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fixed segv in init_forcerec with fr->hwinfo=NULL
2013-02-04
Ber
k
Hess
fixed segv
i
n in
i
t_forcer
e
c wit
h
fr
-
>
hwinfo=NULL
commit
|
commitdiff
|
tree
2013-01-18
Berk
Hess
t
h
read affinity now uses s
o
me topo
l
ogy i
n
formation
commit
|
commitdiff
|
tree
2013-01-17
Berk
Hess
fixed S
D
+
BD in
t
e
gration sl
o
wing down
w
it
h
OpenMP threads
commit
|
commitdiff
|
tree
2013-01-17
Be
r
k Hes
s
impr
o
ved C
U
DA k
e
rne
l
pe
r
formance by p
r
e-loading cj
commit
|
commitdiff
|
tree
2013-01-17
Ber
k
Hes
s
fixed nbnxn h
y
brid
mode with OpenMP
commit
|
commitdiff
|
tree
2013-01-17
Berk H
e
ss
made PME load
b
alancing + DD DLB more efficient
commit
|
commitdiff
|
tree
2013-01-16
Berk Hess
split off
p
ick_nbnxn_r
e
source from
nbnx
n
_pick_n
b
nx
n
commit
|
commitdiff
|
tree
2013-01-13
Berk
Hess
fix
e
d resett
i
n
g
state
s
w
i
th
para
l
lel V
e
rlet sch
e
me
commit
|
commitdiff
|
tree
2013-01-12
Berk Hess
prepared t
h
e
nbnxn code for non-x8
6
SIM
D
commit
|
commitdiff
|
tree
2013-01-11
Berk
Hess
m
ade SHAKE w
o
rk again with particle d
e
compostion
commit
|
commitdiff
|
tree
2013-01-10
Berk Hess
fixed nbnxn no LJ
c
omb
.
rul
e
AVX256
PME kernel
commit
|
commitdiff
|
tree
2013-01-10
B
erk Hess
fixed bug with Verlet + DD + bonded
a
tom commu
n
i
c
ati
o
n
commit
|
commitdiff
|
tree
2013-01-07
Berk He
s
s
f
ix
e
d nbn
x
n
AV
X
-256 Ewald table pointer alignmen
t
commit
|
commitdiff
|
tree
2013-01-02
B
e
rk Hess
minor speed-u
p
and c
o
de clea
n
-up in nbnxn kernels
commit
|
commitdiff
|
tree
2012-12-20
Berk Hess
fix
e
d rece
n
t bugs in LINCS for derivatives
commit
|
commitdiff
|
tree
2012-12-18
Berk
H
e
s
s
r
e
named gmx_x
8
6_simd_macro
s
.
h to g
m
x_simd_macros
.
h
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
implement
e
d nbnxn AVX-256
2x(N
+
N) kernels
commit
|
commitdiff
|
tree
2012-12-11
Ber
k
Hess
r
e
d
u
ced PL
I
NC
S
communic
a
tion with
H
-bond constra
i
nts
commit
|
commitdiff
|
tree
2012-12-07
B
e
rk Hess
fixed GPU
p
air
-
sear
c
h w
i
t
h G
M
X_
C
P
U_ACCE
L
ERATIO
N
=
N
one
commit
|
commitdiff
|
tree
2012-12-06
Berk Hess
removed last OpenM
P
O(nt
h
r
eads) bottleneck
commit
|
commitdiff
|
tree
2012-12-05
Berk
H
e
ss
f
ixed incorre
c
t v
i
ri
a
l w
i
th virtual sites and
O
penMP
commit
|
commitdiff
|
tree
2012-12-05
Berk Hess
fixed
seg
v
in Verlet
p
a
i
r-search w
i
th
t
rilini
c
DD
commit
|
commitdiff
|
tree
2012-11-30
Ber
k
H
e
ss
f
i
xed issue w
i
t
h
-multi
a
nd GPU
s
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
fixed
thread pinni
n
g
w
i
t
h mdrun -multi
commit
|
commitdiff
|
tree
2012-11-28
Berk Hes
s
exten
d
ed
n
bnxn x
8
6 SIMD kernel blendv suppor
t
commit
|
commitdiff
|
tree
2012-11-27
Berk Hess
fixed
bug in nbn
x
n OpenMP non-b
o
nded for
c
e reductio
n
commit
|
commitdiff
|
tree
2012-11-26
