Sprint 5

[QSW-244] Modify the slurm templates to save run data into files. Created: 04/Jul/18  Updated: 05/Jul/18  Resolved: 05/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jonney Huang

Assignee:

Jonney Huang

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

CS18p6

Sprint:

QSW Sprint 5: 1807-1

To avoid scanning and matching errors, make the slurm scripts saves all the data into a file after simulation finished.

[QSW-243] Update HF Coef for Binary Mode Created: 04/Jul/18  Updated: 09/Jul/18  Resolved: 09/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jonney Huang

Assignee:

Jonney Huang

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

CS18p6

Sprint:

QSW Sprint 5: 1807-1

Binary mode HF has significant different runtime, compare to ASCII mode.
Update the Coef for both and modify the submit script to use different coef to est WCT.

[QSW-242] Plan how we add Web interface to interact with CLI-based event-based search Created: 04/Jul/18  Updated: 16/Jul/18  Resolved: 16/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Sung Bae

Assignee:

Unassigned

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

Data sharing

Sprint:

QSW Sprint 5: 1807-1

[QSW-241] Integrate all the components to achieve the behaviour of old event-based search (waveform only) Created: 04/Jul/18  Updated: 10/Jul/18  Resolved: 10/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Sung Bae

Assignee:

sharmila savarimuthu

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

Data sharing

Sprint:

QSW Sprint 5: 1807-1

Comment by sharmila savarimuthu [ 09/Jul/18 ]

The tables IMDB, Station and StationSet can be removed.

The ll file is created from the binary file for which the bin_path is in SimRun table.

The component files (000, 090 and ver) are created and zipped on the fly by using the binary file.

[QSW-240] Understand new code that supersedes old functionalities Created: 04/Jul/18  Updated: 08/Jul/18  Resolved: 08/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Sung Bae

Assignee:

sharmila savarimuthu

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

Data sharing

Sprint:

QSW Sprint 5: 1807-1

Comment by sharmila savarimuthu [ 08/Jul/18 ]

removed the IMDB related code

added binary file path in simrun table

can retrieve component files from binary path based on realisation and event name

[QSW-239] Understand the workflow of existing (broken) event-based search CLI code and identify what is broken Created: 04/Jul/18  Updated: 05/Jul/18  Resolved: 05/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Sung Bae

Assignee:

sharmila savarimuthu

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

1 day

Time Spent:

Not Specified

Original Estimate:

1 day

Epic Link:

Data sharing

Sprint:

QSW Sprint 5: 1807-1

Comment by sharmila savarimuthu [ 05/Jul/18 ]

1. The process is the same until you reach the dat file and get the station name for the lat,lon (using StationQuery)
2. The IMDB table need to be removed from current DB since we no longer need it.
3. Instead we introduce a new column called ‘binary file path’ matching each realisation in the SimRun Table.
4. From this binary file we can retrieve the component files 000,090 and ver for the station name using the qcore API.

[QSW-247] Pull-request for open sha to fix std-dev issue Created: 09/Jul/18  Updated: 10/Jul/18  Resolved: 10/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Jason Motha

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

Empirical Engine

Sprint:

QSW Sprint 5: 1807-1

[QSW-245] Calculate multiple periods for Zhao / Bradley Created: 05/Jul/18  Updated: 11/Jul/18  Resolved: 11/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Jason Motha

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

Empirical Engine

Sprint:

QSW Sprint 5: 1807-1

[QSW-179] Write code that computes an empirical IM Created: 20/Jun/18  Updated: 12/Jul/18  Resolved: 12/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Jason Motha

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

1 day

Time Spent:

Not Specified

Original Estimate:

1 day

Epic Link:

Empirical Engine

Sprint:

QSW Sprint 4, QSW Sprint 5: 1807-1

a function ‘computeEmpiricalIm.py’ (or similar) will then be a wrapper which will take the classes ‘Site’ (e.g. lat/lon/vs30), ‘Rup’ (i.e. SRF and SRF info), ‘ImType’ (e.g. PGA, AI, SA(0.5)), ‘EmpiricalImName’ (e.g. ‘Bradley 2013’, ‘Zhao 2006’) and compute the median and stdev of the IM;

[QSW-178] Calculate estimations of site/fault parameters. Created: 20/Jun/18  Updated: 12/Jul/18  Resolved: 12/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Jason Motha

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

1 day

Time Spent:

Not Specified

Original Estimate:

1 day

Epic Link:

Empirical Engine

Sprint:

QSW Sprint 4, QSW Sprint 5: 1807-1

For a given site:
vs30, Rupture distances
Calculate estimates of the fault parameters specified in [https://wiki.canterbury.ac.nz/display/QuakeCore/Empirical+Engine
]
For a fault:
Determine rupture type and faultstyle

[QSW-231] HF performance report Created: 04/Jul/18  Updated: 06/Jul/18  Resolved: 06/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Story

Priority:

Medium

Reporter:

Sung Bae

Assignee:

Unassigned

Resolution:

Done

Votes:

0

Labels:

None

Σ Remaining Estimate:

Not Specified

Remaining Estimate:

Not Specified

Σ Time Spent:

Not Specified

Time Spent:

Not Specified

Σ Original Estimate:

Not Specified

Original Estimate:

Not Specified

Sub-tasks:

Epic Link:

