Changes

Summary

1. CHG: multithreading ContourToNodes (commit: 1e79391) (details)
2. BUG: mexPrintf is NOT thread safe and crashes. Replace by printf (commit: 9474be9) (details)
3. CHG: Temporary fix for not being able to connect via port 22 (commit: a83fea6) (details)
4. CHG: Need P instead of p option (commit: cf35b4b) (details)
5. 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: a75b963) (details)
6. CHG: minor changed ISSM description (commit: bdd72f6) (details)
7. 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: 43146cb) (details)
8. ADD: interpolate from MEaSUREs monthly averaged velocity Mosaic (2014-2023) : https://doi.org/10.5067/EGKZX6FXXM4P (commit: dbcc688) (details)
9. CHG: use mapping toolbox map if Googlemaps is not available (commit: d980ed3) (details)
10. CHG: fixed zoom level option (commit: 83cdc8c) (details)
11. CHG: adjusted tolerances (commit: 86dd813) (details)
12. CHG: added interactive to disp: (commit: 23bf349) (details)
13. Added time and memory output for CoDiPack. (commit: 31dab70) (details)
14. Make preaccumulation configurable. (commit: b741196) (details)
15. Create c-cpp.yml (commit: 8d1129b) (details)
16. Update c-cpp.yml (commit: 57e71e6) (details)
17. CHG: changed checks on flags (commit: 8a0fac6) (details)
18. CHG: need to initialize as 0 (commit: 1c719e0) (details)
19. Update c-cpp.yml (commit: c6b61c1) (details)
20. Update c-cpp.yml (commit: 533d30c) (details)
21. Update c-cpp.yml (commit: 5a3ec47) (details)
22. Update c-cpp.yml (commit: 571d041) (details)
23. Update c-cpp.yml, add matlab (commit: 2f464c6) (details)
24. Update c-cpp.yml (commit: b78ae06) (details)
25. Update c-cpp.yml (commit: df8b3b6) (details)
26. Create github_linux_basic (commit: 5b34d72) (details)
27. Update c-cpp.yml (commit: d3045ed) (details)
28. Update c-cpp.yml (commit: 42c18ea) (details)
29. change the directory for CI files (commit: 13f902e) (details)
30. Update README.md (commit: cc2ad67) (details)
31. Update README.md (commit: a1131fe) (details)
32. create badge for CI, add it to README (commit: 684ad98) (details)
33. CHG: minor (commit: 9092bf4) (details)
34. BUG: forgot to close parenthesis (commit: 2e01ed8) (details)
35. CHG: upgrading PETSc in order to find latest ZLIB (commit: b3dbeeb) (details)
36. FIX: calculation of VAF based on mask in Tria.cpp (commit: 1f9cd7f) (details)
37. CHG: trying to simplify CI (commit: f1e8d22) (details)
38. CHG: trying to simplify CI (commit: db0c094) (details)
39. CHG: getting PETSc from apt-get (commit: 4fbda8b) (details)
40. CHG: PETSc needs to be installed manually, but we can skip autotools and cmake (commit: 5059e9c) (details)
41. BUG: fixing CI problem (commit: 8350f08) (details)
42. CHG: trying to fix CI (commit: 65c0f6e) (details)
43. CHG: trying to fix CI (commit: 2ed9f19) (details)
44. CHG: trying to fix CI (commit: b6cd13d) (details)
45. CHG: trying to fix CI (commit: 2e0f8b8) (details)
46. Update README.md (commit: 9661eba) (details)
47. NEW: added option 'quitonerror' for GitHub's CI (commit: cc5f201) (details)
48. CHG: fixing matlab tests in GitHub CI (commit: 246bda2) (details)
49. CHG: trying to fix CI with MATLAB (commit: 7f9ba8b) (details)
50. CHG: trying to debug CI (commit: c4ee45e) (details)
51. CHG: trying to add MATLAB tests (commit: 031c116) (details)
52. CHG: fixing MATLAB (commit: a979171) (details)
53. load matlab action manually (commit: 0bc0f3c) (details)
54. FIX: updated archive 540 (commit: 2ba99c0) (details)
55. CHG: checking env (commit: 2538728) (details)
56. CHG: checking env (commit: a359b8b) (details)
57. CHG: checking env (commit: f597fb4) (details)
58. CHG: checking env (commit: ce37a17) (details)
59. CHG: checking env (commit: d5f69f3) (details)
60. CHG: checking env (commit: d2964e7) (details)
61. set environment before running matlab (commit: 76e3036) (details)
62. Update c-cpp.yml (commit: e30c029) (details)
