Changes

Summary

1. Update README.md (commit: 5fad7e8) (details)
2. Update README.md (commit: 804d9cb) (details)
3. CHG: adding other way to download ISSM from GitHub (commit: cd0db55) (details)
4. CHG: Updating paths to Python installation (now using venv) (commit: 48fafb4) (details)
5. CHG: Adjusted tolerances (commit: a7642ec) (details)
6. Delete README (commit: 9c87598) (details)
7. CHG: upgrading to latest PETSc version (commit: 1954c7d) (details)
8. BUG: Path to libgfortran (commit: ade0cdf) (details)
9. CHG: Need libgcc in package (commit: 34edfea) (details)
10. BUG: Path fixes (commit: 06014d2) (details)
11. BUG: Not catching runme error; 'exclude_name' option no longer exists (commit: 7829943) (details)
12. CHG: svn -> git; uncommitted cluster class; clean up of devpath from when we couldn't compile native Silicon MEX-files (commit: 86d56f4) (details)
13. BUG: Incorrect file name (commit: 3f1d135) (details)
14. CHG: Virtual environment not preserved in called script (commit: 6c6e3fc) (details)
15. CHG: removing old scripts (commit: 77ece86) (details)
16. CHG: moved up one directory and removed  from version check (commit: 3da6aa4) (details)
17. CHG: adding more files to gitignore (commit: 71cf980) (details)
18. CHG: Adjusted tolerances (commit: ab5622d) (details)
19. CHG: Minor changes to test fixes to GitHub Webhook -> Jenkins (commit: 5f72777) (details)
20. CHG: removing reference to cshrc, replacing by zshrc (commit: c96bbfd) (details)
21. CHG: Adjusted tolerances (commit: 3aec6f3) (details)
22. CHG: Removing Cmake to avoid conflicts with standalone copy (commit: 71a5854) (details)
23. BUG: Removed 'command' (commit: 23e5006) (details)
24. ADD: Missing empty Models/ dir (commit: d046084) (details)
25. Update of .gitignore. (commit: bef7fd6) (details)
26. Moved all CoDiPack specific functions to CoDiPackGlobal.h. (commit: c637383) (details)
27. CHG: Add default location for libgfortran on Mac to rpath (commit: c21aea7) (details)
28. CHG: adaptive time stepping needs vz in 3d (commit: cfdb310) (details)
29. CHG: throw error message if FCT in 3d (commit: 6693f07) (details)
30. CHG: Use git now to get changes and determine installation type (commit: 9417447) (details)
31. CHG: minor, testing to see if jenkins will recompile (commit: d46094f) (details)
32. CHG: forgot to change path to m/mesh/planet (commit: 48f2f11) (details)
33. CHG: Additions to ignore list (commit: 292ee72) (details)
34. Create codeql.yml (commit: d31839f) (details)
35. Bump the npm_and_yarn group across 1 directory with 2 updates (commit: 224629e) (details)
36. CHG: Fixes for gfortran path in rpath; new config for CodeQL (commit: 49c111d) (details)
37. Update codeql.yml (commit: 17a4dda) (details)
38. Update codeql.yml (commit: 85e70df) (details)
39. Update codeql.yml (commit: a522fbb) (details)
40. Update codeql.yml (commit: a2d5637) (details)
41. CHG: Disabling wrappers on CodeQL build (commit: f3154a6) (details)
42. CHG: Correcting handling of git commit and changes when fetch has not been used (commit: 2e2e447) (details)
43. Delete codeql.yml (commit: 2650861) (details)
44. CHG: Adding whitespace and rerunning jobs (commit: c241279) (details)
45. CHG: removing double blank lines (commit: 501faea) (details)
46. CHG: Adjusted tolerances (commit: befbb36) (details)
47. CHG: Updates to UB CCR config; changed path of gmshplanet.py (commit: b5969f1) (details)
48. CHG: do not rotate matrices if no node is rotated (breaking a golden rule here: this change is NOT tested yet, sorry if I am breaking anything (commit: 746e2a0) (details)
49. CoDiPack type can be defined during the configuration. (commit: 0c86d88) (details)
50. BUG: Need to update previous commit every time we run (commit: 0939b23) (details)
51. CHG: Outstanding commit and test fix to git change polling (commit: f94c8d5) (details)
52. Extracted common computation from StressbalanceAnalysis.cpp. (commit: 1c23b49) (details)
53. Added Preaccumulation helper for sparse row assembly. (commit: a28008d) (details)
54. BUG: Fix for rpath anb libgfortran on Mac; no effect, but make sure MSYS2 is set correctly (commit: f3be32b) (details)
55. CHG: vertical speed needs md.basalforcings.perturbation_melting_rate (commit: 004acae) (details)
56. CHG: vertical speed needs md.basalforcings.perturbation_melting_rate (commit: d4ab726) (details)
57. CHG: missing -fPIC install-linux.sh (commit: ef4f38b) (details)
58. CHG: macOS now only provides python3 and not python, and header files are now in the Headers directory (commit: acf9490) (details)
59. CHG: removing SLEPSC and ADIC2 that we have never used (commit: eb56793) (details)
60. CHG: adding common factor to KMatrices StressBalance (commit: d79f20f) (details)
61. CHG: do not extrude lat/lon if undefined (commit: 542dd67) (details)
62. CHG: refine should deal with lat/long as well (commit: 1c44f94) (details)
63. BUG: output is md2 and not md (commit: 624b32e) (details)
64. CHG: if no observations are provided, we can still use md.initialization.vx/vy to set new spc's (commit: ebfeed6) (details)
65. CHG: New cluster class for submitting jobs to UB CCR; typos (commit: d5ffcb6) (details)
66. CHG: adding factors to analysis (commit: 5221b49) (details)
67. CHG: added Data directory for examples (commit: 3b21465) (details)
68. CHG: adding factors in analysis (commit: 5a7f851) (details)
69. CHG: added factors in analysis (commit: e049dfc) (details)
70. CHG: fixed problem with Glads (commit: 06ba999) (details)
71. BUG: MPI_Wait should wait for the cpu that is receiving for once, which created seg faults with AD (commit: 79e0383) (details)
72. CHG: renaming Viscous Budd (commit: 58ec93e) (details)
73. CHG: Adjusted tolerances (commit: 3d3884b) (details)
74. CHG: multithreading ContourToNodes (commit: a5cce0e) (details)
75. BUG: mexPrintf is NOT thread safe and crashes. Replace by printf (commit: 7031ace) (details)
76. CHG: Temporary fix for not being able to connect via port 22 (commit: 7930043) (details)
77. CHG: Need P instead of p option (commit: 1ae9f62) (details)
78. CHG: added PROJ_LIB env variable to make sure proj.db is found. There are sometimes conflicts with MATLAB's libraries which must be taken care of (commit: ab72887) (details)
79. CHG: minor changed ISSM description (commit: e79d8fc) (details)
80. CHG: ITS_LIVE annual velocity updated to v02, data avaliable from 1985 to 2022. The .nc files are in netCDF4 format, to load in Matlab, we need to use `h5read` (commit: 07d41ed) (details)