Berk Hess
made
n
bnxn an
a
lytical Ewald c
o
nsistent
commit
|
commitdiff
|
tree
2012-11-26
Berk Hess
add
e
d nb
n
xn an
a
lyti
c
al Ewald correction
k
ernels
commit
|
commitdiff
|
tree
2012-11-16
Berk Hess
re
d
uced the c
o
st
o
f
the nbnxn OpenMP n
b
-
force red
u
ction
commit
|
commitdiff
|
tree
2012-11-15
Berk
H
ess
fixed incorr
e
ct 1-4 energies with OpenMP
+
e
nergy
groups
commit
|
commitdiff
|
tree
2012-11-14
Berk He
s
s
fix
e
d nb
n
xn x86 SI
M
D non-
b
onded
perf
o
rma
n
c
e
regression
commit
|
commitdiff
|
tree
2012-11-12
Berk Hess
nbnx
n
CPU forc
e
buffer
r
eduction now uses
S
IMD
commit
|
commitdiff
|
tree
2012-11-06
B
e
rk Hess
Merge "Add option to
install libcudart
"
into release-4-6
commit
|
commitdiff
|
tree
2012-11-06
Berk Hess
Me
r
ge "don't execu
t
e any mp
i
_i
n
fo/mpiname in the path
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
Berk He
s
s
Merge "updated seve
r
a
l
th
i
ng
s
related
with Op
e
nMP thread
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
Berk Hess
updated seve
r
al
t
hi
n
gs related with
OpenMP thread
count
commit
|
commitdiff
|
tree
2012-10-26
Berk
Hess
fixed
inco
r
rect PME load
balan
c
ing limita
t
ion
commit
|
commitdiff
|
tree
2012-10-26
Berk
Hess
set th
e
default
for nstdhdl to 100
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
fixed incorrect group energi
e
s wit
h
nbnxn CPU kernels
commit
|
commitdiff
|
tree
2012-10-23
Berk Hess
f
i
xed bon
d
free
.
c thread
s
afety with f
r
e
e
en
e
rgy
commit
|
commitdiff
|
tree
2012-10-23
Berk Hess
moved part of nbnxn_sear
c
h
.
c to
n
b
n
xn_atomdata
.
c
commit
|
commitdiff
|
tree
2012-10-23
Be
r
k H
e
ss
fixed inco
r
rect LJ energy with GPU
and P
M
E load balancing
commit
|
commitdiff
|
tree
2012-10-22
B
e
rk Hess
added
O
pe
n
MP
pa
r
all
e
lizatio
n
for
v
irtu
a
l s
i
tes
commit
|
commitdiff
|
tree
2012-10-18
B
e
rk Hess
renamed co
n
str
a
int va
r
iab
l
es
rmdr t
o
vir_r_
m
_
dr
commit
|
commitdiff
|
tree
2012-10-18
Berk Hess
adde
d
OpenMP
p
aral
l
elization to LINCS proje
c
tion
commit
|
commitdiff
|
tree
2012-10-17
Berk
H
ess
renamed pme_switch
.
.
.
to
p
me_loadb
a
l
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Berk Hess
made p
a
ir-search with GPU 2
0
%
f
aster
commit
|
commitdiff
|
tree
2012-10-12
B
e
r
k H
e
ss
Merge "Fix illegal
b
arrier in wo
r
ksharing
"
into release-4
-
6
commit
|
commitdiff
|
tree
2012-10-08
Berk Hess
ma
d
e
no
n
-bonded po
t
ent
i
al shifts mdp
o
pt
i
ons
commit
|
commitdiff
|
tree
2012-10-04
B
e
rk Hess
fixed b
a
ckward co
m
patibil
i
ty of tpr files with dihres
commit
|
commitdiff
|
tree
2012-10-03
Berk Hess
i
m
proved th
e
e
n
e
r
gy conser
v
ation with
SETTLE
commit
|
commitdiff
|
tree
2012-09-13
Berk Hess
fixed rece
n
t bug
with gro
m
pp check
for P-
R
P-coupling
commit
|
commitdiff
|
tree
2012-08-29
B
erk H
e
ss
bug f
i
x for pme
.