63. Update c-cpp.yml (commit: 7b61081) (details)
64. Update c-cpp.yml (commit: 168094e) (details)
65. Update c-cpp.yml (commit: 21920c7) (details)
66. CHG: fixed typo (commit: 70b01e1) (details)
67. NEW: added a function that reads a geotiff and outputs x,y,data (commit: d78e873) (details)
68. CHG: better check on METIS header (commit: 05cd86f) (details)
69. CHG: removing PETSc from installation (commit: 8eceb90) (details)
70. CHG: install openMPI (commit: df04386) (details)
71. CHG: figuring out open MPI (commit: f6e9ef8) (details)
72. CHG: mpi-include does not need -I (commit: 44a9842) (details)
73. CHG: scalapack is installed as part of open MPI (commit: dc05929) (details)
74. CHG: do not assume that ParMETIS is installed if MUMPS is provided (commit: a31e6d3) (details)
75. CHG: do not preload petsc files if petsc is not installed (commit: 0a97081) (details)
76. CHG: reverting to installing PETSc (commit: d0fde5f) (details)
77. CHG: simplifying workflow and scripts (commit: 382596b) (details)
78. CHG: change name (commit: 54b070a) (details)
79. CHG: removing MPICH from PETSc to speed up CI (commit: 2f9390b) (details)
80. CHG: adding more libs to mpi (commit: 15d7142) (details)
81. CHG: forgot to change LD_PRELOAD (commit: 7c3cac2) (details)
82. CHG: adding flag to mpiexec to avoid openmpi error message about 'There are not enough slots available' (commit: 48737e1) (details)
83. CHG: do not make MeshPartition a template (commit: 6bfebab) (details)
84. CHG: added example (commit: c8b520e) (details)
85. BUG: do not initialize codi_global if autodiff is false (commit: 4dc2ae2) (details)
86. CHG: Added packages to UB CCR installation; do not compile MeshPartition if METIS is not available (commit: 787af96) (details)
87. try to set two steps for the CI (commit: f400850) (details)
88. try to add cache (commit: ad75a7b) (details)
89. try to set the path for cache (commit: 6ed91f0) (details)
90. try again with env variable (commit: 750c718) (details)
91. update download path in artifact (commit: 13af998) (details)
92. try to also cache matlab (commit: 5de8374) (details)
93. change mpi back to petsc version (commit: 4e142f4) (details)
94. no need to cache matlab (commit: 239ff87) (details)
95. cache matlab (commit: f6f2916) (details)
96. try the uncompress path again (commit: a175878) (details)
97. download to /root (commit: 03b51c1) (details)
98. try to use relative path (commit: 8f3ee6d) (details)
99. add relative path (commit: fa1031b) (details)
100. change relative path again (commit: 91d425f) (details)
101. typo fixed (commit: 1fe7196) (details)
102. update working dir (commit: 1be644a) (details)
103. activate compile (commit: 64d3590) (details)
104. put test back (commit: 8cd2297) (details)
105. remove apt-get installed mpi (commit: 45287e7) (details)
106. try to create a matrix of test (commit: 7baf86f) (details)
107. try matrix with string variables (commit: 6fc2d49) (details)
108. add codipack in CI (commit: 909790b) (details)
109. try to fix codipack configure (commit: 093a11e) (details)
110. add gsl (commit: 884b5f0) (details)
111. seperate basic and codipack (commit: 7283804) (details)
112. Update common-workflow.yml (commit: 0ce30b9) (details)
113. only include ad tests for ccdipack (commit: 92c4d5e) (details)
114. fix bug in main-ci (commit: e2e12b5) (details)
115. set different names for different runs (commit: 0bde952) (details)
116. add type of input.os (commit: bb088f1) (details)
117. try to cache src/c (commit: 1df6ca5) (details)
118. fix error in the test job (commit: 63ba042) (details)
119. remove cache src/c (commit: e253f84) (details)
120. try petsc-3.20 for ad (commit: 69212ab) (details)
121. try to use env to set the id of cache (commit: b7973ce) (details)
122. try github.env (commit: 1e05474) (details)
123. try to fix bugs when using inputs in cache id (commit: 18ac845) (details)
