caddforge-docs 0.3.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (152) hide show
  1. caddforge_docs/__init__.py +1 -0
  2. caddforge_docs/cli.py +20 -0
  3. caddforge_docs/server.py +124 -0
  4. caddforge_docs/site/404.html +2118 -0
  5. caddforge_docs/site/assets/_mkdocstrings.css +237 -0
  6. caddforge_docs/site/assets/images/favicon.png +0 -0
  7. caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js +16 -0
  8. caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js.map +7 -0
  9. caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js +42 -0
  10. caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js.map +7 -0
  11. caddforge_docs/site/assets/licenses/W3C-Software-and-Document-2015.txt +15 -0
  12. caddforge_docs/site/assets/licenses/autogrid-COPYING-GPL-2.txt +339 -0
  13. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt +674 -0
  14. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt +73 -0
  15. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt +24 -0
  16. caddforge_docs/site/assets/licenses/caddforge-opencosmors-COPYING.txt +674 -0
  17. caddforge_docs/site/assets/licenses/caddforge-opencosmors-LICENSE.txt +165 -0
  18. caddforge_docs/site/assets/licenses/caddforge-unidock-tools-LICENSE.txt +202 -0
  19. caddforge_docs/site/assets/licenses/clipboard-LICENSE.txt +19 -0
  20. caddforge_docs/site/assets/licenses/escape-html-LICENSE.txt +2 -0
  21. caddforge_docs/site/assets/licenses/focus-visible-LICENSE.txt +4 -0
  22. caddforge_docs/site/assets/licenses/fontawesome-LICENSE.txt +165 -0
  23. caddforge_docs/site/assets/licenses/fuzzaldrin-plus-LICENSE.txt +21 -0
  24. caddforge_docs/site/assets/licenses/lunr-LICENSE.txt +17 -0
  25. caddforge_docs/site/assets/licenses/material-LICENSE.txt +20 -0
  26. caddforge_docs/site/assets/licenses/material-design-color-LICENSE.txt +31 -0
  27. caddforge_docs/site/assets/licenses/material-shadows-LICENSE.txt +31 -0
  28. caddforge_docs/site/assets/licenses/mkdocs-material-LICENSE.txt +19 -0
  29. caddforge_docs/site/assets/licenses/mkdocs-material-extensions-LICENSE.txt +21 -0
  30. caddforge_docs/site/assets/licenses/mkdocs-section-index-LICENSE.txt +21 -0
  31. caddforge_docs/site/assets/licenses/mkdocstrings-LICENSE.txt +15 -0
  32. caddforge_docs/site/assets/licenses/mkdocstrings-python-LICENSE.txt +15 -0
  33. caddforge_docs/site/assets/licenses/octicons-LICENSE.txt +21 -0
  34. caddforge_docs/site/assets/licenses/preact-LICENSE.txt +19 -0
  35. caddforge_docs/site/assets/licenses/properdocs-LICENSE.txt +26 -0
  36. caddforge_docs/site/assets/licenses/pymdown-extensions-LICENSE.txt +113 -0
  37. caddforge_docs/site/assets/licenses/rxjs-LICENSE.txt +180 -0
  38. caddforge_docs/site/assets/licenses/simple-LICENSE.txt +30 -0
  39. caddforge_docs/site/assets/licenses/tiny-emitter-LICENSE.txt +19 -0
  40. caddforge_docs/site/assets/licenses/tslib-LICENSE.txt +12 -0
  41. caddforge_docs/site/assets/licenses/zeno-rocha-components-LICENSE.txt +22 -0
  42. caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css +1 -0
  43. caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css.map +1 -0
  44. caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css +1 -0
  45. caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css.map +1 -0
  46. caddforge_docs/site/core/cli/index.html +2446 -0
  47. caddforge_docs/site/core/concepts/index.html +2340 -0
  48. caddforge_docs/site/core/configuration/index.html +2300 -0
  49. caddforge_docs/site/core/index.html +2170 -0
  50. caddforge_docs/site/core/jobs-results/index.html +2315 -0
  51. caddforge_docs/site/core/plugins/index.html +2200 -0
  52. caddforge_docs/site/core/slurm/index.html +2562 -0
  53. caddforge_docs/site/development/ci-publishing/index.html +2345 -0
  54. caddforge_docs/site/development/contributing/index.html +2311 -0
  55. caddforge_docs/site/development/documentation/index.html +2380 -0
  56. caddforge_docs/site/development/index.html +2201 -0
  57. caddforge_docs/site/development/release-notes/index.html +2504 -0
  58. caddforge_docs/site/development/release-readiness/index.html +2333 -0
  59. caddforge_docs/site/development/security/index.html +2181 -0
  60. caddforge_docs/site/development/tool-authoring/index.html +2435 -0
  61. caddforge_docs/site/examples/index.html +2465 -0
  62. caddforge_docs/site/examples/manifest.json +158 -0
  63. caddforge_docs/site/examples/minimize/component_overrides.yaml +14 -0
  64. caddforge_docs/site/examples/minimize/ligand_only.yaml +13 -0
  65. caddforge_docs/site/examples/minimize/pipeline_docking.yaml +84 -0
  66. caddforge_docs/site/examples/minimize/pipeline_scatter.yaml +49 -0
  67. caddforge_docs/site/examples/minimize/pocket_free_shell_restrained.yaml +13 -0
  68. caddforge_docs/site/examples/minimize/pocket_restrained.yaml +13 -0
  69. caddforge_docs/site/examples/minimize/prepared_metal.yaml +14 -0
  70. caddforge_docs/site/examples/minimize/sidechains_free_backbone_fixed.yaml +13 -0
  71. caddforge_docs/site/examples/minimize/sidechains_free_backbone_restrained.yaml +13 -0
  72. caddforge_docs/site/examples/pipelines/descriptor-model-and-candidate-filter.yaml +44 -0
  73. caddforge_docs/site/examples/pipelines/dock-extract-and-minimize-poses.yaml +85 -0
  74. caddforge_docs/site/examples/pipelines/docking-screen-and-rescore.yaml +55 -0
  75. caddforge_docs/site/examples/pipelines/flexible-gnina-to-openbpmd-to-md-to-abfe.yaml +189 -0
  76. caddforge_docs/site/examples/pipelines/gnina-flexible-complex-artifacts.yaml +52 -0
  77. caddforge_docs/site/examples/pipelines/minimize-a-multi-pose-sdf.yaml +46 -0
  78. caddforge_docs/site/examples/pipelines/pose-level-md-selection.yaml +95 -0
  79. caddforge_docs/site/examples/pipelines/result-collection-and-diagnostics.yaml +55 -0
  80. caddforge_docs/site/examples/quickstart/diagnostics.yaml +8 -0
  81. caddforge_docs/site/examples/quickstart/index.html +2172 -0
  82. caddforge_docs/site/examples/quickstart/pipeline.yaml +23 -0
  83. caddforge_docs/site/examples/quickstart/run.py +18 -0
  84. caddforge_docs/site/examples/quickstart/run_pipeline.py +6 -0
  85. caddforge_docs/site/examples/quickstart/scores.csv +7 -0
  86. caddforge_docs/site/examples/quickstart/values.csv +31 -0
  87. caddforge_docs/site/examples/run_tool.py +40 -0
  88. caddforge_docs/site/examples/tools/datascience-csv-scatter.yaml +17 -0
  89. caddforge_docs/site/examples/tools/datascience-distribution-diagnostics.yaml +10 -0
  90. caddforge_docs/site/examples/tools/descriptors-ani-conformers.yaml +9 -0
  91. caddforge_docs/site/examples/tools/descriptors-ani-psa.yaml +9 -0
  92. caddforge_docs/site/examples/tools/descriptors-cluster-molecules.yaml +11 -0
  93. caddforge_docs/site/examples/tools/descriptors-phesa.yaml +7 -0
  94. caddforge_docs/site/examples/tools/docking-gnina.yaml +12 -0
  95. caddforge_docs/site/examples/tools/docking-idockya.yaml +8 -0
  96. caddforge_docs/site/examples/tools/docking-unidock.yaml +12 -0
  97. caddforge_docs/site/examples/tools/fep-openfe-abfe.yaml +53 -0
