SIMPLE Test Report - nanox
SIMPLE test run
Execution times
4h 51m 37.4sTotal across 7 timed test steps
| Test step | Program | Duration |
|---|---|---|
| 4_track_particles/tracked_ptcl_1/tracked_ptcl_1/3_autorefine3D_nano | autorefine3D_nano | 1h 55m 14.4s6914.4 seconds |
| 4_track_particles/tracked_ptcl_1/tracked_ptcl_1/2_analysis2D_nano | analysis2D_nano | 6m 07.0s367.0 seconds |
| 4_track_particles/tracked_ptcl_1/tracked_ptcl_1/1_import_particles | import_particles | 6.3s6.3 seconds |
| 4_track_particles | track_particles | 1h 53m 51.2s6831.2 seconds |
| 3_tseries_make_pickavg | tseries_make_pickavg | 9.1s9.1 seconds |
| 2_tseries_motion_correct | tseries_motion_correct | 49m 27.1s2967.1 seconds |
| 1_tseries_import | tseries_import | 6m 42.3s402.3 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_nano1h 55m 14.4s
orthogonal_reprojs_state01.jpg
LOG summary: PROGRAM track_particles
>>> >>> ITERATION 1 >>> >>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.1052 **** SIMPLE_VOLASSEMBLE NORMAL STOP **** >>> ORIENTATION OVERLAP: 0.003 >>> % PARTICLES SAMPLED THIS ITERATION 100.000 (638/638) >>> % PARTICLES UPDATED SO FAR 100.000 >>> % PARTICLES USED FOR UPDATING THE MODEL 100.000 >>> % GREEDY SEARCHES 0.000 >>> DIST BTW BEST ORIS (DEG) AVG/SDEV/MIN/MAX: 85.442 42.629 1.287 177.471 >>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 89.888 52.077 0.168 179.468 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 5.507 2.895 0.187 13.533 >>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 1.005 0.000 1.005 1.005 >>> ESTIMATED LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 0.000 0.000 0.000 0.000 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 8.183 0.000 8.183 8.183 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.738 0.207 0.245 0.991 >>> -------------------- 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: 27.856 >>> AVERAGE GEODESIC DISTANCE: 1.527 **** VIZORIS NORMAL STOP **** **** AUTOREFINE3D_NANO NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 6914.4 seconds
4_track_particles/tracked_ptcl_1/tracked_ptcl_1/2_analysis2D_nano6m 07.0s
cavgs_iter015.jpg
LOG summary: PROGRAM track_particles
>>> ESTIMATED LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 0.000 0.000 0.000 0.000 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 8.856 3.633 0.716 57.280 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.474 0.201 -0.183 0.900 >>> -------------------- SETTINGS -------------------- >>> | REFINEMENT MODE | greedy >>> | PROB NEIGH MODE | state >>> | GAU REGULARIZATION | off >>> | ML REGULARIZATION | off >>> | FILTER MODE | none >>> -------------------------------------------------- >>> CONVERGED: .NO. >>> JPEG /usr/local/data/actions-runner/SIMPLE_data_testing/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: 0.984 >>> % PARTICLES SAMPLED THIS ITERATION 100.000 (12971/12971) >>> % PARTICLES UPDATED SO FAR 100.000 >>> % PARTICLES USED FOR AVERAGING 100.000 >>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 38.058 72.954 0.000 180.000 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 0.545 1.035 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: 8.955 3.641 0.716 57.280 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.475 0.201 -0.091 0.900 >>> -------------------- SETTINGS -------------------- >>> | REFINEMENT MODE | greedy >>> | PROB NEIGH MODE | state >>> | GAU REGULARIZATION | off >>> | ML REGULARIZATION | off >>> | FILTER MODE | none >>> -------------------------------------------------- >>> CONVERGED: .NO. >>> JPEG /usr/local/data/actions-runner/SIMPLE_data_testing/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: a7ca03a6 **** Execution time: 367.0 seconds
4_track_particles/tracked_ptcl_1/tracked_ptcl_1/1_import_particles6.3s
LOG summary: PROGRAM track_particles
>>> PROGRAM: import_particles >>> EXECUTION DIRECTORY: 1_import_particles **** IMPORT_PARTICLES NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 6.3 seconds
4_track_particles1h 53m 51.2s
LOG summary: PROGRAM track_particles