81. ADD: interpolate from MEaSUREs monthly averaged velocity Mosaic (2014-2023) : https://doi.org/10.5067/EGKZX6FXXM4P (commit: 96f163d) (details)
82. CHG: use mapping toolbox map if Googlemaps is not available (commit: 877f97d) (details)
83. CHG: fixed zoom level option (commit: f13265c) (details)
84. CHG: adjusted tolerances (commit: 67ecf56) (details)
85. CHG: added interactive to disp: (commit: 82f74cc) (details)
86. Added time and memory output for CoDiPack. (commit: dee0d08) (details)
87. Make preaccumulation configurable. (commit: 0053772) (details)
88. Create c-cpp.yml (commit: de8cfa1) (details)
89. Update c-cpp.yml (commit: 6ea1be6) (details)
90. CHG: changed checks on flags (commit: 75710aa) (details)
91. CHG: need to initialize as 0 (commit: 206ded5) (details)
92. Update c-cpp.yml (commit: 5f63850) (details)
93. Update c-cpp.yml (commit: c26805a) (details)
94. Update c-cpp.yml (commit: c4d8675) (details)
95. Update c-cpp.yml (commit: 1b9716a) (details)
96. Update c-cpp.yml, add matlab (commit: b0584a0) (details)
97. Update c-cpp.yml (commit: 3de0de9) (details)
98. Update c-cpp.yml (commit: 97b7d9f) (details)
99. Create github_linux_basic (commit: 917aa3b) (details)
100. Update c-cpp.yml (commit: 7e7cb29) (details)
101. Update c-cpp.yml (commit: a09e38a) (details)
102. change the directory for CI files (commit: ed557da) (details)
103. Update README.md (commit: 6f97503) (details)
104. Update README.md (commit: 7ee2aa6) (details)
105. create badge for CI, add it to README (commit: 5b19ff4) (details)
106. CHG: minor (commit: 3155d83) (details)
107. BUG: forgot to close parenthesis (commit: 99e58f8) (details)
108. CHG: upgrading PETSc in order to find latest ZLIB (commit: 0a5d4f8) (details)
109. FIX: calculation of VAF based on mask in Tria.cpp (commit: c76bcad) (details)
110. CHG: trying to simplify CI (commit: 345ce88) (details)
111. CHG: trying to simplify CI (commit: 8ca30ea) (details)
112. CHG: getting PETSc from apt-get (commit: 7653d0b) (details)
113. CHG: PETSc needs to be installed manually, but we can skip autotools and cmake (commit: 0a7c0f0) (details)
114. BUG: fixing CI problem (commit: a762b38) (details)
115. CHG: trying to fix CI (commit: b4cb2c6) (details)
116. CHG: trying to fix CI (commit: 8b5f7e9) (details)
117. CHG: trying to fix CI (commit: 07c5512) (details)
118. CHG: trying to fix CI (commit: 34f659f) (details)
119. Update README.md (commit: 1ad8f26) (details)
120. NEW: added option 'quitonerror' for GitHub's CI (commit: cadec61) (details)
121. CHG: fixing matlab tests in GitHub CI (commit: e29269a) (details)
122. CHG: trying to fix CI with MATLAB (commit: c02ba76) (details)
123. CHG: trying to debug CI (commit: dbb040a) (details)
124. CHG: trying to add MATLAB tests (commit: 9e03058) (details)
125. CHG: fixing MATLAB (commit: 47fec1e) (details)
126. load matlab action manually (commit: 979bccd) (details)
127. FIX: updated archive 540 (commit: 2a46a3e) (details)
128. CHG: checking env (commit: d0b793d) (details)
129. CHG: checking env (commit: 38a30bf) (details)
130. CHG: checking env (commit: cec57fd) (details)
131. CHG: checking env (commit: af5690c) (details)
132. CHG: checking env (commit: a9938ed) (details)
133. CHG: checking env (commit: 9208d86) (details)
134. set environment before running matlab (commit: 4a1a946) (details)
135. Update c-cpp.yml (commit: 32b049b) (details)
136. Update c-cpp.yml (commit: 71c965d) (details)
137. Update c-cpp.yml (commit: d6b4c45) (details)
138. Update c-cpp.yml (commit: f32cecc) (details)
139. CHG: fixed typo (commit: fa5e47b) (details)
140. NEW: added a function that reads a geotiff and outputs x,y,data (commit: d3a11cb) (details)
141. CHG: better check on METIS header (commit: aab5168) (details)
142. CHG: removing PETSc from installation (commit: 2788cec) (details)
143. CHG: install openMPI (commit: 0b37126) (details)
144. CHG: figuring out open MPI (commit: 8b91009) (details)
145. CHG: mpi-include does not need -I (commit: b55430e) (details)
146. CHG: scalapack is installed as part of open MPI (commit: 6f937e4) (details)
147. CHG: do not assume that ParMETIS is installed if MUMPS is provided (commit: 0f97bbc) (details)
148. CHG: do not preload petsc files if petsc is not installed (commit: 2f07102) (details)
149. CHG: reverting to installing PETSc (commit: 9640ebb) (details)
150. CHG: simplifying workflow and scripts (commit: 0319b46) (details)
151. CHG: change name (commit: 482d3f8) (details)
152. CHG: removing MPICH from PETSc to speed up CI (commit: 6d818da) (details)
153. CHG: adding more libs to mpi (commit: e69a782) (details)
154. CHG: forgot to change LD_PRELOAD (commit: b00c721) (details)
155. CHG: adding flag to mpiexec to avoid openmpi error message about 'There are not enough slots available' (commit: 3cb916c) (details)
156. CHG: do not make MeshPartition a template (commit: 7f7505c) (details)
157. CHG: added example (commit: 60d676d) (details)
158. BUG: do not initialize codi_global if autodiff is false (commit: 6aa5da9) (details)
159. CHG: Added packages to UB CCR installation; do not compile MeshPartition if METIS is not available (commit: d1e52e2) (details)
160. try to set two steps for the CI (commit: 5975640) (details)
161. try to add cache (commit: 50190d3) (details)
162. try to set the path for cache (commit: 15a348d) (details)
163. try again with env variable (commit: 1b19f0b) (details)
164. update download path in artifact (commit: 0848c3f) (details)
165. try to also cache matlab (commit: 9b235c5) (details)
166. change mpi back to petsc version (commit: 2e7ff85) (details)
167. no need to cache matlab (commit: d6fe336) (details)
168. cache matlab (commit: 80b3c04) (details)
169. try the uncompress path again (commit: dfc6574) (details)
170. download to /root (commit: 81b8b98) (details)
171. try to use relative path (commit: e864a3b) (details)
172. add relative path (commit: ff1f207) (details)
173. change relative path again (commit: e113efe) (details)
174. typo fixed (commit: 995b94a) (details)
175. update working dir (commit: 84a03dd) (details)
176. activate compile (commit: 8c98e69) (details)
177. put test back (commit: e339299) (details)
178. remove apt-get installed mpi (commit: eaae0d7) (details)
179. try to create a matrix of test (commit: efc7cc7) (details)
180. try matrix with string variables (commit: e91fd41) (details)
181. add codipack in CI (commit: 182c715) (details)
182. try to fix codipack configure (commit: 837a322) (details)
183. add gsl (commit: c71caeb) (details)
184. seperate basic and codipack (commit: 7594905) (details)
185. Update common-workflow.yml (commit: 083c437) (details)
