moebiusband/MD-Bench
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Author SHA1 Message Date
JairoBuitrago
a13a0f3bae Final MPI version 2024-04-15 16:53:25 +02:00
rafaelravedutti
a6a269703d Merge pull request #7 from RRZE-HPC/mucosim23 
Mucosim23
 2024-01-17 15:14:08 +01:00
TejeshPala
7ee250161a omp_get_max_threads instead of omp_get_num_threads for gcc compiler adaption 
Signed-off-by: TejeshPala <tejesh.pala@fau.de>
 2024-01-13 15:09:03 +01:00
TejeshPala
c73efea786 include openmp in ICC 
Signed-off-by: TejeshPala <tejesh.pala@fau.de>
 2024-01-11 17:16:17 +01:00
TejeshPala
4cfa664533 schedule options for force kernels and to print in main fn 
Signed-off-by: TejeshPala <tejesh.pala@fau.de>
 2024-01-11 17:09:18 +01:00
Rafael Ravedutti
1837403326 Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2023-12-13 10:52:55 +01:00
Rafael Ravedutti
02629612a9 Fix explicit types for CUDA and provide option to write initial state of system 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-12-13 10:52:47 +01:00
TEJESH PALA
ce00aa0042 Merge pull request #6 from RRZE-HPC/mucosim23 
omp print threads
 2023-11-21 17:11:18 +01:00
TejeshPala
c4e5e87265 omp print threads 2023-11-21 15:31:27 +01:00
Rafael Ravedutti
da3b1dd53f Add extended parameter option --param 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-11-21 15:27:11 +01:00
Rafael Ravedutti
2f13291817 Change function get_num_threads to get_cuda_num_threads 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-11-21 14:40:19 +01:00
Rafael Ravedutti
a460fffa19 Fix PBC case 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-10-10 12:53:43 +02:00
Jan Eitzinger
19209bdcce Cleanup and move gather-bench to util folder 2023-08-15 15:21:21 +02:00
Rafael Ravedutti
151f0c0e6f Add extendend param option 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-05-29 02:27:32 +02:00
Rafael Ravedutti
72f486f9bf Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2023-04-09 03:44:53 +02:00
Rafael Ravedutti
8253b31ee0 Include masked out interactions from remainder in atoms_outside_cutoff 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-09 03:44:21 +02:00
Rafael Ravedutti
e206c3566d Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2023-04-09 01:23:45 +02:00
Rafael Ravedutti
7ff1673399 Update config.mk with SORT_ATOMS 
Signed-off-by: Rafael Ravedutti <rafael.r.ravedutti@fau.de>
 2023-04-09 01:23:39 +02:00
Rafael Ravedutti
b6982d56f5 Fix atom sorting 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-09 01:19:12 +02:00
Rafael Ravedutti
1ad981a059 Add static analysis for gromacs-avx2-dp on Zen3 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-09 00:07:04 +02:00
Rafael Ravedutti
c438fc6832 Fix GROMACS AVX2 code 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-07 21:54:07 +02:00
Rafael Ravedutti
17e239ed6d Add uiCA reference to its analyses 
Signed-off-by: Rafael Ravedutti <rafael.r.ravedutti@fau.de>
 2023-04-05 23:58:52 +02:00
Rafael Ravedutti
d151b9b3e4 Update scripts with division factor 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-05 23:56:35 +02:00
Rafael Ravedutti
98257b746c Add scripts to properly generate agr data 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-05 23:19:48 +02:00
Rafael Ravedutti
a101f8588a Add analyses with llvm-mca 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-05 22:11:55 +02:00
Rafael Ravedutti
c14a6b2186 Add outputs for uiCA 
Signed-off-by: Rafael Ravedutti <rafael.r.ravedutti@fau.de>
 2023-04-05 19:51:09 +02:00
Rafael Ravedutti
300776f512 Add outputs for new analyses 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-05 19:48:04 +02:00
Rafael Ravedutti
4e5fe27c0f Add object files for new static analyses 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-05 19:46:05 +02:00
Rafael Ravedutti
989bec2c7d Add first analyses with GROMACS changes 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-05 02:44:50 +02:00
Rafael Ravedutti
2971ddcc63 Separate log by hostname and allow to set prefetchers to be used 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-04 21:56:03 +02:00
Rafael Ravedutti
5341938b60 Increase cutoff for Argon case 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-04-03 15:06:32 +02:00
Rafael Ravedutti
039de0be99 Fix stubbed versions and debug messages 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-30 03:49:57 +02:00
Rafael Ravedutti
43259eb3cf Adjust neighbor lists layout to keep neighbor ids contiguous in memory 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-30 01:57:26 +02:00
Rafael Ravedutti
3eb7170a65 Adapt stubbed version for new neighbor lists in GROMACS 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-29 21:54:33 +02:00
Rafael Ravedutti
59145644e3 Last changes to 2xnn kernels 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 23:34:07 +02:00
Rafael Ravedutti
4a460b2c88 Adjust input files indent in output 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 23:04:11 +02:00
Rafael Ravedutti
b15aa2f461 Optimize 4xn kernels 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 23:00:21 +02:00
Rafael Ravedutti
5c000444a4 Pre-compute masks for 4xn kernels 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 22:30:30 +02:00
Rafael Ravedutti
04ade6bcec Pre-compute masks for 2xnn kernel with full neighbor-lists 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 19:33:26 +02:00
Rafael Ravedutti
85f1484449 Specialize force kernel when there are no masks to be checked 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 18:04:18 +02:00
Rafael Ravedutti
965fda3879 Pre-compute masks in the same way as in the master branch 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 17:32:42 +02:00
Rafael Ravedutti
a86d214c73 Add working version with old masking 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 02:19:46 +02:00
Rafael Ravedutti
d138f975f6 Add diagonal checks 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-23 02:17:27 +01:00
Rafael Ravedutti
296a4c4e01 Set interaction masks as gromacs does 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-23 00:58:25 +01:00
Rafael Ravedutti
f5fd3e265a Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2023-03-22 13:50:51 +01:00
Rafael Ravedutti
1fbf9dbdac Update skin for argon case 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-22 13:50:42 +01:00
JanLJL
89e1b9a9b6 Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2023-02-14 14:00:29 +01:00
JanLJL
4e99f7a623 fixed wrong markers and added OSACA output for ICX 2023-02-14 13:52:59 +01:00
Rafael Ravedutti
4607202752 fix markers for gromacs-icx-avx512-sp 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-02-13 16:55:39 +01:00
JanLJL
301274c9b6 Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2023-02-13 14:15:17 +01:00