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Make both ftp and http links for source download
2016-02-19
Be
r
k Hes
s
Fix excessive
l
ist
splitting
commit
|
commitdiff
|
tree
2016-02-07
Be
r
k Hess
Fix incorrec
t
cmap parsing
commit
|
commitdiff
|
tree
2016-02-05
Berk Hess
Fix incorrect cmap parsing
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
F
ix mdrun removing
V
er
l
et buf
f
er
w
ith EM
commit
|
commitdiff
|
tree
2016-02-03
Be
r
k
H
es
s
F
ix SE
T
TLE error hand
l
in
g
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix TPI
ignoring P
M
E mesh con
t
r
i
bution
s
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Add check
for doubl
e
perturbat
i
on
commit
|
commitdiff
|
tree
2016-01-29
Be
r
k H
e
ss
Fix LI
N
CS trian
g
le
constraint thread issu
e
commit
|
commitdiff
|
tree
2016-01-28
Be
r
k Hes
s
Update pair-l
i
st buffer manual
commit
|
commitdiff
|
tree
2016-01-24
Berk H
e
ss
Fix exact con
t
inuation fr
o
m
non-energy steps
commit
|
commitdiff
|
tree
2016-01-24
B
erk
He
s
s
Fix ener
g
y fi
l
e continuation with md-vv
commit
|
commitdiff
|
tree
2016-01-24
B
erk Hess
Fix ener
g
y average with continu
a
tion
commit
|
commitdiff
|
tree
2016-01-08
Berk He
s
s
Fix PM
E
load b
a
lancing sk
i
pping a
s
e
tup
commit
|
commitdiff
|
tree
2015-12-29
Ber
k
Hess
Correct vect
o
r che
c
k of g
m
x ch
e
ck
commit
|
commitdiff
|
tree
2015-12-19
Berk He
s
s
Bring performa
n
ce estimation up
t
o date
commit
|
commitdiff
|
tree
2015-12-11
Berk
H
e
ss
Fix bug wi
t
h
p
ull group weights
commit
|
commitdiff
|
tree
2015-11-19
Berk
H
e
s
s
Rem
o
ved mdrun
f
a
t
a
l_error with
P3M
-
AD
commit
|
commitdiff
|
tree
2015-11-09
B
erk He
s
s
Correct LIN
C
S
dHdl contr
i
bution
commit
|
commitdiff
|
tree
2015-11-02
Berk
H
ess
Fix intermolecu
l
a
r interactions
with small
mol
s
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
Fixe
d
nb
n
x
n
_
4xN pe
r
forman
c
e
regression
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
Fix bugs with intermol i
n
t
eractions and DD
commit
|
commitdiff
|
tree
2015-09-15
Be
r
k Hess
Detect incorrect cycle counting
commit
|
commitdiff
|
tree
2015-08-14
B
e
rk Hess
Make m
d
run -
n
t
work again
commit
|
commitdiff
|
tree
2015-07-06
Berk
H
ess
Fi
x
too small GPU pair cou
n
t estimates
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fix bug in G
P
U
l
ist b
a
lancing
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
F
i
x D
D
DLB
s
t
a
te is
s
ue
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
F
i
x bug in GPU
l
is
t
bal
a
ncing
commit
|
commitdiff
|
tree
2015-07-04
Be
r
k H
e
ss
Obey Open
M
P thread
c
ou
n
t limit with
tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk H
e
ss
Fix two PME DLB trigger iss
u
es
commit
|
commitdiff
|
tree
2015-07-03
Berk Hess
Cor
r
ect grompp pull warning
m
e
s
sage
commit
|
commitdiff
|
tree
2015-06-30
Berk H
e
s
s
Fix inconsistent OpenMP autom
a
tio
n
commit
|
commitdiff
|
tree
2015-06-30
Berk
H
ess
ena
b
led 1 PP +
1 P
M
E
n
ode
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Add
c
h
eck
s
for inefficient resourc
e
usage
commit
|
commitdiff
|
tree
2015-06-29
B
e
rk H
e
ss
Improve D
L
B+PME tunin
g
w
i
th G
P
Us
commit
|
commitdiff
|
tree
2015-06-27
Berk
H
e
s
s
Improve pair
s
earch th
r
e
ad load b
a
lanc
e
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
I
m
pr
o
v
e
d the intra-GPU
load bala
n
cing
commit
|
commitdiff
|
tree
2015-06-27
Be
r
k Hess
Reduce the
u
se
o
f
nbnxn_co
n
sts
.
