Table of Contents
SEP report reproducibility test guideline
Requirement for repro test
If you have more complex reproducing strategies rather than typing make. You need to include a readme file or put the instructions at the top of make file as comment.
The quality of reproducibility will be evaluated in five aspects:
1. All Code compiles on SEP computing environment
2. flow for CR figures is present in makefile
3. ER figures can be reproduced
4. Makefile is written in a clear/concise/neat manner
5. CR figures can be reproduced.
The last two are optional, but rest are mandatory(everyone needs to pass in order to pass the test). Also we will check that proper reproducibility label are assigned to each figures.
It is not rare that your makefile will have dozens of entries. We are not able to check all of these. Therefore, we require the makefile to have several common targets, i.e
1. make burn; burn all the figures in the paper.
2. make clean; burn all figures, and also clean the executables and the intermediate result file (.H).
3. make NR; build NR figures; (this could be a simple copy from a backup folder).
4. make ER; build ER figures
5. make CR; build CR figures
Again, you can back up your figures to a separate folder, but it is not OK to just copy them back to directory Fig in those figures making rules.
1. What is the rule of thumb of choosing NR/ER/CR labels for a plot?
You should have known it while you were writing the report. Please refer to the up-to-date instructions @ vostok:/wrk/sep147/Adm/preface.tex for details.
2. Do I need to include all the .H files I used in the figures in the local directory?
You are not forbidden from doing that just for backup purpose. However, your makefile flows for building these figures should start from the raw input data file, perform the computations and then generate the figures. The only exception is plotting the raw data, since no computation needs to be performed. Simply grabbing backed-up intermediate results (.H files) and plotting them is not considered a valid reproducible flow, unless it is NR.
3. My makefile rules take a long time to compute, how can I test them more efficiently?
'-n' option in Make would show the user nominally all the cmds GNUmake would execute for this target, but without actually executing them. e.g
make -n target.H rather than
make target1.H. This would help you diagnose many of the mistakes you might have in your make file in advance. For example, a filename typo in the dependence list.
1. put a dash '-' at the beginning of the command, if you want Make to continue the flow in case of an error. For eg.
buildx: - mkdir bin make bin/exe.x
Testing score sheet SEP 147
|code||CR Fig Flows||ER figs can||Makefile||CR figs can|
|Papers:||Filename||compiles||present||be rebuilt||Clarity||be rebuilt||note|
-: Not applicable. (for example, if one paper has no CR figures)
Paper1: Jason P. Chang and Sjoerd de Ridder, “Correlation energy between surface and borehole stations at the Valhall Field”
Paper2: Noha S. Farghal and Stewart A. Levin, “Hunting for microseismic reflections using multiplets”
Paper3: Musa Maharramov, “Identifying reservoir depletion patterns from production-induced deformations with applications to seismic imaging”
Paper6: Yi Shen, “Estimation of Q from surface-seismic reflection data in data space and image space”
Paper7: Qiang Fu and Jon Claerbout, “Recently progress regarding logarithm Fourier domain bidirectional deconvolution”
Paper8: Chris Leader and Robert Clapp, “Linearised inversion with GPUs”
Paper9: Chris Leader and Ali Almomin, “How incoherent can we be? Phase encoded linearised inversion with random boundaries”
Paper10: Ali Almomin and Biondo Biondi, “Tomographic full waveform inversion: Practical and computationally feasible approach”
Paper11: Yang Zhang and Biondo Biondi, “Residual moveout based wave equation migration velocity analysis in 3-D”
Paper12: Yang Zhang and Adam D. Halpert, “Enhanced interpreter-aided salt-boundary extraction using shape deformation”
Paper13: Ohad Barak, “P/S separation of OBS data by inversion in a homogeneous media”
Paper14: Mandy Wong, Shuki Ronen, and Biondo Biondi, “Joint imaging with Streamer and ocean bottom data”
Paper15: Mandy Wong, Biondo Biondi, and Shuki Ronen, “Imaging with multiples using linearized full-wave inversion”
Paper16: Yunyue (Elita) Li, Peng Shen, and Colin Perkins, “VTI Migration velocity analysis using RTM”
Paper17: Yunyue (Elita) Li, “Wave-equation migration velocity analysis for anisotropic models on 2-D ExxonMobil field data”
Paper18: Yunyue (Elita) Li, “Wave-equation migration velocity analysis for VTI media using optimized implicit finite difference”
Paper19: Sjoerd de Ridder, “Continuous reservoir monitoring by ambient seismic noise tomography”
Paper20: Sjoerd de Ridder, “Surface wave tomography based on FWI of the 2 dimensional scalar wave equation”
Paper21: Adam Halpert, “Edge-preserving smoothing for segmentation of seismic images”
Paper22: Adam Halpert, “Fast velocity model evaluation with synthesized wavefields”
Paper23: Xukai Shen, “Early-arrival waveform inversion for near-surface velocity and anisotropic parameters: Modeling and sensitivity kernel analysis”
Paper24: Xukai Shen, “Early-arrival waveform inversion for near-surface velocity and anisotropic parameters: Inversion of synthetic data”
Paper25: Xukai Shen and Robert G. Clapp, “Short Note: FWI with different boundary conditions”
Paper26: Xukai Shen and Tieyuan Zhu, “Short Note: Early arrival waveform inversion: Application to crosswell field data”
Paper27: Biondo Biondi and Ali Almomin, “Tomographic full waveform inversion (TFWI) by combining full waveform inversion with wave-equation migration velocity anaylisis”
Paper28: Robert G. Clapp, “Image gather reconstruction using STOMP”
Paper29: Stewart A. Levin, “Integral operator quality from low order interpolation”
Paper30: Jon Claerbout, “Polarity preserving decon in N logN time”
Paper31: Jon Claerbout, Antoine Guitton, and Qiang Fu, “Decon in the log domain with variable gain”