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Fix SETTLE error handling
2016-02-03
Be
r
k
H
e
ss
Fix SET
T
L
E
erro
r
handling
commit
|
commitdiff
|
tree
2016-01-29
B
erk Hess
Fix TPI ig
n
oring P
M
E mes
h
c
ontri
b
u
tions
.
commit
|
commitdiff
|
tree
2016-01-29
Berk
H
ess
Add
c
heck for double pertur
b
a
t
ion
commit
|
commitdiff
|
tree
2016-01-29
Berk
H
es
s
Fix LINCS triang
l
e
constraint threa
d
i
s
sue
commit
|
commitdiff
|
tree
2016-01-28
B
er
k
He
s
s
Update pair-lis
t
buffer
m
a
n
ual
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix exact c
o
ntin
u
ation from no
n
-en
e
rgy s
t
eps
commit
|
commitdiff
|
tree
2016-01-24
Berk He
s
s
Fix ene
r
gy
f
i
le cont
i
nua
t
ion w
i
t
h m
d
-vv
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix ener
g
y ave
r
age with contin
u
ation
commit
|
commitdiff
|
tree
2016-01-08
Berk Hess
Fix
P
ME lo
a
d balancing skippi
n
g
a
setup
commit
|
commitdiff
|
tree
2015-12-29
Berk Hess
Co
r
rect vecto
r
check of gm
x
che
c
k
commit
|
commitdiff
|
tree
2015-12-19
Berk Hess
B
ring
p
erf
o
rmance estimati
o
n up to date
commit
|
commitdiff
|
tree
2015-12-11
Berk Hess
Fi
x
bu
g
w
i
t
h
pull gr
o
u
p
w
e
i
g
h
t
s
commit
|
commitdiff
|
tree
2015-11-19
Ber
k
Hess
Re
m
ove
d
mdrun
f
atal_e
r
ror with P3M-AD
commit
|
commitdiff
|
tree
2015-11-09
Be
r
k Hess
Correc
t
LINCS dHd
l
contribution
commit
|
commitdiff
|
tree
2015-11-02
Berk Hess
Fix in
t
ermolecu
l
ar
i
nteractions wit
h
small mols
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
Fix
e
d nbnxn_4
x
N
p
erf
o
rmance regression
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
Fix bugs with
i
ntermol interac
t
ions a
n
d
DD
commit
|
commitdiff
|
tree
2015-09-15
Berk
Hess
Detect incor
r
ect cycle c
o
u
n
ting
commit
|
commitdiff
|
tree
2015-08-14
Be
r
k Hess
M
ake mdrun -nt
w
ork aga
i
n
commit
|
commitdiff
|
tree
2015-07-06
Ber
k
Hess
Fix too s
m
all
G
PU pair count est
i
mates
commit
|
commitdiff
|
tree
2015-07-06
Be
r
k Hess
F
i
x bug in G
P
U list balancing
commit
|
commitdiff
|
tree
2015-07-05
B
e
rk H
e
ss
Fix DD
D
LB state issue
commit
|
commitdiff
|
tree
2015-07-05
Berk He
s
s
Fix
b
u
g
i
n GPU list ba
l
ancing
commit
|
commitdiff
|
tree
2015-07-04
B
e
rk
Hess
Obey OpenMP
t
hread count limi
t
with
tMPI
commit
|
commitdiff
|
tree
2015-07-04
B
e
rk Hess
Fix two PME D
L
B trigger issues
commit
|
commitdiff
|
tree
2015-07-03
B
e
r
k
H
e
ss
Co
r
r
ect grompp pull w
a
rning mess
a
ge
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
F
ix
i
nconsistent OpenMP automation
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
enabl
e
d 1 PP + 1
P
ME node
commit
|
commitdiff
|
tree
2015-06-30
Ber
k
Hess
A
dd checks f
o
r i
n
effic
i
ent resour
c
e
usage
commit
|
commitdiff
|
tree
2015-06-29
Berk Hess
I
mp
r
ove DLB+PME tuning
w
ith GPUs
commit
|
commitdiff
|
tree
2015-06-27
Berk
H
ess
I
mprove pair
s
e
ar
c
h
t
hread lo
a
d ba
l
ance
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Improved t
h
e
i
ntra-G
P
U l
o
ad b
a
lancing
commit
|
commitdiff
|
tree
2015-06-27
B
e
r
k
H
es
s
Reduce the
u
se of
n
bnxn
_
consts
.
