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Make multi-atom TPI reproducible
2018-03-06
Ber
k
Hess
Mak
e
multi-atom
T
P
I
reprodu
c
ible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Work around
gcc bug
with group kernel ta
b
les
commit
|
commitdiff
|
tree
2018-03-02
B
e
rk Hess
Fix AWH bias-sharing with
p
aral
l
e
l simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Detect AMD S
M
T top
o
logy
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix mdrun multisim with separate P
M
E
r
anks
commit
|
commitdiff
|
tree
2018-02-23
Berk
Hess
Fix md integrator with No
s
e-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-16
Ber
k
H
e
s
s
Correct mult
i
s
im MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
F
ix ran
g
e
bug
i
n
add
_
sel
e
c
t
ion_
g
ro
u
ps in tngio
.
c
p
p
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net charge c
h
e
c
k
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
F
ix grompp net char
g
e ch
e
ck
commit
|
commitdiff
|
tree
2018-02-08
Ber
k
Hess
Use SIM
D
bondeds
w
it
h
out pe
r
turbed in
t
e
r
actions
commit
|
commitdiff
|
tree
2018-02-08
Berk Hess
Al
l
ow bonds
w
ith distance=0
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Set cutoff modifiers in for
c
er
e
c
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
F
ix a
s
s
e
rtion failure in
T
PI
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix C
O
MM remov
a
l
on p
a
rt of the syst
e
m
commit
|
commitdiff
|
tree
2018-01-18
Berk
H
es
s
Add check in grompp
t
o a
v
o
id
a
ssertion
fail
u
re
commit
|
commitdiff
|
tree
2018-01-17
Berk He
s
s
R
e
-enable G
P
U with walls and 1 energy group
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Re
m
o
v
e
tumbling ice
-
cube
warnin
g
with
S
D
commit
|
commitdiff
|
tree
2018-01-16
B
erk
He
s
s
Avoid mdrun
echoing "No option -multi"
commit
|
commitdiff
|
tree
2018-01-09
B
erk
H
ess
Reword
C
PU/GPU im
b
ala
n
ce notes
commit
|
commitdiff
|
tree
2018-01-09
Berk
Hess
D
o
not
t
urn
on
DLB at replica ex
c
hange
commit
|
commitdiff
|
tree
2018-01-08
Berk
H
ess
F
i
x tri
c
l
inic do
m
a
in d
e
compo
s
i
t
i
o
n
bug
commit
|
commitdiff
|
tree
2017-12-19
Berk He
s
s
Make a
c
cel
e
ratio
n
corr
e
ction VC
M
mode wor
k
commit
|
commitdiff
|
tree
2017-12-19
Berk
Hess
Make oversubscr
i
p
t
i
o
n
warning consistent
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Req
u
ire
-
ntmpi
with setting
-
ntom
p
with GPUs
commit
|
commitdiff
|
tree
2017-12-12
B
e
rk
H
e
s
s
Check for large energy at first step
commit
|
commitdiff
|
tree
2017-12-12
Berk
Hess
Avoid yelling about t
h
read pinning twice
commit
|
commitdiff
|
tree
2017-12-11
Berk He
s
s
Add grom
p
p note fo
r
PR pcouple + positi
o
n
r
estraints
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
R
emove
S
IMD
warn
i
ng for AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
T
o
ne
d
o
w
n
not
e
a
b
out
not pinn
i
ng threa
d
s
commit
|
commitdiff
|
tree
2017-12-08
Be
r
k Hess
Co
r
r
ect Shake
test toleran
c
es
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Add
V
iveca
Lind
a
hl
a
s
con
t
ributor
commit
|
commitdiff
|
tree
2017-12-07
B
e
r
k
Hess
Choos
e
faster
nbnxn SIMD kernels
o
n
AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
Fix DD exac
t
continuation bug
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fix pme gather in
d
ouble w
i
th
A
V
X(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