186. only include ad tests for ccdipack (commit: 25b6dfc) (details)
187. fix bug in main-ci (commit: 6e84779) (details)
188. set different names for different runs (commit: b0269ef) (details)
189. add type of input.os (commit: e0b1eed) (details)
190. try to cache src/c (commit: 565963c) (details)
191. fix error in the test job (commit: 0206504) (details)
192. remove cache src/c (commit: feaeafc) (details)
193. try petsc-3.20 for ad (commit: b377c3a) (details)
194. try to use env to set the id of cache (commit: ea1e689) (details)
195. try github.env (commit: 24468bb) (details)
196. try to fix bugs when using inputs in cache id (commit: 1d4ea2d) (details)
197. fix bug in the if condition (commit: c3b3660) (details)
198. fix codipack (commit: d2062bb) (details)
199. try ad again (commit: 28d82e6) (details)
200. CHG: added error message instead of just bypassing (commit: 6594401) (details)
201. CHG: for macOS we now also need to add  -commons use_dylibs (commit: 1a3699f) (details)
202. BUG: need to provide specific LD_FLAGS and tweak setCompiler.py to make it work on Sonoma (commit: e49bead) (details)
203. CHG: cleanup (commit: a8f5547) (details)
204. remove with-petsc in codipack (commit: 9d331f1) (details)
205. reduce matrix size for tests (commit: 2fcdd45) (details)
206. check spaces (commit: 22c2e32) (details)
207. turn off codipack tests (commit: b8d2d51) (details)
208. do not compress petsc/src/ to decrease the size of the artifact (commit: 57d4613) (details)
209. try to exclude petsc/src (commit: f9262f6) (details)
210. add gsl to codipack version (commit: a358592) (details)
211. CHG: calving rate in CalvingMIP use normal vector from the levelset (commit: b181f85) (details)
212. Update README.md (commit: 0fb4465) (details)
213. Update README.md (commit: 3a00056) (details)
214. Update action badge in README.md (commit: f4f10ac) (details)
215. CHG: default md.levelset.reinit_frequency=10. Add more description to stabilization (commit: 2f6a9e3) (details)
216. CHG: make two CIs separately for Ubuntu basic and codipack (commit: 4741ed5) (details)
217. CHG: Update test540, due to update default reinit_frequency (commit: 430b105) (details)
218. change the way to reuse workflow (commit: 0efe728) (details)
219. hard code the version of configure ISSM for now (commit: db8075d) (details)
220. BUG: fix CalvingCalvingMIP in Penta (commit: 2698137) (details)
221. fix bugs in action.yml (commit: 7f6f141) (details)
222. separate prepare externalpackes and build (commit: 584f3a5) (details)
223. test ISSM_DIR (commit: 08d6530) (details)
224. Update action.yml (commit: 37527bd) (details)
225. fix ISSM_DIR issue (commit: 47f8a7b) (details)
226. rerun CI, make input name shorter (commit: f857165) (details)
227. fix bug in action.yml (commit: ff67c9f) (details)
228. CHG: update Archive540 (commit: a30382f) (details)
229. rerun full CI (commit: 323ceb5) (details)
230. fix bug in uploading artifact (commit: b4ae7ad) (details)
231. BUG: fix CalvingCalvingMIP (commit: 92549b0) (details)
232. BUG: recompile ISSM, update test540 Archive (commit: a53cd43) (details)
233. CHG: update Archive affected by levelset.reinit_frequency=10 (commit: 87b72a8) (details)
234. add badges for Ubuntu Basic and CodiPack (commit: feb47a9) (details)
235. CHG: MATLAB -> Python and Javascript (commit: ba72369) (details)
236. NEW: Add contrib/poinelli folder and include Paolo2023 interpolation script (commit: 4436be0) (details)
237. CHG: 1st edit of interpPaolo2023 (commit: 37889e4) (details)
238. CHG: taking care of paths with white spaces (commit: b52a7fa) (details)
239. CHG: relaxed tolerances for test 541 (commit: 17823c6) (details)
240. CHG: Cleanup (commit: 15ceb8f) (details)
241. CHG: update to GEMB merge layers to parallel matlab version updates (commit: e96dabc) (details)
242. CHG: update GEMB tols for latest commit (commit: 6ae19af) (details)
243. CHG: update remaining tols in windows and on git for GEMB (commit: 16ba5ed) (details)
244. CHG: Cleanup of configuration options (commit: a96a4ea) (details)
245. BUG: Needed closing ;; (commit: cde015c) (details)
246. CHG: Removing support for Android (commit: f2dc910) (details)
247. CHG: Synchronized enums after pull and merge (commit: 31a5504) (details)
248. BUG: Cleaned up configs (commit: 52cd3be) (details)
249. BUG: Correcting env var substitution (commit: 53e2064) (details)
250. CHG: Cleanup (commit: ecc8bdf) (details)
251. CHG: Cleanup (commit: f4eedf7) (details)
252. CHG: Moving standard env vars to issm_options for MSYS2 builds (commit: 317ec23) (details)
253. CHG: Cleanup; missing env var for Javascript build (commit: e96bbbb) (details)
254. BUG: Fix for MSYS2 build (commit: efeecc0) (details)
255. merge actions to the workflow file (commit: 426b2b2) (details)
256. use multiple lines for the yml (commit: 731bcc7) (details)
257. try to set matlab outside (commit: 3cf77f7) (details)
258. fix missing type of common-workflow.yml (commit: f596275) (details)
259. fix bug in setting matlab root (commit: ec42822) (details)
260. if cache not hit, then recompile (commit: 20636a0) (details)
261. CHG: added check to tell useers they cannot use both PETSc and CoDiPack (commit: 912b605) (details)
262. BUG: Need to check if supplied gfortran and other libs are files for binaries builds (commit: 3256dd9) (details)
263. CHG: added some explanation (commit: 13ed448) (details)
264. BUG: compute calving rate after extrapolation, so that the direction can be correctly computated in the inactive elements (commit: 34142a6) (details)
265. BUG: update archive 540,541,542 (commit: d00366b) (details)
266. update 806,812 (commit: e0f5c70) (details)
267. BUG: update archive 3203 (commit: 1c2cf34) (details)
268. CHG: Consolidation of C*OPTFLAGS to C*FLAGS; missing parmetis option (commit: 613dd08) (details)
269. BUG: Missing commit from pristine copy (commit: 01418c9) (details)
270. BUG: CXXFLAGS is not empty by default under clang (commit: 03ddf03) (details)
271. BUG: Bad path to gfortran (commit: a6bb061) (details)
272. use json to handle matrix strategy (commit: c700e2b) (details)
273. CHG: Standardizing MATLAB and Python wrapper makefiles; adding more possible NumPy header file locations (commit: f202e0d) (details)
274. BUG: fixed memory leak (commit: 4124654) (details)
275. BUG: Reverting changes for now to get versioned code working (commit: 5922889) (details)
276. CHG: Standardizing MATLAB and Python wrapper makefiles (commit: c1e78be) (details)
277. BUG: Reverting (again, sigh) (commit: 16fcdb0) (details)
