Last modified by teodoramisan on 2026/02/13 10:11
From version 65.4
edited by teodoramisan
on 2026/02/12 11:20
Change comment: There is no comment for this version
To version 66.1
edited by teodoramisan
on 2026/02/12 11:25
Change comment: There is no comment for this version

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37 37  
38 38  From the Jupyter Lab launcher, click on the **Xircuits File** icon, as in the screenshot below.
39 39  
40 -[[image:xircuits-file-icon.png||alt="newxircs.png"]]
40 +[[image:xircuits-file-icon.png||alt="newxircs.png" height="592" width="1100"]]
41 41  
42 42  A new file with the .xircuits extension will be generated under your current working directory. This is where you can start building the workflow diagram interactively.
43 43  
44 -[[image:xircuits-generated-file.png||alt="newfile.png"]]
44 +[[image:xircuits-generated-file.png||alt="newfile.png" height="592" width="1100"]]
45 45  
46 46  You will notice that 2 components are already placed inside the workflow: the __Start__ and the __Finish__ components. They cannot be modified or deleted, and they represent the starting and finishing point of the workflow.
47 47  
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49 49  
50 50  Open the components tray, from the left-side bar icon highlighted below.
51 51  
52 -[[image:xircuits-extension-icon.png||alt="tray.png"]]
52 +[[image:xircuits-extension-icon.png||alt="tray.png" height="591" width="1100"]]
53 53  
54 54  Now, you can browse through the components, select the one you wish to use, then drag and drop it into the workflow area.
55 55  
56 56  Customizable components can be identified by a suffix (e.g. **TVB_**SIMULATOR, **VBI_**SIMULATION_RUNNER).
57 57  
58 -[[image:xircuits-component-browser.png||alt="components.png"]]
58 +[[image:xircuits-component-browser.png||alt="components.png" height="592" width="1100"]]
59 59  
60 60  === **Step 3. Configure the components** ===
61 61  
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69 69  
70 70  Components and parameters include info buttons (i) that explain their purpose and how they are used (e.g. the simulator info panel below).
71 71  
72 -[[image:configure-components.png||alt="diagr.png"]]
72 +[[image:Screenshot 2026-02-12 115445.png||alt="diagr.png" height="592" width="1100"]]
73 73  
74 74  === **Step 4. Make connections** ===
75 75  
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77 77  
78 78  First, link the __Start__ node to the first component of your workflow. Then make the connections between all your components. The last component should be linked to the __Finish__ node, to indicate the end of your workflow (e.g. the blue connections in the screenshot below). These connections will dictate the order of execution of the components in your workflow.
79 79  
80 -[[image:components-connection.png||alt="diagram.png"]]
80 +[[image:components-connection.png||alt="diagram.png" height="592" width="1100"]]
81 81  
82 82  === **Step 5. Run the workflow** ===
83 83  
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89 89  
90 90  * For this you can click on the Run button (▶), which will also implicitly compile the workflow. Make sure that __Local Run__ is selected near the Run button.
91 91  
92 -[[image:local-run-button.png||alt="run.png"]]
92 +[[image:local-run-button.png||alt="run.png" height="592" width="1100"]]
93 93  
94 94  
95 95  2. Remotely on HPC (only if you have access to HPC resources)
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96 96  
97 97  * First choose the __Remote Run__ in the select box and then click the Run button (▶), which will also implicitly compile the workflow.
98 98  
99 -[[image:remote-run-button.png||alt="remote.png"]]
99 +[[image:remote-run-button.png||alt="remote.png" height="385" width="1100"]]
100 100  
101 101  * A dialog will open to request the HPC connection details:
102 102  ** which __HPC Site__ to use
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104 104  ** one checkbox to choose whether you want the __HPC Monitoring__ to be opened up automatically (via tvb-ext-unicore GUI). This can also be opened up manually using the __Monitor HPC__ button or the __U__ icon from the left side-bar.
105 105  ** one checkbox to choose whether you want the results to be __staged out__ automatically or not. If checked, the workflow waits for the HPC jobs to finish and then performs the stage out. If unchecked, the results can be manually downloaded later on by using the GUI of the tvb-ext-unicore.
106 106  
107 -[[image:remote-run-configuration.png||alt="rem.png"]]
107 +[[image:remote-run-configuration.png||alt="rem.png" height="591" width="1100"]]
108 108  
109 109  * The HPC monitoring is done via the GUI of tvb-ext-unicore which is a separate package we have documented under this Wiki. But it can be nicely used together with tvb-ext-xircuits:
110 110  
111 -[[image:hpc-monitoring.png||alt="uni.png"]]
111 +[[image:hpc-monitoring.png||alt="uni.png" height="593" width="1100"]]
112 112  
113 113  
114 114  After clicking on Run, a new Jupyter Output window should appear in the bottom of your Jupyter Lab environment. Here you will see the output of your workflow, such as logs, static plots, etc.
115 115  
116 -[[image:jupyter-output-window.png||alt="out.png"]]
116 +[[image:jupyter-output-window.png||alt="out.png" height="591" width="1100"]]
117 117  
118 118  === **Step 6. Share your work*** ===
119 119  
Screenshot 2026-02-12 115445.png
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