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Make multi-atom TPI reproducible
2018-03-06
Berk Hess
M
a
ke multi-a
t
om TP
I
r
ep
r
oducible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Work around
g
cc
b
ug with g
r
oup kernel tab
l
es
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix AWH
bias-sha
r
ing with parallel s
i
mulation
commit
|
commitdiff
|
tree
2018-03-01
Berk
Hess
Detect AMD
S
MT top
o
l
o
gy
commit
|
commitdiff
|
tree
2018-03-01
Berk
H
ess
Fi
x
mdrun multisim w
i
th se
p
arat
e
P
M
E
ran
k
s
commit
|
commitdiff
|
tree
2018-02-23
B
e
rk Hess
Fi
x
md in
t
egrator with Nose-
H
o
o
v
er coupling
commit
|
commitdiff
|
tree
2018-02-16
B
erk Hess
Correct mul
t
isim MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix ra
n
ge bug
i
n add_select
i
on_groups i
n
tngi
o
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
B
erk
Hess
Fix grompp
n
et charg
e
c
h
e
ck
commit
|
commitdiff
|
tree
2018-02-14
Berk Hes
s
Fi
x
grompp net c
h
arge check
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
ess
Us
e
SIMD bondeds withou
t
p
e
rtur
b
ed interactions
commit
|
commitdiff
|
tree
2018-02-08
Berk Hess
A
l
low bonds with distance=0
commit
|
commitdiff
|
tree
2018-02-05
Berk
He
s
s
Set cutoff mod
i
fiers in f
o
r
c
erec
commit
|
commitdiff
|
tree
2018-02-05
Berk
Hess
Fi
x
assertion failure i
n
TPI
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix COM
M
r
emova
l
on
p
a
rt of
t
he sy
s
tem
commit
|
commitdiff
|
tree
2018-01-18
B
e
rk
Hes
s
Add check in g
r
o
mpp to avo
i
d asse
r
tion fai
l
u
r
e
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
R
e
-en
a
ble GPU with w
a
lls an
d
1 energy gro
u
p
commit
|
commitdiff
|
tree
2018-01-16
Ber
k
Hess
Rem
o
ve tumbling ice-cube wa
r
ni
n
g with
SD
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
A
v
oid mdrun
e
choi
n
g "
N
o option -multi
"
commit
|
commitdiff
|
tree
2018-01-09
Ber
k
H
e
ss
R
e
word
C
P
U/GPU imbalance n
o
tes
commit
|
commitdiff
|
tree
2018-01-09
Berk
Hes
s
D
o not turn on DLB at
replica
exchange
commit
|
commitdiff
|
tree
2018-01-08
Berk Hess
Fix triclin
i
c dom
a
in decomposit
i
on bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make acceleration correction VCM m
o
d
e
work
commit
|
commitdiff
|
tree
2017-12-19
Berk
H
ess
Make over
s
ubscription warning consisten
t
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Requ
i
re -ntmpi
with se
t
ting -
n
tom
p
with GPU
s
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Che
c
k
for
l
ar
g
e energy at
first step
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Avoid ye
l
ling about th
r
ead p
i
n
ni
n
g twice
commit
|
commitdiff
|
tree
2017-12-11
Be
r
k H
e
ss
A
d
d grompp
n
o
t
e for PR p
c
oup
l
e
+ position
restrai
n
ts
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remove SIMD warning
f
or AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Tone dow
n
n
ote ab
o
ut n
o
t
pinning threads
commit
|
commitdiff
|
tree
2017-12-08
B
er
k
Hess
Cor
r
ect
S
h
a
ke
t
est tolerance
s
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Add Vi
v
eca Linda
h
l as
contributor
commit
|
commitdiff
|
tree
2017-12-07
Be
r
k H
e
ss
Choose f
a
ster nbnx
n
SI
M
D
k
erne
l
s on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk He
s
s
F
i
x DD
e
xact con
t
i
n
uat
i
on bug
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
F
i
x pme g
a
ther
in
d
ouble with
A
VX(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