278. add \' in common_workflow (commit: 102f07b) (details)
279. Update common-workflow.yml (commit: 6ec3517) (details)
280. Update common-workflow.yml (commit: 8bdf8d2) (details)
281. Update common-workflow.yml (commit: 92334a9) (details)
282. update workflow using one file for one case (commit: e477fa3) (details)
283. CHG: MATLAB -> Python wrapper Makrfile.am; upgraded nodes to NumPy 2 (commit: e715320) (details)
284. ADD: output melt rate and its components in SHAKTI hydrology (commit: 4bfad50) (details)
285. CHG: removing unused options (commit: 187f80c) (details)
286. CHG: Removed HTTPS protocol as checkout option; added troubleshooting note about HTTPS protocol error (commit: 42ac9cb) (details)
287. CHG: More clarification about HTTPS vs SSH (commit: 66a11ce) (details)
288. NEW: added file to interpolate undercutting forcings from ISMIP6 data files (commit: 3392563) (details)
289. CHG: added ref (commit: 39d675d) (details)
290. CHG: moving file to a better directory (commit: 7621d80) (details)
291. CHG: update ICESat2 ATL14/15 to version 4 (commit: 29bf890) (details)
292. CHG: closed contour should be option #1 (commit: 3814cab) (details)
293. CHG: minor estetics (commit: 909f497) (details)
294. CHG:update script for TACC Frontera (commit: 0af0688) (details)
295. NEW: add option to include subglacial hydrology layer thickness in driving stress calculation of the SSA (commit: 1105aba) (details)
296. CHG: include stressbalance hydrology layer capability in python (commit: da74c91) (details)
297. BUG: fix loading MEaSUREs velocity for individual glaciers (commit: ba48cc8) (details)
298. CHG: update Jakobshavn MEaSUREs velocity to 2024 (commit: f2e798e) (details)
299. BUG: add if for more general model results (commit: d81f05d) (details)
300. BUG: generalize analyzeCalvingfront function (commit: 8448acd) (details)
301. CHG: second iteration of interpPaolo2023- add interpolation routine (commit: bd63da8) (details)
302. CHG: include temporal component in Paolo2023 melt rate (commit: 99209c8) (details)
303. NEW: added error message if cxxoptflags is provided (commit: 08657b9) (details)
304. BUG: python should not need MEXLIB, this introduces dependencies that are problematic (commit: e36b9bf) (details)
305. BUG: bad python syntax (commit: 0142b7c) (details)
306. CHG: simplifying hydro slope code (commit: 338886f) (details)
307. NEW: nightly run test for stressbalance hydrology layer (commit: ad33e61) (details)
308. CHG: add interpolated dates as output (commit: eff452a) (details)
309. CHG: do not use configure.py in installation script, call configure directly (commit: 0ae352e) (details)
310. CHG: fixed RHS (commit: 425b448) (details)
311. ADD: stanage cluster settings for Sheffield University Stanage HPC cluster (commit: 272614d) (details)
312. BUG: ocean-averaged sea level loads (commit: a9afa9f) (details)
313. NEW: retrieving change in gravitational acceleration from ESA solver (commit: 934614b) (details)
314. CHG: fixed bad character from Surendra's commit (commit: 54b4de7) (details)
315. CHG: fixing NR (commit: 973ddb7) (details)
316. CHG: make python test identical to MATLAB test (commit: b4aa682) (details)
317. CHG: making python test identical to MATLAB (commit: e546cd0) (details)
318. ESA nightly updated with a new diagostic (commit: 513a325) (details)
319. CHG: relaxing tolerances (commit: b9e596c) (details)
320. CHG: relaxing tolerances (commit: 77d5533) (details)
321. CHG: relaxing tolerances (commit: eed8df1) (details)
322. CHG: New archives; changes to ext pkg install scripts and Makefiles as needed to account for new changes to macOS linker (commit: 3d2b61e) (details)
323. Update .gitignore (commit: 195664c) (details)
324. CHG: Updated PETSc version (commit: afc8a21) (details)
325. CHG: Renaming of GDAL install scripts (commit: fcff971) (details)
326. CHG: Fixes for latest PETSc version install script (commit: 5f36b1e) (details)
327. BUG: Corrected install script (commit: df66d12) (details)
328. CHG: Adjusted tolerances (commit: 0ed2108) (details)
329. CHG: Disabling test 362 for Silicon-based Mac as it has large errors (commit: f421911) (details)
330. CHG: Adjusted tolerances (commit: fb91a00) (details)
331. CHG: Adjusted tolerances (commit: e4a2c1e) (details)
332. CHG: Corrected install script name (commit: 27ae96f) (details)
333. Update .gitignore (commit: 2b00a6f) (details)
334. CHG: moving functions around (commit: 02c609d) (details)
335. ADD: mac basic CI (commit: fb15aad) (details)
336. CHG: Love core accuracy and stability improved. NEW: Complex solution enabled (commit: 507291f) (details)
337. CHG: Love core accuracy and stability improved. NEW: Complex solution enabled (commit: c7c1b20) (details)
338. fixing merging error in Makefile.am (commit: 80570a2) (details)
339. CHG:cleaned up Love core for final version (commit: cee3df6) (details)
340. FIX: fixing recast of int/double to double precision for some compilers in Love core (commit: 57a34e6) (details)
341. FIX: cleaning up love core (commit: e3030e4) (details)
342. CHG: Bug in Python wrapper; cleanup (commit: f5a7c45) (details)
343. CHG: Updated gitignore; removed test 362 from test suite for distributables on Silicon-based Macs (commit: 0763279) (details)
344. CHG: Committing local changes from UB CCR (commit: a5e6ef6) (details)
345. Update test2085.m (commit: f986dcc) (details)
346. Update test2084.m (commit: 08a9fb4) (details)
347. CHG: minor edit, include larsen-thwaites hosts to interpStal2020 (commit: f58a1a7) (details)
348. CHG: Older versions of PETSc use config/configure.py (may need to change others) (commit: 3fdb691) (details)
349. CHG: Updates for saving model for JavaScript (commit: 0f22121) (details)
350. CHG: Disabling guts of some savemodeljs methods until they are added to issm.js (commit: baca642) (details)
351. CHG: Turning off development mode so we can generate new binaries automatically for use on VESL (commit: 1ae1d97) (details)
352. CHG: Fixes for JavaScript API and Emscripten compilation (commit: 69bbd50) (details)
353. CHG: no error compiler flag still needed (commit: ac7755e) (details)
354. CHG: More JavaScript API fixes; compiler options to disable wasm (commit: 8c4ac40) (details)
355. CHG: Make sure optimization is use for JavaScript binaries, but that certain functions are not optimized out (commit: 93e6151) (details)
356. CHG: Emscripten does not like opt flag (commit: 455e885) (details)
357. BUG: Issue was missing quote, not flag (commit: 025c1f7) (details)
358. CHG: Added missing exported functions for JavaScript binaries (commit: d40778d) (details)
