Commit Graph

198 Commits

Author SHA1 Message Date
Rafael Ravedutti
cd15911a97 When building neighbor lists, skip first iterations until z is in range
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-07 18:28:53 +01:00
Rafael Ravedutti
0eacb2453e Inline getBoundingBoxDistanceSq and avoid redundant loads from bbminz and bbmaxz
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-07 18:00:21 +01:00
Rafael Ravedutti
cdb1d5b9f1 Add version with AVX2 intrinsics for gromacs scheme
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-04 17:52:48 +01:00
Rafael Ravedutti
34ce407f18 Update stats for gromacs scheme
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-04 14:47:37 +01:00
Rafael Ravedutti
6e6a3f6502 Use aligned loads when gathering j atoms
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-04 14:29:32 +01:00
Rafael Ravedutti
7b90800a2b Setting forces to zero before calculation is not required
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-04 14:05:04 +01:00
Rafael Ravedutti
9daf9e5f4d Fix exclusion masks and add SIMD debug tools
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-02 21:54:18 +01:00
Rafael Ravedutti
4c5f013bf4 Assign masked adds results to forces
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-02 18:07:56 +01:00
Rafael Ravedutti
6ad1e58a3e Add first kernel using SIMD instrinsics for 4xn cases
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-02 18:00:44 +01:00
Rafael Ravedutti
5fd2d422ee Adjust kernels to work with MxN loops
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-02 00:49:55 +01:00
Rafael Ravedutti
85e7954932 Check all clusters in cell when building neighbor lists because ghost clusters may not be sorted
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-01 20:16:04 +01:00
Rafael Ravedutti
4a5216a177 Remove bb z-check on while loop when building neighbor lists
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-02-01 00:46:12 +01:00
Rafael Ravedutti
e64c3345bc Fix a few more bugs on gromacs variant
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-31 23:46:20 +01:00
Rafael Ravedutti
e0e6b6a68c Perform a few fixes for gromacs variant
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-31 17:49:22 +01:00
Rafael Ravedutti
6691803910 Add first version of force calculation with cluster scheme
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-28 18:07:41 +01:00
Rafael Ravedutti
eedcc97e4a Remove segfaults
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-28 15:18:54 +01:00
Rafael Ravedutti
a119fcdfdd Fix some segfaults and add function to update single atoms
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-27 03:07:31 +01:00
Rafael Ravedutti
aa0f4048d0 Rename default directory to lammps and reorganize gromacs variant steps
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-25 21:00:11 +01:00
Rafael Ravedutti
cbe42b8149 Fix errors to make gromacs approach compilable so far
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-25 12:19:28 +01:00
Rafael Ravedutti
6291709ae7 Add first draft code with GROMACS approach
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-25 00:43:10 +01:00
Rafael Ravedutti
72730bc27b Update Makefile and config.mk
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-17 14:16:39 +01:00
Rafael Ravedutti
df09c2861e Add first version with more than one optimization scheme
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-17 14:15:02 +01:00
Rafael Ravedutti
489e7ee9d3 Update .gitignore
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-17 11:46:57 +01:00
Rafael Ravedutti
165335cea0 Update compilation flags for all available compilers
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-17 11:40:44 +01:00
Rafael Ravedutti
35c110155e Separate tracing from force computation and fix stubbed version
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2021-12-01 00:07:45 +01:00
Rafael Ravedutti
bb21a885a1 Add new setups for Copper melting with LJ and EAM
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2021-11-30 01:33:55 +01:00
Rafael Ravedutti
f7010113bf Include commented timestamping on asm
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2021-11-10 14:39:44 +01:00
Rafael Ravedutti
841dfb9490 Fix data types for rdr and rdrho
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2021-11-09 20:36:23 +01:00
Rafael Ravedutti
f8b9a095cf Add working version of force.s
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2021-11-09 01:23:15 +01:00
Rafael Ravedutti
b2dada6179 Fix param references and assembler errors for force.s
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2021-11-09 00:05:42 +01:00
Rafael Ravedutti
d8c8733cb2 Update asm force again
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2021-11-08 23:32:24 +01:00
Rafael Ravedutti
cf7ea1460c Update asm version to be integrated
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2021-11-08 22:31:58 +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