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Add one element to state rvec arrays
2015-12-16
B
erk
Hess
Add one element to state r
v
ec arra
y
s
commit
|
commitdiff
|
tree
2015-12-12
Berk Hess
Re
m
ove
d
unus
e
d
mdr
u
n o
p
tion -dn
commit
|
commitdiff
|
tree
2015-12-07
Berk
Hess
Mov
e
d pull p
a
r
ams to md
t
ypes/pull-params
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
In
c
rea
s
e pdb chai
n
ids
t
o 62 in ou
t
p
ut
commit
|
commitdiff
|
tree
2015-12-02
Berk
H
e
s
s
Refactored set_pb
c
_dd
commit
|
commitdiff
|
tree
2015-12-02
B
erk H
e
ss
Mad
e
t_inputrec const in PME load bal
a
nc
i
ng
commit
|
commitdiff
|
tree
2015-12-01
B
e
rk H
e
ss
Pull group cou
n
t for coords s
t
or
e
d in t
p
r
commit
|
commitdiff
|
tree
2015-11-19
B
e
rk Hess
Rem
o
ved mdr
u
n fatal_error with P3
M
-
AD
commit
|
commitdiff
|
tree
2015-11-18
Berk
Hess
Rem
o
ve
d
Reaction-Field
-
nec
commit
|
commitdiff
|
tree
2015-11-14
Berk Hess
Optimized the bonde
d
thread
f
or
c
e reduc
t
ion
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
Fi
x
ed (harml
e
ss) fp exception in wa
l
lc
y
cle_s
u
m
commit
|
commitdiff
|
tree
2015-11-09
Berk Hes
s
Co
r
re
c
t LINCS dH
d
l
contribution
commit
|
commitdiff
|
tree
2015-11-03
Berk H
e
ss
F
i
x no wallcycle support
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Re
m
ove
d
n
b
nxn
kernel blendv optimi
z
ation
commit
|
commitdiff
|
tree
2015-11-02
B
erk Hess
Fi
x
intermo
l
ec
u
la
r
interacti
o
ns wi
t
h small
mols
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
Fixed nbnx
n
_4xN per
f
orm
a
nce regressio
n
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
Fix b
u
gs with intermol interactions and DD
commit
|
commitdiff
|
tree
2015-10-01
Berk Hess
Removed CUD
A
polling wait
commit
|
commitdiff
|
tree
2015-09-27
Berk He
s
s
M
o
v
e
gmx_domdec_comm_t
d
efinition
commit
|
commitdiff
|
tree
2015-09-22
B
erk Hess
Remo
v
ed useless mul
t
ipl
e
s
h
i
f
ts in pbc
.
cpp
commit
|
commitdiff
|
tree
2015-09-16
Berk Hess
Split nbnx
n
_gri
d
.
c
off
from nbnxn_
s
earch
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk Hess
Detect incorr
e
ct cyc
l
e c
o
unting
commit
|
commitdiff
|
tree
2015-08-25
Berk
Hess
Simpli
f
y changing the tpx_
v
ersion
commit
|
commitdiff
|
tree
2015-08-14
B
e
rk Hess
M
a
ke mdrun -
n
t
wo
r
k agai
n
commit
|
commitdiff
|
tree
2015-08-13
Be
r
k
H
ess
Added set_pull_coord
_
reference_val
u
e
commit
|
commitdiff
|
tree
2015-08-12
B
e
rk Hess
A
dded const
q
ualifi
e
r
s to c
o
re MD routine
s
commit
|
commitdiff
|
tree
2015-07-08
Be
r
k Hess
Separate
d
b
o
nded and Ew
a
ld correction threading
commit
|
commitdiff
|
tree
2015-07-06
B
erk Hess
F
i
x too small G
P
U pair count esti
m
a
t
es
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fix bug in GPU
list bal
a
ncing
commit
|
commitdiff
|
tree
2015-07-05
Berk He
s
s
Fix DD DLB state issue
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
Fix bug
in GPU list balancing
commit
|
commitdiff
|
tree
2015-07-04
Berk Hes
s
Obey OpenMP t
h
read count limit w
i
th tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
Fix two PME DLB trigger issues
commit
|
commitdiff
|
tree
2015-07-03
Berk
H
ess
Corr
e
ct g
r
omp
p
pull warning mes
s
age
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Fix
in
c
onsis
t
ent OpenMP automa
t
i
o
n
commit
|
commitdiff
|
tree
2015-06-30
Be
r
k Hess
enabled 1 P
P
+ 1 PME node
commit
|
commitdiff
|
tree
2015-06-30
Be
r
k Hess
Add checks fo
r
i
n
efficient resource
u
sage
commit
|
commitdiff
|
tree
2015-06-29
B
erk Hes
s
I
m
p
r
ove DLB+P
M
E
tun
i
ng with GPUs
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
I
m
prove pair search thread
load balance
commit
|
commitdiff
|
tree
2015-06-27
Ber
k
Hess
Improved th
e
intra-GP
U
l
oa
d
balancing
commit
|
commitdiff
|
tree
2015-06-27
Be
r
k
Hess
Reduce the use of
nbnxn_consts
.
