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Support 4 sized cluster for GPU NBL search
2018-04-27
Berk Hess
R
e
move pull MPI code dupli
c
ation
commit
|
commitdiff
|
tree
2018-04-16
B
e
rk
Hess
Move natoms_
m
ol out
of
gm
x
_molblock_t
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Convert gm
x
_molblock_t t
o
C++
commit
|
commitdiff
|
tree
2018-04-03
Be
r
k Hess
Convert g
m
x_mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
B
e
rk
Hes
s
Change warninp file
n
m to std::stri
n
g
commit
|
commitdiff
|
tree
2018-04-03
Berk H
e
s
s
Do not cal
c
ul
a
te CO
M
for pul
l
group 0
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Mo
v
e file opening out of init_pu
l
l()
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
M
od
u
larize pull_coord_work_
t
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Re
m
ove mol
s
from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Fi
x
gmx dump AWH for
m
atti
n
g issue
commit
|
commitdiff
|
tree
2018-03-20
Be
r
k H
e
ss
Disal
l
ow single si
m
ulation
w
ith multisim
commit
|
commitdiff
|
tree
2018-03-16
Berk He
s
s
Cor
r
ect PMF
s
ign error in
A
WH
bias sha
r
i
ng
commit
|
commitdiff
|
tree
2018-03-16
Berk
Hess
Fix r
e
cent md
r
un sig
n
al
i
n
g bu
g
commit
|
commitdiff
|
tree
2018-03-15
Berk Hess
Fix v
i
r
i
al
with ex
t
e
rnal pull pote
n
tial and MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
I
m
prove in
t
er
-
si
m
ulation si
g
nal
i
ng
commit
|
commitdiff
|
tree
2018-03-14
Berk
Hes
s
Fix mdrun
s
ignalling with AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
Hess
F
ix
COM pulling wi
t
h external po
t
ential with #ranks
>
3
2
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
Hes
s
Fix pull b
u
g with geometr
y
=di
r
e
ction-periodic
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add AWH fix
e
s to release notes
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ensemble
c
heck
p
o
i
nting
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
F
ix AWH deconvolution when sharing a bi
a
s
commit
|
commitdiff
|
tree
2018-03-09
Berk Hes
s
Correct pd
b
2gmx -missing
o
ption
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fix memory leak in PME
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Conv
e
rt t_fil
e
nm
t
o C
+
+
commit
|
commitdiff
|
tree
2018-03-06
Ber
k
Hess
Make mul
t
i-atom TPI r
e
pro
d
ucible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
W
ork a
r
o
und gcc bug with group k
e
r
n
el tables
commit
|
commitdiff
|
tree
2018-03-05
B
e
r
k Hess
Leave
nullptr opt in t_filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix cp
p
c
heck warnin
g
commit
|
commitdiff
|
tree
2018-03-02
Berk Hes
s
Fix AW
H
bias-sha
r
i
n
g w
i
th p
a
rallel s
i
mulat
i
on
commit
|
commitdiff
|
tree
2018-03-01
B
e
rk Hess
Dete
c
t AMD SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Berk
Hess
Fix mdrun
m
ultisim with sep
a
rate PME ranks
commit
|
commitdiff
|
tree
2018-02-23
B
e
rk He
s
s
Fix md integrator with Nos
e
-Hoover c
o
u
pling
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
Simplify mdrun tMPI threa
d
spawning
commit
|
commitdiff
|
tree
2018-02-16
Berk H
e
ss
Corr
e
c
t
m
u
ltisim
M
PI b
a
rrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hes
s
R
e
move
s
upport for
tpx v
e
rsi
o
n bef
o
re 5
8
/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hes
s
Fix range bug i
n
add_selec
t
ion_g
r
oups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Be
r
k Hess
Fix
g
rompp net c
h
a
r
ge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
F
ix grompp net charge c
h
eck
commit
|
commitdiff
|
tree
2018-02-08
Berk He
s
s
U
se SIMD bondeds without perturbed interacti
o
ns
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
e
s
s
Allo
w
b
o
n
d
s w
i
th distance=0
commit
|
commitdiff
|
tree
2018-02-05
B
erk Hess
Set cutoff
m
odifi
e
rs in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk H
e
ss
Fix
a
ssertion failure in TPI
commit
|
commitdiff
|
tree
2018-01-30
Berk
H
ess
Removed unused flag
PCA_CAN_R
E
AD_NODE
commit
|
commitdiff
|
tree
2018-01-18
Berk
Hess
Fix C
O
MM
r
emoval o
n
part
o
f th
e
syst
e
m
commit
|
commitdiff
|
tree
2018-01-18
Berk
H
ess
Add chec
k
in grompp to a
v
o
id assertion
f
ailure
commit
|
commitdiff
|
tree
2018-01-17
Berk Hes
s
Re
p
l
ace stde
r
r
print
s
in
filenm
.
