moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
179 Commits 8 Branches 0 Tags 3.4 MiB
7bad7e84b6
Commit Graph

55 Commits

Author SHA1 Message Date
Martin Bauernfeind
5a6d1851ed Ported updateAtomsPbc to cuda and changed the code to use the cuda version from now on 2022-07-13 14:07:19 +02:00
Martin Bauernfeind
71798f5ec5 🐛 Fixed aforementioned correctness issue by deleting a superflous cudaMemcpy in computeForce() that was overwriting correct data with incorrect data 2022-07-05 00:54:11 +02:00
Martin Bauernfeind
7e8fd96fa4 Fixed some compiler errors - the simulation seems to be off regarding how many ghost atoms are used -> some bugfixing might be needed 2022-07-03 21:14:33 +02:00
Martin Bauernfeind
463de5b1ed Ported the updatePbc method to cuda 2022-07-03 19:53:33 +02:00
Martin Bauernfeind
60ed524dd8 Fixed various compiler errors - now there's probably a memory leak remaining 2022-06-26 18:37:09 +02:00
Martin Bauernfeind
c49278cb21 First crude attempt at parallelizing neighborhood computation (only the part after binning the atoms is parallelized with cuda) 2022-06-26 16:25:59 +02:00
Martin Bauernfeind
b5b4d23c0c 🐛 further refactoring fixing 2022-06-23 19:46:29 +02:00
Martin Bauernfeind
fea1e41daa 🐛 further refactoring step fixing 2022-06-23 19:43:36 +02:00
Martin Bauernfeind
f1998b7acc 🐛 further refactor step fixing 2022-06-23 19:39:36 +02:00
Martin Bauernfeind
7f068a6959 ♻️ Fixing refactoring step 2022-06-23 19:32:09 +02:00
Martin Bauernfeind
62cfc22856 ♻️ Refactoring: pulled definition of the GPU atom and neighbor representation from force.cu and put it into main 2022-06-23 18:54:56 +02:00
Maximilian Gaul
c4080e866e Make integrate kernels aware of neighbour list update 2022-01-24 18:04:50 +01:00
Maximilian Gaul
dc4d5f1a9c Porting atom velocity memory layout to AoS, porting velocity integration to CUDA, adding measurements + logbook update 2022-01-01 18:18:12 +01:00
Maximilian Gaul
50007216ed Implemented atom force AoS memory layout, added performance measurements + logbook Update 2022-01-01 16:09:21 +01:00
Maximilian Gaul
72e4599acc Copy neighbour lists only when reneighbouring happens, added measurements + logbook update 2022-01-01 12:56:42 +01:00
Maximilian Gaul
bf1ae3d013 Removed debug prints, only zero atom forces and not copy them, added measurements 2021-12-28 16:32:54 +01:00
Maximilian Gaul
8009b54113 Trying to debug segfault if cudaMemcpy is limited to neighbour list update 2021-12-25 15:36:08 +01:00
Maximilian Gaul
0ea0587442 Only malloc once at the beginning plus measurement csv 2021-12-25 13:52:33 +01:00
Rafael Ravedutti
ec556eb117 Add EAM without explicit types and update fp for PBC atoms 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-03 00:57:24 +01:00
Rafael Ravedutti
0f1e824507 Fix integration with mass and add VTK output 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-29 16:52:19 +02:00
Rafael Ravedutti
70cc6aeb19 Add first working version of EAM 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 13:55:14 +02:00
Jan Eitzinger
70e24d7c2c Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2021-10-26 09:16:31 +02:00
Jan Eitzinger
3c3d27b48a Introduce separate version for traced force routine. 2021-10-26 09:11:17 +02:00
Rafael Ravedutti
2dac10469c Add EAM force field 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 00:40:39 +02:00
Rafael Ravedutti
43ba28e130 Add ATOMS_LOOP_RUNS option and statistics to stub variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-12 22:39:54 +02:00
Rafael Ravedutti
55d346510e Compute statistics, useful data volume and cycles per SIMD iteration 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-12 15:04:08 +02:00
Rafael Ravedutti
f295f54fca Add useful data volume calculation for force kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-11 16:57:02 +02:00
Rafael Ravedutti
749c4d55ab Provide trace output for all reneighboring steps 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-04 16:47:07 +02:00
Rafael Ravedutti
57041ceed2 Add likwid-perfctr run with CACHES_PMC for 1 timestep on casclakesp2 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-16 00:24:43 +02:00
Rafael Ravedutti
0a2ec6376c Add memory tracer and update config.mk with all options 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-06-16 00:56:00 +02:00
Rafael Ravedutti
4496e91125 Add version with explicit types for atoms 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-05-19 23:51:02 +02:00
Rafael Ravedutti
15de65303e Add version iterating most internal loop multiple times 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-05-05 03:04:41 +02:00
Rafael Ravedutti
3c7dbc833a Allow any values for atoms_per_unit_cell 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-21 13:01:06 +02:00
Rafael Ravedutti
706f1c38f2 Update stubbed force calculation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-07 00:46:51 +02:00
Rafael Ravedutti
77a0774208 Improve stubbed force calculation version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-03-30 22:17:30 +02:00
Rafael Ravedutti
7efd30791a Add version with stubbed force calculation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-03-30 01:54:56 +02:00
Jan Eitzinger
2bc3120112 Put force kernel in separate compilation unit 2021-03-25 06:49:28 +01:00
Jan Eitzinger
6679b6c8aa Simplify macros for data structure access. 
Still segvaults for AoS.
 2021-03-23 09:26:41 +01:00
Rafael Ravedutti
cb0ae2b0bb Replace inline calls by macros 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-03-22 21:51:47 +01:00
Rafael Ravedutti
3f7edb5dbf Add support for AoS data layout 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-03-20 18:32:50 +01:00
Jan Eitzinger
b39957421c Include Likwid Markers. Allow to switch between SP and DP floats. 2020-11-05 12:41:44 +01:00
Jan Eitzinger
0fd51e8a9c Add OpenMP parallelization for computeForce. 2020-08-19 11:19:16 +02:00
Jan Eitzinger
a0acce6cb3 Switch License to LGPL3 2020-08-19 10:47:40 +02:00
Jan Eitzinger
b1f2e23696 Fix more bugs. Enable optimization for CLANG. 2020-08-19 10:00:19 +02:00
Jan Eitzinger
dcee5f97f2 Add timing and result output. 2020-08-19 09:22:43 +02:00
Jan Eitzinger
71ea8dbb0e Refactor. Fix bug in atom initialization. 2020-08-19 09:00:35 +02:00
Jan Eitzinger
e7869286d7 Introduce modular version. 2020-08-18 14:27:28 +02:00
Jan Eitzinger
b20b71ca0b First working code. Clean up. 2020-08-17 14:01:46 +02:00
Jan Eitzinger
49cd67f82f Fix bug in ghost atom setup. 2020-08-17 13:20:54 +02:00
Jan Eitzinger
24a2e87e7e Fix bug in logic of setupBoundary. 2020-08-14 13:51:01 +02:00