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implemented plain-C SIMD macros for reference
2013-07-24
Berk Hes
s
implemen
t
ed plain-C SIMD
macros for
r
eference
commit
|
commitdiff
|
tree
2013-06-20
Berk He
s
s
fixed SD and B
D
integ
r
ator OpenMP performance
commit
|
commitdiff
|
tree
2013-06-20
B
erk Hess
flop
s
table now repo
r
ts CUDA ana
l
ytical
E
w
a
l
d
commit
|
commitdiff
|
tree
2013-06-14
Be
r
k
H
ess
fixed minor g_bar ou
t
put issues
commit
|
commitdiff
|
tree
2013-06-05
Berk Hess
fixed
D
D internal s
t
ate corruption wi
t
h energy
m
inimiz
a
tion
commit
|
commitdiff
|
tree
2013-06-03
Berk Hess
f
i
xed deadlock with repli
c
a exchange
and -
m
axh
commit
|
commitdiff
|
tree
2013-05-08
Berk Hess
f
i
x
ed inc
o
r
rect scali
n
g of cos
-
accel
e
ration vi
s
co
s
ity
commit
|
commitdiff
|
tree
2013-04-29
Berk Hess
g
e
neral
SIMD acc
e
leration for angle
s
+dihedrals
commit
|
commitdiff
|
tree
2013-04-26
B
erk
H
e
s
s
PME load balancing
now checks
f
or PME grid restrictions
commit
|
commitdiff
|
tree
2013-04-18
B
e
r
k
Hess
change
d
mdr
u
n
-nsteps to gmx_large_
i
nt_t
commit
|
commitdiff
|
tree
2013-04-12
B
erk Hess
im
p
roved lo
a
d balancing with Verlet cut-off scheme
commit
|
commitdiff
|
tree
2013-03-27
Ber
k
Hess
remo
v
ed x86 speci
f
ic
s
f
rom
n
bnxn SIMD k
e
rne
l
s
commit
|
commitdiff
|
tree
2013-03-27
Berk Hess
c
orrecte
d
lo
g
file wall time break
d
own
commit
|
commitdiff
|
tree
2013-03-21
Be
r
k Hess
made PME
w
o
r
k
with
a
m
ix of 1
and more
threads
commit
|
commitdiff
|
tree
2013-03-14
Berk
H
ess
corr
e
c
t
ed
grompp rvdw char
g
e-group radii c
h
ec
k
commit
|
commitdiff
|
tree
2013-03-05
Berk
Hess
f
i
x
e
d
bug with DD
c
ut-off check and PME
D
LB
commit
|
commitdiff
|
tree
2013-03-05
Berk Hess
fixed recent bug with sorting ato
m
s for G
P
Us
commit
|
commitdiff
|
tree
2013-02-26
Ber
k
Hess
fixed P
M
E
time print with -nt
o
m
p
_
pme
!