He
s
s
M
erge "Merge branch r
e
l
ea
s
e-
2
016
i
nt
o
rel
e
ase-
2
0
1
8
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fixed ini
t
ia
l
temperatur
e
reportin
g
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Upda
t
e md
r
un signal help t
e
xt
commit
|
commitdiff
|
tree
2017-12-04
Berk
Hess
Only stop a
t
nstlist step
s
with -reprod
commit
|
commitdiff
|
tree
2017-12-03
Berk
Hess
C
lear
vsite velocities for simple in
t
egrators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
T
i
ghten B-spline moduli single precis
i
o
n
t
e
st tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avoi
d
asse
r
tion
fai
l
ure in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
C
han
g
e the GPU S
M
T cut-off to quadr
a
ti
c
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Upda
t
e
documention of No
s
e
-
Hoover
outpu
t
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Ref
a
cto
r
nbnxn exclusion s
e
tting
commit
|
commitdiff
|
tree
2017-11-28
Be
r
k Hess
E
xtend gr
o
m
pp missing energy
t
erm messag
e
commit
|
commitdiff
|
tree
2017-11-27
B
e
r
k Hess
E
nable auto thr
e
ad pinning
wi
t
h thread
limiting
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Fix
PME GPU wit
h
walls
commit
|
commitdiff
|
tree
2017-11-25
B
e
r
k Hess
Fix
c
ompiler w
a
rning wit
h
out MPI
commit
|
commitdiff
|
tree
2017-11-24
Be
r
k Hess
Disabled
CUDA
t
im
i
n
gs
commit
|
commitdiff
|
tree
2017-11-24
Berk
Hess
Speed up nbnxn buff
e
r clearing
commit
|
commitdiff
|
tree
2017-11-24
Berk Hes
s
Limit
SMT with
P
ME on
GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Upda
t
e note
i
n
m
anual on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk
H
ess
Correct PME GPU timin
g
naming
commit
|
commitdiff
|
tree
2017-11-20
Berk H
e
ss
Prevent PME tun
i
ng excessive grid sca
l
in
g
commit
|
commitdiff
|
tree
2017-11-19
Berk Hess
Add SIMD fo
r
AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
A
l
so pri
n
t 1x1 pair-
l
ist setu
p
to log
commit
|
commitdiff
|
tree
2017-11-10
Ber
k
Hess
Fix g
e
ni
o
n charg
e
su
m
mation
a
ccuracy
commit
|
commitdiff
|
tree
2017-11-02
Berk
Hess
Fix Ekin at s
t
ep 0 w
i
th COM removal
commit
|
commitdiff
|
tree
2017-11-02
Berk He
s
s
Ad
d
miss
i
n
g
E
wald cor
r
ection for pme-user
commit
|
commitdiff
|
tree
2017-10-30
Berk
Hess
Re
m
o
v
e unuse
d
sign param
e
ter fro
m
d
ih_angle()
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
Remove inco
r
rect comm
e
nt for CHARMM ti
p
s3p
commit
|
commitdiff
|
tree
2017-10-24
Ber
k
Hess
Fix g
m
x check fo
r
tprs with differ
e
nt #atoms
commit
|
commitdiff
|
tree
2017-10-23
Ber
k
Hess
Fix incorrect
d
V
/dlambda
f
or wa
l
l
s
commit
|
commitdiff
|
tree
2017-10-21
B
e
r
k Hess
Merge "Merge br
a
n
ch release-20
1
6"
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fi
x
warning
f
or confout
w
it
h
p
eriodic mol
e
cule
s
commit
|
commitdiff
|
tree
2017-10-18
Ber
k
Hess
Made CUDA PME te
x
ture reference
con
d
iti
o
n
a
l
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
Im
p
rove vsite p
a
rallel checking
commit
|
commitdiff
|
tree
2017-10-12
Berk Hess
Simplify v
i
rial h
a
ndling
commit
|
commitdiff
|
tree
2017-10-11
Be
r
k Hess
Disable ARM Neon
n
a
t
ive rs
q
rt iter
a
tion
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
A
d
d
acceleration correction VCM mode
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Fix max
_
size() in
allocator
.
