You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: user-guide/docs/curating/bestpractices.md
+3-3Lines changed: 3 additions & 3 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -79,7 +79,7 @@ Users should select the project type that best fits their research method and da
79
79
80
80
Once the project type is selected, the interactive interface in My Project will guide users through the curation and publication steps through detailed onboarding instructions.
81
81
82
-
My Project is a space where users can work during the process of curation and publication and after publication to publish new data products or to analyze their data.
82
+
My Project is a space where users can work during the process of curation and publication and after publication to publish new data products or to analyze their data.
83
83
84
84
Because My Project is a shared space, it is recommended that teams select a data manager to coordinate file organization, transfers, curation, naming, etc.
85
85
@@ -125,7 +125,7 @@ In My Projects, users may upload files and or create folders to keep their files
125
125
126
126
Except for project type "Other" which does not have categories, users will categorize their files or folders according to the corresponding project type. Categories describe and highlight the main components of the dataset in relation to the research method used to obtain it. Each category has a form that needs to be filled with metadata to explain the methods and characteristics of the dataset, and there are onboarding instructions on what kind of information is suitable for each metadata field. In turn, some of these fields are required, which means that they are fundamental for the clarity of the project's description. The best way to approach data curation in My Project, is to organize the files in relation to the data model of choice and have the files already organized and complete before categorizing and tagging. While curating data in My Project, do not move, rename or modify files that have been already categorized. In particular, do not make changes to categorized files through an SSH connection or through Globus. If you need to, please remove the category, deselect the files, and start all over.
127
127
128
-
Within the different project types, there are different layers for describing a dataset. At the project level, it is desirable to provide an overview of the research, including its general goal and outcomes, what is the audience, and how the data can be reused. For large projects we encourage users to provide an outline of the scope and contents of the data. At the categories level, the descriptions need to address technical and methodological aspects involved in obtaining the data.
128
+
Within the different project types, there are different layers for describing a dataset. At the project level, it is desirable to provide an overview of the research, including its general goal and outcomes, what is the audience, and how the data can be reused. For large projects we encourage users to provide an outline of the scope and contents of the data. At the categories level, the descriptions need to address technical and methodological aspects involved in obtaining the data.
129
129
130
130
In addition, users can tag individual files or groups of files for ease of data comprehension and reuse by others. While categories are required, tagging is not, though we recommend that users tag their files because it helps other users to efficiently identify file contents in the publication interface. For each project type the list of tags are agreed upon terms contributed by experts in the field of NH. If the tags available do not apply, feel free to add custom tags and submit tickets informing the curation team about the need to incorporate them in the list. We heard from our users that the list of tags per category reaffirms them of the need to include certain types of documentation to their publication.
131
131
@@ -441,7 +441,7 @@ Due to variations in research methods, users may not need to use all the metadat
441
441
442
442
#### Protected Data { #protecteddata }
443
443
444
-
Protected data in the Data Depot Repository (DDR) are generally (but not always) included within interdisciplinary and social science research projects that study human subjects, which always need to have approval from an Institutional Review Board (IRB). We developed a data model and onboarding instructions <ahref="https://converge.colorado.edu/data/data-publication">in coordination with our CONVERGE partners</a> to manage this type of data within our curation and publication pipelines. Additionally, CONVERGE has a series of <ahref="https://converge.colorado.edu/resources/check-sheets/ethical-considerations/">check sheets</a> that outline how researchers should manage data that could contain sensitive information; these check sheets have also been published in <ahref="http://doi.org/10.17603/ds2-7r74-1021">the DDR</a>.
444
+
Protected data in the Data Depot Repository (DDR) are generally (but not always) included within interdisciplinary and social science research projects that study human subjects, which always need to have approval from an Institutional Review Board (IRB). We developed a data model and onboarding instructions <ahref="https://converge.colorado.edu/data/data-publication">in coordination with our CONVERGE partners</a> to manage this type of data within our curation and publication pipelines. Additionally, CONVERGE has a series of <ahref="https://converge.colorado.edu/resources/check-sheets/ethical-considerations/">check sheets</a> that outline how researchers should manage data that could contain sensitive information; these check sheets have also been published in <ahref="http://doi.org/10.17603/ds2-7r74-1021">the DDR</a>.
