moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
131 Commits 8 Branches 0 Tags 3.4 MiB
0586ef150a
Commit Graph

131 Commits

This Branch
This Branch
All Branches
Author SHA1 Message Date
Maximilian Gaul
0586ef150a Fix num of threads instead of num of blocks, add logbook template 2021-11-15 19:39:09 +01:00
Maximilian Gaul
2e5d973f7d Rough rewrite to execute outer loop of force calculation in parallel, not inner loop 2021-11-14 10:02:23 +01:00
Maximilian Gaul
e2fd1a0476 Fixed bug, results are now equal to master branch (but still slow) 2021-11-11 21:00:30 +01:00
Maximilian Gaul
4105c844c6 Runs fine (but slow), results seem to be slightly off from original 2021-11-11 20:47:06 +01:00
Maximilian Gaul
1f5c9c4b23 Fixed segfault error, added more cudaErrorChecks, added cudaFree to avoid memory leak 2021-11-11 20:29:14 +01:00
Maximilian Gaul
29e115464b Fixed cudaMemcpy for AOS data layout, added debug outputs, added cudaErrorChecks 2021-11-11 20:14:30 +01:00
Maximilian Gaul
1a54314c8b First run but segfault at the moment after a few seconds 2021-11-11 15:23:46 +01:00
Maximilian Gaul
280f595b7f Fixed linker error by putting includes and cuda function in extern 'C' 2021-11-11 14:49:29 +01:00
Maximilian Gaul
3428974730 getTimeStamp() couldn't get linked 2021-11-11 08:03:56 +01:00
Maximilian Gaul
b54842f764 Added Makefile instructions for .cu files 2021-11-11 07:27:12 +01:00
Maximilian Gaul
9730164e6f Rename force.c to force.cu because of cuda build errors 2021-11-10 16:20:04 +01:00
Maximilian Gaul
0f5fdd3708 Sum results after cuda function executed 2021-11-10 16:02:05 +01:00
Maximilian Gaul
3f7fb7f22a cudaMemcpy of Atom and other properties, first draft implementation of CUDA kernel 2021-11-09 16:40:25 +01:00
Maximilian Gaul
bfa6c581c3 Copy necessary values for force calculation into cuda memory 2021-11-09 08:37:37 +01:00
Maximilian Gaul
fd886e77eb Added make config for NVCC 2021-11-08 20:32:12 +01:00
Rafael Ravedutti
9b615cf0b3 Update force kernel to be integrated 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-08 14:05:29 +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
d9c9cba12d Set EAM parameters for same case as miniMD 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-27 01:38:56 +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
Rafael Ravedutti
7db14b2ffe Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2021-10-26 12:34:43 +02:00
Rafael Ravedutti
d7056f09f4 Fix illegal accesses due to invalid type of ghost atoms 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 12:34:35 +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
99d6a4bdd8 Fix Funcfl reference to avoid segfaults 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 01:40:02 +02:00
Rafael Ravedutti
40ddc9ad50 Fix errors introduced by last changes 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 01:19:11 +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
9d16bb46c8 Include average neighbors and SIMD iterations per atom on stats 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-20 22:43:08 +02:00
Rafael Ravedutti
557c5e4d3f IUpdate logbook again and do not check for variant on ATOMS_LOOP_RUNS effect 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-14 00:46:30 +02:00
Rafael Ravedutti
40bbaac078 Add hardware information on logbook 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-13 22:27:34 +02:00
Rafael Ravedutti
c46e4ee4df Include ATOMS_LOOP_RUNS option in config.mk file 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-12 23:35:58 +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
4e0390404a Add correct version (without traces) of CACHES_PMC results with and without force calculation on casclakesp2 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-06 16:08:46 +02:00
Rafael Ravedutti
b1f8e91f0f Add cache measurements for versions with and without force computation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-04 18:13:17 +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
2889577a3b Add neighbor lists capacity to index tracer file 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-08-10 17:28:59 +02:00
Rafael Ravedutti
b8d71090aa Add number of atoms in index tracer file 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-08-10 16:43:51 +02:00
Rafael Ravedutti
6b75c158d6 Include atom reference on index tracer and add only_mem ASM version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-08-10 01:19:26 +02:00
Rafael Ravedutti
9d79f0248f Add config option to switch between asm syntaxes 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-08-09 21:37:18 +02:00
Rafael Ravedutti
effd961f29 Add cache sets histogram script, update gather plot script and add results for icx32 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-29 17:01:30 +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
8e1542c87d Sort elements within vector to fix distance calculation on index tracer 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-15 23:51:00 +02:00
Rafael Ravedutti
d97fc577b0 Add first version of index and distance tracer 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-09 23:49:14 +02:00
Rafael Ravedutti
e6062e8f79 Update script to plot stubbed data and add results for casclakesp2 with AoS 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-03 03:07:35 +02:00
Rafael Ravedutti
eef44e97d7 Update cache settings for casclakesp2 and results 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-02 02:57:31 +02:00
Rafael Ravedutti
4bde1944cf Update script for plotting gather data and AOS results for casclakesp2 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-01 20:02:59 +02:00
Rafael Ravedutti
5534f1b195 Modify gather script to include raw data and update results without prefetchers 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-06-30 16:09:34 +02:00
Rafael Ravedutti
ecb5ccf6ff Adjust likwid markers for force region 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-06-30 13:44:02 +02:00