359. CHG: Adjusted tolerances (commit: 46ed7a1) (details)
360. CHG: Fixes for outputting transient class to JavaScript model (commit: 9a73fc2) (details)
361. BUG: gmsl was not the same as bslc. Now fixed. test2011 modified. (commit: 2fc48ba) (details)
362. CHG: Updated archives (commit: b9a0f5c) (details)
363. FIX: Bug in frequency love number output format when np>1; CHG: updated love core tests and archives (commit: c7e1e66) (details)
364. FIX: love core: recast some integers to doubletype to help some mac compilers (commit: c597ea0) (details)
365. FIX: Missing synched enum files for Love core update (commit: de53456) (details)
366. Update test2075.m (commit: 346cdbe) (details)
367. Update test2071.m (commit: 3bfeb3d) (details)
368. CHG: Adjusted tolerances (commit: 6b4611e) (details)
369. CHG: Fixes for love numbers and related tests under Python API (commit: 15cf622) (details)
370. BUG: Fixed parens (commit: 189738f) (details)
371. CHG: Do not assume that system/subprocess call will use bash as shell; cleanup (commit: 7fa8267) (details)
372. CHG: Translated test2085 from MATLAB -> Python (commit: de6aa4a) (details)
373. fix penta section normals and remove duplicate code (commit: 68a1198) (details)
374. fix indentation (commit: ba34a19) (details)
375. CHG: Adjusted tolerances; do not run test 2085 on Silicon (commit: adf71c2) (details)
376. CHG: Adjusted tolerances (commit: 6164a6e) (details)
377. remove unused indices in  Tria::NormalTop (commit: 2b35078) (details)
378. CHG: Updated path to gfortran (commit: b41fcb4) (details)
379. CHG: extract AD cost functions (commit: 58fe6ce) (details)
380. CHG: Modified all basic external package installation scripts to use developers' download links, where possible (commit: 957ed85) (details)
381. CHG: Check if LDFLAGS is set (commit: f275274) (details)
382. CHG: Updated all install scripts for external packages needed for extended capabilities (commit: 2f62628) (details)
383. CHG: Uploading Chaco source to repository as it does not download properly from Sandia's GitHub repo (commit: 8a018b9) (details)
384. CHG: Moved Adjoinable MPI source to repo because developer's Mercurial repo appears to be down (commit: 9270a30) (details)
385. CHG: More external package fixes (commit: b4d061b) (details)
386. CHG: Adjusted tolerances (commit: 419bba7) (details)
387. CHG: Need to ignore download script in directory to properly download datasets (commit: 648c7e7) (details)
388. CHG: Rolling back to HDF5 1.14.3 as newer versions do not properly compile on Intel-based Macs (known issue) (commit: 551c597) (details)
389. BUG: Expode hidden NumPy symbols in newer versions; cleanup (commit: 3438d0b) (details)
390. CHG: Adjusted tolerances (commit: c6abcf6) (details)
391. CHG: Fix bug in src/c/analyses/SmbAnalysis.cpp (commit: 45dcbbb) (details)
392. CHG: Update SmbSEMIC modules (commit: 7eed5a3) (details)
393. ADD: MATLAB - interpolate netcdf file with using xarray in python. (commit: 318919a) (details)
394. CHG: Resolve memory leakage in SEMIC. (commit: 0dda306) (details)
395. CHG: model.refine MATLAB -> Python; clean up (commit: 50c4f95) (details)
396. BUG: Bad indexing of bamgmesh out (commit: c6bade2) (details)
397. CHG: Catch unsupported draw function; clean up (commit: d641506) (details)
398. CHG: Adjusted tolerances (commit: 5d36a67) (details)
399. FIX: Output of Tidal love numbers in Love core (commit: 89066e2) (details)
400. CHG: do not assume hemisphere (commit: 73416d6) (details)
401. BUG: if minor version of python is greater than 9 the last digit was removed. Now fixed (commit: 36a100d) (details)
402. CHG: Fix SEMIC enables to run surface mass and energy balance with albedo scheme of Alex. Fix Documentation for SMBsemic with albedo scheme of Denby and ISBA. (commit: 06e43c8) (details)
403. ADD: flag `with_matlab` in CI with matlab (commit: 4088830) (details)
404. CHG: input.with_matlab -> input.interface (commit: bcd7f0e) (details)
405. ADD: ubuntu python test (commit: c45e791) (details)
406. ADD: install python-dev (commit: 5d792ba) (details)
407. ADD: python tests (commit: ab6f5c2) (details)
408. BUG: fix .yml (commit: 5f1f739) (details)
409. CHG: python path for CI (commit: b07f2ea) (details)
410. BUG: fix python path (commit: 307f8a0) (details)
411. CHG: get python path from python action (commit: 06adc93) (details)
412. CHG: use env (commit: 97a4ea5) (details)
413. Update ubuntu-python.yml (commit: 002f28d) (details)
414. CHG: output python path after setup (commit: a9da2df) (details)
415. change to v5 python action (commit: 0de8889) (details)
416. update python path (commit: 1f4c9cc) (details)
417. fix bug in python_version (commit: 939717a) (details)
418. CHG: wrong place holder for string (commit: 1428b1e) (details)
419. currentlt test with only python (commit: ca2f893) (details)
420. add libpython (commit: 219ebf2) (details)
421. update CI (commit: c7136a8) (details)
422. update CI (commit: df8e6a1) (details)
423. set python path (commit: 175c34a) (details)
424. update numpy path (commit: e6f88df) (details)
425. check the folder (commit: 5ef1549) (details)
426. add path to numpy (commit: ba7cb7d) (details)
427. add path to numpy (commit: b92e094) (details)
428. update numpy (commit: 3d580b5) (details)
429. add test numpy (commit: 52705c4) (details)
430. print more (commit: 138ee42) (details)
431. look into _core (commit: 062bd2a) (details)
432. add python to test (commit: 547646e) (details)
433. add netCDF4 (commit: 8536c41) (details)
434. add source ISSM (commit: c88d507) (details)
435. ADD: ubuntu python CI test (commit: 7f7ee10) (details)
436. Revert "add python CI" (commit: 101481c) (details)
437. Revert "Revert "add python CI"" (commit: dd63a1b) (details)
438. CHG: Eased tolerances (commit: 868cbe1) (details)
439. CHG: Moving certain external packages to new repo (commit: 672689d) (details)
440. ADD: `cutoff` option in flowlines.m (commit: 950c755) (details)
441. BUG: revert issmscpin to previous version (commit: 23b709c) (details)
442. CHG: adding dynamic function name (commit: dd8dc91) (details)
443. CHG: automatically remove checkpoint file once done to save disk space (commit: 3a24974) (details)
444. CHG: Cleanup; MATLAB -> Python; documentation (commit: 61ab59f) (details)
445. CHG: Merging Inwoo's fix for MATLAB + Python APIs with minor changes (commit: 6b9c9fc) (details)
446. BUG: should not capitalize Matlab and Python so that they can be picked up by modules (commit: 08c867c) (details)
447. BUG: Lowercasing JavaScript (commit: 90ee39e) (details)