=
-ntomp
commit
|
commitdiff
|
tree
2013-02-20
Be
r
k Hess
added mdrun
check for Ve
r
let+p
e
rturb
e
d at
o
m
s
commit
|
commitdiff
|
tree
2013-02-20
B
erk Hess
f
i
xed issues
with
F
EP soft-core and cut-off's
commit
|
commitdiff
|
tree
2013-02-18
Ber
k
H
e
ss
fixed GPU pa
r
tic
l
e
gridding p
e
rformance issue
commit
|
commitdiff
|
tree
2013-02-15
Berk
H
ess
i
mprov
e
d P
M
E
loa
d
balancing
rep
o
r
ting
commit
|
commitdiff
|
tree
2013-02-06
Berk Hess
fix
e
d bug with sd inte
g
rato
r
and OpenMP threa
d
i
n
g
commit
|
commitdiff
|
tree
2013-02-05
Berk
H
ess
improved load ba
l
ancing on the GPU
commit
|
commitdiff
|
tree
2013-02-04
Berk He
s
s
fixed segv in
init_fo
r
cerec with fr->hwinfo=NULL
commit
|
commitdiff
|
tree
2013-02-01
Berk Hess
PME-only counters are now
r
es
e
t with -
m
axh
-
resethway
commit
|
commitdiff
|
tree
2013-01-18
Berk Hess
thread
a
f
finity
now
uses some topolog
y
information
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
fixed S
D
+
BD integration sl
o
w
ing down with OpenMP
t
hreads
commit
|
commitdiff
|
tree
2013-01-17
B
erk Hes
s
i
mproved CUDA kernel
performance
by p
r
e-loading
cj
commit
|
commitdiff
|
tree
2013-01-17
Berk H
e
ss
fixed nbnxn h
y
brid mod
e
w
ith
OpenMP
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
made PME
loa
d
balancing
+
DD DLB more eff
i
ci
e
nt
commit
|
commitdiff
|
tree
2013-01-16
Berk Hess
split off p
i
ck_n
b
nxn_resource from nbnxn_pick_nbn
x
n
commit
|
commitdiff
|
tree
2013-01-13
Berk Hess
fixed resetting
s
tates w
i
t
h parallel Verle
t
scheme
commit
|
commitdiff
|
tree
2013-01-12
Berk Hess
p
repared
the nbnxn
code for non-x
8
6 SI
M
D
commit
|
commitdiff
|
tree
2013-01-11
B
erk Hes
s
made SHAKE
w
ork again with particle
d
e
c
o
m
postion
commit
|
commitdiff
|
tree
2013-01-10
Berk Hess
fix
e
d
n
bnxn no LJ comb
.
rule AVX256 PME kernel
commit
|
commitdiff
|
tree
2013-01-10
Ber
k
Hess
fixe
d
bug with Verlet +
D
D +
b
onded atom communication
commit
|
commitdiff
|
tree
2013-01-07
B
erk
Hess
fix
e
d
nbnxn A
V
X-
2
56
Ewald table pointer
ali
g
nment
commit
|
commitdiff
|
tree
2013-01-02
Berk Hess
minor sp
e
ed-up
a
nd
c
ode clean
-
up in nbnxn k
e
rnels
commit
|
commitdiff
|
tree
2012-12-20
Berk
Hess
f
ixed
recent bug
s
in LINCS
f
or deriva
t
ives
commit
|
commitdiff
|
tree
2012-12-18
Berk
H
e
ss
renamed gmx_x86
_
simd_m
a
cros
.
h to
gmx_s
i
md_macros
.
h
commit
|
commitdiff
|
tree
2012-12-18
B
erk
H
ess
i
mplem
e
nted
n
bnxn AVX-256
2
x
(
N+N) kerne
l
s
commit
|
commitdiff
|
tree
2012-12-11
Berk
H
ess
r
educed PLINCS
communicat
i
on with H-bond constraints
commit
|
commitdiff
|
tree
2012-12-07
Berk Hess
fixed GPU pair-s
e
arch with GMX_CPU
_
A
CC
E
L
ERAT
I
ON=
N
one
commit
|
commitdiff
|
tree
2012-12-06
B
erk
Hess
r
e
mov
e
d last OpenMP O(n
t
hreads)
b
ottlene
c
k
commit
|
commitdiff
|
tree
2012-12-05
B
erk H
e
s
s
f
ixed incorrec
t
vi
r
i
a
l
w
i
th virtua
l
si
t
es and OpenMP
commit
|
commitdiff
|
tree
2012-12-05
Berk
H
ess
fixed segv
i
n Verlet pair-search with trilinic
D
D
commit
|
commitdiff
|
tree
2012-11-30
Berk He
s
s
f
i
x
ed issue with
-multi and GPUs
commit
|
commitdiff
|
tree