HF/BB

Sprint:

QSW Sprint 5: 1807-1

[QSW-224] Checkpointing on BB Created: 04/Jul/18  Updated: 06/Jul/18  Resolved: 06/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Viktor Polak

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

HF/BB

Sprint:

QSW Sprint 5: 1807-1

[QSW-223] Checkpointing on HF Created: 04/Jul/18  Updated: 05/Jul/18  Resolved: 05/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Viktor Polak

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

HF/BB

Sprint:

QSW Sprint 5: 1807-1

[QSW-218] Rename IM_calc metadata to specify it is IM_calc metadata file Created: 02/Jul/18  Updated: 09/Jul/18  Resolved: 09/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Melody Zhu

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

IMCalc

Sprint:

QSW Sprint 5: 1807-1

Comment by Melody Zhu [ 09/Jul/18 ]

The following changes are in check_point branch and not merged

1. Changed .info file to .meta_info as this is the quickest fix to all scripts that using im_calucation. eg. visulization/im_plot.py, test_im_plot, test_calculate_ims.
2. Updated IM_calcuation doc in wiki to reflect the change in point1
3. Updated scripts that uses IM_calculation in accordance to point 1

[QSW-213] [Generate slurm] make optional parameters actually optional Created: 27/Jun/18  Updated: 11/Jul/18  Resolved: 11/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Melody Zhu

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

IMCalc

Sprint:

QSW Sprint 4, QSW Sprint 5: 1807-1

Comment by Melody Zhu [ 11/Jul/18 ]

waiting for pull request from checkpoint branch to master

[QSW-208] Rrup wrapper to get list of stations from FD-station list Created: 26/Jun/18  Updated: 26/Jul/18

Status:

In Progress

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Melody Zhu

Resolution:

Unresolved

Votes:

0

Labels:

None

Remaining Estimate:

4 hours

Time Spent:

Not Specified

Original Estimate:

4 hours

Epic Link:

IMCalc

Sprint:

QSW Sprint 4, QSW Sprint 5: 1807-1

Comment by Melody Zhu [ 09/Jul/18 ]

Should fd_file path be parsed as an argument or fetched from params_base.py?

Comment by Melody Zhu [ 11/Jul/18 ]

waiting for pull request from checkpoint branch to master

[QSW-168] Residuals with respect to distance Created: 11/Jun/18  Updated: 04/Jul/18  Resolved: 04/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Jason Motha

Assignee:

Viktor Polak

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

IMplot

Sprint:

QSW Sprint 4, QSW Sprint 5: 1807-1

Comment by Jason Motha [ 11/Jun/18 ]

based on im_plots.py

[QSW-237] Run R code with the aggregated IMs (prototype) Created: 04/Jul/18  Updated: 12/Jul/18  Resolved: 12/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Sung Bae

Assignee:

Unassigned

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

Validation

Sprint:

QSW Sprint 5: 1807-1

[QSW-236] Test Viktor's combine_IM_files for non-ergodic with real data Created: 04/Jul/18  Updated: 12/Jul/18  Resolved: 12/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Sung Bae

Assignee:

Robin Lee

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

Validation

Sprint:

QSW Sprint 5: 1807-1

It is expected that there may be emerging issues with this task, which will be added as we go.

[QSW-235] MMI Fix (Na -> 1) Created: 04/Jul/18  Updated: 06/Jul/18  Resolved: 06/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Bug

Priority:

Medium

Reporter:

Sung Bae

Assignee:

Jason Motha

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

Validation

Sprint:

QSW Sprint 5: 1807-1

[QSW-149] Create input data for non-ergodic workflow Created: 06/Jun/18  Updated: 11/Jul/18  Resolved: 11/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Sung Bae

Assignee:

Viktor Polak

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Epic Link:

Validation

Sprint:

QSW Sprint 3, QSW Sprint 4, QSW Sprint 5: 1807-1

[QSW-252] srfinfo2vm parameters for VM topo and version Created: 13/Jul/18  Updated: 13/Jul/18  Resolved: 13/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Viktor Polak

Assignee:

Viktor Polak

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Sprint:

QSW Sprint 5: 1807-1

[QSW-48] fixed animation doesn't need params.py Created: 14/May/18  Updated: 13/Jul/18  Resolved: 13/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Viktor Polak

Assignee:

Viktor Polak

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Sprint:

QSW Sprint 5: 1807-1

[QSW-38] fixed animation joins PNG layers instead of PS Created: 14/May/18  Updated: 12/Jul/18  Resolved: 12/Jul/18

Status:

Done

Project:

QuakeCoRE SW

Component/s:

None

Affects Version/s:

None

Fix Version/s:

None

Type:

Task

Priority:

Medium

Reporter:

Viktor Polak

Assignee:

Viktor Polak

Resolution:

Done

Votes:

0

Labels:

None

Remaining Estimate:

2 hours

Time Spent:

Not Specified

Original Estimate:

2 hours

Sprint:

QSW Sprint 5: 1807-1

ffmpeg can layer PNGs. Will be major performance boost.

Comment by Viktor Polak [ 14/May/18 ]

https://superuser.com/questions/1182021/ffmpeg-how-do-i-overlay-a-png-over-another-png?utm_medium=organic&utm_source=google_rich_qa&utm_campaign=google_rich_qa