  98. caddforge_docs/site/examples/tools/fep-openfe-rbfe-septop.yaml +23 -0
  99. caddforge_docs/site/examples/tools/md-center-and-align.yaml +16 -0
  100. caddforge_docs/site/examples/tools/md-cluster-representative.yaml +16 -0
  101. caddforge_docs/site/examples/tools/md-extract-frames.yaml +17 -0
  102. caddforge_docs/site/examples/tools/md-fix-structure.yaml +20 -0
  103. caddforge_docs/site/examples/tools/md-grand.yaml +28 -0
  104. caddforge_docs/site/examples/tools/md-inducia.yaml +29 -0
  105. caddforge_docs/site/examples/tools/md-minimize.yaml +13 -0
  106. caddforge_docs/site/examples/tools/md-openbpmd.yaml +11 -0
  107. caddforge_docs/site/examples/tools/md-plain-md.yaml +28 -0
  108. caddforge_docs/site/examples/tools/ml-explore-classifier.yaml +5 -0
  109. caddforge_docs/site/examples/tools/ml-model-factory.yaml +32 -0
  110. caddforge_docs/site/examples/tools/ml-model-zoo.yaml +16 -0
  111. caddforge_docs/site/examples/tools/ml-pca.yaml +10 -0
  112. caddforge_docs/site/examples/tools/ml-simple-gp.yaml +17 -0
  113. caddforge_docs/site/examples/tools/qm-transfer-free-energy.yaml +11 -0
  114. caddforge_docs/site/explanation/references/index.html +2218 -0
  115. caddforge_docs/site/explanation/reproducibility/index.html +2306 -0
  116. caddforge_docs/site/explanation/third-party-notices/index.html +2599 -0
  117. caddforge_docs/site/getting-started/first-pipeline/index.html +2195 -0
  118. caddforge_docs/site/getting-started/first-workflow/index.html +2329 -0
  119. caddforge_docs/site/getting-started/index.html +2200 -0
  120. caddforge_docs/site/getting-started/installation/index.html +2541 -0
  121. caddforge_docs/site/gui/index.html +2267 -0
  122. caddforge_docs/site/gui/plugin-authoring/index.html +2280 -0
  123. caddforge_docs/site/gui/walkthrough/index.html +2181 -0
  124. caddforge_docs/site/how-to/jobs/index.html +2195 -0
  125. caddforge_docs/site/how-to/scatter/index.html +2193 -0
  126. caddforge_docs/site/how-to/troubleshooting/index.html +2429 -0
  127. caddforge_docs/site/index.html +2359 -0
  128. caddforge_docs/site/objects.inv +0 -0
  129. caddforge_docs/site/pipelines/artifacts/index.html +2314 -0
  130. caddforge_docs/site/pipelines/built-ins/index.html +2670 -0
  131. caddforge_docs/site/pipelines/examples/index.html +3186 -0
  132. caddforge_docs/site/pipelines/index.html +2164 -0
  133. caddforge_docs/site/pipelines/specification/index.html +2278 -0
  134. caddforge_docs/site/plugins/datascience/index.html +2405 -0
  135. caddforge_docs/site/plugins/descriptors/index.html +2609 -0
  136. caddforge_docs/site/plugins/docking/index.html +2480 -0
  137. caddforge_docs/site/plugins/fep/index.html +2508 -0
  138. caddforge_docs/site/plugins/index.html +2216 -0
  139. caddforge_docs/site/plugins/md/index.html +3795 -0
  140. caddforge_docs/site/plugins/ml/index.html +2815 -0
  141. caddforge_docs/site/plugins/qm/index.html +2309 -0
  142. caddforge_docs/site/plugins/version-matrix/index.html +2449 -0
  143. caddforge_docs/site/reference/api/index.html +4414 -0
  144. caddforge_docs/site/reference/index.html +2166 -0
  145. caddforge_docs/site/search/search_index.json +1 -0
  146. caddforge_docs/site/sitemap.xml +191 -0
  147. caddforge_docs/site/sitemap.xml.gz +0 -0
  148. caddforge_docs-0.3.0.dist-info/METADATA +158 -0
  149. caddforge_docs-0.3.0.dist-info/RECORD +152 -0
  150. caddforge_docs-0.3.0.dist-info/WHEEL +4 -0
  151. caddforge_docs-0.3.0.dist-info/entry_points.txt +2 -0
  152. caddforge_docs-0.3.0.dist-info/licenses/LICENSE +21 -0
caddforge_docs/site/how-to/troubleshooting/index.html ADDED
@@ -0,0 +1,2429 @@
1
+
2
+ <!doctype html>
3
+ <html lang="en" class="no-js">
4
+ <head>
5
+
6
+ <meta charset="utf-8">
7
+ <meta name="viewport" content="width=device-width,initial-scale=1">
8
+
9
+ <meta name="description" content="Central documentation for the CADDForge CADD toolbox framework.">
10
+
11
+
12
+
13
+ <link rel="canonical" href="https://idorsia.github.io/caddforge-docs/how-to/troubleshooting/">
14
+
15
+
16
+ <link rel="prev" href="../scatter/">
17
+
18
+
19
+ <link rel="next" href="../../core/">
20
+
21
+
22
+
23
+
24
+
25
+ <link rel="icon" href="../../assets/images/favicon.png">
26
+ <meta name="generator" content="mkdocs-ProperDocs 1.6.7, mkdocs-material-9.7.7">
27
+
28
+
29
+
30
+ <title>Troubleshooting - CADDForge</title>
31
+
32
+
33
+
34
+ <link rel="stylesheet" href="../../assets/stylesheets/main.ec1eaa64.min.css">
35
+
36
+
37
+ <link rel="stylesheet" href="../../assets/stylesheets/palette.ab4e12ef.min.css">
38
+
39
+
40
+
41
+
42
+
43
+
44
+
45
+
46
+
47
+
48
+
49
+
50
+ <link rel="stylesheet" href="../../assets/_mkdocstrings.css">
51
+
52
+ <script>__md_scope=new URL("../..",location),__md_hash=e=>[...e].reduce(((e,_)=>(e<<5)-e+_.charCodeAt(0)),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
53
+
54
+
55
+
56
+
57
+
58
+ </head>
59
+
60
+
61
+
62
+
63
+
64
+
65
+
66
+
67
+
68
+ <body dir="ltr" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="teal">
69
+
70
+
71
+ <input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
72
+ <input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
73
+ <label class="md-overlay" for="__drawer"></label>
74
+ <div data-md-component="skip">
75
+
76
+
77
+ <a href="#troubleshooting" class="md-skip">
78
+ Skip to content
79
+ </a>
80
+
81
+ </div>
82
+ <div data-md-component="announce">
83
+
84
+ </div>
85
+
86
+
87
+
88
+
89
+
90
+
91
+ <header class="md-header md-header--shadow" data-md-component="header">
92
+ <nav class="md-header__inner md-grid" aria-label="Header">
93
+ <a href="../.." title="CADDForge" class="md-header__button md-logo" aria-label="CADDForge" data-md-component="logo">
94
+
95
+
96
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
97
+
98
+ </a>
99
+ <label class="md-header__button md-icon" for="__drawer">
100
+
101
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z"/></svg>
102
+ </label>
103
+ <div class="md-header__title" data-md-component="header-title">
104
+ <div class="md-header__ellipsis">
105
+ <div class="md-header__topic">
106
+ <span class="md-ellipsis">
107
+ CADDForge
108
+ </span>
109
+ </div>
110
+ <div class="md-header__topic" data-md-component="header-topic">
111
+ <span class="md-ellipsis">
112
+
113
+ Troubleshooting
114
+
115
+ </span>
116
+ </div>
117
+ </div>
118
+ </div>
119
+
120
+
121
+ <form class="md-header__option" data-md-component="palette">
122
+
123
+
124
+
125
+
126
+ <input class="md-option" data-md-color-media="(prefers-color-scheme: light)" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="teal" aria-label="Switch to dark mode" type="radio" name="__palette" id="__palette_0">
127
+
128
+ <label class="md-header__button md-icon" title="Switch to dark mode" for="__palette_1" hidden>
129
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="m17.75 4.09-2.53 1.94.91 3.06-2.63-1.81-2.63 1.81.91-3.06-2.53-1.94L12.44 4l1.06-3 1.06 3zm3.5 6.91-1.64 1.25.59 1.98-1.7-1.17-1.7 1.17.59-1.98L15.75 11l2.06-.05L18.5 9l.69 1.95zm-2.28 4.95c.83-.08 1.72 1.1 1.19 1.85-.32.45-.66.87-1.08 1.27C15.17 23 8.84 23 4.94 19.07c-3.91-3.9-3.91-10.24 0-14.14.4-.4.82-.76 1.27-1.08.75-.53 1.93.36 1.85 1.19-.27 2.86.69 5.83 2.89 8.02a9.96 9.96 0 0 0 8.02 2.89m-1.64 2.02a12.08 12.08 0 0 1-7.8-3.47c-2.17-2.19-3.33-5-3.49-7.82-2.81 3.14-2.7 7.96.31 10.98 3.02 3.01 7.84 3.12 10.98.31"/></svg>