h
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Corrected nstcalclr/ns
t
fep/nst_repl_e
x
c
heck
s
commit
|
commitdiff
|
tree
2015-06-26
Berk Hess
Fixed Verlet buffer issue with 2-wide SIMD
commit
|
commitdiff
|
tree
2015-06-25
Berk Hess
Intermo
l
ecular bonded int
e
raction support added
commit
|
commitdiff
|
tree
2015-06-25
Be
r
k Hess
Reena
b
led SIMD
k
erne
l
s wi
t
ho
u
t cut-o
f
fs
commit
|
commitdiff
|
tree
2015-06-24
Be
r
k
H
ess
G
P
U
Ewald
t
able
kernel now uses
CPU spa
c
ing
commit
|
commitdiff
|
tree
2015-06-24
Berk
H
ess
Avoid GPU sel
e
c
t
i
on
w
it
h
G
P
U emula
t
i
o
n
commit
|
commitdiff
|
tree
2015-06-24
Berk
Hess
Mino
r
reformatting of SIMD mismatch mes
s
age
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Add sugar
to
print empty line in printBi
n
ary
I
nformation
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Fix g_ener
g
y a
v
erage/RMSD
bug
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Update l
a
u
n
c
h configuration for physical nodes
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Avoi
d
fp exceptions
i
n pair searc
h
debug
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Re
p
laced har
d
ware th
r
eads by l
o
gical cor
e
s in output
commit
|
commitdiff
|
tree
2015-06-18
Ber
k
Hess
R
e
du
c
ed the cost of
the pull comm
u
ni
c
ation
commit
|
commitdiff
|
tree
2015-06-17
B
e
rk H
e
ss
Refacto
r
ed pull data structures
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
A
d
ded missing
DD cycle counting
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
A
utoma
t
ed
t
he -gpu_id option
commit
|
commitdiff
|
tree
2015-06-14
Be
r
k
H
ess
Refac
t
ored mdrun resou
r
ce div
i
s
ion
commit
|
commitdiff
|
tree
2015-06-13
Berk Hess
Hardwa
r
e reporting now
c
overs all nod
e
s
commit
|
commitdiff
|
tree
2015-06-05
Be
r
k
Hess
D
on
'
t u
s
e PME r
a
n
k
s with
G
P
Us and -npme=-1
commit
|
commitdiff
|
tree
2015-05-27
Berk Hes
s
Refactoring of
P
M
E load balancing
commit
|
commitdiff
|
tree
2015-05-23
Berk He
s
s
Rem
o
ved sta
t
ic f
r
om variables in gmx_lapack
commit
|
commitdiff
|
tree
2015-05-16
Berk Hess
LINCS thread tasks can now be independ
e
nt
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fixed CUDA
e
rror with empty domains
commit
|
commitdiff
|
tree
2015-05-13
Berk
He
s
s
Fix segv in g_covar
commit
|
commitdiff
|
tree
2015-05-11
Be
r
k
Hess
Changed F
F
T
W warning fr
o
m AVX
t
o
n
o
SSE
commit
|
commitdiff
|
tree
2015-05-07
Berk
Hess
Removed non
-
ff atomtypes from oplsaa and
c
harmm27
commit
|
commitdiff
|
tree
2015-05-04
Ber
k
Hess
Fixed GPU non-local F cop
y
loc
a
l condit
i
onal
commit
|
commitdiff
|
tree
2015-04-28
Be
r
k Hess
Re-en
a
b
l
e
d FMA for AVX-128-FMA
commit
|
commitdiff
|
tree
2015-04-22
Berk Hess
Me
r
ge bran
c
h 'release-5-0'
commit
|
commitdiff
|
tree
2015-04-17
Be
r
k H
e
ss
Add value_ref and val
u
e to pull_coord_t