124. fix bug in the if condition (commit: 1f4a9f4) (details)
125. fix codipack (commit: fae90a5) (details)
126. try ad again (commit: 66e4f82) (details)
127. CHG: added error message instead of just bypassing (commit: 1aa4555) (details)
128. CHG: for macOS we now also need to add  -commons use_dylibs (commit: eddbc51) (details)
129. BUG: need to provide specific LD_FLAGS and tweak setCompiler.py to make it work on Sonoma (commit: 2364937) (details)
130. CHG: cleanup (commit: 14d761f) (details)
131. remove with-petsc in codipack (commit: b35a114) (details)
132. reduce matrix size for tests (commit: 4671a46) (details)
133. check spaces (commit: 5ccd274) (details)
134. turn off codipack tests (commit: 3f44b86) (details)
135. do not compress petsc/src/ to decrease the size of the artifact (commit: 38f993e) (details)
136. try to exclude petsc/src (commit: 29dbe16) (details)
137. add gsl to codipack version (commit: 8bb700f) (details)
138. CHG: calving rate in CalvingMIP use normal vector from the levelset (commit: 8b089ab) (details)
139. Update README.md (commit: 81ee094) (details)
140. Update README.md (commit: d3c04a9) (details)
141. Update action badge in README.md (commit: ba30c85) (details)
142. CHG: default md.levelset.reinit_frequency=10. Add more description to stabilization (commit: b5d77dd) (details)
143. CHG: make two CIs separately for Ubuntu basic and codipack (commit: 2b5a6ff) (details)
144. CHG: Update test540, due to update default reinit_frequency (commit: 3e9e691) (details)
145. change the way to reuse workflow (commit: 1e8a29b) (details)
146. hard code the version of configure ISSM for now (commit: 80151a8) (details)
147. BUG: fix CalvingCalvingMIP in Penta (commit: b2de648) (details)
148. fix bugs in action.yml (commit: 830d14b) (details)
149. separate prepare externalpackes and build (commit: d8e2dd1) (details)
150. test ISSM_DIR (commit: fa789b6) (details)
151. Update action.yml (commit: 5aa39ba) (details)
152. fix ISSM_DIR issue (commit: 8bd8575) (details)
153. rerun CI, make input name shorter (commit: ca8a4ee) (details)
154. fix bug in action.yml (commit: 73c3538) (details)
155. CHG: update Archive540 (commit: 8c4f19d) (details)
156. rerun full CI (commit: 886c972) (details)
157. fix bug in uploading artifact (commit: c64a63f) (details)
158. BUG: fix CalvingCalvingMIP (commit: d8bbe33) (details)
159. BUG: recompile ISSM, update test540 Archive (commit: bdff019) (details)
160. CHG: update Archive affected by levelset.reinit_frequency=10 (commit: 96b1b80) (details)
161. add badges for Ubuntu Basic and CodiPack (commit: a79de1e) (details)
162. CHG: MATLAB -> Python and Javascript (commit: 6a2b0e0) (details)
163. CHG: taking care of paths with white spaces (commit: b801141) (details)
164. CHG: relaxed tolerances for test 541 (commit: 74b8289) (details)
165. CHG: Cleanup (commit: 5495d62) (details)
166. CHG: update to GEMB merge layers to parallel matlab version updates (commit: e068d33) (details)
167. CHG: update GEMB tols for latest commit (commit: 1b6b531) (details)
168. CHG: update remaining tols in windows and on git for GEMB (commit: a727659) (details)
169. CHG: Cleanup of configuration options (commit: 2561795) (details)
170. BUG: Needed closing ;; (commit: bdf2ded) (details)
171. CHG: Removing support for Android (commit: 0db7fc2) (details)
172. CHG: Synchronized enums after pull and merge (commit: 8d404e5) (details)
173. BUG: Cleaned up configs (commit: 9655481) (details)
174. BUG: Correcting env var substitution (commit: 3148eb2) (details)
175. CHG: Cleanup (commit: 36c824f) (details)
176. CHG: Cleanup (commit: fd4f45b) (details)
177. CHG: Moving standard env vars to issm_options for MSYS2 builds (commit: 4977f2a) (details)
178. CHG: Cleanup; missing env var for Javascript build (commit: 53ee210) (details)
179. BUG: Fix for MSYS2 build (commit: 3a68cbf) (details)

