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Clean up PME domain count passing
2018-05-15
Berk He
s
s
Clean up PME domain count
passing
commit
|
commitdiff
|
tree
2018-05-03
B
erk Hess
Enable SIMD version of up
d
ate
commit
|
commitdiff
|
tree
2018-04-27
Berk Hess
Remove
p
ull MPI code dup
l
ication
commit
|
commitdiff
|
tree
2018-04-24
Be
r
k Hess
Fi
x
in
d
exing
issue in the pull co
d
e
commit
|
commitdiff
|
tree
2018-04-16
Berk
H
e
s
s
Move natom
s
_mol o
u
t of gmx_m
o
lblock_t
commit
|
commitdiff
|
tree
2018-04-09
Be
r
k He
s
s
Co
n
v
e
rt
g
mx_molbloc
k
_
t
to C++
commit
|
commitdiff
|
tree
2018-04-03
Be
r
k
H
ess
Convert gmx_m
t
o
p_t to C+
+
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Change warninp filenm
t
o
std::string
commit
|
commitdiff
|
tree
2018-04-03
Berk He
s
s
Do not calc
u
late COM for
pull group 0
commit
|
commitdiff
|
tree
2018-03-29
Berk
H
ess
Move fi
l
e
o
p
e
n
ing out of in
i
t_pull()
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modulariz
e
pu
l
l_co
o
r
d_wo
r
k_t
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Rem
o
ve mol
s
f
r
om gmx_mtop_
t
commit
|
commitdiff
|
tree
2018-03-20
Ber
k
He
s
s
Fix gmx
d
ump AWH
f
ormatt
i
ng
i
ssue
commit
|
commitdiff
|
tree
2018-03-20
Berk H
e
ss
Disal
l
ow sin
g
le sim
u
lation with m
u
ltisim
commit
|
commitdiff
|
tree
2018-03-16
Berk
H
ess
Correct PMF sign
e
r
ror in AWH bias sha
r
ing
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Fi
x
recen
t
mdrun
s
i
g
n
a
ling bug
commit
|
commitdiff
|
tree
2018-03-15
B
e
rk H
e
s
s
Fix vi
r
i
a
l
w
i
t
h
ex
t
e
r
n
al pull pote
n
tial and MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve inte
r
-sim
u
lation sign
a
l
i
ng
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
F
i
x mdrun signalling
wit
h
AWH bia
s
s
h
aring
commit
|
commitdiff
|
tree
2018-03-14
Berk Hes
s
Fix COM pulli
n
g with external
p
o
tential with #ranks>
3
2
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
He
s
s
Fix
p
ull bu
g
with geometry=dir
e
cti
o
n-peri
o
dic
commit
|
commitdiff
|
tree
2018-03-13
Ber
k
Hess
Add AWH
f
ixes to re
l
e
a
se notes
commit
|
commitdiff
|
tree
2018-03-13
Be
r
k
Hess
Fix AWH en
s
emble c
h
eckpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk
H
e
ss
F
i
x AWH deconvolutio
n
when sh
a
ring a bias
commit
|
commitdiff
|
tree
2018-03-09
B
er
k
H
ess
Correct
pdb2gmx -missing option
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fix memory leak in PME
commit
|
commitdiff
|
tree
2018-03-06
Berk
Hess
C
onvert
t
_fi
l
e
n
m to C++
commit
|
commitdiff
|
tree
2018-03-06
B
erk Hess
Mak
e
multi-atom
T
PI reprodu
c
ible
commit
|
commitdiff
|
tree
2018-03-05
B
erk Hess
Work ar
o
und gcc bug
with group kernel tabl
e
s
commit
|
commitdiff
|
tree
2018-03-05
Be
r
k Hess
Leave nullptr o
p
t
i
n
t_fi
l
enm
commit
|
commitdiff
|
tree
2018-03-02
B
e
rk
Hes
s
Fix cppch
e
ck warning
commit
|
commitdiff
|
tree
2018-03-02
Berk
H
ess
Fi
x
AWH bias-sharing wi
t
h parall
e
l simu
l
a
t
i
o
n
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
De
t
ect
A
M
D
SM
T
topo
l
ogy
commit
|
commitdiff
|
tree
2018-03-01
Berk H
e
ss
F
i
x mdrun multis
i
m with sepa
r
ate P
M
E ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix
md inte
g
r
a
tor with Nose-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-22
Berk He
s
s
Simpl
i
fy mdrun tMP
I
thr
e
a
d spaw
n
ing
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Cor
r
e
ct mul
t
isim
M
P
I barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Remove support for tpx
version be
f
ore 58
/
gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix ra
n
ge bug in add_selection_groups in tngio
.
c
p
p
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix gr
o
m
pp net cha
r
ge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net charg
e
check
commit
|
commitdiff
|
tree
2018-02-08
B
erk Hess
U
s
e
SIMD bondeds with
o
ut p
e
rturbe
d
interaction
s
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
ess
Allow bonds wi
t
h di
s
tance=0
commit
|
commitdiff
|
tree
2018-02-05
Berk Hes
s
Set c
u
t
off modifiers in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Be
r
k
H
ess
Fix ass
e
rtion failur
e
in
TPI
commit
|
commitdiff
|
tree
2018-01-30
B
e
rk Hess
Removed un
u
sed flag PCA_CAN_RE
A
D_NOD
E
commit
|
commitdiff
|
tree
2018-01-18
Ber
k
Hess
Fix
C
OM
M
removal on part of th
e
system
commit
|
commitdiff
|
tree
2018-01-18
Be
r
k
He
s
s
Add check
in
g
rompp to avo
i
d assertion failu
r
e
commit
|
commitdiff
|
tree
2018-01-17
Berk Hes
s
Rep
l
ace
stder
r
prin
t
s in f
i
lenm
.