130
+ </label>
131
+
132
+
133
+
134
+
135
+
136
+ <input class="md-option" data-md-color-media="(prefers-color-scheme: dark)" data-md-color-scheme="slate" data-md-color-primary="blue" data-md-color-accent="teal" aria-label="Switch to light mode" type="radio" name="__palette" id="__palette_1">
137
+
138
+ <label class="md-header__button md-icon" title="Switch to light mode" for="__palette_0" hidden>
139
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 7a5 5 0 0 1 5 5 5 5 0 0 1-5 5 5 5 0 0 1-5-5 5 5 0 0 1 5-5m0 2a3 3 0 0 0-3 3 3 3 0 0 0 3 3 3 3 0 0 0 3-3 3 3 0 0 0-3-3m0-7 2.39 3.42C13.65 5.15 12.84 5 12 5s-1.65.15-2.39.42zM3.34 7l4.16-.35A7.2 7.2 0 0 0 5.94 8.5c-.44.74-.69 1.5-.83 2.29zm.02 10 1.76-3.77a7.131 7.131 0 0 0 2.38 4.14zM20.65 7l-1.77 3.79a7.02 7.02 0 0 0-2.38-4.15zm-.01 10-4.14.36c.59-.51 1.12-1.14 1.54-1.86.42-.73.69-1.5.83-2.29zM12 22l-2.41-3.44c.74.27 1.55.44 2.41.44.82 0 1.63-.17 2.37-.44z"/></svg>
140
+ </label>
141
+
142
+
143
+ </form>
144
+
145
+
146
+
147
+ <script>var palette=__md_get("__palette");if(palette&&palette.color){if("(prefers-color-scheme)"===palette.color.media){var media=matchMedia("(prefers-color-scheme: light)"),input=document.querySelector(media.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: dark)']");palette.color.media=input.getAttribute("data-md-color-media"),palette.color.scheme=input.getAttribute("data-md-color-scheme"),palette.color.primary=input.getAttribute("data-md-color-primary"),palette.color.accent=input.getAttribute("data-md-color-accent")}for(var[key,value]of Object.entries(palette.color))document.body.setAttribute("data-md-color-"+key,value)}</script>
148
+
149
+
150
+
151
+
152
+
153
+ <label class="md-header__button md-icon" for="__search">
154
+
155
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.52 6.52 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5"/></svg>
156
+ </label>
157
+ <div class="md-search" data-md-component="search" role="dialog">
158
+ <label class="md-search__overlay" for="__search"></label>
159
+ <div class="md-search__inner" role="search">
160
+ <form class="md-search__form" name="search">
161
+ <input type="text" class="md-search__input" name="query" aria-label="Search" placeholder="Search" autocapitalize="off" autocorrect="off" autocomplete="off" spellcheck="false" data-md-component="search-query" required>
162
+ <label class="md-search__icon md-icon" for="__search">
163
+
164
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.52 6.52 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5"/></svg>
165
+
166
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11z"/></svg>
167
+ </label>
168
+ <nav class="md-search__options" aria-label="Search">
169
+
170
+ <button type="reset" class="md-search__icon md-icon" title="Clear" aria-label="Clear" tabindex="-1">
171
+
172
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12z"/></svg>
173
+ </button>
174
+ </nav>
175
+
176
+ <div class="md-search__suggest" data-md-component="search-suggest"></div>
177
+
178
+ </form>
179
+ <div class="md-search__output">
180
+ <div class="md-search__scrollwrap" tabindex="0" data-md-scrollfix>
181
+ <div class="md-search-result" data-md-component="search-result">
182
+ <div class="md-search-result__meta">
183
+ Initializing search
184
+ </div>
185
+ <ol class="md-search-result__list" role="presentation"></ol>
186
+ </div>
187
+ </div>
188
+ </div>
189
+ </div>
190
+ </div>
191
+
192
+
193
+
194
+ <div class="md-header__source">
195
+ <a href="https://github.com/idorsia/caddforge-docs" title="Go to repository" class="md-source" data-md-component="source">
196
+ <div class="md-source__icon md-icon">
197
+
198
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 7.1.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2025 Fonticons, Inc.--><path d="M439.6 236.1 244 40.5c-5.4-5.5-12.8-8.5-20.4-8.5s-15 3-20.4 8.4L162.5 81l51.5 51.5c27.1-9.1 52.7 16.8 43.4 43.7l49.7 49.7c34.2-11.8 61.2 31 35.5 56.7-26.5 26.5-70.2-2.9-56-37.3L240.3 199v121.9c25.3 12.5 22.3 41.8 9.1 55-6.4 6.4-15.2 10.1-24.3 10.1s-17.8-3.6-24.3-10.1c-17.6-17.6-11.1-46.9 11.2-56v-123c-20.8-8.5-24.6-30.7-18.6-45L142.6 101 8.5 235.1C3 240.6 0 247.9 0 255.5s3 15 8.5 20.4l195.6 195.7c5.4 5.4 12.7 8.4 20.4 8.4s15-3 20.4-8.4l194.7-194.7c5.4-5.4 8.4-12.8 8.4-20.4s-3-15-8.4-20.4"/></svg>
199
+ </div>
200
+ <div class="md-source__repository">
201
+ caddforge-docs
202
+ </div>
203
+ </a>
204
+ </div>
205
+
206
+ </nav>
207
+
208
+ </header>
209
+
210
+ <div class="md-container" data-md-component="container">
211
+
212
+
213
+
214
+
215
+
216
+
217
+ <main class="md-main" data-md-component="main">
218
+ <div class="md-main__inner md-grid">
219
+
220
+
221
+
222
+ <div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" >
223
+ <div class="md-sidebar__scrollwrap">
224
+ <div class="md-sidebar__inner">
225
+
226
+
227
+
228
+
229
+ <nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
230
+ <label class="md-nav__title" for="__drawer">
231
+ <a href="../.." title="CADDForge" class="md-nav__button md-logo" aria-label="CADDForge" data-md-component="logo">
232
+
233
+
234
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
235
+
236
+ </a>
237
+ CADDForge
238
+ </label>
239
+
240
+ <div class="md-nav__source">
241
+ <a href="https://github.com/idorsia/caddforge-docs" title="Go to repository" class="md-source" data-md-component="source">
242
+ <div class="md-source__icon md-icon">
243
+
244
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 7.1.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2025 Fonticons, Inc.--><path d="M439.6 236.1 244 40.5c-5.4-5.5-12.8-8.5-20.4-8.5s-15 3-20.4 8.4L162.5 81l51.5 51.5c27.1-9.1 52.7 16.8 43.4 43.7l49.7 49.7c34.2-11.8 61.2 31 35.5 56.7-26.5 26.5-70.2-2.9-56-37.3L240.3 199v121.9c25.3 12.5 22.3 41.8 9.1 55-6.4 6.4-15.2 10.1-24.3 10.1s-17.8-3.6-24.3-10.1c-17.6-17.6-11.1-46.9 11.2-56v-123c-20.8-8.5-24.6-30.7-18.6-45L142.6 101 8.5 235.1C3 240.6 0 247.9 0 255.5s3 15 8.5 20.4l195.6 195.7c5.4 5.4 12.7 8.4 20.4 8.4s15-3 20.4-8.4l194.7-194.7c5.4-5.4 8.4-12.8 8.4-20.4s-3-15-8.4-20.4"/></svg>
245
+ </div>
246
+ <div class="md-source__repository">
247
+ caddforge-docs
248
+ </div>
249
+ </a>
250
+ </div>
251
+
252
+ <ul class="md-nav__list" data-md-scrollfix>
253
+
254
+
255
+
256
+
257
+
258
+
259
+
260
+ <li class="md-nav__item">
261
+ <a href="../.." class="md-nav__link">
262
+
263
+
264
+
265
+ <span class="md-ellipsis">
266
+
267
+
268
+ Home
269
+
270
+
271
+
272
+ </span>
273
+
274
+
275
+
276
+ </a>
277
+ </li>
278
+
279
+
280
+
281
+
282
+
283
+
284
+
285
+
286
+
287
+
288
+
289
+
290
+
291
+
292
+
293
+
294
+
295
+
296
+
297
+
298
+
299
+
300
+
301
+
302
+
303
+
304
+
305
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
306
+
307
+
308
+
309
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