CHG: multithreading ContourToNodes
 (commit: 1e79391)

BUG: mexPrintf is NOT thread safe and crashes. Replace by printf
 (commit: 9474be9)

CHG: Temporary fix for not being able to connect via port 22
 (commit: a83fea6)

CHG: Need P instead of p option
 (commit: cf35b4b)

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: a75b963)

CHG: minor changed ISSM description
 (commit: bdd72f6)

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: 43146cb)

ADD: interpolate from MEaSUREs monthly averaged velocity Mosaic (2014-2023) : https://doi.org/10.5067/EGKZX6FXXM4P
 (commit: dbcc688)

CHG: use mapping toolbox map if Googlemaps is not available
 (commit: d980ed3)

CHG: fixed zoom level option
 (commit: 83cdc8c)

CHG: adjusted tolerances
 (commit: 86dd813)

CHG: added interactive to disp:
 (commit: 23bf349)

Added time and memory output for CoDiPack.
 (commit: 31dab70)

Make preaccumulation configurable.
 (commit: b741196)

Create c-cpp.yml
 (commit: 8d1129b)

Update c-cpp.yml
 (commit: 57e71e6)

CHG: changed checks on flags
 (commit: 8a0fac6)

CHG: need to initialize as 0
 (commit: 1c719e0)

Update c-cpp.yml
 (commit: c6b61c1)

Update c-cpp.yml
 (commit: 533d30c)

Update c-cpp.yml
 (commit: 5a3ec47)

Update c-cpp.yml
 (commit: 571d041)

Update c-cpp.yml, add matlab
 (commit: 2f464c6)

Update c-cpp.yml
 (commit: b78ae06)

Update c-cpp.yml
 (commit: df8b3b6)

Create github_linux_basic
 (commit: 5b34d72)

Update c-cpp.yml
 (commit: d3045ed)

Update c-cpp.yml
 (commit: 42c18ea)

change the directory for CI files
 (commit: 13f902e)

Update README.md
 (commit: cc2ad67)

Update README.md
 (commit: a1131fe)

create badge for CI, add it to README
 (commit: 684ad98)

CHG: minor
 (commit: 9092bf4)

BUG: forgot to close parenthesis
 (commit: 2e01ed8)

CHG: upgrading PETSc in order to find latest ZLIB
 (commit: b3dbeeb)

FIX: calculation of VAF based on mask in Tria.cpp
 (commit: 1f9cd7f)

CHG: trying to simplify CI
 (commit: f1e8d22)

CHG: trying to simplify CI
 (commit: db0c094)

CHG: getting PETSc from apt-get
 (commit: 4fbda8b)

CHG: PETSc needs to be installed manually, but we can skip autotools and cmake
 (commit: 5059e9c)

BUG: fixing CI problem
 (commit: 8350f08)

CHG: trying to fix CI
 (commit: 65c0f6e)

CHG: trying to fix CI
 (commit: 2ed9f19)

CHG: trying to fix CI
 (commit: b6cd13d)

CHG: trying to fix CI
 (commit: 2e0f8b8)

Update README.md

Added commit notes (and testing fixes for Jenkins workflow)
 (commit: 9661eba)

NEW: added option 'quitonerror' for GitHub's CI
 (commit: cc5f201)

CHG: fixing matlab tests in GitHub CI
 (commit: 246bda2)

CHG: trying to fix CI with MATLAB
 (commit: 7f9ba8b)

CHG: trying to debug CI
 (commit: c4ee45e)

CHG: trying to add MATLAB tests
 (commit: 031c116)