h
commit
|
commitdiff
|
tree
2015-06-27
Be
r
k Hess
Co
r
r
e
cted nst
c
alclr/nstf
e
p
/
nst_repl_ex ch
e
ck
s
commit
|
commitdiff
|
tree
2015-06-26
B
erk
H
ess
Fixed Verlet b
u
ff
e
r issu
e
wit
h
2-wide SIMD
commit
|
commitdiff
|
tree
2015-06-25
Berk Hess
Inte
r
molecular
bonded intera
c
tion support added
commit
|
commitdiff
|
tree
2015-06-25
B
e
rk Hess
Reenabled SIMD kernels with
o
u
t cut-offs
commit
|
commitdiff
|
tree
2015-06-24
Berk Hes
s
GPU Ewald table
k
er
n
el now
u
ses CPU spacing
commit
|
commitdiff
|
tree
2015-06-24
B
erk Hess
Avo
i
d GPU selec
t
ion with GPU emulation
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Min
o
r
reform
a
tt
i
n
g
of SIMD mismatch
m
e
s
sage
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Add sugar to print empty line in
pr
i
ntBinaryI
n
formation
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Fix g_energy average/RMSD bug
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Update launch configur
a
t
i
o
n f
o
r physical node
s
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Avoid fp exceptions in pair se
a
rch debug
commit
|
commitdiff
|
tree
2015-06-22
Berk He
s
s
Replaced hardware
threads
b
y logical cores in outpu
t
commit
|
commitdiff
|
tree
2015-06-18
Berk Hess
R
e
duced t
h
e
cost of the pull communi
c
ation
commit
|
commitdiff
|
tree
2015-06-17
B
erk Hess
Refactore
d
pull data structures
commit
|
commitdiff
|
tree
2015-06-16
B
e
rk
H
es
s
Ad
d
e
d
missing
D
D cyc
l
e counting
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Automated the -gpu_id
o
ption
commit
|
commitdiff
|
tree
2015-06-14
Berk
Hess
R
e
f
a
ctored
m
d
r
u
n
r
e
source divi
s
ion
commit
|
commitdiff
|
tree
2015-06-13
B
erk
H
ess
Hardware reportin
g
no
w
c
o
v
e
r
s
all nodes
commit
|
commitdiff
|
tree
2015-06-05
Berk Hes
s
Don't use PME ranks
w
i
th GPUs a
n
d -npme=-1
commit
|
commitdiff
|
tree
2015-05-27
Berk Hess
Refa
c
tor
i
ng
of PME
l
oad b
a
lancing
commit
|
commitdiff
|
tree
2015-05-23
Berk He
s
s
Re
m
ove
d
sta
t
ic from variables i
n
gmx_la
p
ac
k
commit
|
commitdiff
|
tree
2015-05-16
Berk Hess
LINCS thread tasks can n
o
w be independent
commit
|
commitdiff
|
tree
2015-05-13
Berk Hes
s
F
ixed CUDA
e
rror with empty domai
n
s
commit
|
commitdiff
|
tree
2015-05-13
B
e
rk Hess
F
ix segv in g_covar
commit
|
commitdiff
|
tree
2015-05-11
Berk Hess
C
h
a
n
ged FF
T
W warning from AVX to
n
o
S
S
E
commit
|
commitdiff
|
tree
2015-05-07
B
e
rk Hes
s
Remov
e
d non-ff atom
t
y
p
es from op
l
saa a
n
d
c
harmm27
commit
|
commitdiff
|
tree
2015-05-04
Ber
k
Hess
Fi
x
ed G
P
U non-local F cop
y
lo
c
al co
n
di
t
ional
commit
|
commitdiff
|
tree
2015-04-28
Berk Hess
R
e
-
enabled FMA for
A
VX
-
128-FMA
commit
|
commitdiff
|
tree
2015-04-22
Be
r
k Hess
Merge branch 'r
e
lease-5-
0
'
commit
|
commitdiff
|
tree
2015-04-17
Berk
H
ess
A
d
d
value_ref and value to pull_c
o
ord_t
commit
|
commitdiff
|
tree
2015-04-17
B
e
rk Hess
Correct
-
n
tmpi
a
uto fo
r
intel nehalem and older
commit
|
commitdiff
|
tree
2015-04-08
Berk
Hess
A
d
ded
p
ull
geome
t
ry direc
t
i
o
n-relative
commit
|
commitdiff
|
tree
2015-04-01
Berk H
e
ss
C
o
rrected force-swit
c
h
m
anual section
commit
|
commitdiff
|
tree
2015-03-19
Berk Hess
Removed r
e
duction
of dH/dl without FE
commit
|
commitdiff
