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P-SV wave field inside a spherically symmetric Earth (source: G. Jahnke)
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Survey Results

by admin last modified 2008-03-10 22:35

Scientific software in the Earth sciences:



Scientific software in the Earth sciences: “Seismology”

1. What methodologies are you primarily using for your research/data modelling:
Ray theory/Gaussian beams   37.0% (20)
Normal modes   11.1% (6)
Reflectivity method   35.2% (19)
Numerical approaches (finite differences, elements, volumes, pseudospectral, etc)   64.8% (35)
Other: GEMINI   1.9% (1)
Other: Gemini   1.9% (1)
Other: Monte-Carlo simulations of energy propagation   1.9% (1)
Other: PROMAX   1.9% (1)
Other: stochastic simulation   1.9% (1)
Other: stochastic, EGF   1.9% (1)
Other: wavelet analyse   1.9% (1)
2. What computationally intensive methodologies are you using?
Finite differences   59.3% (32)
Finite/spectral elements   16.7% (9)
Finite volumes   9.3% (5)
Pseudo-spectral method   9.3% (5)
Particle methods   7.4% (4)
Hybrid approaches
(0)
Other: ADER-DG   1.9% (1)
Other: FD and scattering methods in future projects   1.9% (1)
Other: Genetic algorithms for inversion   1.9% (1)
Other: inversion   1.9% (1)
Other: Multiple scattering, mode coupling   1.9% (1)
Other: none   1.9% (1)
Other: Reflection Tomography and migration   1.9% (1)
Other: Runge-Kutta; SVD   1.9% (1)
Other: spectral methods   1.9% (1)
3. Are you developing or using parallel algorithms?
Developing   27.8% (15)
Using   42.6% (23)
Neither   22.2% (12)
TOTAL   92.6% 54

4. Do you have professional software engineering support for your developments?
Yes   5.6% (3)
Partly   14.8% (8)
No   72.2% (39)
TOTAL   92.6% 54
5. Are you using High-Performance Computing (HPC) Hardware?
No access   13.0% (7)
PC-Cluster   44.4% (24)
Supercomputer   46.3% (25)
Other: I have access to HPC but am not using it   1.9% (1)
Other: Not yet   1.9% (1)
Other: SUN servers & workstations   1.9% (1)
6. Where is the HPC hardware located?
Local (e.g., at your department)   51.9% (28)
Local Supercomputer Centre   33.3% (18)
National Supercomputer Centre   25.9% (14)
GRID Access (e.g., DEISA)   1.9% (1)
Other: n.a.   1.9% (1)
7. How much RAM do your “standard” applications require at present?
1 GByte   33.3% (18)
10 GByte   42.6% (23)
100 GByte   22.2% (12)
1 TByte   3.7% (2)
Other: 4 GByte   1.9% (1)
Other: 60   1.9% (1)
Other: < 1GByte   1.9% (1)

8. Would you make use of and benefit from engineered (benchmarked, version-controlled, multi-platform, optimised, interfaced) seismological applications in a common software environment (examples see questions 1+2)?
Yes   57.4% (31)
Partly   24.1% (13)
No   9.3% (5)
TOTAL   90.7% 54
9. Would you make us of and benefit from easy (i.e. hidden) access to parallel computational resources through web interfaces for specific cpu-rich scientific applications (e.g., seismograms for 3-D reference models, wave fields for data modelling, etc.)?
Yes   59.3% (32)
Partly   22.2% (12)
No   11.1% (6)
TOTAL   92.6% 54
10. Would you be able to provide computational algorithms for an Earth Science software library?
Yes   55.6% (30)
No   35.2% (19)
TOTAL   90.7% 54

