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Moved pull initialization back to mdrunner
2016-03-21
Berk Hes
s
Moved pull initializ
a
t
i
on back to m
d
r
u
n
ner
commit
|
commitdiff
|
tree
2016-03-12
B
er
k
Hess
Split off Fermi kernel fr
o
m
CUDA
k
er
n
el
commit
|
commitdiff
|
tree
2016-03-04
Berk He
s
s
Converted
c
s
e
ttle
(
)
t
o use real/
S
imdReal tem
p
late
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Use SIMD transpose scat
t
e
r
in
bonde
d
s
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Use rvec4
f
or listed force buff
e
r
commit
|
commitdiff
|
tree
2016-02-27
Ber
k
Hess
Re
m
ove
epsfac from G
P
U k
e
rnel
i
n
ner-loops
commit
|
commitdiff
|
tree
2016-02-27
B
e
rk Hess
Min
o
r
code re
o
rdering in GPU ke
r
nel
s
commit
|
commitdiff
|
tree
2016-02-26
Be
r
k
H
ess
Fix
c
o
m
pilat
i
on with Sim
d
4Float, w
i
thout
Simd4Do
u
ble
commit
|
commitdiff
|
tree
2016-02-19
Be
r
k Hess
Fix excessiv
e
l
i
st splitting
commit
|
commitdiff
|
tree
2016-02-17
Ber
k
Hes
s
Renamed nbnxn stat
i
c const ints
commit
|
commitdiff
|
tree
2016-02-11
Berk H
e
s
s
Add S
I
MD
version of pbc_dx_aiuc
commit
|
commitdiff
|
tree
2016-02-09
Berk
H
es
s
Replaced nbnxn
sea
r
ch+grid
simd macros
commit
|
commitdiff
|
tree
2016-02-07
Berk Hess
Fix incorrect c
m
ap
p
a
r
sing
commit
|
commitdiff
|
tree
2016-02-05
Berk Hess
Fix incorrect cmap parsing
commit
|
commitdiff
|
tree
2016-02-03
B
erk
H
e
ss
Repla
c
ed
l
i
terals in n
b
nxn
l
ists by in
t
s
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix mdrun
remo
v
ing Verl
e
t
b
uffer
w
ith EM
commit
|
commitdiff
|
tree
2016-02-03
Berk
Hess
Fix
SETTLE error handling
commit
|
commitdiff
|
tree
2016-01-29
Be
r
k Hess
Added
documenta
t
ion for pme grid i
n
dexing
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix TPI
ign
o
ring
P
M
E
mesh
contributi
o
n
s
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Update -ntomp_pme -npme c
h
eck
commit
|
commitdiff
|
tree
2016-01-29
Ber
k
Hess
Add check for double p
e
r
turbation
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix LINCS t
r
i
a
ngle constrai
n
t
thread
i
ss
u
e
commit
|
commitdiff
|
tree
2016-01-28
Berk H
e
ss
U
p
date
p
air-l
i
st bu
f
f
e
r manual
commit
|
commitdiff
|
tree
2016-01-24
B
erk H
e
ss
Fix
exact
co
n
tinuatio
n
f
rom
non-energy st
e
ps
commit
|
commitdiff
|
tree
2016-01-24
Berk
Hess
Fix energy file continuation with md-v
v
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix en
e
rgy av
e
rage w
i
t
h
con
t
inuation
commit
|
commitdiff
|
tree
2016-01-08
B
erk Hess
Fix PME load balanci
n
g s
k
ippi
n
g a setup
commit
|
commitdiff
|
tree
2015-12-29
B
e
r
k
Hess
C
orrect
v
ector ch
e
ck of gm
x
check
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
Re
o
rganized d
o
mdec i
n
itialization
commit
|
commitdiff
|
tree
2015-12-20
Berk Hess
Merge releas
e
-5-1 into m
a
st
e
r
commit
|
commitdiff
|
tree
2015-12-19
Berk H
e
ss
Bring p
e
rformanc
e
estimation
up to date
commit
|
commitdiff
|
tree
2015-12-17
Berk Hess
Removed top
o
logy point
e
r
s f
r
om DD stru
c
t
commit
|
commitdiff
|
tree
2015-12-16
Berk
Hess
A
d
d one e
l
e
ment to state rv
e
c a
r
rays
commit
|
commitdiff
|
tree
2015-12-12
Berk Hess
Removed unused mdrun option
-dn
commit
|
commitdiff
|
tree
2015-12-11
Berk Hess
Fix
bug with pull
g
roup
w
e
ights
commit
|
commitdiff
|
tree
2015-12-07
Berk H
e
ss
Move
d
pull
par
a
ms to
m
dtypes/pull
-
params
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Increase