Update README.md
 (commit: 5fad7e8)

Update README.md
 (commit: 804d9cb)

CHG: adding other way to download ISSM from GitHub
 (commit: cd0db55)

CHG: Updating paths to Python installation (now using venv)
 (commit: 48fafb4)

CHG: Adjusted tolerances
 (commit: a7642ec)

Delete README
 (commit: 9c87598)

CHG: upgrading to latest PETSc version
 (commit: 1954c7d)

BUG: Path to libgfortran
 (commit: ade0cdf)

CHG: Need libgcc in package
 (commit: 34edfea)

BUG: Path fixes
 (commit: 06014d2)

BUG: Not catching runme error; 'exclude_name' option no longer exists
 (commit: 7829943)

CHG: svn -> git; uncommitted cluster class; clean up of devpath from when we couldn't compile native Silicon MEX-files
 (commit: 86d56f4)

BUG: Incorrect file name
 (commit: 3f1d135)

CHG: Virtual environment not preserved in called script
 (commit: 6c6e3fc)

CHG: removing old scripts
 (commit: 77ece86)

CHG: moved up one directory and removed  from version check
 (commit: 3da6aa4)

CHG: adding more files to gitignore
 (commit: 71cf980)

CHG: Adjusted tolerances
 (commit: ab5622d)

CHG: Minor changes to test fixes to GitHub Webhook -> Jenkins
 (commit: 5f72777)

CHG: removing reference to cshrc, replacing by zshrc
 (commit: c96bbfd)

CHG: Adjusted tolerances
 (commit: 3aec6f3)

CHG: Removing Cmake to avoid conflicts with standalone copy
 (commit: 71a5854)

BUG: Removed 'command'
 (commit: 23e5006)

ADD: Missing empty Models/ dir
 (commit: d046084)

Update of .gitignore.
 (commit: bef7fd6)

Moved all CoDiPack specific functions to CoDiPackGlobal.h.
 (commit: c637383)

CHG: Add default location for libgfortran on Mac to rpath
 (commit: c21aea7)

CHG: adaptive time stepping needs vz in 3d
 (commit: cfdb310)

CHG: throw error message if FCT in 3d
 (commit: 6693f07)

CHG: Use git now to get changes and determine installation type
 (commit: 9417447)

CHG: minor, testing to see if jenkins will recompile
 (commit: d46094f)

CHG: forgot to change path to m/mesh/planet
 (commit: 48f2f11)

CHG: Additions to ignore list
 (commit: 292ee72)

Create codeql.yml

Adding code scanning for security vulnerabilities
 (commit: d31839f)

Bump the npm_and_yarn group across 1 directory with 2 updates

Bumps the npm_and_yarn group with 2 updates in the /jenkins/javascript/karma directory: [karma](https://github.com/karma-runner/karma) and [mathjs](https://github.com/josdejong/mathjs).