11. What other software/applications should be provided/maintained within an Earth Science software library?
Grid generation   50.0% (27)
Visualization   70.4% (38)
Processing   44.4% (24)
Model and data format specifications/converters   72.2% (39)
Other: any kind of seismological software tools, for example, petrophysical modelling, elastic tensor data base   1.9% (1)
Other: imaging/inversion algorithms   1.9% (1)
Other: inverison, 3D event location   1.9% (1)
Other: inversion routines e.g. waveform inversion, genetic algorithms   1.9% (1)
Other: numerical library for coordinate-type independent PDE   1.9% (1)
Other: Receiver Functions, seismic anisotropy,   1.9% (1)
Other: time series analysis in a way that is prsented in small modules and extendable by the user due to standardized data structure interfaces   1.9% (1)
Other: updated seismometer transfer function info   1.9% (1)
12. Should seismological software be connectable to other areas/applications (e.g., geodynamics, crustal deformation, geophysical fluid flows, etc) for example through common model specifications etc. ?
Yes   55.6% (30)
Partly   33.3% (18)
No   3.7% (2)
TOTAL   92.6% 54
13. Would you participate in training courses offered in connection with Earth science simulation software/High Performance Computing?
Yes   83.3% (45)
No   7.4% (4)
TOTAL   90.7% 54

14. Please indicate your level?
Undergraduate student   1.9% (1)
PhD student   25.9% (14)
Postdoc   14.8% (8)
Staff scientist   31.5% (17)
Professor   18.5% (10)
TOTAL   92.6% 54
15. Please provide any further comments/suggestions, e.g., by referring to specific questions, topics, etc.
# Response
1 100% support for this initiative
1 A tool for phase identification in full waveform synthetics would be good to have. In the moment my research would benefit most from spherical Earth, full waveofrm seismograms for the extended source in 3D.
1 earthquake location in 3D media with quick access to 3D ray tracing for the whole spectrum of seismic phases would be very interesting.
1 For my research projects there are no canned solutions available yet. Hence I plan to write my own new code or else adopt an existing one.
1 I think it is very important to exchange synthetic data in a simple and robust way. Scientific exchange between the computational and "real" seismologist would be much easier if the computational community would adapt standards for data storage and exchange which where developed in the "real"-data world. I am thinking of standards/protocols like SeedLink and ArcLink.
1 It is really necessary for the seismology community to develop a new software-package. The existing ones are really old-fashioned and far away from an intuitive handling. It would be great if the software would have a nice graphic interface, from which I e.g. could cut time-series, make rotations, filtering, calculate the eigenvalues of covariance matrix, calculate receiver functions, making plots etc. As Luther-King said: I had a dream... Maybe that dream becomes true for seismology.
1 Library should include imaging/migration/inversion algorithms (for active and passive seismic data sets), e.g. waveform inversion, PSDM, event location techniques, etc.
1 numerical library for combined FD-FV-FE (partly or shared) useful for research; seismic wave propagation on poro-thermo-visco-elastic media;
1 On top of creating an e-infrastructure more effort should be made to build stronger links between modellers and observers!
1 Our group at the Technical University Freiberg is devloping Finite-Difference Modelling codes that are applied for reflection seismic modelling and imaging (e.g. tunnel seismics, borehole seismics) . The current main focus is on 2-D/3-D time domain full waveform tomography for viscoelastic media. We could provide parallel FD MPI codes (2-D, 2.5-D and 3-D) to a Earth Science library.
1 some of my opinions: - professional (software engineering) support would be highly desirable for the development, maintenance and sharing of scientific software - if possible, this should be organized within the community with free licenses since young researchers have to rely on transfering their software solutions from one research place to another (e.g. on the opposite: the license model of Matlab is an obstacle) - software should be provided in small modules that can easily be extended; for research work it will always be essential to extend existing software; monolithic solutions are only useful for routine work; I prefer concepts like used in SeismicUnix - software libraries are most useful if they are not restricted (by implementation) to one specific area (e.g. normal mode calculation can not only be used in global seismology but is also needed in shallow seismic studies) - seismologists are used to share their software since many years now, but most of the code is only sparsely documented, has undergone several stages of modifications by different researchers, use incompatible data or parameter formats, etc.; to improve this situation is only possible by a permanent and long-term support and maintenance by software engineers - due to the rapidly evolving hardware, highly complex algorithms (e.g. to calculate wavefield partial derivatives) will become more and more applicable in routine applications - remote access computing facilities will only be useful if high bandwidth data transmission is provided as well



Scientific software in the Earth sciences: “Geodynamics”

