moebiusband/MD-Bench
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131 Commits

Author SHA1 Message Date
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
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
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
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
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
ecb5ccf6ff Adjust likwid markers for force region 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-06-30 13:44:02 +02:00
Rafael Ravedutti
7ae22a5695 Add forces reading operation on memory tracer and include ampersand in TRACER_PRINT 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-06-21 22:56:44 +02:00
Rafael Ravedutti
0a2ec6376c Add memory tracer and update config.mk with all options 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-06-16 00:56:00 +02:00
Rafael Ravedutti
56ad09156b Fix explicit types for stubbed version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-05-20 00:08:10 +02:00
Rafael Ravedutti
4496e91125 Add version with explicit types for atoms 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-05-19 23:51:02 +02:00
Rafael Ravedutti
6c03ea3f3c Adjust output when computing invalid values 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-05-07 02:31:53 +02:00
Rafael Ravedutti
e53d9961ef Fix compilation when INTERNAL_LOOP_NTIMES is not set and create avx512 directory 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-05-06 13:59:02 +02:00
Rafael Ravedutti
15de65303e Add version iterating most internal loop multiple times 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-05-05 03:04:41 +02:00
Rafael Ravedutti
0a81407948 Fix invalid values for cycles per neighbor 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-29 20:29:00 +02:00
Rafael Ravedutti
11b2d4bcc1 Update results for arch_analysis and stub script 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-29 17:57:37 +02:00
Rafael Ravedutti
c356336dbd Show cycles per atom and neighbor 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-22 16:50:22 +02:00
Rafael Ravedutti
4c53519c73 Add output as CSV 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-22 01:22:18 +02:00
Rafael Ravedutti
fd108d97d8 Fix problem when atoms_per_unit_cell is less or equal than 4 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-22 00:07:42 +02:00
Rafael Ravedutti
3c7dbc833a Allow any values for atoms_per_unit_cell 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-21 13:01:06 +02:00
Rafael Ravedutti
d3121ee08f Adjust computeForce parameters for stub 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-21 11:28:02 +02:00
Rafael Ravedutti
78e6e5c773 Merge master branch into stub 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-15 20:12:36 +02:00
Jan Eitzinger
06ba3b2726 Restructure timing and instrumentation. Add performance metric. 2021-04-15 14:55:02 +02:00
Rafael Ravedutti
a0699dde4c Merge branch 'master' into stub 2021-04-12 23:10:36 +02:00
Jan Eitzinger
35273c491b Introduce generic variant targets 
Change Makefiles to allow multiple binary targets specified by VARIANT
environment variabel. For specified variants a matching main-<VARIANT>.c
source file must be present.
 2021-04-12 08:24:27 +02:00
Rafael Ravedutti
706f1c38f2 Update stubbed force calculation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-04-07 00:46:51 +02:00
Rafael Ravedutti
77a0774208 Improve stubbed force calculation version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-03-30 22:17:30 +02:00
Rafael Ravedutti
7efd30791a Add version with stubbed force calculation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-03-30 01:54:56 +02:00
Jan Eitzinger
2bc3120112 Put force kernel in separate compilation unit 2021-03-25 06:49:28 +01:00
Jan Eitzinger
d026028439 Streamline build system 2021-03-24 08:43:44 +01:00
Rafael Ravedutti
4b481bb407 Fix macros for AoS 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-03-23 16:21:08 +01:00
Jan Eitzinger
fc1fc9fd45 Port pbc to new macros. Enable debugging flags. 2021-03-23 10:03:55 +01:00
Jan Eitzinger
6679b6c8aa Simplify macros for data structure access. 
Still segvaults for AoS.
 2021-03-23 09:26:41 +01:00
Rafael Ravedutti
cb0ae2b0bb Replace inline calls by macros 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-03-22 21:51:47 +01:00
Rafael Ravedutti
3f7edb5dbf Add support for AoS data layout 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-03-20 18:32:50 +01:00
Jan Eitzinger
b39957421c Include Likwid Markers. Allow to switch between SP and DP floats. 2020-11-05 12:41:44 +01:00
Jan Eitzinger
0fd51e8a9c Add OpenMP parallelization for computeForce. 2020-08-19 11:19:16 +02:00
Jan Eitzinger
a0acce6cb3 Switch License to LGPL3 2020-08-19 10:47:40 +02:00
Jan Eitzinger
b1f2e23696 Fix more bugs. Enable optimization for CLANG. 2020-08-19 10:00:19 +02:00
Jan Eitzinger
dcee5f97f2 Add timing and result output. 2020-08-19 09:22:43 +02:00
Jan Eitzinger
71ea8dbb0e Refactor. Fix bug in atom initialization. 2020-08-19 09:00:35 +02:00
Jan Eitzinger
e7869286d7 Introduce modular version. 2020-08-18 14:27:28 +02:00
Jan Eitzinger
b20b71ca0b First working code. Clean up. 2020-08-17 14:01:46 +02:00
Jan Eitzinger
49cd67f82f Fix bug in ghost atom setup. 2020-08-17 13:20:54 +02:00
Jan Eitzinger
24a2e87e7e Fix bug in logic of setupBoundary. 2020-08-14 13:51:01 +02:00
Jan Eitzinger
9e7cbf5687 Finish border treatment. 2020-08-14 09:31:04 +02:00
Jan Eitzinger
7d0c47da72 Add alternative for setup of ghost atoms. 2020-08-14 08:32:36 +02:00
Jan Eitzinger
a4c2860130 Add boundary ghost layer setup without atom relocation. 2020-08-13 09:43:29 +02:00
Jan Eitzinger
fb763f0dfc Debug. Runs with wrong temp. 2020-08-12 15:38:08 +02:00
Jan Eitzinger
ff45b07749 Initial checkin of simplified miniMD port. Does not work yet. 2020-08-11 16:34:22 +02:00