Updates `karma` from 0.13.22 to 6.4.3
- [Release notes](https://github.com/karma-runner/karma/releases)
- [Changelog](https://github.com/karma-runner/karma/blob/master/CHANGELOG.md)
- [Commits](https://github.com/karma-runner/karma/compare/v0.13.22...v6.4.3)

Updates `mathjs` from 3.20.2 to 13.0.0
- [Changelog](https://github.com/josdejong/mathjs/blob/develop/HISTORY.md)
- [Commits](https://github.com/josdejong/mathjs/compare/v3.20.2...v13.0.0)

---
updated-dependencies:
- dependency-name: karma
  dependency-type: direct:development
  dependency-group: npm_and_yarn
- dependency-name: mathjs
  dependency-type: direct:development
  dependency-group: npm_and_yarn
...

Signed-off-by: dependabot[bot] <support@github.com>
 (commit: 224629e)

CHG: Fixes for gfortran path in rpath; new config for CodeQL
 (commit: 49c111d)

Update codeql.yml
 (commit: 17a4dda)

Update codeql.yml
 (commit: 85e70df)

Update codeql.yml
 (commit: a522fbb)

Update codeql.yml
 (commit: a2d5637)

CHG: Disabling wrappers on CodeQL build
 (commit: f3154a6)

CHG: Correcting handling of git commit and changes when fetch has not been used
 (commit: 2e2e447)

Delete codeql.yml

Deleting for now until external packages can be offloaded to package managers.
 (commit: 2650861)

CHG: Adding whitespace and rerunning jobs
 (commit: c241279)

CHG: removing double blank lines
 (commit: 501faea)

CHG: Adjusted tolerances
 (commit: befbb36)

CHG: Updates to UB CCR config; changed path of gmshplanet.py
 (commit: b5969f1)

CHG: do not rotate matrices if no node is rotated (breaking a golden rule here: this change is NOT tested yet, sorry if I am breaking anything
 (commit: 746e2a0)

CoDiPack type can be defined during the configuration.
 (commit: 0c86d88)

BUG: Need to update previous commit every time we run
 (commit: 0939b23)

CHG: Outstanding commit and test fix to git change polling
 (commit: f94c8d5)

Extracted common computation from StressbalanceAnalysis.cpp.
 (commit: 1c23b49)

Added Preaccumulation helper for sparse row assembly.
 (commit: a28008d)

BUG: Fix for rpath anb libgfortran on Mac; no effect, but make sure MSYS2 is set correctly
 (commit: f3be32b)

CHG: vertical speed needs md.basalforcings.perturbation_melting_rate
 (commit: 004acae)

CHG: vertical speed needs md.basalforcings.perturbation_melting_rate
 (commit: d4ab726)

CHG: missing -fPIC install-linux.sh
 (commit: ef4f38b)

CHG: macOS now only provides python3 and not python, and header files are now in the Headers directory
 (commit: acf9490)

CHG: removing SLEPSC and ADIC2 that we have never used
 (commit: eb56793)

CHG: adding common factor to KMatrices StressBalance
 (commit: d79f20f)

CHG: do not extrude lat/lon if undefined
 (commit: 542dd67)

CHG: refine should deal with lat/long as well
 (commit: 1c44f94)

BUG: output is md2 and not md
 (commit: 624b32e)

CHG: if no observations are provided, we can still use md.initialization.vx/vy to set new spc's
 (commit: ebfeed6)

CHG: New cluster class for submitting jobs to UB CCR; typos
 (commit: d5ffcb6)

CHG: adding factors to analysis
 (commit: 5221b49)

CHG: added Data directory for examples
 (commit: 3b21465)

CHG: adding factors in analysis
 (commit: 5a7f851)

CHG: added factors in analysis
 (commit: e049dfc)

CHG: fixed problem with Glads
 (commit: 06ba999)

BUG: MPI_Wait should wait for the cpu that is receiving for once, which created seg faults with AD
 (commit: 79e0383)

CHG: renaming Viscous Budd
 (commit: 58ec93e)

CHG: Adjusted tolerances
 (commit: 3d3884b)

CHG: multithreading ContourToNodes
 (commit: a5cce0e)

BUG: mexPrintf is NOT thread safe and crashes. Replace by printf
 (commit: 7031ace)

CHG: Temporary fix for not being able to connect via port 22
 (commit: 7930043)

CHG: Need P instead of p option
 (commit: 1ae9f62)

CHG: added PROJ_LIB env variable to make sure proj.db is found. There are sometimes conflicts with MATLAB's libraries which must be taken care of
 (commit: ab72887)

CHG: minor changed ISSM description
 (commit: e79d8fc)

CHG: ITS_LIVE annual velocity updated to v02, data avaliable from 1985 to 2022. The .nc files are in netCDF4 format, to load in Matlab, we need to use `h5read`
 (commit: 07d41ed)

ADD: interpolate from MEaSUREs monthly averaged velocity Mosaic (2014-2023) : https://doi.org/10.5067/EGKZX6FXXM4P
 (commit: 96f163d)

CHG: use mapping toolbox map if Googlemaps is not available
 (commit: 877f97d)

CHG: fixed zoom level option
 (commit: f13265c)

CHG: adjusted tolerances
 (commit: 67ecf56)

CHG: added interactive to disp:
 (commit: 82f74cc)

Added time and memory output for CoDiPack.
 (commit: dee0d08)

Make preaccumulation configurable.
 (commit: 0053772)

Create c-cpp.yml
 (commit: de8cfa1)

Update c-cpp.yml
 (commit: 6ea1be6)

CHG: changed checks on flags
 (commit: 75710aa)

CHG: need to initialize as 0
 (commit: 206ded5)

Update c-cpp.yml
 (commit: 5f63850)