445
445
446
446
Natural Hazards also encompasses data that have granular geographical locations and images that may capture humans that are not the focus of the research/would not fall under the purview of an IRB. See both the Privacy Policy within our <ahref="https://www.designsafe-ci.org/account/terms-conditions/">Terms of Use</a>,
Copy file name to clipboardExpand all lines: user-guide/docs/tools/simulation/clawpack.md
+1-1Lines changed: 1 addition & 1 deletion
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -17,5 +17,5 @@ The Clawpack 5.4.0 suite has been installed into the DesignSafe Jupyter Hub envi
17
17
### Example Clawpack Use Case
18
18
19
19
An example GeoClaw notebook in Jupyter can be seen by navigating to 'community / Jupyter Notebooks / Workspace Application Sample Notebooks / GeoClaw' and opening 'GeoClaw_topotools_example.ipynb', and can be previewed and copied to your own space from <ahref="https://www.designsafe-ci.org/data/browser/public/designsafe.storage.community//Jupyter%20Notebooks/Workspace%20Application%20Sample%20Notebooks/GeoClaw"target="_blank">here</a>.<br>
Copy file name to clipboardExpand all lines: user-guide/docs/tools/simulation/openfoam.md
+4-4Lines changed: 4 additions & 4 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -2,7 +2,7 @@
2
2
3
3
The OpenFOAM (Open Field Operation and Manipulation) CFD (Computational Fluid Dynamics) Toolbox is a free, open source CFD software package which has a large user base across most areas of engineering and science, from both commercial and academic organizations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. It includes tools for meshing, notably snappyHexMesh, a parallelised mesher for complex CAD geometries, and for pre- and post-processing. Almost everything (including meshing, and pre- and post-processing) runs in parallel as standard, enabling users to take full advantage of high performance computing resources.
4
4
5
-
More detailed information and OpenFOAM user documentation can be found at the <ahref="https://openfoam.org/"target="_blank">OpenFOAM website</a>.
5
+
More detailed information and OpenFOAM user documentation can be found at the <ahref="https://openfoam.org/"target="_blank">OpenFOAM website</a>.
6
6
7
7
8
8
### How to Submit an OpenFOAM Job in the Workspace
@@ -11,19 +11,19 @@ More detailed information and OpenFOAM user documentation can be found at the <a
11
11
12
12
13
13
14
-
* Select the version of OpenFOAM you wanted to work with (Designsafe supports version 6 and 7).
14
+
* Select the version of OpenFOAM you wanted to work with (Designsafe supports version 6 and 7).
15
15
16
16
17
17
18
-
* Locate your Case Directory (Folder) with your input files that are in the Data Depot and follow the onscreen directions to enter this directory in the form. The following figure shows the example case in the community data.
18
+
* Locate your Case Directory (Folder) with your input files that are in the Data Depot and follow the onscreen directions to enter this directory in the form. The following figure shows the example case in the community data.
19
19
20
20
21
21
22
22
* Select your Solver from the dropdown menu. The workspace has options for 5 OpenFOAM solvers i.e. interFOAM, simpleFOAM, icoFOAM, potentialFOAM and olaFlow. If you need any other specfic solver please submit a ticket.
23
23
24
24
25
25
26
-
* Choose decompostion and mesh generation options from the dropdown menu.
26
+
* Choose decompostion and mesh generation options from the dropdown menu.