h
commit
|
commitdiff
|
tree
2015-06-27
Berk H
e
ss
Correc
t
ed
nstc
a
lclr/nstfep/
n
st_repl_ex c
h
ecks
commit
|
commitdiff
|
tree
2015-06-26
B
e
rk Hess
Fixed
Verlet buffer
i
ssue
w
ith 2-wide SIMD
commit
|
commitdiff
|
tree
2015-06-25
Be
r
k Hess
Intermolecular bonded
i
n
teraction support adde
d
commit
|
commitdiff
|
tree
2015-06-25
Berk Hess
Reenabled S
I
MD
k
ernels without cut-offs
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
GP
U
Ewal
d
ta
b
l
e
k
e
r
n
el now us
e
s
CPU spacing
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Avoid GPU selection wi
t
h
GPU emulation
commit
|
commitdiff
|
tree
2015-06-24
Berk
Hess
Mino
r
reformatting of SIMD m
i
s
match m
e
ssage
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Add sugar to
p
r
i
nt empty line in printBinaryInfo
r
matio
n
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Fix g_
e
n
ergy
a
v
erage/RMSD bug
commit
|
commitdiff
|
tree
2015-06-22
Berk He
s
s
Update launch conf
i
guration for physical nod
e
s
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Avoid fp exceptions in pair s
e
arch debug
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Replaced ha
r
d
ware threads
by logical cores in ou
t
put
commit
|
commitdiff
|
tree
2015-06-18
Ber
k
Hess
Reduce
d
the cost of the pull c
o
mmunication
commit
|
commitdiff
|
tree
2015-06-17
B
erk Hess
Refactored
p
ull
data st
r
uctures
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Added missing DD cy
c
l
e
counting
commit
|
commitdiff
|
tree
2015-06-16
B
erk Hes
s
Automated th
e
-gpu_id option
commit
|
commitdiff
|
tree
2015-06-14
Berk Hess
Refacto
r
ed mdrun
r
esource divi
s
ion
commit
|
commitdiff
|
tree
2015-06-13
Berk H
e
ss
Ha
r
dware
r
e
po
r
t
ing n
o
w cov
e
rs all
nodes
commit
|
commitdiff
|
tree
2015-06-05
B
e
rk He
s
s
Don't use PM
E
ranks
with GPUs and
-n
p
me
=
-1
commit
|
commitdiff
|
tree
2015-05-27
Berk Hess
Refactoring of PME load
balancing
commit
|
commitdiff
|
tree
2015-05-23
Berk Hess
Rem
o
ve
d
static f
r
om va
r
iables in gmx_lapa
c
k
commit
|
commitdiff
|
tree
2015-05-16
Berk Hess
LINCS thread tasks can now be independ
e
nt
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
F
ixe
d
CUDA err
o
r with empty dom
a
ins
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fix s
e
gv in g_covar
commit
|
commitdiff
|
tree
2015-05-11
Berk Hess
Changed FFTW wa
r
nin
g
fro
m
AVX t
o
no
SSE
commit
|
commitdiff
|
tree
2015-05-07
Berk Hess
Removed
non-ff
at
o
mtypes f
r
om oplsaa and c
h
armm27
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fixed
G
PU non-local
F
copy local
c
o
n
ditio
n
al
commit
|
commitdiff
|
tree
2015-04-28
Berk H
e
ss
Re-enabled FMA for A
V
X-128-FM
A
commit
|
commitdiff
|
tree
2015-04-22
Be
r
k
Hess
Merge
b
ranch '
r
e
l
ease-5-0'
commit
|
commitdiff
|
tree
2015-04-17
Berk H
e
s
s
Add va
l
u
e
_r
e
f
a
nd va
l
u
e
to
pul
l
_coord_t
commit
|
commitdiff
|
tree
2015-04-17
Ber
k
Hess
Correct -ntmpi auto fo
r
intel neh
a
l
em and ol
d
e
r
commit
|
commitdiff
|
tree
2015-04-08
B
e
r
k Hess
Adde
d
p
u
l
l
geome
t
r
y
d
irection-relative