cpp by asserts
commit
|
commitdiff
|
tree
2018-01-17
B
e
r
k Hess
R
e-enable GP
U
wi
t
h wall
s
and 1 energy
group
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Remove
t
umbli
n
g ice-
c
ube warning with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk
Hes
s
Av
o
id
m
d
r
un ech
o
i
n
g
"No option -multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Reword CPU/GPU imbal
a
nce notes
commit
|
commitdiff
|
tree
2018-01-09
B
erk Hess
Do not
t
u
rn on
DL
B
at replica
e
xchange
commit
|
commitdiff
|
tree
2018-01-08
B
e
r
k Hess
Fix tri
c
linic dom
a
i
n
decompos
i
tion bug
commit
|
commitdiff
|
tree
2017-12-19
Be
r
k Hess
Make
a
c
celeratio
n
correctio
n
VCM mode work
commit
|
commitdiff
|
tree
2017-12-19
Ber
k
Hes
s
Make oversubscr
i
ption warning
c
onsistent
commit
|
commitdiff
|
tree
2017-12-14
B
e
rk Hess
Require -nt
m
pi with setting
-
ntom
p
with
G
PUs
commit
|
commitdiff
|
tree
2017-12-12
Berk
Hess
Check for large energy at first
step
commit
|
commitdiff
|
tree
2017-12-12
B
e
rk
Hess
Avoid yelling about thr
e
ad pinning twice
commit
|
commitdiff
|
tree
2017-12-11
Berk H
e
ss
Add g
r
o
m
pp note f
o
r PR pcouple +
po
s
i
t
ion restraints
commit
|
commitdiff
|
tree
2017-12-10
B
erk Hess
Remove
S
IMD warning
f
or AMD Ze
n
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Ton
e
down n
o
te about not pinning th
r
e
ads
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
C
o
rrect Shake
test t
o
leranc
e
s
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Add Viveca L
i
ndahl as cont
r
ib
u
tor
commit
|
commitdiff
|
tree
2017-12-07
Berk Hess
Choose fa
s
te
r
nbnxn
S
IM
D
kernels on
AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Ber
k
Hess
Fix
DD exact continu
a
ti
o
n bug
commit
|
commitdiff
|
tree
2017-12-04
Berk He
s
s
Fix p
m
e
gather
in double with AVX(2)_
1
28
commit
|
commitdiff
|
tree
2017-12-04
B
erk Hess
Mer
g
e
"Merge
bran
c
h rele
a
s
e
-2
0
1
6
into release-20
1
8
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
B
er
k
Hess
Fi
x
e
d
initial temperatu
r
e reporting
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
Update mdrun
sign
a
l help text
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
O
nly stop at
nstli
s
t step
s
with -reprod
commit
|
commitdiff
|
tree
2017-12-03
B
erk Hess
Clear vsi
t
e velociti
e
s for simple integ
r
ators
commit
|
commitdiff
|
tree
2017-12-03
Ber
k
Hess
Tig
h
ten B-spline m
o
d
u
l
i single
p
recision
test tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
B
e
r
k Hess
Avoid asse
r
t
i
o
n
failure in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk H
e
ss
Change
t
he GPU SMT cut-off to quadr
a
tic
commit
|
commitdiff
|
tree
2017-11-28
Berk
Hes
s
Update docu
m
ention of
N
o
s
e-Hoover output
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Refactor nbnxn
e
xclusion setting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Extend
g
romp
p
mis
s
ing energy term messa
g
e
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
E
n
able auto th
r
ead
pinni
n
g
with
thread lim
i
ting
commit
|
commitdiff
|
tree
2017-11-27
Berk He
s
s
Fix P
M
E GPU with
walls
commit
|
commitdiff
|
tree
2017-11-25
Berk H
e
ss
Fix compile
r
warning
without MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
D
isabled CUDA t
i
mings
commit
|
commitdiff
|
tree
2017-11-24
Berk Hes
s
Speed up nbnxn
b
u
ffe
r
clearing
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Lim
i
t SMT w
i
th PM
E
on GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Update note in man
u
al on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Correct PME G
P
U timing
n
aming
commit
|
commitdiff
|
tree
2017-11-20
Berk
Hess
P
r
ev
e
nt PME tunin
g
e
x
cessive grid scaling
commit
|
commitdiff
|
tree
2017-11-19
B
erk Hess
Add
SIMD for
A
WH
commit
|
commitdiff
|
tree
2017-11-16
Berk
H
es
s
Also pr
i
nt
1x1 pair
-
list setup to log
commit
|
commitdiff
|
tree
2017-11-10
Berk
H
e
ss
Fix geni
o
n charge summa
t
ion accurac
y
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix Eki
n
at step 0 with
C
OM removal
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Add mis
s
ing Ewald correction for pme-user
commit
|
commitdiff
|
tree
2017-10-30
Berk
Hess
Remove unused sign pa
r
a
mete
r
from dih_a
n
gle()
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
R
emove incorrect comment for CHARMM tips3p
commit
|
commitdiff
|
tree
2017-10-24
Berk Hess
Fix
g
m
x check fo
r
tpr
s
wi
t
h d
i
fferent #ato
m
s
commit
|
commitdiff
|
tree
2017-10-23
Ber
k
Hes
s
Fix in
c
or
r
ect dV/dlambda
f
o
r
walls
commit
|
commitdiff
|
tree
2017-10-21
B
e
rk Hess
Merge "Merg
e
br
a
nch re
l
e
ase-2016"
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix warning for con
f
out
w
it
h
periodic m
o
lecules
commit
|
commitdiff
|
tree
2017-10-18
Berk Hess
Made
C
UDA PME
t
e
xture
r
eference conditional
commit
|
commitdiff
|
tree
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