p
d
b chain ids to 62 in
o
u
t
put
commit
|
commitdiff
|
tree
2015-12-02
B
e
rk Hess
Refactored set_p
b
c_dd
commit
|
commitdiff
|
tree
2015-12-02
Berk Hes
s
Made t_i
n
putrec c
o
nst in PME load balancing
commit
|
commitdiff
|
tree
2015-12-01
B
erk Hess
P
ul
l
group count f
o
r coo
r
ds
s
tor
e
d
i
n tpr
commit
|
commitdiff
|
tree
2015-11-19
B
e
r
k Hess
Removed mdrun fatal_error with P3M-AD
commit
|
commitdiff
|
tree
2015-11-18
B
erk Hess
R
e
move
d
Reactio
n
-
Field-nec
commit
|
commitdiff
|
tree
2015-11-14
Berk Hess
Optimize
d
the bon
d
ed thread
fo
r
ce reduc
t
ion
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
F
i
x
ed (harmless) fp
e
x
c
eption
i
n wallc
y
cle_sum
commit
|
commitdiff
|
tree
2015-11-09
Ber
k
Hess
Correc
t
LINCS dHdl contribution
commit
|
commitdiff
|
tree
2015-11-03
Be
r
k
H
ess
Fix no wa
l
lcycle suppo
r
t
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Removed nbnxn
k
ernel blendv
optimization
commit
|
commitdiff
|
tree
2015-11-02
Berk Hess
Fix intermolecular
i
n
t
eractions with sm
a
l
l mols
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
F
ixe
d
nb
n
x
n
_4
x
N performance regressi
o
n
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
Fix bugs wit
h
intermo
l
in
t
e
r
action
s
and DD
commit
|
commitdiff
|
tree
2015-10-01
Berk Hess
Remo
v
ed
CUDA poll
i
ng wai
t
commit
|
commitdiff
|
tree
2015-09-27
B
er
k
Hess
Move gmx_domdec_com
m
_t definition
commit
|
commitdiff
|
tree
2015-09-22
Berk H
e
ss
Removed useless multipl
e
shifts
i
n pbc
.
cp
p
commit
|
commitdiff
|
tree
2015-09-16
Berk
H
ess
Spl
i
t nbnxn_g
r
id
.
c
o
ff
f
r
om nbnxn_
s
earch
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk
H
es
s
D
etect i
n
correct cycle coun
t
ing
commit
|
commitdiff
|
tree
2015-08-25
Berk He
s
s
Simplify
c
hanging the
t
px_
v
e
r
s
i
on
commit
|
commitdiff
|
tree
2015-08-14
B
erk Hess
M
a
ke mdrun -nt work again
commit
|
commitdiff
|
tree
2015-08-13
B
erk Hess
Added set_pull_coord_reference_value
commit
|
commitdiff
|
tree
2015-08-12
Berk Hess
Added const qual
i
fi
e
rs to
core M
D
routines
commit
|
commitdiff
|
tree
2015-07-08
Berk Hess
Separated b
o
nded and Ewal
d
correction
t
hreadin
g
commit
|
commitdiff
|
tree
2015-07-06
Berk
H
e
s
s
Fix too sma
l
l GPU pair cou
n
t est
i
m
a
tes
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
F
ix bug
i
n GPU list
balancing
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
F
ix
D
D D
L
B state issue
commit
|
commitdiff
|
tree
2015-07-05
Berk
H
ess
Fix bug
in
GPU li
s
t
ba
l
a
n
cing
commit
|
commitdiff
|
tree
2015-07-04
Berk H
e
ss
Obey OpenMP th
r
ead cou
n
t
l
imi
t
with tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk He
s
s
Fix tw
o
P
M
E DLB trigger is
s
ues
commit
|
commitdiff
|
tree
2015-07-03
Berk Hess
Correct grompp
p
ull
warning message
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Fix inconsistent Open
M
P
automatio
n
commit
|
commitdiff
|
tree
2015-06-30
Berk Hes
s
enab
l
ed
1 PP + 1 PME
n
o
de
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Add
c
he
c
ks for ineff
i
cient resource usage
commit
|
commitdiff
|
tree
2015-06-29
Berk
H
ess
Improve DL
B
+P
M
E tuning with
G
PUs
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
I
mpr
o
ve pair search thread load b
a
lance
commit
|
commitdiff
|
tree
2015-06-27
Be
r
k H
e
ss
Improved the intr
a
-GP
U
load balancing
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk
He
s
s
Redu
c
e t
h
e use
of nbnxn_consts
.