CHG: fixing MATLAB
 (commit: a979171)

load matlab action manually

as suggested https://github.com/matlab-actions/run-command/issues/53
 (commit: 0bc0f3c)

FIX: updated archive 540
 (commit: 2ba99c0)

CHG: checking env
 (commit: 2538728)

CHG: checking env
 (commit: a359b8b)

CHG: checking env
 (commit: f597fb4)

CHG: checking env
 (commit: ce37a17)

CHG: checking env
 (commit: d5f69f3)

CHG: checking env
 (commit: d2964e7)

set environment before running matlab
 (commit: 76e3036)

Update c-cpp.yml
 (commit: e30c029)

Update c-cpp.yml
 (commit: 7b61081)

Update c-cpp.yml
 (commit: 168094e)

Update c-cpp.yml
 (commit: 21920c7)

CHG: fixed typo
 (commit: 70b01e1)

NEW: added a function that reads a geotiff and outputs x,y,data
 (commit: d78e873)

CHG: better check on METIS header
 (commit: 05cd86f)

CHG: removing PETSc from installation
 (commit: 8eceb90)

CHG: install openMPI
 (commit: df04386)

CHG: figuring out open MPI
 (commit: f6e9ef8)

CHG: mpi-include does not need -I
 (commit: 44a9842)

CHG: scalapack is installed as part of open MPI
 (commit: dc05929)

CHG: do not assume that ParMETIS is installed if MUMPS is provided
 (commit: a31e6d3)

CHG: do not preload petsc files if petsc is not installed
 (commit: 0a97081)

CHG: reverting to installing PETSc
 (commit: d0fde5f)

CHG: simplifying workflow and scripts
 (commit: 382596b)

CHG: change name
 (commit: 54b070a)

CHG: removing MPICH from PETSc to speed up CI
 (commit: 2f9390b)

CHG: adding more libs to mpi
 (commit: 15d7142)

CHG: forgot to change LD_PRELOAD
 (commit: 7c3cac2)

CHG: adding flag to mpiexec to avoid openmpi error message about 'There are not enough slots available'
 (commit: 48737e1)

CHG: do not make MeshPartition a template
 (commit: 6bfebab)

CHG: added example
 (commit: c8b520e)

BUG: do not initialize codi_global if autodiff is false
 (commit: 4dc2ae2)

CHG: Added packages to UB CCR installation; do not compile MeshPartition if METIS is not available
 (commit: 787af96)

try to set two steps for the CI
 (commit: f400850)

try to add cache
 (commit: ad75a7b)

try to set the path for cache
 (commit: 6ed91f0)

try again with env variable
 (commit: 750c718)

update download path in artifact
 (commit: 13af998)

try to also cache matlab
 (commit: 5de8374)

change mpi back to petsc version
 (commit: 4e142f4)

no need to cache matlab
 (commit: 239ff87)

cache matlab
 (commit: f6f2916)

try the uncompress path again
 (commit: a175878)

download to /root
 (commit: 03b51c1)

try to use relative path
 (commit: 8f3ee6d)

add relative path
 (commit: fa1031b)

change relative path again
 (commit: 91d425f)

typo fixed
 (commit: 1fe7196)

update working dir
 (commit: 1be644a)

activate compile
 (commit: 64d3590)

put test back
 (commit: 8cd2297)

remove apt-get installed mpi
 (commit: 45287e7)

try to create a matrix of test
 (commit: 7baf86f)

try matrix with string variables
 (commit: 6fc2d49)

add codipack in CI
 (commit: 909790b)

try to fix codipack configure
 (commit: 093a11e)

add gsl
 (commit: 884b5f0)

seperate basic and codipack
 (commit: 7283804)

Update common-workflow.yml
 (commit: 0ce30b9)

only include ad tests for ccdipack
 (commit: 92c4d5e)

fix bug in main-ci
 (commit: e2e12b5)

set different names for different runs
 (commit: 0bde952)

add type of input.os
 (commit: bb088f1)

try to cache src/c
 (commit: 1df6ca5)

fix error in the test job
 (commit: 63ba042)

remove cache src/c
 (commit: e253f84)

try petsc-3.20 for ad
 (commit: 69212ab)

try to use env to set the id of cache
 (commit: b7973ce)

try github.env
 (commit: 1e05474)

try to fix bugs when using inputs in cache id
 (commit: 18ac845)

fix bug in the if condition
 (commit: 1f4a9f4)

fix codipack
 (commit: fae90a5)

try ad again
 (commit: 66e4f82)