310
+
311
+
312
+ <div class="md-nav__link md-nav__container">
313
+ <a href="../../getting-started/" class="md-nav__link ">
314
+
315
+
316
+
317
+ <span class="md-ellipsis">
318
+
319
+
320
+ Getting Started
321
+
322
+
323
+
324
+ </span>
325
+
326
+
327
+
328
+ </a>
329
+
330
+
331
+ <label class="md-nav__link " for="__nav_2" id="__nav_2_label" tabindex="">
332
+ <span class="md-nav__icon md-icon"></span>
333
+ </label>
334
+
335
+ </div>
336
+
337
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
338
+ <label class="md-nav__title" for="__nav_2">
339
+ <span class="md-nav__icon md-icon"></span>
340
+
341
+
342
+ Getting Started
343
+
344
+
345
+ </label>
346
+ <ul class="md-nav__list" data-md-scrollfix>
347
+
348
+
349
+
350
+
351
+
352
+
353
+
354
+ <li class="md-nav__item">
355
+ <a href="../../getting-started/installation/" class="md-nav__link">
356
+
357
+
358
+
359
+ <span class="md-ellipsis">
360
+
361
+
362
+ Installation
363
+
364
+
365
+
366
+ </span>
367
+
368
+
369
+
370
+ </a>
371
+ </li>
372
+
373
+
374
+
375
+
376
+
377
+
378
+
379
+
380
+
381
+
382
+ <li class="md-nav__item">
383
+ <a href="../../getting-started/first-workflow/" class="md-nav__link">
384
+
385
+
386
+
387
+ <span class="md-ellipsis">
388
+
389
+
390
+ First Workflow
391
+
392
+
393
+
394
+ </span>
395
+
396
+
397
+
398
+ </a>
399
+ </li>
400
+
401
+
402
+
403
+
404
+
405
+
406
+
407
+
408
+
409
+
410
+ <li class="md-nav__item">
411
+ <a href="../../getting-started/first-pipeline/" class="md-nav__link">
412
+
413
+
414
+
415
+ <span class="md-ellipsis">
416
+
417
+
418
+ First Pipeline
419
+
420
+
421
+
422
+ </span>
423
+
424
+
425
+
426
+ </a>
427
+ </li>
428
+
429
+
430
+
431
+
432
+ </ul>
433
+ </nav>
434
+
435
+ </li>
436
+
437
+
438
+
439
+
440
+
441
+
442
+
443
+
444
+
445
+
446
+
447
+
448
+
449
+
450
+
451
+
452
+
453
+
454
+
455
+
456
+
457
+
458
+
459
+
460
+
461
+
462
+
463
+
464
+
465
+ <li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
466
+
467
+
468
+
469
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
470
+
471
+
472
+ <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="">
473
+
474
+
475
+
476
+ <span class="md-ellipsis">
477
+
478
+
479
+ How-to Guides
480
+
481
+
482
+
483
+ </span>
484
+
485
+
486
+
487
+ <span class="md-nav__icon md-icon"></span>
488
+ </label>
489
+
490
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
491
+ <label class="md-nav__title" for="__nav_3">
492
+ <span class="md-nav__icon md-icon"></span>
493
+
494
+
495
+ How-to Guides
496
+
497
+
498
+ </label>
499
+ <ul class="md-nav__list" data-md-scrollfix>
500
+
501
+
502
+
503
+
504
+
505
+
506
+
507
+ <li class="md-nav__item">
508
+ <a href="../jobs/" class="md-nav__link">
509
+
510
+
511
+
512
+ <span class="md-ellipsis">
513
+
514
+
515
+ Jobs and Results
516
+
517
+
518
+
519
+ </span>
520
+
521
+
522
+
523
+ </a>
524
+ </li>
525
+
526
+
527
+
528
+
529
+
530
+
531
+
532
+
533
+
534
+
535
+ <li class="md-nav__item">
536
+ <a href="../scatter/" class="md-nav__link">
537
+
538
+
539
+
540
+ <span class="md-ellipsis">
541
+
542
+
543
+ Scatter and Reduce
544
+
545
+
546
+
547
+ </span>
548
+
549
+
550
+
551
+ </a>
552
+ </li>
553
+
554
+
555
+
556
+
557
+
558
+
559
+
560
+
561
+
562
+
563
+
564
+
565
+ <li class="md-nav__item md-nav__item--active">
566
+
567
+ <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
568
+
569
+
570
+
571
+
572
+
573
+ <label class="md-nav__link md-nav__link--active" for="__toc">
574
+
575
+
576
+
577
+ <span class="md-ellipsis">
578
+
579
+
580
+ Troubleshooting
581
+
582
+
583
+
584
+ </span>
585
+
586
+
587
+
588
+ <span class="md-nav__icon md-icon"></span>
589
+ </label>
590
+
591
+ <a href="./" class="md-nav__link md-nav__link--active">
592
+
593
+
594
+
595
+ <span class="md-ellipsis">
596
+
597
+
598
+ Troubleshooting
599
+
600
+
601
+
602
+ </span>
603
+
604
+
605
+
606
+ </a>
607
+
608
+
609
+
610
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
611
+
612
+
613
+
614
+
615
+
616
+
617
+ <label class="md-nav__title" for="__toc">
618
+ <span class="md-nav__icon md-icon"></span>
619
+ Table of contents
620
+ </label>
621
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
622
+
623
+ <li class="md-nav__item">
624
+ <a href="#installation-or-tool-discovery-fails" class="md-nav__link">
625
+ <span class="md-ellipsis">
626
+
627
+ Installation or tool discovery fails
628
+
629
+ </span>
630
+ </a>
631
+
632
+ </li>
633
+
634
+ <li class="md-nav__item">
635
+ <a href="#pyocl-or-java-fails" class="md-nav__link">
636
+ <span class="md-ellipsis">
637
+
638
+ PyOCL or Java fails
639
+
640
+ </span>
641
+ </a>
642
+
643
+ </li>
644
+
645
+ <li class="md-nav__item">
646
+ <a href="#configuration-or-input-paths-are-rejected" class="md-nav__link">
647
+ <span class="md-ellipsis">
648
+
649
+ Configuration or input paths are rejected
650
+
651
+ </span>
652
+ </a>
653
+
654
+ </li>
655
+
656
+ <li class="md-nav__item">
657
+ <a href="#job-is-missing-or-failed" class="md-nav__link">
658
+ <span class="md-ellipsis">
659
+
660
+ Job is missing or failed
661
+
662
+ </span>
663
+ </a>
664
+
665
+ </li>
666
+
667
+ <li class="md-nav__item">
668
+ <a href="#slurm-submission-or-execution-fails" class="md-nav__link">
669
+ <span class="md-ellipsis">
670
+
671
+ Slurm submission or execution fails
672
+
673
+ </span>
674
+ </a>
675
+
676
+ </li>
677
+
678
+ <li class="md-nav__item">
679
+ <a href="#browser-based-interfaces-do-not-open" class="md-nav__link">
680
+ <span class="md-ellipsis">
681
+
682
+ Browser-based interfaces do not open
683
+
684
+ </span>
685
+ </a>
686
+
687
+ </li>
688
+
689
+ <li class="md-nav__item">
690
+ <a href="#prepare-a-useful-bug-report" class="md-nav__link">
691
+ <span class="md-ellipsis">
692
+
693
+ Prepare a useful bug report
694
+
695
+ </span>
696
+ </a>
697
+
698
+ </li>
699
+
700
+ </ul>
701
+
702
+ </nav>
703
+
704
+ </li>
705
+
706
+
707
+
708
+
709
+ </ul>
710
+ </nav>
711
+
712
+ </li>
713
+
714
+
715
+
716
+
717
+
718
+
719
+
720
+
721
+
722
+
723
+
724
+
725
+
726
+
727
+
728
+
729
+
730
+
731
+
732
+
733
+
734
+
735
+
736
+
737
+
738
+
739
+
740
+
741
+
742
+
743
+
744
+
745
+
746
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
747
+
748
+
749
+
750
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
751
+
752
+
753
+ <div class="md-nav__link md-nav__container">
754
+ <a href="../../core/" class="md-nav__link ">
755
+
756
+
757
+
758
+ <span class="md-ellipsis">
759
+
760
+
761
+ Core
762
+
763
+
764
+
765
+ </span>
766
+
767
+
768
+
769
+ </a>
770
+
771
+
772
+ <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
773
+ <span class="md-nav__icon md-icon"></span>
774
+ </label>
775
+
776
+ </div>
777
+
778
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
779
+ <label class="md-nav__title" for="__nav_4">
780
+ <span class="md-nav__icon md-icon"></span>
781
+
782
+
783
+ Core
784
+
785
+
786
+ </label>
787
+ <ul class="md-nav__list" data-md-scrollfix>
788
+
789
+
790
+
791
+
792
+
793
+
794
+
795
+ <li class="md-nav__item">