1. What computationally intensive methodologies are you using?
Finite differences   36.4% (8)
Finite/spectral elements   31.8% (7)
Finite volumes   27.3% (6)
Pseudo-spectral method   4.5% (1)
Particle methods   18.2% (4)
Hybrid approaches   9.1% (2)
Other: Boundary Element method   4.5% (1)
Other: genetic algorithms, adaptive grid inversion methods   4.5% (1)
Other: simplex   4.5% (1)
2. Are you developing or using parallel algorithms?
Developing   31.8% (7)
Using   22.7% (5)
Neither   31.8% (7)
TOTAL   86.4% 22
3. Do you have professional software engineering support for your developments?
Yes   4.5% (1)
Partly   18.2% (4)
No   63.6% (14)
TOTAL   86.4% 22

4. Are you using High-Performance Computing (HPC) Hardware?
No access   9.1% (2)
PC-Cluster   68.2% (15)
Supercomputer   27.3% (6)
Other: SGI Altix with 12 CPU's   4.5% (1)
5. Where is the HPC hardware located?
Local (e.g., at your department)   68.2% (15)
Local Supercomputer Centre   13.6% (3)
National Supercomputer Centre   27.3% (6)
GRID Access (e.g., DEISA)
(0)
6. How much RAM do your “standard” applications require at present?
1 GByte   40.9% (9)
10 GByte   45.5% (10)
100 GByte   9.1% (2)
1 TByte
(0)
Other: can be exceptionally 100Gb but rare so far   4.5% (1)
Other: up to 2 GByte   4.5% (1)

7. Would you make use of and benefit from engineered (benchmarked, version-controlled, multi-platform, optimised, interfaced) geodynamical applications in a common software environment (examples see questions 1+2)?
Yes   18.2% (4)
Partly   59.1% (13)
No   9.1% (2)
TOTAL   86.4% 22
8. Would you make us of and benefit from easy (i.e. hidden) access to parallel computational resources through web interfaces for specific cpu-rich scientific applications?
Yes   31.8% (7)
Partly   36.4% (8)
No   18.2% (4)
TOTAL   86.4% 22
9. Would you be able to provide computational algorithms for an Earth Science software library?
Yes   50.0% (11)
No   36.4% (8)
TOTAL   86.4% 22

10. What other software/applications should be provided/maintained within an Earth Science software library?
Grid generation   50.0% (11)
Visualization   86.4% (19)
Processing   36.4% (8)
Model and data format specifications/converters   72.7% (16)
Other: benchmarks for validation and verification   4.5% (1)
Other: inversion   4.5% (1)
11. Should geodynamical software be connectable to other areas/applications (e.g., seismology, crustal deformation, geophysical fluid flows, etc) for example through common model specifications etc. ?
Yes   59.1% (13)
Partly   27.3% (6)
No
(0)
TOTAL   86.4% 22
12. Would you participate in training courses offered in connection with Earth science simulation software/High Performance Computing?
Yes   68.2% (15)
No   18.2% (4)
TOTAL   86.4% 22

13. Please indicate your level?
Undergraduate student
(0)
PhD student   18.2% (4)
Postdoc   27.3% (6)
Staff scientist   22.7% (5)
Professor   18.2% (4)
TOTAL   86.4% 22
14. Please provide any further comments/suggestions, e.g., by referring to specific questions, topics, etc.
# Response
1 It's a very good idea to propose training courses for CFD and PARALLEL Visualization of large data sets
1 Many modelling frameworks of the type suggested are already in development (e.g. Cactus Code), the difficulty lies in persuading a majority of researchers to use them when that have already invested significant time and energy into their own codes. Whatever code emerges will have to be fully open source, benchmark favorably against existing codes and be easily extensible (standardised way of writing one's own modules) before any wider community will take notice. That said, this sort of project really does need doing.
1 may be I have missed it in the survey... of utmost importance for any succesful software project is DOCUMENTATION. Code should contain some visual formatting, but also a lot of comment. My experience is that the ratio between executable code lines and comment lines should be close to 1:1 (most comments in routine headers that provide precise definitions about input and output, format descriptions, algorithm descriptiobs etc). AND, of course, user documentation is needed, i.e. technical references as well as cookbooks and tutorials.
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