Update c-cpp.yml
 (commit: c26805a)

Update c-cpp.yml
 (commit: c4d8675)

Update c-cpp.yml
 (commit: 1b9716a)

Update c-cpp.yml, add matlab
 (commit: b0584a0)

Update c-cpp.yml
 (commit: 3de0de9)

Update c-cpp.yml
 (commit: 97b7d9f)

Create github_linux_basic
 (commit: 917aa3b)

Update c-cpp.yml
 (commit: 7e7cb29)

Update c-cpp.yml
 (commit: a09e38a)

change the directory for CI files
 (commit: ed557da)

Update README.md
 (commit: 6f97503)

Update README.md
 (commit: 7ee2aa6)

create badge for CI, add it to README
 (commit: 5b19ff4)

CHG: minor
 (commit: 3155d83)

BUG: forgot to close parenthesis
 (commit: 99e58f8)

CHG: upgrading PETSc in order to find latest ZLIB
 (commit: 0a5d4f8)

FIX: calculation of VAF based on mask in Tria.cpp
 (commit: c76bcad)

CHG: trying to simplify CI
 (commit: 345ce88)

CHG: trying to simplify CI
 (commit: 8ca30ea)

CHG: getting PETSc from apt-get
 (commit: 7653d0b)

CHG: PETSc needs to be installed manually, but we can skip autotools and cmake
 (commit: 0a7c0f0)

BUG: fixing CI problem
 (commit: a762b38)

CHG: trying to fix CI
 (commit: b4cb2c6)

CHG: trying to fix CI
 (commit: 8b5f7e9)

CHG: trying to fix CI
 (commit: 07c5512)

CHG: trying to fix CI
 (commit: 34f659f)

Update README.md

Added commit notes (and testing fixes for Jenkins workflow)
 (commit: 1ad8f26)

NEW: added option 'quitonerror' for GitHub's CI
 (commit: cadec61)

CHG: fixing matlab tests in GitHub CI
 (commit: e29269a)

CHG: trying to fix CI with MATLAB
 (commit: c02ba76)

CHG: trying to debug CI
 (commit: dbb040a)

CHG: trying to add MATLAB tests
 (commit: 9e03058)

CHG: fixing MATLAB
 (commit: 47fec1e)

load matlab action manually

as suggested https://github.com/matlab-actions/run-command/issues/53
 (commit: 979bccd)

FIX: updated archive 540
 (commit: 2a46a3e)

CHG: checking env
 (commit: d0b793d)

CHG: checking env
 (commit: 38a30bf)

CHG: checking env
 (commit: cec57fd)

CHG: checking env
 (commit: af5690c)

CHG: checking env
 (commit: a9938ed)

CHG: checking env
 (commit: 9208d86)

set environment before running matlab
 (commit: 4a1a946)

Update c-cpp.yml
 (commit: 32b049b)

Update c-cpp.yml
 (commit: 71c965d)

Update c-cpp.yml
 (commit: d6b4c45)

Update c-cpp.yml
 (commit: f32cecc)

CHG: fixed typo
 (commit: fa5e47b)

NEW: added a function that reads a geotiff and outputs x,y,data
 (commit: d3a11cb)

CHG: better check on METIS header
 (commit: aab5168)

CHG: removing PETSc from installation
 (commit: 2788cec)

CHG: install openMPI
 (commit: 0b37126)

CHG: figuring out open MPI
 (commit: 8b91009)

CHG: mpi-include does not need -I
 (commit: b55430e)

CHG: scalapack is installed as part of open MPI
 (commit: 6f937e4)

CHG: do not assume that ParMETIS is installed if MUMPS is provided
 (commit: 0f97bbc)

CHG: do not preload petsc files if petsc is not installed
 (commit: 2f07102)

CHG: reverting to installing PETSc
 (commit: 9640ebb)

CHG: simplifying workflow and scripts
 (commit: 0319b46)

CHG: change name
 (commit: 482d3f8)

CHG: removing MPICH from PETSc to speed up CI
 (commit: 6d818da)

CHG: adding more libs to mpi
 (commit: e69a782)

CHG: forgot to change LD_PRELOAD
 (commit: b00c721)

CHG: adding flag to mpiexec to avoid openmpi error message about 'There are not enough slots available'
 (commit: 3cb916c)

CHG: do not make MeshPartition a template
 (commit: 7f7505c)

CHG: added example
 (commit: 60d676d)

BUG: do not initialize codi_global if autodiff is false
 (commit: 6aa5da9)

CHG: Added packages to UB CCR installation; do not compile MeshPartition if METIS is not available
 (commit: d1e52e2)

try to set two steps for the CI
 (commit: 5975640)

try to add cache
 (commit: 50190d3)

try to set the path for cache
 (commit: 15a348d)

try again with env variable
 (commit: 1b19f0b)

update download path in artifact
 (commit: 0848c3f)

try to also cache matlab
 (commit: 9b235c5)

change mpi back to petsc version
 (commit: 2e7ff85)

no need to cache matlab
 (commit: d6fe336)

cache matlab
 (commit: 80b3c04)

try the uncompress path again
 (commit: dfc6574)

download to /root
 (commit: 81b8b98)

try to use relative path
 (commit: e864a3b)

add relative path
 (commit: ff1f207)

change relative path again
 (commit: e113efe)

typo fixed
 (commit: 995b94a)

update working dir
 (commit: 84a03dd)

activate compile
 (commit: 8c98e69)

put test back
 (commit: e339299)

remove apt-get installed mpi
 (commit: eaae0d7)

try to create a matrix of test
 (commit: efc7cc7)

try matrix with string variables
 (commit: e91fd41)

add codipack in CI
 (commit: 182c715)

try to fix codipack configure
 (commit: 837a322)

add gsl
 (commit: c71caeb)

seperate basic and codipack
 (commit: 7594905)

Update common-workflow.yml
 (commit: 083c437)

only include ad tests for ccdipack
 (commit: 25b6dfc)

fix bug in main-ci
 (commit: 6e84779)

set different names for different runs
 (commit: b0269ef)

add type of input.os
 (commit: e0b1eed)

try to cache src/c
 (commit: 565963c)

fix error in the test job
 (commit: 0206504)

remove cache src/c
 (commit: feaeafc)

try petsc-3.20 for ad
 (commit: b377c3a)