CHG: added error message instead of just bypassing
 (commit: 1aa4555)

CHG: for macOS we now also need to add  -commons use_dylibs
 (commit: eddbc51)

BUG: need to provide specific LD_FLAGS and tweak setCompiler.py to make it work on Sonoma
 (commit: 2364937)

CHG: cleanup
 (commit: 14d761f)

remove with-petsc in codipack
 (commit: b35a114)

reduce matrix size for tests
 (commit: 4671a46)

check spaces
 (commit: 5ccd274)

turn off codipack tests
 (commit: 3f44b86)

do not compress petsc/src/ to decrease the size of the artifact
 (commit: 38f993e)

try to exclude petsc/src
 (commit: 29dbe16)

add gsl to codipack version
 (commit: 8bb700f)

CHG: calving rate in CalvingMIP use normal vector from the levelset
 (commit: 8b089ab)

Update README.md

Testing Jenkins status badge
 (commit: 81ee094)

Update README.md
 (commit: d3c04a9)

Update action badge in README.md
 (commit: ba30c85)

CHG: default md.levelset.reinit_frequency=10. Add more description to stabilization
 (commit: b5d77dd)

CHG: make two CIs separately for Ubuntu basic and codipack
 (commit: 2b5a6ff)

CHG: Update test540, due to update default reinit_frequency
 (commit: 3e9e691)

change the way to reuse workflow
 (commit: 1e8a29b)

hard code the version of configure ISSM for now
 (commit: 80151a8)

BUG: fix CalvingCalvingMIP in Penta
 (commit: b2de648)

fix bugs in action.yml
 (commit: 830d14b)

separate prepare externalpackes and build
 (commit: d8e2dd1)

test ISSM_DIR
 (commit: fa789b6)

Update action.yml
 (commit: 5aa39ba)

fix ISSM_DIR issue
 (commit: 8bd8575)

rerun CI, make input name shorter
 (commit: ca8a4ee)

fix bug in action.yml
 (commit: 73c3538)

CHG: update Archive540
 (commit: 8c4f19d)

rerun full CI
 (commit: 886c972)

fix bug in uploading artifact
 (commit: c64a63f)

BUG: fix CalvingCalvingMIP
 (commit: d8bbe33)

BUG: recompile ISSM, update test540 Archive
 (commit: bdff019)

CHG: update Archive affected by levelset.reinit_frequency=10
 (commit: 96b1b80)

add badges for Ubuntu Basic and CodiPack
 (commit: a79de1e)

CHG: MATLAB -> Python and Javascript
 (commit: 6a2b0e0)

CHG: taking care of paths with white spaces
 (commit: b801141)

CHG: relaxed tolerances for test 541
 (commit: 74b8289)

CHG: Cleanup
 (commit: 5495d62)

CHG: update to GEMB merge layers to parallel matlab version updates
 (commit: e068d33)

CHG: update GEMB tols for latest commit
 (commit: 1b6b531)

CHG: update remaining tols in windows and on git for GEMB
 (commit: a727659)

CHG: Cleanup of configuration options
 (commit: 2561795)

BUG: Needed closing ;;
 (commit: bdf2ded)

CHG: Removing support for Android
 (commit: 0db7fc2)

CHG: Synchronized enums after pull and merge
 (commit: 8d404e5)

BUG: Cleaned up configs
 (commit: 9655481)

BUG: Correcting env var substitution
 (commit: 3148eb2)

CHG: Cleanup
 (commit: 36c824f)

CHG: Cleanup
 (commit: fd4f45b)

CHG: Moving standard env vars to issm_options for MSYS2 builds
 (commit: 4977f2a)

CHG: Cleanup; missing env var for Javascript build
 (commit: 53ee210)

BUG: Fix for MSYS2 build
 (commit: 3a68cbf)