796
+ <a href="../../core/concepts/" class="md-nav__link">
797
+
798
+
799
+
800
+ <span class="md-ellipsis">
801
+
802
+
803
+ Concepts
804
+
805
+
806
+
807
+ </span>
808
+
809
+
810
+
811
+ </a>
812
+ </li>
813
+
814
+
815
+
816
+
817
+
818
+
819
+
820
+
821
+
822
+
823
+ <li class="md-nav__item">
824
+ <a href="../../core/configuration/" class="md-nav__link">
825
+
826
+
827
+
828
+ <span class="md-ellipsis">
829
+
830
+
831
+ Configuration
832
+
833
+
834
+
835
+ </span>
836
+
837
+
838
+
839
+ </a>
840
+ </li>
841
+
842
+
843
+
844
+
845
+
846
+
847
+
848
+
849
+
850
+
851
+ <li class="md-nav__item">
852
+ <a href="../../core/cli/" class="md-nav__link">
853
+
854
+
855
+
856
+ <span class="md-ellipsis">
857
+
858
+
859
+ CLI
860
+
861
+
862
+
863
+ </span>
864
+
865
+
866
+
867
+ </a>
868
+ </li>
869
+
870
+
871
+
872
+
873
+
874
+
875
+
876
+
877
+
878
+
879
+ <li class="md-nav__item">
880
+ <a href="../../core/jobs-results/" class="md-nav__link">
881
+
882
+
883
+
884
+ <span class="md-ellipsis">
885
+
886
+
887
+ Jobs and Results
888
+
889
+
890
+
891
+ </span>
892
+
893
+
894
+
895
+ </a>
896
+ </li>
897
+
898
+
899
+
900
+
901
+
902
+
903
+
904
+
905
+
906
+
907
+ <li class="md-nav__item">
908
+ <a href="../../core/slurm/" class="md-nav__link">
909
+
910
+
911
+
912
+ <span class="md-ellipsis">
913
+
914
+
915
+ Slurm Backend
916
+
917
+
918
+
919
+ </span>
920
+
921
+
922
+
923
+ </a>
924
+ </li>
925
+
926
+
927
+
928
+
929
+
930
+
931
+
932
+
933
+
934
+
935
+ <li class="md-nav__item">
936
+ <a href="../../core/plugins/" class="md-nav__link">
937
+
938
+
939
+
940
+ <span class="md-ellipsis">
941
+
942
+
943
+ Plugins
944
+
945
+
946
+
947
+ </span>
948
+
949
+
950
+
951
+ </a>
952
+ </li>
953
+
954
+
955
+
956
+
957
+ </ul>
958
+ </nav>
959
+
960
+ </li>
961
+
962
+
963
+
964
+
965
+
966
+
967
+
968
+
969
+
970
+
971
+
972
+
973
+
974
+
975
+
976
+
977
+
978
+
979
+
980
+
981
+
982
+
983
+
984
+
985
+
986
+
987
+
988
+
989
+
990
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
991
+
992
+
993
+
994
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
995
+
996
+
997
+ <div class="md-nav__link md-nav__container">
998
+ <a href="../../pipelines/" class="md-nav__link ">
999
+
1000
+
1001
+
1002
+ <span class="md-ellipsis">
1003
+
1004
+
1005
+ Pipelines
1006
+
1007
+
1008
+
1009
+ </span>
1010
+
1011
+
1012
+
1013
+ </a>
1014
+
1015
+
1016
+ <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
1017
+ <span class="md-nav__icon md-icon"></span>
1018
+ </label>
1019
+
1020
+ </div>
1021
+
1022
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
1023
+ <label class="md-nav__title" for="__nav_5">
1024
+ <span class="md-nav__icon md-icon"></span>
1025
+
1026
+
1027
+ Pipelines
1028
+
1029
+
1030
+ </label>
1031
+ <ul class="md-nav__list" data-md-scrollfix>
1032
+
1033
+
1034
+
1035
+
1036
+
1037
+
1038
+
1039
+ <li class="md-nav__item">
1040
+ <a href="../../pipelines/specification/" class="md-nav__link">
1041
+
1042
+
1043
+
1044
+ <span class="md-ellipsis">
1045
+
1046
+
1047
+ Specification
1048
+
1049
+
1050
+
1051
+ </span>
1052
+
1053
+
1054
+
1055
+ </a>
1056
+ </li>
1057
+
1058
+
1059
+
1060
+
1061
+
1062
+
1063
+
1064
+
1065
+
1066
+
1067
+ <li class="md-nav__item">
1068
+ <a href="../../pipelines/artifacts/" class="md-nav__link">
1069
+
1070
+
1071
+
1072
+ <span class="md-ellipsis">
1073
+
1074
+
1075
+ Artifacts
1076
+
1077
+
1078
+
1079
+ </span>
1080
+
1081
+
1082
+
1083
+ </a>
1084
+ </li>
1085
+
1086
+
1087
+
1088
+
1089
+
1090
+
1091
+
1092
+
1093
+
1094
+
1095
+ <li class="md-nav__item">
1096
+ <a href="../../pipelines/built-ins/" class="md-nav__link">
1097
+
1098
+
1099
+
1100
+ <span class="md-ellipsis">
1101
+
1102
+
1103
+ Built-in Stages
1104
+
1105
+
1106
+
1107
+ </span>
1108
+
1109
+
1110
+
1111
+ </a>
1112
+ </li>
1113
+
1114
+
1115
+
1116
+
1117
+
1118
+
1119
+
1120
+
1121
+
1122
+
1123
+ <li class="md-nav__item">
1124
+ <a href="../../pipelines/examples/" class="md-nav__link">
1125
+
1126
+
1127
+
1128
+ <span class="md-ellipsis">
1129
+
1130
+
1131
+ Examples
1132
+
1133
+
1134
+
1135
+ </span>
1136
+
1137
+
1138
+
1139
+ </a>
1140
+ </li>
1141
+
1142
+
1143
+
1144
+
1145
+ </ul>
1146
+ </nav>
1147
+
1148
+ </li>
1149
+
1150
+
1151
+
1152
+
1153
+
1154
+
1155
+
1156
+
1157
+
1158
+
1159
+
1160
+
1161
+
1162
+
1163
+
1164
+
1165
+
1166
+
1167
+
1168
+
1169
+
1170
+
1171
+
1172
+
1173
+
1174
+
1175
+
1176
+
1177
+
1178
+
1179
+
1180
+
1181
+
1182
+
1183
+
1184
+
1185
+
1186
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1187
+
1188
+
1189
+
1190
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
1191
+
1192
+
1193
+ <div class="md-nav__link md-nav__container">
1194
+ <a href="../../plugins/" class="md-nav__link ">
1195
+
1196
+
1197
+
1198
+ <span class="md-ellipsis">
1199
+
1200
+
1201
+ Plugins
1202
+
1203
+
1204
+
1205
+ </span>
1206
+
1207
+
1208
+
1209
+ </a>
1210
+
1211
+
1212
+ <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
1213
+ <span class="md-nav__icon md-icon"></span>
1214
+ </label>
1215
+
1216
+ </div>
1217
+
1218
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
1219
+ <label class="md-nav__title" for="__nav_6">
1220
+ <span class="md-nav__icon md-icon"></span>
1221
+
1222
+
1223
+ Plugins
1224
+
1225
+
1226
+ </label>
1227
+ <ul class="md-nav__list" data-md-scrollfix>
1228
+
1229
+
1230
+
1231
+
1232
+
1233
+
1234
+
1235
+ <li class="md-nav__item">
1236
+ <a href="../../plugins/version-matrix/" class="md-nav__link">
1237
+
1238
+
1239
+
1240
+ <span class="md-ellipsis">
1241
+
1242
+
1243
+ Version Matrix
1244
+
1245
+
1246
+
1247
+ </span>
1248
+
1249
+
1250
+
1251
+ </a>
1252
+ </li>
1253
+
1254
+
1255
+
1256
+
1257
+
1258
+
1259
+
1260
+
1261
+
1262
+
1263
+ <li class="md-nav__item">
1264
+ <a href="../../plugins/docking/" class="md-nav__link">
1265
+
1266
+
1267
+
1268
+ <span class="md-ellipsis">
1269
+
1270
+
1271
+ Docking
1272
+
1273
+
1274
+
1275
+ </span>
1276
+
1277
+
1278
+
1279
+ </a>
1280
+ </li>
1281
+
1282
+
1283
+
1284
+
1285
+
1286
+
1287
+
1288
+
1289
+
1290
+
1291
+ <li class="md-nav__item">
1292
+ <a href="../../plugins/descriptors/" class="md-nav__link">
1293
+
1294
+
1295
+
1296
+ <span class="md-ellipsis">
1297
+
1298
+
1299
+ Descriptors
1300
+
1301
+
1302
+
1303
+ </span>
1304
+
1305
+
1306
+
1307
+ </a>
1308
+ </li>
1309
+
1310
+
1311
+
1312
+
1313
+
1314
+
1315
+
1316
+
1317
+
1318
+
1319
+ <li class="md-nav__item">
1320
+ <a href="../../plugins/md/" class="md-nav__link">
1321
+
1322
+
1323
+
1324
+ <span class="md-ellipsis">
1325
+
1326
+
1327
+ MD
1328
+
1329
+
1330
+
1331
+ </span>
1332
+
1333
+
1334
+
1335
+ </a>
1336
+ </li>
1337
+
1338
+
1339
+
1340
+
1341
+
1342
+
1343
+
1344
+
1345
+
1346
+
1347
+ <li class="md-nav__item">
1348
+ <a href="../../plugins/fep/" class="md-nav__link">
1349
+
1350
+
1351
+
1352
+ <span class="md-ellipsis">
1353
+
1354
+
1355
+ FEP
1356
+
1357
+
1358
+
1359
+ </span>
1360
+
1361
+
1362
+
1363
+ </a>
1364
+ </li>
1365
+
1366
+
1367
+
1368
+
1369
+
1370
+
1371
+
1372
+
1373
+
1374