>>> tracked_ptcl_2 : 11001 FRAMES PROCESSED >>> tracked_ptcl_1 : 11126 FRAMES PROCESSED >>> tracked_ptcl_2 : 11126 FRAMES PROCESSED >>> tracked_ptcl_2 : 11251 FRAMES PROCESSED >>> tracked_ptcl_1 : 11251 FRAMES PROCESSED >>> tracked_ptcl_1 : 11376 FRAMES PROCESSED >>> tracked_ptcl_2 : 11376 FRAMES PROCESSED >>> tracked_ptcl_1 : 11501 FRAMES PROCESSED >>> tracked_ptcl_2 : 11501 FRAMES PROCESSED >>> tracked_ptcl_2 : 11626 FRAMES PROCESSED >>> tracked_ptcl_1 : 11626 FRAMES PROCESSED >>> tracked_ptcl_2 : 11751 FRAMES PROCESSED >>> tracked_ptcl_1 : 11751 FRAMES PROCESSED >>> tracked_ptcl_2 : 11876 FRAMES PROCESSED >>> tracked_ptcl_1 : 11876 FRAMES PROCESSED >>> tracked_ptcl_2 : 12001 FRAMES PROCESSED >>> tracked_ptcl_1 : 12001 FRAMES PROCESSED >>> tracked_ptcl_1 : 12126 FRAMES PROCESSED >>> tracked_ptcl_2 : 12126 FRAMES PROCESSED >>> tracked_ptcl_2 : 12251 FRAMES PROCESSED >>> tracked_ptcl_1 : 12251 FRAMES PROCESSED >>> tracked_ptcl_2 : 12376 FRAMES PROCESSED >>> tracked_ptcl_1 : 12376 FRAMES PROCESSED >>> tracked_ptcl_2 : 12501 FRAMES PROCESSED >>> tracked_ptcl_1 : 12501 FRAMES PROCESSED >>> tracked_ptcl_1 : 12626 FRAMES PROCESSED >>> tracked_ptcl_2 : 12626 FRAMES PROCESSED >>> tracked_ptcl_2 : 12751 FRAMES PROCESSED >>> tracked_ptcl_1 : 12751 FRAMES PROCESSED >>> tracked_ptcl_2 : 12876 FRAMES PROCESSED >>> tracked_ptcl_1 : 12876 FRAMES PROCESSED >>> WRITING PARTICLES, NEIGHBOURS & SPECTRUM >>> WRITING PARTICLES, NEIGHBOURS & SPECTRUM **** single_tseries_tracker NORMAL STOP **** **** single_tseries_tracker NORMAL STOP **** **** Execution time: 6830.0 seconds **** Execution time: 6830.0 seconds **** single_tseries_tracker NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 6831.2 seconds
3_tseries_make_pickavg9.1s
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: a7ca03a6 **** Execution time: 9.1 seconds
2_tseries_motion_correct49m 27.1s
tseries_win01826_thumb.jpg
tseries_win02688_thumb.jpg
tseries_win02921_thumb.jpg
tseries_win03165_thumb.jpg
tseries_win06860_thumb.jpg
tseries_win07983_thumb.jpg
tseries_win09506_thumb.jpg
tseries_win09971_thumb.jpg
tseries_win10179_thumb.jpg
tseries_win11436_thumb.jpg
LOG summary: PROGRAM tseries_motion_correct
>>> PATCH-BASED REFINEMENT (10 x 10) >>> AVERAGE PATCH & FRAMES CORRELATION: 0.587 >>> AVERAGE PATCH & FRAMES CORRELATION: 0.582 >>> PROCESSING MOVIE: frames2align_part5.mrc >>> # DEAD/HOT PIXELS / AVE / SDEV: 19 1042.1 230.6 >>> WEIGHTS AVE/SDEV/MIN/MAX : 0.2000 0.0030 0.1968 0.2034 >>> PATCH-BASED REFINEMENT (10 x 10) >>> PROCESSING MOVIE: frames2align_part6.mrc >>> # DEAD/HOT PIXELS / AVE / SDEV: 15 1041.1 229.9 >>> AVERAGE PATCH & FRAMES CORRELATION: 0.588 >>> WEIGHTS AVE/SDEV/MIN/MAX : 0.2000 0.0028 0.1968 0.2029 >>> PATCH-BASED REFINEMENT (10 x 10) >>> AVERAGE PATCH & FRAMES CORRELATION: 0.584 >>> PROCESSING MOVIE: frames2align_part5.mrc >>> # DEAD/HOT PIXELS / AVE / SDEV: 19 1041.7 230.1 >>> WEIGHTS AVE/SDEV/MIN/MAX : 0.2000 0.0033 0.1957 0.2032 >>> PATCH-BASED REFINEMENT (10 x 10) >>> PROCESSING MOVIE: frames2align_part6.mrc >>> # DEAD/HOT PIXELS / AVE / SDEV: 15 1041.1 229.9 >>> AVERAGE PATCH & FRAMES CORRELATION: 0.587 >>> WEIGHTS AVE/SDEV/MIN/MAX : 0.2000 0.0028 0.1968 0.2029 >>> PATCH-BASED REFINEMENT (10 x 10) >>> AVERAGE PATCH & FRAMES CORRELATION: 0.584 >>> PROCESSING MOVIE: frames2align_part5.mrc >>> # DEAD/HOT PIXELS / AVE / SDEV: 18 1041.8 229.8 >>> WEIGHTS AVE/SDEV/MIN/MAX : 0.2000 0.0030 0.1966 0.2038 >>> PATCH-BASED REFINEMENT (10 x 10) >>> PROCESSING MOVIE: frames2align_part6.mrc >>> # DEAD/HOT PIXELS / AVE / SDEV: 15 1041.1 229.9 >>> AVERAGE PATCH & FRAMES CORRELATION: 0.586 >>> WEIGHTS AVE/SDEV/MIN/MAX : 0.2000 0.0028 0.1968 0.2029 >>> PATCH-BASED REFINEMENT (10 x 10) >>> AVERAGE PATCH & FRAMES CORRELATION: 0.584 **** SIMPLE_TSERIES_MOTION_CORRECT NORMAL STOP **** **** Execution time: 2963.0 seconds **** SIMPLE_TSERIES_MOTION_CORRECT NORMAL STOP **** **** Execution time: 2963.4 seconds **** SIMPLE_DISTR_TSERIES_MOTION_CORRECT NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 2967.1 seconds
1_tseries_import6m 42.3s
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: a7ca03a6 **** Execution time: 402.3 seconds