moebiusband/MD-Bench
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Author SHA1 Message Date
Rafael Ravedutti
cd1fbfb3c8 Reorganize SIMD files and split AVX and AVX2 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-15 00:55:46 +01:00
Rafael Ravedutti
f293cec960 Call CPU version of updatePbc within setupPbc 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-14 19:19:57 +01:00
Rafael Ravedutti
6eedf1776e Small fixes into GROMACS GPU code 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-14 18:21:14 +01:00
Rafael Ravedutti
93188d1383 Adjust NVCC flags to avoid issues with atomicAdd with doubles 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-14 18:01:46 +01:00
Rafael Ravedutti
c70ebce4c1 Integrate GROMACS GPU implementation into master branch 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-08 18:33:23 +01:00
Rafael Ravedutti
493915fe95 Fix code for AVX and remove warnings 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-08 15:30:37 +01:00
Rafael Ravedutti
437b380229 Adjust NVCC flags 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-07 20:37:01 +01:00
Rafael Ravedutti
c4304e3619 Update figure widths again 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 18:41:40 +02:00
Rafael Ravedutti
b774e771ba Update width of figures in table 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 18:38:32 +02:00
Rafael Ravedutti
e86caa92b1 Fix Verlet Lists figure href 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 18:24:16 +02:00
Rafael Ravedutti
b201055658 Update table with HTML 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 18:23:29 +02:00
Rafael Ravedutti
8fce79dda6 Update README.md 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 17:56:37 +02:00
Rafael Ravedutti
1421a023a9 Remove gather-bench image 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 17:50:24 +02:00
Rafael Ravedutti
d3811c35c6 Update table with figures 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 17:48:39 +02:00
Rafael Ravedutti
239eea86b4 Update gather_bench figure 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 17:44:35 +02:00
Rafael Ravedutti
2ddb8a2934 Add gather-bench as submodule 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 14:55:11 +02:00
Rafael Ravedutti
1af19ad586 Update gather_bench image to PNG 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 14:47:45 +02:00
Rafael Ravedutti
b9fadd7fbf Update introduction text and add gather bench figure 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 14:46:24 +02:00
Rafael Ravedutti
12e7718a5f Insert stubbed case into table as well 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 14:38:08 +02:00
Rafael Ravedutti
4ddd84ef9d Insert table with figures 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 14:37:11 +02:00
Rafael Ravedutti
c0a54190d8 Update figures again 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 14:35:30 +02:00
Rafael Ravedutti
bc8f0e7c35 Update figs 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 14:28:18 +02:00
Rafael Ravedutti
9301610f7c Add more figures 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-09-29 14:23:34 +02:00
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