diff --git a/tutorial_data/master/betalactamase/dials.integrate.log b/tutorial_data/master/betalactamase/dials.integrate.log index 830dd0d1..82fe0905 100644 --- a/tutorial_data/master/betalactamase/dials.integrate.log +++ b/tutorial_data/master/betalactamase/dials.integrate.log @@ -132,11 +132,11 @@ Modelling reflection profiles Split 13 reflections overlapping job boundaries Memory situation report: - Available system memory (excluding swap) :128.6 GB - Available swap memory : 7.7 GB - Available system memory (including swap) :136.3 GB - Maximum memory for processing (including swap) :122.7 GB - Maximum memory for processing (excluding swap) :115.7 GB + Available system memory (excluding swap) :128.8 GB + Available swap memory : 8.5 GB + Available system memory (including swap) :137.3 GB + Maximum memory for processing (including swap) :123.5 GB + Maximum memory for processing (excluding swap) :115.9 GB no memory ulimit set Memory required per process : 0.0 GB @@ -849,12 +849,12 @@ Processing reflections in the following blocks of images: Timing information for reference profile formation +-------------------+---------------+ -| Read time | 64.51 seconds | -| Extract time | 0.40 seconds | +| Read time | 64.30 seconds | +| Extract time | 0.58 seconds | | Pre-process time | 0.08 seconds | -| Process time | 26.74 seconds | +| Process time | 26.28 seconds | | Post-process time | 0.00 seconds | -| Total time | 92.07 seconds | +| Total time | 91.39 seconds | +-------------------+---------------+ ================================================================================ @@ -864,11 +864,11 @@ Integrating reflections Split 109 reflections overlapping job boundaries Memory situation report: - Available system memory (excluding swap) :128.6 GB - Available swap memory : 7.7 GB - Available system memory (including swap) :136.3 GB - Maximum memory for processing (including swap) :122.7 GB - Maximum memory for processing (excluding swap) :115.7 GB + Available system memory (excluding swap) :128.8 GB + Available swap memory : 8.5 GB + Available system memory (including swap) :137.3 GB + Maximum memory for processing (including swap) :123.5 GB + Maximum memory for processing (excluding swap) :115.9 GB no memory ulimit set Memory required per process : 0.0 GB @@ -1709,12 +1709,12 @@ Processing reflections in the following blocks of images: Timing information for integration +-------------------+----------------+ -| Read time | 65.56 seconds | -| Extract time | 2.71 seconds | -| Pre-process time | 0.39 seconds | -| Process time | 139.62 seconds | +| Read time | 64.56 seconds | +| Extract time | 2.57 seconds | +| Pre-process time | 0.35 seconds | +| Process time | 138.80 seconds | | Post-process time | 0.00 seconds | -| Total time | 209.46 seconds | +| Total time | 207.49 seconds | +-------------------+----------------+ Removing 41622 unintegrated reflections of 368699 total diff --git a/tutorial_data/master/betalactamase/dials.scale.log b/tutorial_data/master/betalactamase/dials.scale.log index 4bfe7516..d104a21a 100644 --- a/tutorial_data/master/betalactamase/dials.scale.log +++ b/tutorial_data/master/betalactamase/dials.scale.log @@ -125,7 +125,7 @@ A round of outlier rejection has been performed, Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 0.99 +Time taken for refinement 1.21 Refinement steps: +--------+--------+----------+ @@ -177,7 +177,7 @@ are expected to be ~1.0 for reliable errors (sigmas). Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 3.74 +Time taken for refinement 3.79 Refinement steps: +--------+--------+----------+ @@ -248,7 +248,7 @@ are expected to be ~1.0 for reliable errors (sigmas). The reflection table variances have been adjusted to account for the uncertainty in the scaling model -Total time taken: 19.0162s +Total time taken: 19.2279s ================================================================================ diff --git a/tutorial_data/master/betalactamase/dials.scale_cut.log b/tutorial_data/master/betalactamase/dials.scale_cut.log index 6750e89a..b56252b2 100644 --- a/tutorial_data/master/betalactamase/dials.scale_cut.log +++ b/tutorial_data/master/betalactamase/dials.scale_cut.log @@ -68,7 +68,7 @@ Completed preprocessing and initialisation for this dataset. Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 0.98 +Time taken for refinement 0.97 Refinement steps: +--------+--------+----------+ @@ -161,7 +161,7 @@ are expected to be ~1.0 for reliable errors (sigmas). Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 2.43 +Time taken for refinement 2.42 Refinement steps: +--------+--------+----------+ @@ -180,7 +180,7 @@ RMSD no longer decreasing Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 1.18 +Time taken for refinement 1.17 Refinement steps: +--------+--------+----------+ @@ -230,7 +230,7 @@ are expected to be ~1.0 for reliable errors (sigmas). The reflection table variances have been adjusted to account for the uncertainty in the scaling model -Total time taken: 13.5817s +Total time taken: 13.4853s ================================================================================ diff --git a/tutorial_data/master/last_update b/tutorial_data/master/last_update index 12d94902..3f5c7071 100644 --- a/tutorial_data/master/last_update +++ b/tutorial_data/master/last_update @@ -1 +1 @@ -2023-W43 +2023-W44 diff --git a/tutorial_data/master/mpro_x0692/dials.integrate.log b/tutorial_data/master/mpro_x0692/dials.integrate.log index 79cc6b8b..0ec6bbee 100644 --- a/tutorial_data/master/mpro_x0692/dials.integrate.log +++ b/tutorial_data/master/mpro_x0692/dials.integrate.log @@ -122,11 +122,11 @@ Modelling reflection profiles Split 27 reflections overlapping job boundaries Memory situation report: - Available system memory (excluding swap) :128.9 GB - Available swap memory : 7.7 GB - Available system memory (including swap) :136.6 GB - Maximum memory for processing (including swap) :122.9 GB - Maximum memory for processing (excluding swap) :116.0 GB + Available system memory (excluding swap) :129.1 GB + Available swap memory : 8.5 GB + Available system memory (including swap) :137.6 GB + Maximum memory for processing (including swap) :123.8 GB + Maximum memory for processing (excluding swap) :116.2 GB no memory ulimit set Memory required per process : 0.0 GB @@ -551,12 +551,12 @@ Processing reflections in the following blocks of images: Timing information for reference profile formation +-------------------+---------------+ -| Read time | 21.93 seconds | -| Extract time | 0.40 seconds | +| Read time | 20.16 seconds | +| Extract time | 0.38 seconds | | Pre-process time | 0.02 seconds | -| Process time | 8.54 seconds | +| Process time | 8.39 seconds | | Post-process time | 0.00 seconds | -| Total time | 30.93 seconds | +| Total time | 29.09 seconds | +-------------------+---------------+ ================================================================================ @@ -566,11 +566,11 @@ Integrating reflections Split 681 reflections overlapping job boundaries Memory situation report: - Available system memory (excluding swap) :128.8 GB - Available swap memory : 7.7 GB - Available system memory (including swap) :136.6 GB - Maximum memory for processing (including swap) :122.9 GB - Maximum memory for processing (excluding swap) :116.0 GB + Available system memory (excluding swap) :129.1 GB + Available swap memory : 8.5 GB + Available system memory (including swap) :137.5 GB + Maximum memory for processing (including swap) :123.8 GB + Maximum memory for processing (excluding swap) :116.2 GB no memory ulimit set Memory required per process : 0.3 GB @@ -1091,12 +1091,12 @@ Processing reflections in the following blocks of images: Timing information for integration +-------------------+----------------+ -| Read time | 24.19 seconds | -| Extract time | 6.86 seconds | +| Read time | 24.34 seconds | +| Extract time | 6.54 seconds | | Pre-process time | 0.20 seconds | -| Process time | 129.67 seconds | +| Process time | 130.09 seconds | | Post-process time | 0.00 seconds | -| Total time | 161.95 seconds | +| Total time | 162.44 seconds | +-------------------+----------------+ Removing 22837 unintegrated reflections of 199394 total diff --git a/tutorial_data/master/mpro_x0692/dials.scale.log b/tutorial_data/master/mpro_x0692/dials.scale.log index a05af188..2b242e84 100644 --- a/tutorial_data/master/mpro_x0692/dials.scale.log +++ b/tutorial_data/master/mpro_x0692/dials.scale.log @@ -67,7 +67,7 @@ Completed preprocessing and initialisation for this dataset. Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 5.89 +Time taken for refinement 5.87 Refinement steps: +--------+--------+----------+ @@ -139,7 +139,7 @@ A round of outlier rejection has been performed, Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 2.44 +Time taken for refinement 2.43 Refinement steps: +--------+--------+----------+ @@ -199,7 +199,7 @@ are expected to be ~1.0 for reliable errors (sigmas). Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 4.45 +Time taken for refinement 4.48 Refinement steps: +--------+--------+----------+ @@ -223,7 +223,7 @@ RMSD no longer decreasing Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 0.93 +Time taken for refinement 0.96 Refinement steps: +--------+--------+----------+ @@ -273,7 +273,7 @@ are expected to be ~1.0 for reliable errors (sigmas). The reflection table variances have been adjusted to account for the uncertainty in the scaling model -Total time taken: 19.3069s +Total time taken: 19.3101s ================================================================================ diff --git a/tutorial_data/master/mpro_x0692/dials.scale_cut.log b/tutorial_data/master/mpro_x0692/dials.scale_cut.log index b9abb77f..73591b94 100644 --- a/tutorial_data/master/mpro_x0692/dials.scale_cut.log +++ b/tutorial_data/master/mpro_x0692/dials.scale_cut.log @@ -68,7 +68,7 @@ Completed preprocessing and initialisation for this dataset. Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 0.67 +Time taken for refinement 0.66 Refinement steps: +--------+--------+----------+ @@ -108,7 +108,7 @@ A round of outlier rejection has been performed, Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 0.68 +Time taken for refinement 0.66 Refinement steps: +--------+--------+----------+ @@ -158,7 +158,7 @@ are expected to be ~1.0 for reliable errors (sigmas). Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 3.07 +Time taken for refinement 3.03 Refinement steps: +--------+--------+----------+ @@ -179,7 +179,7 @@ RMSD no longer decreasing Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 0.98 +Time taken for refinement 0.94 Refinement steps: +--------+--------+----------+ @@ -229,7 +229,7 @@ are expected to be ~1.0 for reliable errors (sigmas). The reflection table variances have been adjusted to account for the uncertainty in the scaling model -Total time taken: 9.3055s +Total time taken: 9.0388s ================================================================================ diff --git a/tutorial_data/master/multi_crystal/dials.merge.log b/tutorial_data/master/multi_crystal/dials.merge.log index 05c30491..da225805 100644 --- a/tutorial_data/master/multi_crystal/dials.merge.log +++ b/tutorial_data/master/multi_crystal/dials.merge.log @@ -295,7 +295,7 @@ Number of crystals: 2 Number of Miller indices: 20799 Resolution range: 68.3603 1.78117 History: - From DIALS 3.dev.1044-g103ed65a1, run on 2023-10-28 at 08:20:51 BST (2023-10-28 + From DIALS 3.dev.1044-g103ed65a1, run on 2023-11-04 at 08:19:44 GMT Crystal 1: Name: HKL_base Project: HKL_base diff --git a/tutorial_data/master/multi_crystal/dials.scale.log b/tutorial_data/master/multi_crystal/dials.scale.log index 4887b11c..be9e2e0b 100644 --- a/tutorial_data/master/multi_crystal/dials.scale.log +++ b/tutorial_data/master/multi_crystal/dials.scale.log @@ -227,7 +227,7 @@ Completed configuration of MultiScaler. Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 31.02 +Time taken for refinement 26.68 Refinement steps: +--------+--------+----------+ @@ -402,7 +402,7 @@ Combined outlier rejection has been performed across multiple datasets, Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 2.76 +Time taken for refinement 2.47 Refinement steps: +--------+--------+----------+ @@ -462,7 +462,7 @@ are expected to be ~1.0 for reliable errors (sigmas). Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 19.50 +Time taken for refinement 15.72 Refinement steps: +--------+--------+----------+ @@ -485,7 +485,7 @@ RMSD no longer decreasing Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 4.94 +Time taken for refinement 3.84 Refinement steps: +--------+--------+----------+ @@ -539,7 +539,7 @@ The reflection table variances have been adjusted to account for the uncertainty in the scaling models for all datasets Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) -Total time taken: 66.3793s +Total time taken: 55.2976s ================================================================================ diff --git a/tutorial_data/master/multi_crystal/dials.scale_cut.log b/tutorial_data/master/multi_crystal/dials.scale_cut.log index ef55b3a7..82c765aa 100644 --- a/tutorial_data/master/multi_crystal/dials.scale_cut.log +++ b/tutorial_data/master/multi_crystal/dials.scale_cut.log @@ -222,7 +222,7 @@ Completed configuration of MultiScaler. Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 2.12 +Time taken for refinement 1.72 Refinement steps: +--------+--------+----------+ @@ -267,7 +267,7 @@ Combined outlier rejection has been performed across multiple datasets, Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 1.42 +Time taken for refinement 1.15 Refinement steps: +--------+--------+----------+ @@ -320,7 +320,7 @@ are expected to be ~1.0 for reliable errors (sigmas). Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 14.45 +Time taken for refinement 11.80 Refinement steps: +--------+--------+----------+ @@ -341,7 +341,7 @@ RMSD no longer decreasing Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 4.63 +Time taken for refinement 3.83 Refinement steps: +--------+--------+----------+ @@ -395,7 +395,7 @@ The reflection table variances have been adjusted to account for the uncertainty in the scaling models for all datasets Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) -Total time taken: 30.0638s +Total time taken: 24.7397s ================================================================================ diff --git a/tutorial_data/master/multi_crystal/dials.scale_exclude.log b/tutorial_data/master/multi_crystal/dials.scale_exclude.log index 0a5776aa..6a5f6955 100644 --- a/tutorial_data/master/multi_crystal/dials.scale_exclude.log +++ b/tutorial_data/master/multi_crystal/dials.scale_exclude.log @@ -222,7 +222,7 @@ Completed configuration of MultiScaler. Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 0.92 +Time taken for refinement 0.77 Refinement steps: +--------+--------+----------+ @@ -262,7 +262,7 @@ Combined outlier rejection has been performed across multiple datasets, Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with an LBFGS minimizer. -Time taken for refinement 0.94 +Time taken for refinement 0.77 Refinement steps: +--------+--------+----------+ @@ -313,7 +313,7 @@ are expected to be ~1.0 for reliable errors (sigmas). Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 11.99 +Time taken for refinement 9.73 Refinement steps: +--------+--------+----------+ @@ -333,7 +333,7 @@ RMSD no longer decreasing Components to be refined in this cycle for all datasets: scale, decay, absorption Performing a round of scaling with a Levenberg-Marquardt minimizer. -Time taken for refinement 4.51 +Time taken for refinement 3.80 Refinement steps: +--------+--------+----------+ @@ -387,7 +387,7 @@ The reflection table variances have been adjusted to account for the uncertainty in the scaling models for all datasets Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) -Total time taken: 25.4405s +Total time taken: 21.2753s ================================================================================ diff --git a/tutorial_data/master/thaumatin/dials.export.log b/tutorial_data/master/thaumatin/dials.export.log index 07b3abf0..80ede4a5 100644 --- a/tutorial_data/master/thaumatin/dials.export.log +++ b/tutorial_data/master/thaumatin/dials.export.log @@ -29,7 +29,7 @@ Number of crystals: 1 Number of Miller indices: 324700 Resolution range: 150.004 1.16829 History: - From DIALS 3.dev.1044-g103ed65a1, run on 2023-10-28 at 08:14:44 BST (2023-10-28 + From DIALS 3.dev.1044-g103ed65a1, run on 2023-11-04 at 08:14:38 GMT Crystal 1: Name: XTAL