c
M
PI_COMM_NULL fix dcf8b67e
commit
|
commitdiff
|
tree
2012-08-09
B
e
rk Hess
fixed
t
rjconv not
w
r
iting veloc
i
t
ies wit
h
c
pt input
commit
|
commitdiff
|
tree
2012-08-06
Berk Hess
fixed incorr
e
ct TPI r
e
sults with dynamic
b
ox
commit
|
commitdiff
|
tree
2012-07-18
Berk Hess
fixed
D
D charge gro
u
p displacement error
c
heck
commit
|
commitdiff
|
tree
2012-07-17
Berk Hess
fix a segfau
l
t in s
s
e_mask_init
commit
|
commitdiff
|
tree
2012-07-04
Berk
Hess
set default for rcoulomb,
rv
d
w a
n
d rl
i
st to -1
commit
|
commitdiff
|
tree
2012-06-25
Berk Hes
s
fixed
segv/hang with EM and foreign lambda values
commit
|
commitdiff
|
tree
2012-06-25
Berk Hess
a
d
d
ed check for log fp!=
N
ULL w
h
en
disa
b
ling a
c
ce
l
e
r
ation
commit
|
commitdiff
|
tree
2012-05-24
Berk Hess
now mdrun always initializes MPI
commit
|
commitdiff
|
tree
2012-05-21
Berk Hess
g
romp
p
now r
e
tains the o
r
der o
f
bonds con
v
erted to
.
.
.
commit
|
commitdiff
|
tree
2012-05-21
Berk Hess
re-int
r
oduced fix for
r
ea
l
/double issue in gmx_d
e
n
s
ity
commit
|
commitdiff
|
tree
2012-05-08
Berk Hes
s
fixed mdrun -cpi SD an
d
p
coupl
initialization
commit
|
commitdiff
|
tree
2012-04-28
Berk Hess
fixed PME forces wi
t
h FE, fix
e
s #
9
29 int
r
oduced in
.
.
.
commit
|
commitdiff
|
tree
2012-04-27
Berk Hess
fixed
s
egv in TPI w
i
th PME, f
i
xes #927
commit
|
commitdiff
|
tree
2012-04-27
Berk
H
ess
changed
P
ME MPI_Comm compari
s
i
o
ns to M
P
I_COMM_NULL
.
.
.
commit
|
commitdiff
|
tree
2012-04-27
Berk Hess
c
h
an
g
ed n
u
mber of iat
o
ms for F_SETTLE
from 1 to 3
commit
|
commitdiff
|
tree
2012-04-26
Berk
Hess
added suppor
t
for graphs not st
a
r
ting at 0
commit
|
commitdiff
|
tree
2012-04-26
Berk Hess
Merg
e
"Merge release-
4
-
5
-
patches i
n
t
o releas
e
-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
Berk Hess
Merge release-4-
5
-
patches into re
l
ease-4-6
commit
|
commitdiff
|
tree
2012-04-26
B
erk Hess
fix
e
d the reported
tempe
r
ature wit
h
Brownian dy
n
amics
commit
|
commitdiff
|
tree
2012-04-26
Be
r
k
Hess
fi
x
ed
d
is
p
ersion corre
c
tion wi
t
h para
l
lel
EM
commit
|
commitdiff
|
tree
2012-04-25
B
e
rk Hess
replac
e
d PPP
M
by P3M-AD:
a
few lines
i
n pme
.
c
commit
|
commitdiff
|
tree
2012-04-25
B
e
rk H
e
ss
fixed initial COM motion removal w
i
th mult
i
ple groups
commit
|
commitdiff
|
tree
2012-04-24
Berk
H
e
s
s
Merge "all
o
w -append to overrule unsupp
o
rt
e
d file locking
.
