moebiusband/MD-Bench
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Author SHA1 Message Date
Rafael Ravedutti
15d43dcce5 Explicitly set half_neigh to zero on stubbed versions 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-12-14 17:21:09 +01:00
Rafael Ravedutti
292138b270 Write debug_printf to avoid warnings and fix latency/cfd script 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-12-14 16:17:28 +01:00
Rafael Ravedutti
0e952964f7 Update script 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-12-13 15:47:17 +01:00
Rafael Ravedutti
cd37746d07 Add script to automate latency and CFD evaluation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-12-13 15:35:41 +01:00
Rafael Ravedutti
d76d044a00 Update build options for each compiler and include ICX 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-12-13 01:06:59 +01:00
Rafael Ravedutti
a7cb888517 Fix compilation for ICX compiler 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-12-13 00:59:31 +01:00
Rafael Ravedutti
416f042fc0 Fix readline() when fgets returns NULL even on success 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-30 17:43:35 +01:00
Rafael Ravedutti
fa4e38c6c4 Add IACA and stubbed measurements for GROMACS 4x8 FN kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-18 01:00:20 +01:00
Rafael Ravedutti
04ea1b027e Print kernel and precision info in gromacs-stub 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-16 16:15:15 +01:00
Rafael Ravedutti
56d9613028 Implement stubbed version for GROMACS 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-15 16:01:13 +01:00
Rafael Ravedutti
bc06220aeb Remove AVX512 reciprocal usage in AVX2 file 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-15 01:40:37 +01:00
Rafael Ravedutti
efa462d0af Add AVX_FMA ISA 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-15 01:24:30 +01:00
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