2012-11-28
Ber
k
Hess
fixed thread
pinning with
m
drun -mult
i
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
ext
e
nd
e
d
nbnxn x86 SIMD kernel blendv support
commit
|
commitdiff
|
tree
2012-11-27
B
e
r
k Hess
fixed bug in
n
bnxn Op
e
nMP non-bond
e
d force
r
e
d
u
c
t
ion
commit
|
commitdiff
|
tree
2012-11-26
Berk H
e
ss
m
a
de nb
n
xn analytical Ew
a
ld
c
onsistent
commit
|
commitdiff
|
tree
2012-11-26
B
e
r
k
Hess
added nbnxn analytical Ewald correction
k
erne
l
s
commit
|
commitdiff
|
tree
2012-11-16
Berk Hess
reduced the cost of
t
h
e
nbn
x
n
O
penMP nb-f
o
rce r
e
d
u
ction
commit
|
commitdiff
|
tree
2012-11-15
B
e
rk Hess
fi
x
e
d inco
r
rect 1
-
4 energie
s
wit
h
OpenMP +
energy groups
commit
|
commitdiff
|
tree
2012-11-14
Ber
k
Hess
fix
e
d nbnxn x86 SIMD non-bo
n
d
ed performa
n
ce regre
s
sion
commit
|
commitdiff
|
tree
2012-11-12
Berk
H
e
ss
n
bn
x
n CPU force buffer
reduction n
o
w uses S
I
M
D
commit
|
commitdiff
|
tree
2012-11-06
Berk Hess
Merge "Add option
t
o install
l
ibcuda
r
t" into r
e
lease-4-6
commit
|
commitdiff
|
tree
2012-11-06
Berk
Hess
Me
r
ge "don't
e
xecute any
mpi_info/mpiname in the path
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
Berk Hess
Merge "up
d
ated several things rela
t
ed with OpenMP
t
hr
e
ad
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
Be
r
k Hess
updated several things
r
elated
with Op
e
nMP thread count
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
fix
e
d
i
ncorrect PME load balancin
g
limitation
commit
|
commitdiff
|
tree
2012-10-26
Berk
H
ess
set the defa
u
lt for nstdhdl to 100
commit
|
commitdiff
|
tree
2012-10-26
Ber
k
Hess
fixed incorr
e
ct
gr
o
up energies with nbnxn C
P
U kernels
commit
|
commitdiff
|
tree
2012-10-23
B
e
r
k Hess
fixed bondfree
.
c thread safety with
f
ree energy
commit
|
commitdiff
|
tree
2012-10-23
B
e
rk He
s
s
moved
p
a
r
t
of
n
bnxn_search
.
c
to nbnxn
_
atomdata
.
c
commit
|
commitdiff
|
tree
2012-10-23
Be
r
k
Hess
fixed inco
r
r
e
ct LJ ene
r
gy with GPU and P
M
E load balancin
g
commit
|
commitdiff
|
tree
2012-10-22
Berk Hess
added
O
penMP parallelization for vi
r
tual sites
commit
|
commitdiff
|
tree
2012-10-18
Ber
k
H
e
ss
renamed c
o
nstraint
v
aria
b
les rmdr to vir_r_m_dr
commit
|
commitdiff
|
tree
2012-10-18
Ber
k
H
e
ss
add
e
d OpenMP
p
a
ralleliza
t
ion to LINCS
p
rojection
commit
|
commitdiff
|
tree
2012-10-17
Berk Hess
renamed pme_sw
i
tch
.
.
.
to pme_loadbal
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Be
r
k Hess
mad
e
p
a
ir-search with
G
PU 2
0
% faster
commit
|
commitdiff
|
tree
2012-10-12
Berk Hess
Merge "Fix
i
llegal barrier
in w
o
rksharing" into re
l
ease-4-6
commit
|
commitdiff
|
tree
2012-10-08
Berk Hess
made non
-
bonded
p
otential shifts mdp options
commit
|
commitdiff
|
tree
2012-10-04
Berk
Hess
fixed backward comp
a
tibility of
t
pr fil
e
s w
i
th dihres
commit
|
commitdiff
|
tree
2012-10-03
B
e
rk
H
ess
improve
d
th
e
energy cons
e
rvation with SETTL
E
commit
|
commitdiff
|
tree
2012-09-13
B
erk Hess
fixed
recen
t
bug with grompp
c
h
e
ck for P-R P-coupling
commit
|
commitdiff
|
tree
2012-08-29
Ber
k
Hess
bug fix for pme
.