h
commit
|
commitdiff
|
tree
2015-06-27
Ber
k
Hess
Corrected nstcalclr/n
s
tfe
p
/nst
_
repl_e
x
checks
commit
|
commitdiff
|
tree
2015-06-26
Ber
k
Hess
Fixed V
e
rlet buffer issue
with 2-wi
d
e
S
I
MD
commit
|
commitdiff
|
tree
2015-06-25
Berk Hess
Intermolecula
r
bonded interac
t
ion
s
upport added
commit
|
commitdiff
|
tree
2015-06-25
Berk Hess
R
e
e
n
a
bled SIMD kern
e
ls
wit
h
out
cut-o
f
fs
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
GPU Ewald ta
b
le kernel
now u
s
es
C
P
U spacing
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Avoid GPU se
l
ectio
n
wit
h
GP
U
emulation
commit
|
commitdiff
|
tree
2015-06-24
B
e
r
k Hess
Mino
r
r
e
formattin
g
of SIMD mismatch mess
a
ge
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Add sugar to pr
i
nt em
p
ty line
i
n printB
i
nar
y
Informa
t
ion
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
F
i
x
g_ene
r
gy avera
g
e/RMSD bug
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Update
lau
n
ch configuration f
o
r physical
no
d
e
s
commit
|
commitdiff
|
tree
2015-06-22
Berk
H
ess
Avoi
d
f
p exceptions in pair sear
c
h debug
commit
|
commitdiff
|
tree
2015-06-22
Ber
k
Hess
Replaced
h
a
rdware threads by logical cores
in o
u
tput
commit
|
commitdiff
|
tree
2015-06-18
Berk Hess
Reduced th
e
c
o
s
t
o
f t
h
e pull
communication
commit
|
commitdiff
|
tree
2015-06-17
Berk Hess
Refacto
r
e
d pull data s
t
ructures
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
A
dded mis
s
ing
D
D cycle counti
n
g
commit
|
commitdiff
|
tree
2015-06-16
B
e
rk
Hess
Automated the -gpu_id optio
n
commit
|
commitdiff
|
tree
2015-06-14
B
erk Hes
s
Refactored
m
drun resource division
commit
|
commitdiff
|
tree
2015-06-13
Berk
Hess
Hard
w
are reporting now
c
ove
r
s all nodes
commit
|
commitdiff
|
tree
2015-06-05
Berk H
e
ss
Don't use PME ra
n
ks with GPUs and -npme
=
-1
commit
|
commitdiff
|
tree
2015-05-27
Berk
H
es
s
Refactoring of PME load balancing
commit
|
commitdiff
|
tree
2015-05-23
Berk Hess
Remo
v
ed static fro
m
vari
a
bles
in gm
x
_
l
apack
commit
|
commitdiff
|
tree
2015-05-16
Berk Hess
LINCS thread task
s
can now be independ
e
nt
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fix
e
d
CUDA error wi
t
h emp
t
y do
m
ains
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fix
segv in g_covar
commit
|
commitdiff
|
tree
2015-05-11
Berk
H
e
ss
Chan
g
e
d
F
FTW war
n
ing
f
r
o
m
A
VX to no SSE
commit
|
commitdiff
|
tree
2015-05-07
B
e
rk H
e
ss
Re
m
oved non-ff atomtypes
f
r
om o
p
lsaa a
n
d
c
harmm27
commit
|
commitdiff
|
tree
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