | 2h 00m 40.2s7240.2 seconds |
| 4_track_particles/tracked_ptcl_1/tracked_ptcl_1/2_analysis2D_nano | analysis2D_nano | 5m 47.2s347.2 seconds |
| 4_track_particles/tracked_ptcl_1/tracked_ptcl_1/1_import_particles | import_particles | 0.1s0.1 seconds |
| 4_track_particles | track_particles | 1h 03m 58.7s3838.7 seconds |
| 3_tseries_make_pickavg | tseries_make_pickavg | 14.9s14.9 seconds |
| 2_tseries_motion_correct | tseries_motion_correct | 49m 25.5s2965.5 seconds |
| 1_tseries_import | tseries_import | 7m 09.3s429.3 seconds |
Total is the sum of execution times recorded by SIMPLE in this test LOG.
4_track_particles/tracked_ptcl_1/tracked_ptcl_1/3_autorefine3D_nano2h 00m 40.2s
orientations_distribution_state01.jpg
orthogonal_reprojs_state01.jpg
LOG summary: PROGRAM track_particles
>>> FSC MODE: STATE 1, backend=gridding support=sphere posthoc_mask=none phase_randomization=no >>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.6844 **** SIMPLE_VOLASSEMBLE NORMAL STOP **** >>> RECONSTRUCTION MASTER PHASE (gridding): 6.8 s on 16 threads = 109.2 thread-s, peak RSS 8.75 GiB >>> ORIENTATION OVERLAP: 0.899 >>> % PARTICLES SAMPLED THIS ITERATION 100.000 (12971/12971) >>> % PARTICLES UPDATED SO FAR 100.000 >>> % PARTICLES USED FOR UPDATING THE MODEL 100.000 >>> % GREEDY SEARCHES 0.000 >>> % CONTINUOUS IN-PLANE RUNS IMPROVED 85.853 (12971 attempts) >>> DIST BTW BEST ORIS (DEG) AVG/SDEV/MIN/MAX: 3.143 9.821 0.000 133.929 >>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 1.850 12.457 0.000 180.000 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 0.103 0.472 0.000 9.033 >>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT (THIS ITERATION) 1.005 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 0.716 0.000 0.716 0.716 >>> RESOLUTION @ FSC=0.5 AVG/SDEV/MIN/MAX: 0.818 0.000 0.818 0.818 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.601 0.195 0.000 0.951 >>> -------------------- SETTINGS -------------------- >>> | REFINEMENT MODE | neigh >>> | PROB NEIGH MODE | state >>> | NSPACE PROJECTION DIRECTIONS | 20000 >>> | GAU REGULARIZATION | off >>> | ML REGULARIZATION | off >>> | ICM REGULARIZATION | on, LAMBDA: 0.100000001 >>> | AUTOMASKING | off >>> | FILTER MODE | none >>> -------------------------------------------------- >>> CONVERGED: no **** SIMPLE_REFINE3D NORMAL STOP **** >>> GENERATING PROJECTIONS **** SIMPLE_REPROJECT NORMAL STOP **** >>> GENERATING PROJECTIONS **** SIMPLE_REPROJECT NORMAL STOP **** >>> AVERAGE EULER DISTANCE: 32.702 >>> AVERAGE GEODESIC DISTANCE: 1.474 **** VIZORIS NORMAL STOP **** **** AUTOREFINE3D_NANO NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 7240.2 seconds
4_track_particles/tracked_ptcl_1/tracked_ptcl_1/2_analysis2D_nano5m 47.2s
cavgs_iter015.jpg
LOG summary: PROGRAM track_particles
>>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 9.145 3.972 0.716 57.280 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.473 0.200 -0.029 0.903 >>> -------------------- SETTINGS -------------------- >>> | REFINEMENT MODE | greedy >>> | PROB NEIGH MODE | state >>> | GAU REGULARIZATION | off >>> | ML REGULARIZATION | off >>> | FILTER MODE | none >>> -------------------------------------------------- >>> CONVERGED: .NO. >>> JPEG /usr/local/cache/actions-runner/_work/SIMPLE_data_testing/SIMPLE_data_testing/nanox/4_track_particles/tracked_ptcl_1/tracked_ptcl_1/2_analysis2D_nano/cavgs_iter014.jpg >>> >>> ITERATION 15 >>> >>> CLASS OVERLAP: 0.981 >>> % PARTICLES SAMPLED THIS ITERATION 100.000 (12971/12971) >>> % PARTICLES UPDATED SO FAR 100.000 >>> % PARTICLES USED FOR AVERAGING 100.000 >>> % CONTINUOUS IN-PLANE RUNS IMPROVED 0.000 (0 attempts) >>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 41.249 75.043 0.000 180.000 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 0.582 1.055 0.000 7.071 >>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 1.000 0.000 1.000 1.000 >>> ESTIMATED LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 0.000 0.000 0.000 0.000 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 9.163 3.971 0.716 57.280 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.474 0.200 -0.026 0.903 >>> -------------------- SETTINGS -------------------- >>> | REFINEMENT MODE | greedy >>> | PROB NEIGH MODE | state >>> | GAU REGULARIZATION | off >>> | ML REGULARIZATION | off >>> | FILTER MODE | none >>> -------------------------------------------------- >>> CONVERGED: .NO. >>> JPEG /usr/local/cache/actions-runner/_work/SIMPLE_data_testing/SIMPLE_data_testing/nanox/4_track_particles/tracked_ptcl_1/tracked_ptcl_1/2_analysis2D_nano/cavgs_iter015.jpg **** SIMPLE_CLUSTER2D NORMAL STOP **** **** SIMPLE_CLUSTER2D_NANO NORMAL STOP **** **** SIMPLE_ANALYSIS2D_NANO NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 347.2 seconds
4_track_particles/tracked_ptcl_1/tracked_ptcl_1/1_import_particles0.1s
LOG summary: PROGRAM track_particles
>>> PROGRAM: import_particles >>> EXECUTION DIRECTORY: 1_import_particles **** IMPORT_PARTICLES NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 0.1 seconds
4_track_particles1h 03m 58.7s
LOG summary: PROGRAM track_particles
>>> PROGRAM: track_particles >>> EXECUTION DIRECTORY: 4_track_particles >>> particles to track : 2 >>> concurrent particle tracking jobs : 2 >>> TRACK_PARTICLES: 2 PART(S) COMPLETED IN 3838.5 s **** single_tseries_tracker NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 3838.7 seconds
3_tseries_make_pickavg14.9s
frames2align_thumb.jpg
LOG summary: PROGRAM tseries_make_pickavg
>>> PROGRAM: tseries_make_pickavg >>> EXECUTION DIRECTORY: 3_tseries_make_pickavg >>> PROCESSING MOVIE: frames2align.mrc >>> # DEAD/HOT PIXELS / AVE / SDEV: 22 20816.2 1909.3 >>> WEIGHTS AVE/SDEV/MIN/MAX : 0.0100 0.0032 0.0000 0.0151 >>> PATCH-BASED REFINEMENT ( 3 x 3) >>> AVERAGE PATCH & FRAMES CORRELATION: 0.347 **** SIMPLE_TSERIES_MAKE_PICKAVG NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 14.9 seconds
2_tseries_motion_correct49m 25.5s
tseries_win01576_thumb.jpg
tseries_win02705_thumb.jpg
tseries_win02739_thumb.jpg
tseries_win03913_thumb.jpg
tseries_win04631_thumb.jpg
tseries_win05058_thumb.jpg
tseries_win05195_thumb.jpg
tseries_win08673_thumb.jpg
tseries_win08910_thumb.jpg
tseries_win09893_thumb.jpg
LOG summary: PROGRAM tseries_motion_correct
>>> PROGRAM: tseries_motion_correct >>> EXECUTION DIRECTORY: 2_tseries_motion_correct >>> TSERIES_MOTION_CORRECT: 6 PART(S) COMPLETED IN 2964.4 s **** SIMPLE_DISTR_TSERIES_MOTION_CORRECT NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 2965.5 seconds
1_tseries_import7m 09.3s
LOG summary: PROGRAM tseries_import
>>> PROGRAM: tseries_import >>> EXECUTION DIRECTORY: 1_tseries_import >>> IMPORTED 12971 FRAME(S) >>> TOTAL NUMBER OF FRAME(S): 12971 **** TSERIES_IMPORT NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 429.3 seconds