+
1375
+ <li class="md-nav__item">
1376
+ <a href="../../plugins/qm/" class="md-nav__link">
1377
+
1378
+
1379
+
1380
+ <span class="md-ellipsis">
1381
+
1382
+
1383
+ QM
1384
+
1385
+
1386
+
1387
+ </span>
1388
+
1389
+
1390
+
1391
+ </a>
1392
+ </li>
1393
+
1394
+
1395
+
1396
+
1397
+
1398
+
1399
+
1400
+
1401
+
1402
+
1403
+ <li class="md-nav__item">
1404
+ <a href="../../plugins/ml/" class="md-nav__link">
1405
+
1406
+
1407
+
1408
+ <span class="md-ellipsis">
1409
+
1410
+
1411
+ ML
1412
+
1413
+
1414
+
1415
+ </span>
1416
+
1417
+
1418
+
1419
+ </a>
1420
+ </li>
1421
+
1422
+
1423
+
1424
+
1425
+
1426
+
1427
+
1428
+
1429
+
1430
+
1431
+ <li class="md-nav__item">
1432
+ <a href="../../plugins/datascience/" class="md-nav__link">
1433
+
1434
+
1435
+
1436
+ <span class="md-ellipsis">
1437
+
1438
+
1439
+ Data Science
1440
+
1441
+
1442
+
1443
+ </span>
1444
+
1445
+
1446
+
1447
+ </a>
1448
+ </li>
1449
+
1450
+
1451
+
1452
+
1453
+ </ul>
1454
+ </nav>
1455
+
1456
+ </li>
1457
+
1458
+
1459
+
1460
+
1461
+
1462
+
1463
+
1464
+
1465
+
1466
+
1467
+
1468
+
1469
+
1470
+
1471
+
1472
+
1473
+
1474
+
1475
+
1476
+
1477
+
1478
+
1479
+
1480
+
1481
+
1482
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1483
+
1484
+
1485
+
1486
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_7" >
1487
+
1488
+
1489
+ <div class="md-nav__link md-nav__container">
1490
+ <a href="../../gui/" class="md-nav__link ">
1491
+
1492
+
1493
+
1494
+ <span class="md-ellipsis">
1495
+
1496
+
1497
+ GUI
1498
+
1499
+
1500
+
1501
+ </span>
1502
+
1503
+
1504
+
1505
+ </a>
1506
+
1507
+
1508
+ <label class="md-nav__link " for="__nav_7" id="__nav_7_label" tabindex="">
1509
+ <span class="md-nav__icon md-icon"></span>
1510
+ </label>
1511
+
1512
+ </div>
1513
+
1514
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
1515
+ <label class="md-nav__title" for="__nav_7">
1516
+ <span class="md-nav__icon md-icon"></span>
1517
+
1518
+
1519
+ GUI
1520
+
1521
+
1522
+ </label>
1523
+ <ul class="md-nav__list" data-md-scrollfix>
1524
+
1525
+
1526
+
1527
+
1528
+
1529
+
1530
+
1531
+ <li class="md-nav__item">
1532
+ <a href="../../gui/walkthrough/" class="md-nav__link">
1533
+
1534
+
1535
+
1536
+ <span class="md-ellipsis">
1537
+
1538
+
1539
+ Walkthrough
1540
+
1541
+
1542
+
1543
+ </span>
1544
+
1545
+
1546
+
1547
+ </a>
1548
+ </li>
1549
+
1550
+
1551
+
1552
+
1553
+
1554
+
1555
+
1556
+
1557
+
1558
+
1559
+ <li class="md-nav__item">
1560
+ <a href="../../gui/plugin-authoring/" class="md-nav__link">
1561
+
1562
+
1563
+
1564
+ <span class="md-ellipsis">
1565
+
1566
+
1567
+ Plugin GUI Authoring
1568
+
1569
+
1570
+
1571
+ </span>
1572
+
1573
+
1574
+
1575
+ </a>
1576
+ </li>
1577
+
1578
+
1579
+
1580
+
1581
+ </ul>
1582
+ </nav>
1583
+
1584
+ </li>
1585
+
1586
+
1587
+
1588
+
1589
+
1590
+
1591
+
1592
+
1593
+
1594
+
1595
+
1596
+
1597
+
1598
+
1599
+
1600
+
1601
+
1602
+
1603
+
1604
+
1605
+
1606
+
1607
+
1608
+
1609
+
1610
+
1611
+
1612
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1613
+
1614
+
1615
+
1616
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_8" >
1617
+
1618
+
1619
+ <div class="md-nav__link md-nav__container">
1620
+ <a href="../../reference/" class="md-nav__link ">
1621
+
1622
+
1623
+
1624
+ <span class="md-ellipsis">
1625
+
1626
+
1627
+ Reference
1628
+
1629
+
1630
+
1631
+ </span>
1632
+
1633
+
1634
+
1635
+ </a>
1636
+
1637
+
1638
+ <label class="md-nav__link " for="__nav_8" id="__nav_8_label" tabindex="">
1639
+ <span class="md-nav__icon md-icon"></span>
1640
+ </label>
1641
+
1642
+ </div>
1643
+
1644
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_8_label" aria-expanded="false">
1645
+ <label class="md-nav__title" for="__nav_8">
1646
+ <span class="md-nav__icon md-icon"></span>
1647
+
1648
+
1649
+ Reference
1650
+
1651
+
1652
+ </label>
1653
+ <ul class="md-nav__list" data-md-scrollfix>
1654
+
1655
+
1656
+
1657
+
1658
+
1659
+
1660
+
1661
+ <li class="md-nav__item">
1662
+ <a href="../../reference/api/" class="md-nav__link">
1663
+
1664
+
1665
+
1666
+ <span class="md-ellipsis">
1667
+
1668
+
1669
+ Public Python API
1670
+
1671
+
1672
+
1673
+ </span>
1674
+
1675
+
1676
+
1677
+ </a>
1678
+ </li>
1679
+
1680
+
1681
+
1682
+
1683
+
1684
+
1685
+
1686
+
1687
+
1688
+
1689
+ <li class="md-nav__item">
1690
+ <a href="../../examples/" class="md-nav__link">
1691
+
1692
+
1693
+
1694
+ <span class="md-ellipsis">
1695
+
1696
+
1697
+ Example Library
1698
+
1699
+
1700
+
1701
+ </span>
1702
+
1703
+
1704
+
1705
+ </a>
1706
+ </li>
1707
+
1708
+
1709
+
1710
+
1711
+
1712
+
1713
+
1714
+
1715
+
1716
+
1717
+ <li class="md-nav__item">
1718
+ <a href="../../examples/quickstart/" class="md-nav__link">
1719
+
1720
+
1721
+
1722
+ <span class="md-ellipsis">
1723
+
1724
+
1725
+ Example Data Provenance
1726
+
1727
+
1728
+
1729
+ </span>
1730
+
1731
+
1732
+
1733
+ </a>
1734
+ </li>
1735
+
1736
+
1737
+
1738
+
1739
+ </ul>
1740
+ </nav>
1741
+
1742
+ </li>
1743
+
1744
+
1745
+
1746
+
1747
+
1748
+
1749
+
1750
+
1751
+
1752
+
1753
+
1754
+
1755
+
1756
+
1757
+
1758
+
1759
+
1760
+
1761
+
1762
+
1763
+
1764
+
1765
+
1766
+
1767
+
1768
+
1769
+
1770
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1771
+
1772
+
1773
+
1774
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
1775
+
1776
+
1777
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
1778
+
1779
+
1780
+
1781
+ <span class="md-ellipsis">
1782
+
1783
+
1784
+ Explanation
1785
+
1786
+
1787
+
1788
+ </span>
1789
+
1790
+
1791
+
1792
+ <span class="md-nav__icon md-icon"></span>
1793
+ </label>
1794
+
1795
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
1796
+ <label class="md-nav__title" for="__nav_9">
1797
+ <span class="md-nav__icon md-icon"></span>
1798
+
1799
+
1800
+ Explanation
1801
+
1802
+
1803
+ </label>
1804
+ <ul class="md-nav__list" data-md-scrollfix>
1805
+
1806
+
1807
+
1808
+
1809
+
1810
+
1811
+
1812
+ <li class="md-nav__item">
1813
+ <a href="../../explanation/reproducibility/" class="md-nav__link">
1814
+
1815
+
1816
+
1817
+ <span class="md-ellipsis">
1818
+
1819
+
1820
+ Reproducibility
1821
+
1822
+
1823
+
1824
+ </span>
1825
+
1826
+
1827
+
1828
+ </a>
1829
+ </li>
1830
+
1831
+
1832
+
1833
+
1834
+
1835
+
1836
+
1837
+
1838
+
1839
+
1840
+ <li class="md-nav__item">
1841
+ <a href="../../explanation/references/" class="md-nav__link">
1842
+
1843
+
1844
+
1845
+ <span class="md-ellipsis">
1846
+
1847
+
1848
+ Method References
1849
+
1850
+
1851
+
1852
+ </span>
1853
+
1854
+
1855
+
1856
+ </a>
1857
+ </li>
1858
+
1859
+
1860
+
1861
+
1862
+
1863
+
1864
+
1865
+
1866
+
1867
+
1868
+ <li class="md-nav__item">
1869
+ <a href="../../explanation/third-party-notices/" class="md-nav__link">
1870
+
1871
+
1872
+
1873
+ <span class="md-ellipsis">
1874
+
1875
+
1876
+ Third-party Notices
1877
+
1878
+
1879
+
1880
+ </span>
1881
+
1882
+
1883
+
1884
+ </a>
1885
+ </li>
1886
+
1887
+
1888
+
1889
+
1890
+ </ul>
1891
+ </nav>
1892
+
1893
+ </li>
1894
+
1895
+
1896
+
1897
+
1898
+
1899
+
1900
+
1901
+
1902
+
1903
+
1904
+
1905
+
1906
+
1907
+