Copy file name to clipboardExpand all lines: user-guide/docs/tools/simulation/opensees.md
+5-5Lines changed: 5 additions & 5 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -16,7 +16,7 @@ OpenSeesSP is an OpenSees interpreter intended for high performance computers fo
16
16
17
17
OpenSeesMP is an OpenSees interpreter intended for high performance computers for performing finite element simulations with parameteric studies and very large models on parallel machines. OpenSeesMP requires understanding of parallel processing and the capabilities to write parallel scripts. <!-- OpenSeesMP runs on up to 12 KNL Nodes on Stampede2, with 64 cores per Node. -->
18
18
19
-
### How to Submit an OpenSees Job in the Workspace { #submit }
19
+
### How to Submit an OpenSees Job in the Workspace { #submit }
20
20
21
21
1. Select the OpenSees application from the simulation tab in the workspace.
22
22
@@ -38,7 +38,7 @@ OpenSeesMP is an OpenSees interpreter intended for high performance computers fo
38
38
39
39
6. Enter a job name (Optional).
40
40
41
-
7. Enter an output archive location or use the default provided.
41
+
7. Enter an output archive location or use the default provided.
42
42
43
43
8. Node Count: Number of requested process nodes for the job.
44
44
@@ -55,7 +55,7 @@ OpenSeesMP is an OpenSees interpreter intended for high performance computers fo
55
55
56
56
57
57
58
-
### DesignSafe Tutorial: OpenSees & DesignSafe, October 31, 2018 { #tutorial }
58
+
### DesignSafe Tutorial: OpenSees & DesignSafe, October 31, 2018 { #tutorial }
Copy file name to clipboardExpand all lines: user-guide/docs/tools/simulation/opensees/OSDesignSafe.md
+5-5Lines changed: 5 additions & 5 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -25,14 +25,14 @@ DesignSafe provides different platforms to run the OpenSees applications. These
25
25
1. The <b>Jupyter Hub</b> provides a versatile Jupyter-based IDE for developing a complete workflow that integrates pre- and post-processing with the OpenSees analyses interactively via Jupyter Notebooks. The Jupyter Hub can be run in a dedicated VM, which requires no allocation, or in an allocation in HPC. While OpenSeesPy can be run directly in a Python-based Jupyter Notebook, Julia, Matlab, and R can also be used interactively within a Jupyter Notebook to create the OpenSees input files, submit them to HPC, and post-process the results.
26
26
1. An <b>HPC allocation</b> allows the user to submit very large jobs to the larger queues available on DesignSafe and TACC.
27
27
28
-
The choice of OpenSees Application and DesignSafe platform depends on your project needs.
28
+
The choice of OpenSees Application and DesignSafe platform depends on your project needs.
29
29
30
30
31
31
### OpenSees-Project "Size"
32
32
33
33
As you plan your OpenSees project on DesignSafe, you need to have an idea of the project's "size," which is defined by its scope. The project scope is defined by the size of your model and the type and number of parametric analyses.
34
34
35
-
Understanding the scope of your project, and how that scope grows in "size", will help you choose the right OpenSees application as well as DesignSafe platform.
35
+
Understanding the scope of your project, and how that scope grows in "size", will help you choose the right OpenSees application as well as DesignSafe platform.
36
36
37
37
1. The <b>Model Size</b> affects the size of the system of equations that must be solved (the matrix that needs to be inverted) as well as the number of nonlinear state determinations which can be iterative. <br>
38
38
Here are a few items that affect Model Size:
@@ -66,12 +66,12 @@ The following figure provides the decision matrix: a visual tool for quick asses
66
66
67
67
68
68
69
-
Choose the right OpenSees application to make the best use of resources such as modeler time, run time, and computer resources.
69
+
Choose the right OpenSees application to make the best use of resources such as modeler time, run time, and computer resources.
70
70
71
71
72
72
### Decision Matrix for DesignSafe Platform for OpenSees
73
73
74
-
The following table provides a comparison of all the ways you can run OpenSees on the DesignSafe CI execution platforms and configurations. Each platform has different interfaces for you to interact with OpenSees. Items in the table are placed in order of complexity and recommendation.
74
+
The following table provides a comparison of all the ways you can run OpenSees on the DesignSafe CI execution platforms and configurations. Each platform has different interfaces for you to interact with OpenSees. Items in the table are placed in order of complexity and recommendation.