|
tree
2015-03-12
Be
r
k
H
ess
Fixed md
r
u
n
fp
e
x
c
ep
t
ion with -debug
commit
|
commitdiff
|
tree
2015-03-11
B
erk Hess
Add
e
d updat
e
x copy-back to updat
e
t
i
mer
commit
|
commitdiff
|
tree
2015-03-11
B
e
rk Hess
Redu
c
ed cost of Berendsen pressure coupling
commit
|
commitdiff
|
tree
2015-03-06
Berk He
s
s
Improv
e
th
r
e
adin
g
of bondeds
commit
|
commitdiff
|
tree
2015-03-05
Ber
k
Hess
Made DD exclusio
n
proces
s
ing m
o
re efficient
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
S
I
MD accele
r
ation for L
I
NCS
commit
|
commitdiff
|
tree
2015-03-04
Be
r
k Hess
Allow pull group
s
of 1 atom
w
ith mass 0
commit
|
commitdiff
|
tree
2015-03-04
Berk
H
e
ss
COM pulling
options p
e
r coord
,
imp
r
o
v
e
d
cyl
i
nd
e
r
commit
|
commitdiff
|
tree
2015-03-03
Be
r
k
H
ess
Fix div by zero in P
P
/
PME r
a
t
i
o
commit
|
commitdiff
|
tree
2015-03-02
Berk Hess
Adde
d
pa
r
entheses for casts in SIMD m
a
cros
commit
|
commitdiff
|
tree
2015-02-24
Be
r
k Hess
Fixe
d
pa
r
a
l
l
el distribution
a
n
d
thread
c
o
u
nt reportin
g
commit
|
commitdiff
|
tree
2015-02-12
Berk Hes
s
Re-fixed PME
b
ug with high Ope
n
MP thread
c
ount
commit
|
commitdiff
|
tree
2015-02-06
Be
r
k Hess
R
e-enabled SIMD
f
or a
n
gles and
d
ihedrals
commit
|
commitdiff
|
tree
2015-02-04
Berk Hes
s
Correct CUDA kernel en
e
rg
y
flag
commit
|
commitdiff
|
tree
2015-01-21
Berk Hess
Cor
r
e
c
ted RDTSCP warn
i
ng te
x
t
commit
|
commitdiff
|
tree
2015-01-15
B
erk Hess
Fix allo
c
ati
o
n is
s
u
e with VV integr
a
tor
commit
|
commitdiff
|
tree
2014-12-22
Berk Hess
Fixed pbc=
x
y + 2 walls +
Verlet scheme
commit
|
commitdiff
|
tree
2014-12-22
Berk H
e
ss
Fix bug
FE + GPU + 2
/
3D domain
de
c
o
mposition
commit
|
commitdiff
|
tree
2014-12-11
Berk He
s
s
Added grompp erro
r
fo
r
pullin
g
to nega
t
ive dist
a
nce
commit
|
commitdiff
|
tree
2014-12-09
Berk
H
ess
Fix recent bug with
trilinic 1D DD
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Fixed pull coord init
with r
a
te!=0
,
t_sta
r
t!=0
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
A
dded PB
C
note to comm
-
mode=a
n
gular w
a
rning
commit
|
commitdiff
|
tree
2014-12-05
Berk H
e
ss
Make domdec
a prope
r
m
od
u
le
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Clarified grompp pull error
m
e
s
s
a
ges
commit
|
commitdiff
|
tree
2014-12-05
Berk
Hess
Avoid ra
c
e on dvdl wit
h
Ve
r
let+OpenMP+LINCS+FE+VV
commit
|
commitdiff
|
tree
2014-12-01
Berk Hess
Added warning
for un
n
ece
s
sary
s
oft-core
commit
|
commitdiff
|
tree
2014-11-26
Berk Hess
Fix
e
d triclinic
1
x
N
x1
domain de
c
o
mposit
i
on
commit
|
commitdiff
|
tree
2014-11-25
Berk Hess
F
i
xed twin-r
a
nge + free
z
e +
c
onstr
a
int
s
commit
|
commitdiff
|
tree
2014-11-24
Berk Hess
Avoi
d
N
a
N in rli
s
t buffer calculation
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
C
o
r
r
e
ct
e
d
paramet
e
r for sorting on search grid
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
Fix DD bo
n
ded intera
c
tion ran
g
e print
commit
|
commitdiff
|
tree
2014-10-20
B
e
rk H
e
ss
Rem
o
v
ed
f
_no
v
irsum
r
ed
u
ction in Verlet sc
h
eme
commit
|
commitdiff
|
tree
2014-10-07
B
e
rk Hess
Fixes
i
s
s
ue wit
h
vsiten and Verlet b
u
ffers
commit
|
commitdiff
|
tree
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