Project: DIALS diff --git a/tutorial_data/master/thaumatin/dials.integrate.log b/tutorial_data/master/thaumatin/dials.integrate.log index f2503455..17f96be7 100644 --- a/tutorial_data/master/thaumatin/dials.integrate.log +++ b/tutorial_data/master/thaumatin/dials.integrate.log @@ -127,11 +127,11 @@ Modelling reflection profiles Split 61 reflections overlapping job boundaries Memory situation report: - Available system memory (excluding swap) :127.9 GB - Available swap memory : 7.7 GB - Available system memory (including swap) :135.7 GB - Maximum memory for processing (including swap) :122.1 GB - Maximum memory for processing (excluding swap) :115.1 GB + Available system memory (excluding swap) :128.8 GB + Available swap memory : 8.5 GB + Available system memory (including swap) :137.2 GB + Maximum memory for processing (including swap) :123.5 GB + Maximum memory for processing (excluding swap) :115.9 GB no memory ulimit set Memory required per process : 0.0 GB @@ -349,12 +349,12 @@ Processing reflections in the following blocks of images: Timing information for reference profile formation +-------------------+---------------+ -| Read time | 36.78 seconds | -| Extract time | 1.20 seconds | -| Pre-process time | 0.11 seconds | -| Process time | 31.60 seconds | +| Read time | 31.50 seconds | +| Extract time | 0.91 seconds | +| Pre-process time | 0.09 seconds | +| Process time | 28.91 seconds | | Post-process time | 0.00 seconds | -| Total time | 70.09 seconds | +| Total time | 61.71 seconds | +-------------------+---------------+ ================================================================================ @@ -364,11 +364,11 @@ Integrating reflections Split 374 reflections overlapping job boundaries Memory situation report: - Available system memory (excluding swap) :124.8 GB - Available swap memory : 7.7 GB - Available system memory (including swap) :132.5 GB - Maximum memory for processing (including swap) :119.2 GB - Maximum memory for processing (excluding swap) :112.3 GB + Available system memory (excluding swap) :128.7 GB + Available swap memory : 8.5 GB + Available system memory (including swap) :137.2 GB + Maximum memory for processing (including swap) :123.5 GB + Maximum memory for processing (excluding swap) :115.9 GB no memory ulimit set Memory required per process : 0.0 GB @@ -1029,12 +1029,12 @@ Processing reflections in the following blocks of images: Timing information for integration +-------------------+----------------+ -| Read time | 30.99 seconds | -| Extract time | 3.63 seconds | -| Pre-process time | 0.38 seconds | -| Process time | 120.96 seconds | +| Read time | 32.17 seconds | +| Extract time | 3.41 seconds | +| Pre-process time | 0.42 seconds | +| Process time | 118.95 seconds | | Post-process time | 0.00 seconds | -| Total time | 157.34 seconds | +| Total time | 156.29 seconds | +-------------------+----------------+ Removing 40904 unintegrated reflections of 384160 total diff --git a/tutorial_data/master/thaumatin/dials.report.log b/tutorial_data/master/thaumatin/dials.report.log index b7a25aa2..e7ea14d2 100644 --- a/tutorial_data/master/thaumatin/dials.report.log +++ b/tutorial_data/master/thaumatin/dials.report.log @@ -9,7 +9,7 @@ Analysing strong spots Selected 110371 strong reflections........................................0.03s Analysing reflection centroids Removing 9990 partial reflections - Selected 323347 summation-integrated reflections..........................0.10s + Selected 323347 summation-integrated reflections..........................0.07s Analysing centroid differences with I/Sigma > 10 Analysing centroid differences in x/y with I/Sigma > 10 Analysing centroid differences in z with I/Sigma > 10 @@ -24,7 +24,7 @@ Analysing reflection intensities Analysing distribution of partialities Analysing QE map Analysing reference profiles - Selected 324855 integrated reflections....................................0.08s + Selected 324855 integrated reflections....................................0.07s Analysing reference profile distribution vs x/y Analysing reference profile distribution vs z Analysing reflection correlations vs resolution