commit
|
commitdiff
|
tree
2015-04-17
Berk
H
e
ss
Correct -
n
t
mpi auto
for intel n
e
halem an
d
older
commit
|
commitdiff
|
tree
2015-04-08
B
e
r
k
H
e
ss
Added pul
l
geometry direction-rela
t
i
ve
commit
|
commitdiff
|
tree
2015-04-01
Berk Hess
Correc
t
e
d
f
o
rce-swi
t
ch ma
n
ual section
commit
|
commitdiff
|
tree
2015-03-19
B
erk
H
ess
Removed reduction
o
f dH/dl
without FE
commit
|
commitdiff
|
tree
2015-03-12
Berk Hess
Fixed m
d
run fp exception with -debug
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Added update
x copy-b
a
c
k
to up
d
ate timer
commit
|
commitdiff
|
tree
2015-03-11
B
e
rk Hess
Reduc
e
d cost of Berendsen pressure coupling
commit
|
commitdiff
|
tree
2015-03-06
Berk Hess
Im
p
ro
v
e threading
o
f bondeds
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
Made DD e
x
clusion proces
s
ing more eff
i
c
i
ent
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
SIMD acceleration for
LIN
C
S
commit
|
commitdiff
|
tree
2015-03-04
Ber
k
Hess
A
l
low pull groups of 1 atom wi
t
h mass 0
commit
|
commitdiff
|
tree
2015-03-04
Be
r
k Hess
COM pu
l
li
n
g
op
t
i
on
s
per coord, improve
d
cylinder
commit
|
commitdiff
|
tree
2015-03-03
B
erk Hess
F
i
x di
v
by zero in PP/PM
E
ratio
commit
|
commitdiff
|
tree
2015-03-02
Berk Hess
Added par
e
nthe
s
es
f
or ca
s
ts in SIMD mac
r
os
commit
|
commitdiff
|
tree
2015-02-24
Berk Hess
F
ixed parallel
dist
r
ibution
and thread count reporting
commit
|
commitdiff
|
tree
2015-02-12
Berk H
e
ss
Re-fix
e
d
PME bug with high OpenMP th
r
e
a
d
count
commit
|
commitdiff
|
tree
2015-02-06
Berk Hess
Re-
e
nabled SIMD
f
o
r
angl
e
s and d
i
hedrals
commit
|
commitdiff
|
tree
2015-02-04
B
erk He
s
s
Correct CUDA kerne
l
en
e
rgy
f
lag
commit
|
commitdiff
|
tree
2015-01-21
Be
r
k Hess
Corrected RDTSCP w
a
r
n
ing t
e
xt
commit
|
commitdiff
|
tree
2015-01-15
B
e
rk Hess
Fix alloca
t
ion issue
w
ith VV integrator
commit
|
commitdiff
|
tree
2014-12-22
Berk
H
e
ss
F
i
xed pb
c
=xy
+
2
wal
l
s + V
e
rle
t
sc
h
eme
commit
|
commitdiff
|
tree
2014-12-22
Berk
He
s
s
Fix bug FE
+ G
P
U + 2/3D
d
omain decomposition
commit
|
commitdiff
|
tree
2014-12-11
Be
r
k Hess
A
dded grompp error fo
r
pulling to n
e
gative distance
commit
|
commitdiff
|
tree
2014-12-09
B
e
r
k Hess
Fix recent bug with
t
ri
l
inic
1D DD
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Fixed pull coord init w
i
th
r
at
e
!=0
,
t_star
t
!=0
commit
|
commitdiff
|
tree
2014-12-08
Berk He
s
s
Added PBC note to comm
-
mode=angular w
a
rning
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Make domdec a proper module
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Cla
r
ified grompp pull error m
e
ssag
e
s
commit
|
commitdiff
|
tree
2014-12-05
B
e
rk Hes
s
Avoid race on dvdl wi
t
h Verlet+O
p
e
nMP+LI
N
C
S
+FE+V
V
commit
|
commitdiff
|
tree
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