1908
+
1909
+
1910
+
1911
+
1912
+
1913
+
1914
+
1915
+
1916
+
1917
+
1918
+
1919
+
1920
+
1921
+
1922
+
1923
+
1924
+
1925
+
1926
+
1927
+
1928
+
1929
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1930
+
1931
+
1932
+
1933
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_10" >
1934
+
1935
+
1936
+ <div class="md-nav__link md-nav__container">
1937
+ <a href="../../development/" class="md-nav__link ">
1938
+
1939
+
1940
+
1941
+ <span class="md-ellipsis">
1942
+
1943
+
1944
+ Development
1945
+
1946
+
1947
+
1948
+ </span>
1949
+
1950
+
1951
+
1952
+ </a>
1953
+
1954
+
1955
+ <label class="md-nav__link " for="__nav_10" id="__nav_10_label" tabindex="">
1956
+ <span class="md-nav__icon md-icon"></span>
1957
+ </label>
1958
+
1959
+ </div>
1960
+
1961
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_10_label" aria-expanded="false">
1962
+ <label class="md-nav__title" for="__nav_10">
1963
+ <span class="md-nav__icon md-icon"></span>
1964
+
1965
+
1966
+ Development
1967
+
1968
+
1969
+ </label>
1970
+ <ul class="md-nav__list" data-md-scrollfix>
1971
+
1972
+
1973
+
1974
+
1975
+
1976
+
1977
+
1978
+ <li class="md-nav__item">
1979
+ <a href="../../development/release-notes/" class="md-nav__link">
1980
+
1981
+
1982
+
1983
+ <span class="md-ellipsis">
1984
+
1985
+
1986
+ Release Notes
1987
+
1988
+
1989
+
1990
+ </span>
1991
+
1992
+
1993
+
1994
+ </a>
1995
+ </li>
1996
+
1997
+
1998
+
1999
+
2000
+
2001
+
2002
+
2003
+
2004
+
2005
+
2006
+ <li class="md-nav__item">
2007
+ <a href="../../development/tool-authoring/" class="md-nav__link">
2008
+
2009
+
2010
+
2011
+ <span class="md-ellipsis">
2012
+
2013
+
2014
+ Tool Authoring
2015
+
2016
+
2017
+
2018
+ </span>
2019
+
2020
+
2021
+
2022
+ </a>
2023
+ </li>
2024
+
2025
+
2026
+
2027
+
2028
+
2029
+
2030
+
2031
+
2032
+
2033
+
2034
+ <li class="md-nav__item">
2035
+ <a href="../../development/documentation/" class="md-nav__link">
2036
+
2037
+
2038
+
2039
+ <span class="md-ellipsis">
2040
+
2041
+
2042
+ Documentation
2043
+
2044
+
2045
+
2046
+ </span>
2047
+
2048
+
2049
+
2050
+ </a>
2051
+ </li>
2052
+
2053
+
2054
+
2055
+
2056
+
2057
+
2058
+
2059
+
2060
+
2061
+
2062
+ <li class="md-nav__item">
2063
+ <a href="../../development/contributing/" class="md-nav__link">
2064
+
2065
+
2066
+
2067
+ <span class="md-ellipsis">
2068
+
2069
+
2070
+ Contributing
2071
+
2072
+
2073
+
2074
+ </span>
2075
+
2076
+
2077
+
2078
+ </a>
2079
+ </li>
2080
+
2081
+
2082
+
2083
+
2084
+
2085
+
2086
+
2087
+
2088
+
2089
+
2090
+ <li class="md-nav__item">
2091
+ <a href="../../development/security/" class="md-nav__link">
2092
+
2093
+
2094
+
2095
+ <span class="md-ellipsis">
2096
+
2097
+
2098
+ Security Reporting
2099
+
2100
+
2101
+
2102
+ </span>
2103
+
2104
+
2105
+
2106
+ </a>
2107
+ </li>
2108
+
2109
+
2110
+
2111
+
2112
+
2113
+
2114
+
2115
+
2116
+
2117
+
2118
+ <li class="md-nav__item">
2119
+ <a href="../../development/release-readiness/" class="md-nav__link">
2120
+
2121
+
2122
+
2123
+ <span class="md-ellipsis">
2124
+
2125
+
2126
+ Release Readiness
2127
+
2128
+
2129
+
2130
+ </span>
2131
+
2132
+
2133
+
2134
+ </a>
2135
+ </li>
2136
+
2137
+
2138
+
2139
+
2140
+
2141
+
2142
+
2143
+
2144
+
2145
+
2146
+ <li class="md-nav__item">
2147
+ <a href="../../development/ci-publishing/" class="md-nav__link">
2148
+
2149
+
2150
+
2151
+ <span class="md-ellipsis">
2152
+
2153
+
2154
+ CI and Publishing
2155
+
2156
+
2157
+
2158
+ </span>
2159
+
2160
+
2161
+
2162
+ </a>
2163
+ </li>
2164
+
2165
+
2166
+
2167
+
2168
+ </ul>
2169
+ </nav>
2170
+
2171
+ </li>
2172
+
2173
+
2174
+
2175
+ </ul>
2176
+ </nav>
2177
+ </div>
2178
+ </div>
2179
+ </div>
2180
+
2181
+
2182
+
2183
+ <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
2184
+ <div class="md-sidebar__scrollwrap">
2185
+ <div class="md-sidebar__inner">
2186
+
2187
+
2188
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
2189
+
2190
+
2191
+
2192
+
2193
+
2194
+
2195
+ <label class="md-nav__title" for="__toc">
2196
+ <span class="md-nav__icon md-icon"></span>
2197
+ Table of contents
2198
+ </label>
2199
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
2200
+
2201
+ <li class="md-nav__item">
2202
+ <a href="#installation-or-tool-discovery-fails" class="md-nav__link">
2203
+ <span class="md-ellipsis">
2204
+
2205
+ Installation or tool discovery fails
2206
+
2207
+ </span>
2208
+ </a>
2209
+
2210
+ </li>
2211
+
2212
+ <li class="md-nav__item">
2213
+ <a href="#pyocl-or-java-fails" class="md-nav__link">
2214
+ <span class="md-ellipsis">
2215
+
2216
+ PyOCL or Java fails
2217
+
2218
+ </span>
2219
+ </a>
2220
+
2221
+ </li>
2222
+
2223
+ <li class="md-nav__item">
2224
+ <a href="#configuration-or-input-paths-are-rejected" class="md-nav__link">
2225
+ <span class="md-ellipsis">
2226
+
2227
+ Configuration or input paths are rejected
2228
+
2229
+ </span>
2230
+ </a>
2231
+
2232
+ </li>
2233
+
2234
+ <li class="md-nav__item">
2235
+ <a href="#job-is-missing-or-failed" class="md-nav__link">
2236
+ <span class="md-ellipsis">
2237
+
2238
+ Job is missing or failed
2239
+
2240
+ </span>
2241
+ </a>
2242
+
2243
+ </li>
2244
+
2245
+ <li class="md-nav__item">
2246
+ <a href="#slurm-submission-or-execution-fails" class="md-nav__link">
2247
+ <span class="md-ellipsis">
2248
+
2249
+ Slurm submission or execution fails
2250
+
2251
+ </span>
2252
+ </a>
2253
+
2254
+ </li>
2255
+
2256
+ <li class="md-nav__item">
2257
+ <a href="#browser-based-interfaces-do-not-open" class="md-nav__link">
2258
+ <span class="md-ellipsis">
2259
+
2260
+ Browser-based interfaces do not open
2261
+
2262
+ </span>
2263
+ </a>
2264
+
2265
+ </li>
2266
+
2267
+ <li class="md-nav__item">
2268
+ <a href="#prepare-a-useful-bug-report" class="md-nav__link">
2269
+ <span class="md-ellipsis">
2270
+
2271
+ Prepare a useful bug report
2272
+
2273
+ </span>
2274
+ </a>
2275
+
2276
+ </li>
2277
+
2278
+ </ul>
2279
+
2280
+ </nav>
2281
+ </div>
2282
+ </div>
2283
+ </div>
2284
+
2285
+
2286
+
2287
+ <div class="md-content" data-md-component="content">
2288
+
2289
+ <article class="md-content__inner md-typeset">
2290
+
2291
+
2292
+
2293
+
2294
+
2295
+
2296
+
2297
+
2298
+ <h1 id="troubleshooting">Troubleshooting<a class="headerlink" href="#troubleshooting" title="Permanent link">&para;</a></h1>
2299
+ <p>Start with the smallest local example before troubleshooting a scientific engine or cluster.</p>
2300
+ <h2 id="installation-or-tool-discovery-fails">Installation or tool discovery fails<a class="headerlink" href="#installation-or-tool-discovery-fails" title="Permanent link">&para;</a></h2>
2301
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>check
2302
+ <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>show<span class="w"> </span>caddforge-core
2303
+ <a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>caddforge<span class="w"> </span>list-tools
2304
+ </code></pre></div>
2305
+ <p>Use the same environment for installation and execution. Plugins install core
2306
+ automatically but may need external executables or conda-managed dependencies.