commit
|
commitdiff
|
tree
2015-04-01
B
e
r
k Hess
Correct
e
d force-switch ma
n
ual section
commit
|
commitdiff
|
tree
2015-03-19
Be
r
k Hess
Re
m
oved reduction of dH/dl without F
E
commit
|
commitdiff
|
tree
2015-03-12
Berk He
s
s
Fixed mdrun fp exception with -deb
u
g
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Adde
d
update x copy-back to update ti
m
er
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
R
e
d
uced cost
o
f Ber
e
ndsen
p
ress
u
re coupl
i
ng
commit
|
commitdiff
|
tree
2015-03-06
Berk H
e
ss
Improve threading of bond
e
ds
commit
|
commitdiff
|
tree
2015-03-05
B
e
rk Hess
M
a
de D
D
exclusion proc
e
s
sin
g
mor
e
e
f
f
ic
i
e
n
t
commit
|
commitdiff
|
tree
2015-03-05
B
erk Hess
SIMD acc
e
leration for L
I
NCS
commit
|
commitdiff
|
tree
2015-03-04
Berk H
e
ss
Allow
p
ull gr
o
up
s
of
1 ato
m
with m
a
ss 0
commit
|
commitdiff
|
tree
2015-03-04
Berk Hess
COM
p
ulli
n
g optio
n
s
p
er
c
o
ord,
improv
e
d cylind
e
r
commit
|
commitdiff
|
tree
2015-03-03
Berk Hess
Fix div b
y
zero in PP/PM
E
rati
o
commit
|
commitdiff
|
tree
2015-03-02
Berk Hess
Added pare
n
theses for cast
s
in SIMD macros
commit
|
commitdiff
|
tree
2015-02-24
B
erk
Hess
Fix
e
d
p
a
r
all
e
l distr
i
b
ution and thread count reporting
commit
|
commitdiff
|
tree
2015-02-12
Berk Hess
Re-fixed
PME bug with high Open
M
P thread count
commit
|
commitdiff
|
tree
2015-02-06
Berk Hess
Re-
e
n
a
bled
SIMD for angles and dihedrals
commit
|
commitdiff
|
tree
2015-02-04
Berk Hess
Corr
e
ct CUDA kernel
e
nergy flag
commit
|
commitdiff
|
tree
2015-01-21
Be
r
k Hess
C
o
rrec
t
e
d RDTSCP warning text
commit
|
commitdiff
|
tree
2015-01-15
Berk
H
ess
Fi
x
alloca
t
ion issue wit
h
VV
integrator
commit
|
commitdiff
|
tree
2014-12-22
Berk Hess
Fixed pbc
=
xy + 2 walls
+ V
e
r
l
et s
c
heme
commit
|
commitdiff
|
tree
2014-12-22
Berk
H
ess
Fix bug FE + G
P
U + 2/3D domain
d
e
compositi
o
n
commit
|
commitdiff
|
tree
2014-12-11
B
er
k
He
s
s
A
d
d
e
d
gr
o
mpp error for pulling
t
o
neg
a
t
ive distance
commit
|
commitdiff
|
tree
2014-12-09
Berk Hess
Fix
r
ecent
b
ug
w
ith trilinic
1
D D
D
commit
|
commitdiff
|
tree
2014-12-08
Berk
H
ess
Fixe
d
pull
co
o
rd
init
w
i
th r
a
te!=0, t_start
!
=0
commit
|
commitdiff
|
tree
2014-12-08
Berk
H
ess
Added PBC no
t
e
t
o comm-mode=angular w
a
rni
n
g
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Make domdec a
p
r
o
per mo
d
ule
commit
|
commitdiff
|
tree
2014-12-05
Berk H
e
ss
C
l
a
rified grompp pull error message
s
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Avo
i
d race
on dvdl with Verlet+OpenMP+LINCS+FE+VV
commit
|
commitdiff
|
tree
2014-12-01
Berk Hess
Added
w
arning f
o
r un
n
ecessary soft-core
commit
|
commitdiff
|
tree
2014-11-26
Berk Hess
Fixed triclinic 1xNx1
domain decom
p
osi
t
i
on
commit
|
commitdiff
|
tree
2014-11-25
B
e
rk
Hess
Fixed twin-
r
ang
e
+ freeze + constrai
n
ts
commit
|
commitdiff
|
tree
2014-11-24
Berk Hess
A
v
oi
d
NaN in rl
i
st bu
f
fer calculat
i
o
n
commit
|
commitdiff
|
tree
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