@@ -114,7 +114,7 @@ However, for case of the platforms that have the integrated Jupyter environment,
114
114
The Tcl-Interpreter OpenSees applications (OpenSees-Express, OpenSeesSP, and OpenSeesMP) are compiled executable programs. The MPI, therefore, will run NP processes of this executable.<br>
115
115
OpenSeesPy, on the other hand, is a python library that has been pre-installed in the VM and is called within the python environment. In this case, therefore, the MPI will run NP Python processes and each process will call its own Python library. In addition, all three OpenSees applications are integrated into a single library, OpenSeesPy.</p>
116
116
117
-
#### Examples
117
+
#### Examples
118
118
119
119
The following examples give you the command to executed as well as a demonstration of the Interaction with OpenSees:
Copy file name to clipboardExpand all lines: user-guide/docs/tools/simulation/opensees/opensees.md
+6-6Lines changed: 6 additions & 6 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -28,14 +28,14 @@ DesignSafe provides different platforms to run the OpenSees applications. These
28
28
1. The <b>Jupyter Hub</b> provides a versatile Jupyter-based IDE for developing a complete workflow that integrates pre- and post-processing with the OpenSees analyses interactively via Jupyter Notebooks. The Jupyter Hub can be run in a dedicated VM, which requires no allocation, or in an allocation in HPC. While OpenSeesPy can be run directly in a Python-based Jupyter Notebook, Julia, Matlab, and R can also be used interactively within a Jupyter Notebook to create the OpenSees input files, submit them to HPC, and post-process the results.
29
29
1. An <b>HPC allocation</b> allows the user to submit very large jobs to the larger queues available on DesignSafe and TACC.
30
30
31
-
The choice of OpenSees Application and DesignSafe platform depends on your project needs.
31
+
The choice of OpenSees Application and DesignSafe platform depends on your project needs.
32
32
33
33
34
34
### OpenSees-Project "Size"
35
35
36
36
As you plan your OpenSees project on DesignSafe, you need to have an idea of the project's "size," which is defined by its scope. The project scope is defined by the size of your model and the type and number of parametric analyses.
37
37
38
-
Understanding the scope of your project, and how that scope grows in "size", will help you choose the right OpenSees application as well as DesignSafe platform.
38
+
Understanding the scope of your project, and how that scope grows in "size", will help you choose the right OpenSees application as well as DesignSafe platform.
39
39
40
40
1. The <b>Model Size</b> affects the size of the system of equations that must be solved (the matrix that needs to be inverted) as well as the number of nonlinear state determinations which can be iterative. <br>
41
41
Here are a few items that affect Model Size:
@@ -69,12 +69,12 @@ The following figure provides the decision matrix: a visual tool for quick asses
69
69
70
70
71
71
72
-
Choose the right OpenSees application to make the best use of resources such as modeler time, run time, and computer resources.
72
+
Choose the right OpenSees application to make the best use of resources such as modeler time, run time, and computer resources.
73
73
74
74
75
75
### Decision Matrix for DesignSafe Platform for OpenSees
76
76
77
-
The following table provides a comparison of all the ways you can run OpenSees on the DesignSafe CI execution platforms and configurations. Each platform has different interfaces for you to interact with OpenSees. Items in the table are placed in order of complexity and recommendation.
77
+
The following table provides a comparison of all the ways you can run OpenSees on the DesignSafe CI execution platforms and configurations. Each platform has different interfaces for you to interact with OpenSees. Items in the table are placed in order of complexity and recommendation.
@@ -117,7 +117,7 @@ However, for case of the platforms that have the integrated Jupyter environment,
117
117
The Tcl-Interpreter OpenSees applications (OpenSees-Express, OpenSeesSP, and OpenSeesMP) are compiled executable programs. The MPI, therefore, will run NP processes of this executable.<br>
118
118
OpenSeesPy, on the other hand, is a python library that has been pre-installed in the VM and is called within the python environment. In this case, therefore, the MPI will run NP Python processes and each process will call its own Python library. In addition, all three OpenSees applications are integrated into a single library, OpenSeesPy.</p>
119
119
120
-
#### Examples
120
+
#### Examples
121
121
122
122
The following examples give you the command to executed as well as a demonstration of the Interaction with OpenSees:
0 commit comments