cpp by as
s
erts
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
Re-enable GPU with w
a
lls and 1 energy group
commit
|
commitdiff
|
tree
2018-01-16
Ber
k
Hess
Remo
v
e tumblin
g
ic
e
-cube warning with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Avoi
d
mdrun echoin
g
"N
o
op
t
ion -multi"
commit
|
commitdiff
|
tree
2018-01-09
B
erk Hess
Reword CPU/
G
PU i
m
balance n
o
t
es
commit
|
commitdiff
|
tree
2018-01-09
Be
r
k
H
ess
Do not turn o
n
DLB at repl
i
ca
e
x
c
h
an
g
e
commit
|
commitdiff
|
tree
2018-01-08
Berk
Hes
s
Fix triclinic dom
a
in
d
ecomposition
bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make accel
e
ration correctio
n
VCM mode work
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Ma
k
e
oversubscriptio
n
wa
r
n
ing consiste
n
t
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Require -nt
m
pi with sett
i
ng -nto
m
p
with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Be
r
k
Hess
Check for
large energ
y
at firs
t
step
commit
|
commitdiff
|
tree
2017-12-12
Be
r
k Hess
Avoi
d
y
e
lling abo
u
t threa
d
pinning twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add grompp note
for PR pcouple + p
o
sit
i
on re
s
tr
a
ints
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
R
em
o
ve SIMD warning for AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
To
n
e dow
n
not
e
abou
t
n
ot pin
n
ing
t
hreads
commit
|
commitdiff
|
tree
2017-12-08
B
erk Hes
s
Cor
r
ect Shake test tolerances
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Add Vivec
a
Lindahl as
c
o
ntri
b
utor
commit
|
commitdiff
|
tree
2017-12-07
Berk Hess
Cho
o
se faster nb
n
xn S
I
MD kernels on
A
M
D Zen
commit
|
commitdiff
|
tree
2017-12-05
Be
r
k Hess
Fix DD e
x
ac
t
continuati
o
n bug
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
Fix pme gat
h
er in dou
b
l
e
w
i
t
h
A
V
X
(
2
)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
M
e
rge "Merge branc
h
release-2016 into r
e
lease-20
1
8
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
ess
Fixed initi
a
l
temperature reporting
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k
Hess
Update mdrun
s
ignal help text
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Only stop at nstlist steps with -
r
epr
o
d
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Clear vs
i
te veloci
t
ies
f
or simple int
e
g
r
at
o
r
s
commit
|
commitdiff
|
tree
2017-12-03
Berk Hes
s
Tig
h
ten B-spline mod
u
li sin
g
le precision test toler
a
nce
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk
He
s
s
Avoid assertion failure in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
Change the
GPU SMT cut-off to
qu
a
dratic
commit
|
commitdiff
|
tree
2017-11-28
Berk Hes
s
U
p
date documention o
f
N
o
s
e
-H
o
o
v
er o
u
tput
commit
|
commitdiff
|
tree
2017-11-28
B
erk Hess
Refactor nbnxn ex
c
l
usion setting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Extend
grompp
mis
s
ing ene
r
g
y term
m
e
ssage
commit
|
commitdiff
|
tree
2017-11-27
Ber
k
Hess
E
n
able
a
ut
o
thread pinning w
i
t
h
t
hre
a
d limiting
commit
|
commitdiff
|
tree
2017-11-27
B
erk Hess
Fi
x
PME GPU with w
a
lls
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
F
ix co
m
p
i
ler warning w
i
t
h
o
u
t MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk He
s
s
D
i
sabled CUDA timi
n
gs
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Speed u
p
nbnxn
b
u
ffer clearin
g
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Limit SMT
wi
t
h P
M
E on GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk H
e
ss
Update note in m
a
nual on
S
D
commit
|
commitdiff
|
tree
2017-11-23
Berk H
e
ss
Correct PM
E
GPU t
i
ming naming
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
Preven
t
PME tuning
e
xcessive
g
rid scaling
commit
|
commitdiff
|
tree
2017-11-19
B
e
r
k
Hess
Add SIMD fo
r
AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
Also print
1
x1 pair
-
l
ist setup to
log
commit
|
commitdiff
|
tree
2017-11-10
Berk Hess
Fix genion charge summation ac
c
u
r
a
cy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix Ekin
at step 0 with
C
OM
remo
v
al
commit
|
commitdiff
|
tree
2017-11-02
Ber
k
Hess
Add miss
i
ng E
w
a
l
d cor
r
ection for pme
-
user
commit
|
commitdiff
|
tree
2017-10-30
Berk He
s
s
Remove unu
s
ed sig
n
parameter fro
m
d
i
h
_angle()
commit
|
commitdiff
|
tree
2017-10-29
Berk
Hess
Rem
o
ve incorrect comment fo
r
CHARMM tips3p
commit
|
commitdiff
|
tree
2017-10-24
Berk Hess
Fix gmx check fo
r
tprs
w
i
th differen
t
#a
t
oms
commit
|
commitdiff
|
tree
2017-10-23
B
erk
H
e
s
s
Fi
x
in
c
o
rre
c
t
dV/d
l
amb
d
a for wa
l
ls
commit
|
commitdiff
|
tree
2017-10-21
Berk
H
ess
Merge "
M
erge br
a
nch
release-
2
016
"
commit
|
commitdiff
|
tree
2017-10-20
Berk He
s
s
Fi
x
warn
i
ng for
confout with periodi
c
molecu
l
e
s
commit
|
commitdiff
|
tree
2017-10-18
Berk Hess
Made CUDA PME texture referenc
e
cond
i
tional
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
Improve vsite parallel checking
commit
|
commitdiff
|
tree
2017-10-12
B
e
r
k
H
e
ss
Sim
p
lify virial hand
l
ing
commit
|
commitdiff
|
tree
2017-10-11
B
e
r
k
Hess
D
i
sa
b
le A
R
M Ne
o
n
native
rsqrt iterat
i
on
commit
|
commitdiff
|
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