Merge "Merge b
r
anch relea
s
e
-
2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk Hess
F
i
x
ed initial
t
emperatu
r
e reportin
g
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Update md
r
un si
g
n
al help te
x
t
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk
Hess
Only stop at nst
l
is
t
st
e
ps with
-
repr
o
d
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Clear vsit
e
ve
l
o
c
it
i
es for simple int
e
grators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hes
s
Tighten
B-
s
pline moduli
s
ingle precision test tol
e
rance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk
H
e
ss
Avoid assert
i
on failu
r
e in
A
WH
commit
|
commitdiff
|
tree
2017-11-29
B
e
rk He
s
s
Change the GPU
SMT cut
-
off to qua
d
ratic
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
U
pdate documenti
o
n
of Nose
-
H
o
over output
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Re
f
actor nbnxn
exclusion setting
commit
|
commitdiff
|
tree
2017-11-28
Ber
k
Hess
Extend grompp
m
iss
i
n
g
energy term mes
s
a
ge
commit
|
commitdiff
|
tree
2017-11-27
Berk He
s
s
Enable auto thread pinning
with
thread li
m
i
ting
commit
|
commitdiff
|
tree
2017-11-27
B
e
rk Hess
Fix P
M
E
G
PU with walls
commit
|
commitdiff
|
tree
2017-11-25
Ber
k
Hess
Fi
x
c
ompiler
warning without MPI
commit
|
commitdiff
|
tree
2017-11-24
B
e
rk Hess
D
i
sab
l
ed
CU
D
A timings
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Spe
e
d
up
nbnx
n
b
uf
f
er clearing
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
L
imit SMT with PME on G
P
U
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Upda
t
e note in
m
a
nual on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Correct PME GPU timing
naming
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
P
revent PME tuning exc
e
s
s
ive grid scaling
commit
|
commitdiff
|
tree
2017-11-19
B
e
rk Hess
Add
SIM
D
for AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
Also pr
i
nt
1
x1 pa
i
r-list
s
etup
to lo
g
commit
|
commitdiff
|
tree
2017-11-10
B
erk H
e
s
s
Fix genio
n
charge sum
m
ation accura
c
y
commit
|
commitdiff
|
tree
2017-11-02
Berk He
s
s
F
ix Ek
i
n at step 0 wit
h
COM removal
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Add missing
E
wald corr
e
cti
o
n for pme-
u
ser
commit
|
commitdiff
|
tree
2017-10-30
Berk
H
ess
Remove
u
nused
s
ign
p
aram
e
ter from dih_
a
ngle()
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
Remove incorrect
comme
n
t for CHARMM tips3p
commit
|
commitdiff
|
tree
2017-10-24
Berk
Hess
F
ix gmx check
f
or t
p
rs with di
f
ferent
#
a
toms
commit
|
commitdiff
|
tree
2017-10-23
Ber
k
Hes
s
Fix incorrect
d
V/dlambda
for walls
commit
|
commitdiff
|
tree
2017-10-21
B
e
r
k H
e
ss
Merge "Merge branch release-2016
"
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix warning fo
r
conf
o
ut with periodic mol
e
cules
commit
|
commitdiff
|
tree
2017-10-18
Be
r
k
Hess
Mad
e
CUDA PME
texture re
f
erence
condition
a
l
commit
|
commitdiff
|
tree
2017-10-15
Berk
Hess
Imp
r
ove
v
site paral
l
el
c
hec
k
ing
commit
|
commitdiff
|
tree
2017-10-12
Berk He
s
s
Simplify virial handling
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Di
s
abl
e
ARM
N
e
o
n nati
v
e
r
sqrt iteration
commit
|
commitdiff
|
tree
2017-10-06
Be
r
k Hess
Add acceleration cor
r
e
c
tion V
C
M
mode
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Fix max_size()
in al
l
o
c
ator
.
