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Author SHA1 Message Date
Max Lübke
d5744191a1 feat: Add PinnableMemory class for allocating pinned memory 
refactor: Field class now relies on Pinnable memory
 2024-05-07 09:59:20 +00:00
Max Lübke
3da5b8eb20 feat: Add PinnableMemory class for allocating pinned memory 
This commit adds a new class called PinnableMemory, which is used to allocate memory that can be pinned for RDMA access. The PinnableMemory class provides methods to access and modify the allocated memory, as well as convert it to a span for easy iteration.

The PinnableMemory class is implemented in the PinnableMemory.hpp file, and a test case is added in the testPinnableMemory.cpp file to verify its functionality.
 2024-05-07 09:59:20 +00:00
Max Lübke
e79881d9c5 chore: Update subproject commit in ext/iphreeqc 2024-05-07 09:52:31 +00:00
Max Lübke
44775ea018 fix: Correct logic for updating output values in WorkerRunWorkPackage 2024-05-07 08:34:18 +00:00
Max Lübke
4da95e385b Merge branch 'ml/build' into 'main' 
Update CMakeLists.txt to conditionally add the bench subdirectory based on the...

See merge request naaice/poet!29
 2024-05-06 13:27:27 +02:00
Max Lübke
d399ca8190 Update CMakeLists.txt to conditionally add the bench subdirectory based on the POET_PREPROCESS_BENCHS option 2024-05-06 11:26:13 +00:00
Max Lübke
22458b41f4 Merge branch 'ml/ci' into 'main' 
Refactor CI/CD pipeline

See merge request naaice/poet!28
 2024-05-06 13:17:40 +02:00
Max Lübke
aec3d8f63a Refactor CI/CD pipeline 2024-05-06 13:17:39 +02:00
Max Lübke
74bafca4b8 Merge branch 'ml/surfex' into 'main' 
Enable Surfex/Exchange reactants using IPhreeqc/POET API

See merge request naaice/poet!27
 2024-05-06 12:11:50 +02:00
Max Lübke
2e265443b9 Update Readme 2024-05-06 10:09:28 +00:00
Max Lübke
20a0c453b0 Add EGU debug model 2024-05-06 10:09:28 +00:00
Max Lübke
480dd146f4 BREAKING CHANGE: Enable Surface/Exchange using new API of PhreeqcEngine 2024-05-06 10:01:57 +00:00
Max Luebke
d7c23c6b3c Fix build process to only produce benchmarks when needed 2024-04-15 09:10:11 +00:00
Max Lübke
e11caba0b3 Fix grid size assignment in GridInit.cpp 2024-04-12 12:35:43 +00:00
Max Lübke
6d36dd7a2e Refactor R_lib/kin_r_library.R to use setup$maxiter instead of iter for calculating max digits 2024-04-10 10:24:00 +00:00
Max Lübke
7ee438b667 Remove doctest submodule 2024-04-10 10:24:00 +00:00
Max Lübke
f4661a591c Fix diffusion and chem field update order in RunMasterLoop 2024-04-10 10:24:00 +00:00
Max Lübke
103b26a097 Refactor process to output as DataFrames 2024-04-10 10:24:00 +00:00
Max Lübke
f2c5caf307 Refactor R package dependencies in Dockerfile 2024-04-09 08:09:47 +00:00
Max Luebke
e27ce205fb Add minimal flag to importList function in InitialList 2024-04-08 20:47:38 +00:00
Max Luebke
8856825c23 Refactor Field.cpp to use Rcpp DataFrame for conversion to SEXP 2024-04-08 20:31:36 +00:00
Max Luebke
c42b335aae Refactor build file generation 2024-04-08 20:31:36 +00:00
Max Luebke
a2f04836a4 Refactor benchmark files to current POET input expectations 2024-04-08 20:31:36 +00:00
Max Luebke
7febb31bf9 Refactor command line argument handling and improve script sourcing in initializer.cpp 2024-04-08 12:49:58 +00:00
Max Luebke
c9ff062514 Refactor initializer.cpp to handle command line arguments and improve script sourcing 2024-04-08 12:02:47 +00:00
Max Luebke
62e734e0d5 Refactor code for grid creation and result storage 2024-04-08 11:27:06 +00:00
Max Luebke
3ea3412516 Fix inner_boundaries handling in DiffusionModule and InitialList 2024-04-08 10:32:00 +00:00
Max Luebke
8d64c83123 Update minimum required CMake version to 3.14 2024-04-08 10:31:47 +00:00
Max Luebke
fa916cc66e Refactor code according to static analyzers 2024-04-08 09:19:48 +00:00
Max Luebke
e6092c9166 Add dolo_inner benchmark 2024-04-05 08:34:41 +00:00
Max Luebke
a24b4f5f51 Move old benchmark files into old subdir 
Move new benchmark files from `het` folder
 2024-04-05 08:33:26 +00:00
Max Luebke
5cc161e25e Add inner_boundaries handling in DiffusionModule and InitialList 2024-04-05 08:31:32 +00:00
Max Luebke
35049e1a77 Update .gitignore to ignore .codechecker directory 2024-04-05 07:05:09 +00:00
Max Luebke
6a88de5c5d Refactor code for grid creation and result storage 2024-04-04 09:27:52 +00:00
Max Luebke
d07cfd3465 Add functions for checking sign and negativity in dol.pqi and dolo_200.R 2024-04-04 09:27:27 +00:00
Max Luebke
004977b2ea Add file extension replacement and print output filename 2024-04-03 21:19:39 +00:00
Max Luebke
0a00ea86e6 Update Dockerfile with required dependencies and install R packages 2024-04-03 21:03:16 +00:00
Max Luebke
5ce40617b8 Refactor R functions and how they are called 2024-04-03 21:03:10 +00:00
Max Lübke
2b6f17f18c Update iterations and dt values in dolo_200_rt.R 2024-04-03 16:46:50 +02:00
Max Luebke
33f3368d6e Add parallel grid creation function and update pqc_to_grid function 2024-04-03 14:25:04 +00:00
Max Luebke
24b2ed5b46 Fix initialization of transport_names in ChemistryInit and GridInit 2024-04-03 14:25:04 +00:00
Max Luebke
9976538c11 Update solution parameters in dol.pqi 2024-04-03 14:25:04 +00:00
Max Luebke
38053fd4d0 Add support for missing species in init grid, which are injected (by boundary condition) 2024-04-03 14:25:04 +00:00
Max Luebke
57aaff4d69 Update iphreeqc subproject commit 2024-04-03 10:47:33 +00:00
Max Luebke
ffd076047d Update chem.GetField() to chem.getField() in poet.cpp 2024-04-03 10:47:32 +00:00
Max Luebke
41b811f048 Update runtime and test scripts 2024-04-03 10:46:54 +00:00
Max Lübke
7aea66387a Update units in dol.pqi 2024-04-03 10:59:31 +02:00
Max Lübke
f2e0942737 Update GIT_SUBMODULE_STRATEGY in .gitlab-ci.yml 2024-04-03 10:10:02 +02:00
Max Lübke
13b6cf6549 Update Calcite and Dolomite parameters in dol.pqi 2024-04-03 10:08:37 +02:00
Max Lübke
4468945dec Update out_save in dolo_200_rt.R 2024-04-03 10:08:02 +02:00