h
commit
|
commitdiff
|
tree
2017-10-06
Ber
k
H
e
s
s
Add SIMD
i
n
trinsics version
o
f
simpl
e
update
commit
|
commitdiff
|
tree
2017-10-06
Ber
k
H
e
ss
Impr
o
v
e Pa
d
d
e
dRVec
V
e
c
tor resi
z
ing
commit
|
commitdiff
|
tree
2017-10-05
Berk
H
ess
M
ake SIMD ambiguous tes
t
work with
f
l
o
at/doub
l
e onl
y
commit
|
commitdiff
|
tree
2017-10-04
B
e
rk Hess
Remove a fo
r
ce bu
f
fer argument from IForcePr
o
vider
commit
|
commitdiff
|
tree
2017-10-03
B
e
rk
H
e
ss
Move cal
l
ing of special force functions
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
Remove
h
y
b
rid gpu+cpu nonbon
d
ed
mo
d
e
commit
|
commitdiff
|
tree
2017-09-25
B
erk Hess
Pu
t
rerun state prepa
r
ation in a fun
c
tion
commit
|
commitdiff
|
tree
2017-09-25
Berk
H
ess
Set globa
l
state
o
n ma
s
ter rank only
commit
|
commitdiff
|
tree
2017-09-23
Berk Hess
Fix grompp w
i
th Andersen massive and no COM removal
commit
|
commitdiff
|
tree
2017-09-20
Berk He
s
s
Chan
g
e
n
bn
x
n i
n
dexing to tem
p
late
s
commit
|
commitdiff
|
tree
2017-09-15
B
e
rk Hess
R
emove nb-para
m
eters from
t_forcerec
commit
|
commitdiff
|
tree
2017-09-14
B
e
r
k Hess
Fix nbnxn SI
M
D 2xNN PME tabulated kernel
commit
|
commitdiff
|
tree
2017-09-12
B
e
rk Hess
Fix excep
t
ion in S
I
MD LJ PME solve
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Do no
t
pass state t
o
in
i
t_r
e
plica
_
exc
h
a
nge
commit
|
commitdiff
|
tree
2017-09-11
Berk He
s
s
Fix
P
BC bugs
i
n th
e
swap code
commit
|
commitdiff
|
tree
2017-09-09
Berk Hes
s
Avoid i
n
f
i
n SI
M
D double
s
qrt()
commit
|
commitdiff
|
tree
2017-09-07
Ber
k
Hess
Fix FEP state wi
t
h rerun
commit
|
commitdiff
|
tree
2017-09-04
B
erk He
s
s
Fix two nbnxn sea
r
ch indexing bug
s
commit
|
commitdiff
|
tree
2017-09-04
Berk H
e
s
s
Consolidate
arc
h
i
tecture booleans
commit
|
commitdiff
|
tree
2017-09-03
B
erk
H
ess
Put m
d
run options
in struc
t
s
commit
|
commitdiff
|
tree
2017-09-02
B
erk H
e
ss
P
u
t all domdec o
p
tion
s
i
n
a struct
commit
|
commitdiff
|
tree
2017-09-02
Ber
k
Hess
Fix m
d
run -nb opt
i
o
n pointer
commit
|
commitdiff
|
tree
2017-09-01
Berk
H
ess
Fix mdrun
-
nb optio
n
p
o
inter
commit
|
commitdiff
|
tree
2017-08-29
Berk Hess
Make
p
ul
l
p
otential r
e
gistratio
n
thread
-
s
afe
commit
|
commitdiff
|
tree
2017-08-29
Berk Hess
Set defaul
t
GMX_OPENMP
_
MAX_THREADS
to 64
commit
|
commitdiff
|
tree
2017-08-28
B
e
rk Hess
A
void bond
e
d fo
r
ces loops/timers on inpu
t
s with no
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
B
e
rk Hess
Enabl
e
dynamic
pair l
i
st prunin
g
commit
|
commitdiff
|
tree
2017-08-18
Ber
k
H
ess
Add CPU reference and SIM
D
p
runin
g
kerne
l
s
commit
|
commitdiff
|
tree
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