h
commit
|
commitdiff
|
tree
2017-10-06
B
erk
Hess
Ad
d
SIMD
intrinsics version of simpl
e
update
commit
|
commitdiff
|
tree
2017-10-06
Berk
H
e
s
s
Improve PaddedRVec
V
ecto
r
res
i
z
ing
commit
|
commitdiff
|
tree
2017-10-05
Berk
He
s
s
Make SIMD ambi
g
u
o
us test work with flo
a
t/double only
commit
|
commitdiff
|
tree
2017-10-04
Berk Hes
s
Remov
e
a for
c
e buffer a
r
gument f
r
o
m IForceP
r
ovider
commit
|
commitdiff
|
tree
2017-10-03
Berk Hess
Mov
e
calli
n
g of special force f
u
nctio
n
s
commit
|
commitdiff
|
tree
2017-10-02
Berk
H
es
s
Remove hybrid gpu+cp
u
n
o
n
bonded mode
commit
|
commitdiff
|
tree
2017-09-25
Berk He
s
s
Put rerun state prepara
t
ion i
n
a
f
unctio
n
commit
|
commitdiff
|
tree
2017-09-25
Berk Hess
Set
g
lobal state on maste
r
ra
n
k onl
y
commit
|
commitdiff
|
tree
2017-09-23
Berk Hess
Fix grompp with An
d
ers
e
n
m
a
ss
i
ve
a
n
d
no C
O
M
removal
commit
|
commitdiff
|
tree
2017-09-20
Berk
Hess
Cha
n
g
e
n
b
nxn indexing
to temp
l
ates
commit
|
commitdiff
|
tree
2017-09-15
Berk Hess
Remove nb-paramete
r
s
from t
_
f
o
rce
r
ec
commit
|
commitdiff
|
tree
2017-09-14
Berk Hess
Fi
x
nbnxn S
I
M
D 2xNN PM
E
tabulated
kernel
commit
|
commitdiff
|
tree
2017-09-12
Be
r
k Hes
s
Fix exception
i
n SIMD LJ
PME sol
v
e
commit
|
commitdiff
|
tree
2017-09-12
Berk
Hess
Do not pass st
a
t
e to i
n
it
_
rep
l
ica_
e
xchange
commit
|
commitdiff
|
tree
2017-09-11
Berk He
s
s
Fix
P
BC bugs in the swap code
commit
|
commitdiff
|
tree
2017-09-09
Berk He
s
s
Avoid inf in SIMD double
s
q
r
t()
commit
|
commitdiff
|
tree
2017-09-07
B
erk Hess
Fix FEP
s
tate with rer
u
n
commit
|
commitdiff
|
tree
2017-09-04
Berk
H
e
ss
Fix tw
o
nbn
x
n searc
h
index
i
ng bu
g
s
commit
|
commitdiff
|
tree
2017-09-04
Be
r
k Hess
Consolidate arc
h
ite
c
t
u
r
e booleans
commit
|
commitdiff
|
tree
2017-09-03
Ber
k
Hes
s
Put m
d
ru
n
opti
o
ns i
n
structs
commit
|
commitdiff
|
tree
2017-09-02
Ber
k
Hess
Put a
l
l domdec option
s
in
a
st
r
uct
commit
|
commitdiff
|
tree
2017-09-02
Be
r
k
H
ess
F
i
x
m
drun -n
b
opti
o
n poi
n
ter
commit
|
commitdiff
|
tree
2017-09-01
Berk Hess
Fix mdrun -nb
o
pti
o
n pointer
commit
|
commitdiff
|
tree
2017-08-29
Berk Hes
s
Make pull potential
r
egi
s
tration thread-sa
f
e
commit
|
commitdiff
|
tree
2017-08-29
B
e
r
k Hess
Se
t
defa
u
lt GMX_OP
E
NMP_MAX_THREA
D
S t
o
64
commit
|
commitdiff
|
tree
2017-08-28
Berk Hess
Avoid bonded forces lo
o
ps/tim
e
rs on
i
n
puts with no
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
Berk Hess
Enable dynami
c
pair list pruni
n
g
commit
|
commitdiff
|
tree
2017-08-18
B
e
rk Hess
Add CPU referen
c
e and SI
M
D
p
ru
n
ing kernels
commit
|
commitdiff
|
tree
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