moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
277 Commits 8 Branches 0 Tags 3.4 MiB
8aad7e87a0
Commit Graph

277 Commits

This Branch
This Branch
All Branches
Author SHA1 Message Date
Rafael Ravedutti
70a2f48d64 Add links and figures to README 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 14:08:10 +02:00
Rafael Ravedutti
94abf8b362 Add new sections 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 12:52:54 +02:00
Rafael Ravedutti
da75f2cc36 Add usage section 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 12:39:09 +02:00
Rafael Ravedutti
880b82a86d Update README.md with config.mk options 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 12:21:29 +02:00
Rafael Ravedutti
35a8e3eeb7 Fix header of likwid-marker.h 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 11:48:05 +02:00
Jan Eitzinger
3c02a3fb7a Update README.md 2022-09-14 11:05:57 +02:00
Jan Eitzinger
3d0f4b97ee Switch copyright header in source files. 2022-09-05 10:39:42 +02:00
Rafael Ravedutti
28d3946072 Move common modules to common directory 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-17 17:56:31 +02:00
Rafael Ravedutti
47db9e86b0 Introduce common directory 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-17 17:20:57 +02:00
Rafael Ravedutti
418f392a11 Update .gitignore 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-16 19:33:38 +02:00
Rafael Ravedutti
29fa08fa7f Enhance output for gromacs variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-16 19:32:49 +02:00
Rafael Ravedutti
911ba63336 Adjust ISA options and improve output 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-16 18:36:47 +02:00
Rafael Ravedutti
0caeea0494 Rename cuda.c to device.c 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 18:17:07 +02:00
Rafael Ravedutti
90609a2b5f Adjust file structure for CUDA 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 18:12:29 +02:00
Rafael Ravedutti
939197a785 Create separate structs DeviceAtom and DeviceNeighbor with device pointers 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 17:28:06 +02:00
Rafael Ravedutti
065b596074 Initial refactoring of CUDA code 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 04:19:38 +02:00
Rafael Ravedutti
959ff65126 Fix macro condition 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 01:29:40 +02:00
Rafael Ravedutti
87d006d418 Fix GPU version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-11 16:42:41 +02:00
Rafael Ravedutti
3d95ec4b0a Small fixes 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-09 19:19:48 +02:00
Rafael Ravedutti
c18124b066 Integrate LAMMPS CUDA versions into master branch 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-09 18:53:53 +02:00
Rafael Ravedutti
eb77e1a3bd Fix DEM setup 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-19 04:13:06 +02:00
Rafael Ravedutti
2e77f6207b Avoid errors when compiling for AVX2 due to SIMD LJ implementation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-19 02:30:26 +02:00
Rafael Ravedutti
577955dfb7 Apply first changes to DEM kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-13 02:34:33 +02:00
Rafael Ravedutti
99237241fb Include domain box on DEM input file 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-08 23:15:30 +02:00
Rafael Ravedutti
3b85da83a7 Update timestep size for dem 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-08 02:56:56 +02:00
Rafael Ravedutti
814f561993 Allow PBC in just some directions 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-08 02:30:03 +02:00
Rafael Ravedutti
32836eebcb Setup first DEM example with input file from lecture 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-07 02:11:50 +02:00
Rafael Ravedutti
9ffc09f497 Add DEM kernel to parameter options 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-07 00:47:38 +02:00
Rafael Ravedutti
79483a446e Adjust code with DEM to be compilable 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-06 01:07:39 +02:00
Rafael Ravedutti
bb599c9ea8 Add first version of DEM kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-05 15:33:31 +02:00
Rafael Ravedutti
e4d7faf91b Adjust cutforce and atom positions in stubbed version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-05-14 01:02:08 +02:00
Rafael Ravedutti
bbdcaf2983 New stubbed version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-05-14 00:55:33 +02:00
Rafael Ravedutti
14838389ff Fix stubbed variant for LAMMPS algorithm 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-04-30 04:08:18 +02:00
Rafael Ravedutti
ab2eb1ff50 Write LAMMPS kernel with SIMD intrinsics and implement AVX512 with double-precision functions 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-04-05 02:57:23 +02:00
Rafael Ravedutti
af1756bfe4 Fix skin for Argon simulation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-04-04 22:22:35 +02:00
Rafael Ravedutti
4d11c5a3c2 Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2022-04-04 21:52:47 +02:00
Rafael Ravedutti
e48b3fb653 Add option to check if cj is local before applying reaction force 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-04-04 21:52:40 +02:00
Jan Eitzinger
7a0d6479a1 Merge branch 'master' of https://github.com/RRZE-HPC/MD-Bench 2022-04-01 15:58:05 +02:00
Jan Eitzinger
5585ebcf42 Add ONEAPI config. Remove omp simd for full neigh. 2022-04-01 15:57:54 +02:00
Rafael Ravedutti
fdbeed4368 Fix AVX2 versions with half neighbor lists 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-27 16:39:39 +02:00
Rafael Ravedutti
0e742766b7 Add working version of Simd4xn kernel with half neighbor lists 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-23 15:54:18 +01:00
Rafael Ravedutti
e72323ab6a Fix Simd2xnn Kernel with half neighbor lists and add AVX512 intrinsics with double 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-23 15:21:07 +01:00
Rafael Ravedutti
94521f03b3 Fix reference version with half neighbor lists 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-23 14:31:47 +01:00
Rafael Ravedutti
8709bc2a06 Add first version for half neighbor lists in GROMACS variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-22 23:47:05 +01:00
Rafael Ravedutti
2a555a7deb Add simd reduction pragma to vectorize innermost loop on half-neighbor variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-21 17:02:09 +01:00
Rafael Ravedutti
719330807b Change data layout for force arrays according to position 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-18 01:40:51 +01:00
Rafael Ravedutti
e7737e9151 Refactor half neighbor lists code 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-18 01:28:11 +01:00
Rafael Ravedutti
5df544637f Fix force calculation time in LAMMPS variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-17 02:53:58 +01:00
Rafael Ravedutti
887f41871c Add parameter reading for LAMMPS variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-17 02:44:34 +01:00
Rafael Ravedutti
d4b34e1fa4 Fix intrinsics for AVX2 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-17 00:35:21 +01:00