2307
+ <code>pip check</code> checks Python dependency metadata; it cannot verify an engine or GPU.
2308
+ See <a href="../../getting-started/installation/">installation</a> and the selected plugin page.
2309
+ Candidate versions are not necessarily published; use compatible source tags until release.</p>
2310
+ <p>If discovery raises an import error, inspect its first failing module and install
2311
+ the plugin's declared requirements. Ordinary tool discovery loads installed entry
2312
+ points; a broken scientific plugin can prevent discovery. Do not assume it is ignored.</p>
2313
+ <h2 id="pyocl-or-java-fails">PyOCL or Java fails<a class="headerlink" href="#pyocl-or-java-fails" title="Permanent link">&para;</a></h2>
2314
+ <p>Install the distribution <code>pyocl-idor&gt;=0.8.3</code>; Python code imports it as <code>pyocl</code>.
2315
+ For a missing Python dependency:</p>
2316
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span><span class="s2">"pyocl-idor&gt;=0.8.3"</span>
2317
+ </code></pre></div>
2318
+ <p>PyOCL requires Java 21 or newer. Set <code>JAVA_HOME</code> to the intended Java installation.
2319
+ If JPype cannot find <code>libjvm</code>, verify that this runtime is installed and discoverable.
2320
+ An <code>UnsupportedClassVersionError</code> can indicate an older Java runtime loading the
2321
+ bundled Java 21 helper classes. Check the runtime JPype finds:</p>
2322
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>java<span class="w"> </span>-version
2323
+ <a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>python<span class="w"> </span>-c<span class="w"> </span><span class="s2">"import jpype; print(jpype.getDefaultJVMPath())"</span>
2324
+ </code></pre></div>
2325
+ <p>If the old <code>pyocl</code> distribution is installed, remove it before installing
2326
+ <code>pyocl-idor</code>: both distributions own the same Python import namespace.
2327
+ Restart Python or the notebook kernel after changing a running JVM.</p>
2328
+ <h2 id="configuration-or-input-paths-are-rejected">Configuration or input paths are rejected<a class="headerlink" href="#configuration-or-input-paths-are-rejected" title="Permanent link">&para;</a></h2>
2329
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>datascience<span class="w"> </span>distribution-diagnostics
2330
+ <a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>caddforge<span class="w"> </span>run<span class="w"> </span>datascience<span class="w"> </span>distribution-diagnostics<span class="w"> </span>--help
2331
+ </code></pre></div>
2332
+ <p>Compare fields and types with the installed tool's template. Supply required paths,
2333
+ including authoritative ligand chemistry for molecular workflows. CLI workflow
2334
+ inputs are resolved from the submission directory. Built-in pipeline <code>input_path</code>
2335
+ values resolve relative to the pipeline YAML. Use absolute paths when diagnosing ambiguity.
2336
+ A schema-valid file can still refer to missing or scientifically unsuitable input.</p>
2337
+ <h2 id="job-is-missing-or-failed">Job is missing or failed<a class="headerlink" href="#job-is-missing-or-failed" title="Permanent link">&para;</a></h2>
2338
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>caddforge<span class="w"> </span>list-jobs
2339
+ <a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>caddforge<span class="w"> </span>status<span class="w"> </span>&lt;job-id&gt;
2340
+ <a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>caddforge<span class="w"> </span>logs<span class="w"> </span>&lt;job-id&gt;
2341
+ </code></pre></div>
2342
+ <p>Use the original working directory and registry. The logs command shows stdout;
2343
+ inspect <code>stderr.log</code> directly in the recorded run directory when needed. Inspect saved configuration,
2344
+ <code>metadata.json</code>, and the canonical result, then the first error in the logs.
2345
+ An absent result may mean the job is still running, not that it succeeded.
2346
+ Preserve the original run; use a new run directory for a corrected submission.</p>
2347
+ <h2 id="slurm-submission-or-execution-fails">Slurm submission or execution fails<a class="headerlink" href="#slurm-submission-or-execution-fails" title="Permanent link">&para;</a></h2>
2348
+ <p>Run <code>caddforge backend-check --help</code> and test the intended environment with that command.
2349
+ Check scheduler state, partition/account/time limits, environment accessibility,
2350
+ node filesystem permissions, and engine availability on the compute node.
2351
+ A successful <code>sbatch</code> submission does not establish scientific completion.
2352
+ See <a href="../../core/slurm/">Slurm setup</a> for packed environments and wheelhouses.</p>
2353
+ <h2 id="browser-based-interfaces-do-not-open">Browser-based interfaces do not open<a class="headerlink" href="#browser-based-interfaces-do-not-open" title="Permanent link">&para;</a></h2>
2354
+ <p>For installed docs, verify <code>caddforge-docs</code> is installed in the CLI environment:</p>
2355
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>caddforge<span class="w"> </span>docs<span class="w"> </span>--host<span class="w"> </span>localhost<span class="w"> </span>--no-browser
2356
+ </code></pre></div>
2357
+ <p>Open the printed URL manually. Choose a different <code>--port</code> if the requested port
2358
+ is occupied. For a remote server, select a reachable <code>--host</code> and an appropriate
2359
+ network or SSH tunnel; loopback addresses are local to the machine running the server.
2360
+ GUI configuration and docs serving are separate commands.</p>
2361
+ <h2 id="prepare-a-useful-bug-report">Prepare a useful bug report<a class="headerlink" href="#prepare-a-useful-bug-report" title="Permanent link">&para;</a></h2>
2362
+ <p>Include package versions, platform, backend, a minimal synthetic reproducer,
2363
+ expected behavior, actual behavior, and the relevant error. Remove credentials,
2364
+ personal paths, unpublished compounds, receptor structures, and research data
2365
+ before sharing configurations, logs, screenshots, or registry files.
2366
+ See <a href="../../development/contributing/">contributing</a>.</p>
2367
+
2368
+
2369
+
2370
+
2371
+
2372
+
2373
+
2374
+
2375
+
2376
+
2377
+
2378
+
2379
+
2380
+ </article>
2381
+ </div>
2382
+
2383
+
2384
+ <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
2385
+ </div>
2386
+
2387
+ <button type="button" class="md-top md-icon" data-md-component="top" hidden>
2388
+
2389
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8z"/></svg>
2390
+ Back to top
2391
+ </button>
2392
+
2393
+ </main>
2394
+
2395
+ <footer class="md-footer">
2396
+
2397
+ <div class="md-footer-meta md-typeset">
2398
+ <div class="md-footer-meta__inner md-grid">
2399
+ <div class="md-copyright">
2400
+
2401
+
2402
+ Made with
2403
+ <a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
2404
+ Material for MkDocs
2405
+ </a>
2406
+
2407
+ </div>
2408
+
2409
+ </div>
2410
+ </div>
2411
+ </footer>
2412
+
2413
+ </div>
2414
+ <div class="md-dialog" data-md-component="dialog">
2415
+ <div class="md-dialog__inner md-typeset"></div>
2416
+ </div>
2417
+
2418
+
2419
+
2420
+
2421
+
2422
+ <script id="__config" type="application/json">{"annotate": null, "base": "../..", "features": ["navigation.instant", "navigation.sections", "navigation.indexes", "navigation.top", "search.highlight", "search.suggest", "content.code.copy"], "search": "../../assets/javascripts/workers/search.2c215733.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
2423
+
2424
+
2425
+ <script src="../../assets/javascripts/bundle.d7400e89.min.js"></script>
2426
+
2427
+
2428
+ </body>
2429
+ </html>