.
.
commit
|
commitdiff
|
tree
2012-04-18
Berk Hess
fixed segfa
u
lt in g
r
aph code wi
t
h coordinate su
b
sets
commit
|
commitdiff
|
tree
2012-04-18
Berk He
s
s
allow -appen
d
to
o
verrule unsupp
o
rt
e
d
file locking
commit
|
commitdiff
|
tree
2012-04-17
Berk Hess
changed mdrun file lock
i
ng n
o
t s
u
pported error to a
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
Berk
Hess
changed de
f
ault for nstxout, nstvout a
n
d
nstlog
commit
|
commitdiff
|
tree
2012-04-16
Berk Hess
checkpoint files now
c
ontain a d
o
uble pr
e
c
ision
f
lag
commit
|
commitdiff
|
tree
2012-03-27
B
e
r
k
Hess
added c
o
rrect
i
on
f
or PME vir
i
a
l
with
n
on-linear virtual
.
.
.
commit
|
commitdiff
|
tree
2012-03-23
Berk Hes
s
fix
e
d g
_
bar xvg re
a
ding issue
commit
|
commitdiff
|
tree
2012-03-17
B
e
r
k Hess
fixe
d
increasing memory usage w
i
th SHAKE and DD
commit
|
commitdiff
|
tree
2012-03-16
B
erk
H
e
ss
fixe
d
inc
o
rrect table allocat
i
on
commit
|
commitdiff
|
tree
2012-03-13
Berk Hess
mdrun -npme without PME
o
r with P
D
now gener
a
tes a
.
.
.
commit
|
commitdiff
|
tree
2012-03-05
B
erk H
e
ss
fixed g_a
n
aeig incorrect
m
ultiple extremes, fixes #87
0
commit
|
commitdiff
|
tree
2012-03-05
Ber
k
Hess
ad
d
ed check for mass
-
weighting with g
_
anaeig -entropy
.
.
.
commit
|
commitdiff
|
tree
2012-03-05
Berk
H
ess
removed i
n
i
t
ial te
m
per
a
t
u
re w
i
th Ope
n
MM, fi
x
e
s
#757
commit
|
commitdiff
|
tree
2012-02-28
B
e
rk
Hess
fixed array index out of bounds in EM force trr
s
t
ora
g
e
commit
|
commitdiff
|
tree
2012-02-26
B
erk
H
ess
us
e
s
eparate PME nodes with
#nodes>18
commit
|
commitdiff
|
tree
2012-02-23
Berk Hess
added tpx fi
l
e
t
ag stri
n
g
commit
|
commitdiff
|
tree
2012-02-20
Berk Hess
change
d
default epsilon
-
rf v
a
lue to 0
commit
|
commitdiff
|
tree
2012-02-19
Berk H
e
ss
Merge "G
e
n
erate warnings
for
Q
MMM us
a
ge"
i
nto
r
e
lease-4-6
commit
|
commitdiff
|
tree
2012-02-10
B
e
rk Hess
fixed gmxche
c
k segv with tpr files without AdResS
commit
|
commitdiff
|
tree
2012-02-06
Berk Hess
Fixed bug wi
t
h
C
OM m
o
tion remova
l
on par
t
of t
h
e system
commit
|
commitdiff
|
tree
2012-02-02
Berk Hes
s
Improved
t
he accura
c
y of the sd1 in
t
e
grator
commit
|
commitdiff
|
tree
2012-01-25
B
e
rk
H
ess
Me
r
ge "Added t
w
o new
bon
d
ed fun
c
tion
s
.
"
into releas
e
-4-6
commit
|
commitdiff
|
tree
2011-11-27
Berk Hess
fix
e
d pull c
o
n
s
traint
p
e
r
i
odici
t
y
co
n
si
s
tency check
.
.
.
commit
|
commitdiff
|
tree
2011-11-15
Ber
k
H
e
ss
fixed
dd load print frequ
e
ncy with
n
steps=-1, fixes
.
.
.
commit
|
commitdiff
|
tree
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