c
M
P
I_COMM_NULL fi
x
dcf8b
6
7e
commit
|
commitdiff
|
tree
2012-08-09
Berk H
e
ss
f
ixed trjconv not
writing ve
l
ocities with cp
t
i
n
p
ut
commit
|
commitdiff
|
tree
2012-08-06
Berk He
s
s
f
ixed incorrect
T
PI res
u
lts with d
y
namic b
o
x
commit
|
commitdiff
|
tree
2012-07-18
Berk Hess
fixed DD charge group d
i
splacement error check
commit
|
commitdiff
|
tree
2012-07-17
Berk He
s
s
fix a seg
f
ault in sse_mask_init
commit
|
commitdiff
|
tree
2012-07-04
Berk He
s
s
set default for rcoulom
b
,
rvdw and rlist
to
-
1
commit
|
commitdiff
|
tree
2012-06-25
B
e
rk Hes
s
fixed segv/hang with EM an
d
foreign lambda values
commit
|
commitdiff
|
tree
2012-06-25
Ber
k
H
ess
added
c
heck fo
r
log fp!=NULL when
disabling a
c
c
e
l
eration
commit
|
commitdiff
|
tree
2012-05-24
Berk Hess
n
o
w mdrun always
init
i
alizes MPI
commit
|
commitdiff
|
tree
2012-05-21
B
erk Hess
grompp now retains
the o
r
der of
b
ond
s
c
o
nverted to
.
.
.
commit
|
commitdiff
|
tree
2012-05-21
Berk H
e
ss
re-
i
ntroduced fix for
r
eal
/
dou
b
le issue
i
n gmx_density
commit
|
commitdiff
|
tree
2012-05-08
B
e
rk Hess
fi
x
e
d mdr
u
n
-
cpi SD and
pcoupl initia
l
ization
commit
|
commitdiff
|
tree
2012-04-28
Berk Hes
s
fixed P
M
E forc
e
s
w
i
th FE,
fixes #92
9
introd
u
ced in
.
.
.
commit
|
commitdiff
|
tree
2012-04-27
Berk H
e
s
s
fixed segv in TPI wi
t
h PM
E
, fixes #92
7
commit
|
commitdiff
|
tree
2012-04-27
B
erk
He
s
s
ch
a
nged P
M
E
MPI_Comm c
o
mparisions to MPI_COMM_NULL
.
.
.
commit
|
commitdiff
|
tree
2012-04-27
Berk
Hess
changed numbe
r
o
f
i
a
toms for F_SETTLE
f
rom 1 to 3
commit
|
commitdiff
|
tree
2012-04-26
B
e
rk H
e
ss
added support for
gra
p
hs not star
t
ing at 0
commit
|
commitdiff
|
tree
2012-04-26
Berk He
s
s
M
e
r
ge "
M
erge
release-4-5-patches
into relea
s
e-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
Berk Hess
Mer
g
e rel
e
a
s
e
-4-5-p
a
tches into re
l
ease-4
-
6
commit
|
commitdiff
|
tree
2012-04-26
Berk
H
ess
fixed the r
e
p
orted temperat
u
re with Brownian
dy
n
a
mics
commit
|
commitdiff
|
tree
2012-04-26
Berk He
s
s
fixed dispersion correction with parall
e
l EM
commit
|
commitdiff
|
tree
2012-04-25
Berk Hess
repl
a
c
ed
P
PPM by P3M-A
D
: a few
li
n
e
s
in pme
.
c
commit
|
commitdiff
|
tree
2012-04-25
Berk Hess
fixed initial
C
OM moti
o
n removal with multiple groups
commit
|
commitdiff
|
tree
next