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Merge branch release-5-1
2016-02-19
M
ark
A
braham
Merge bran
c
h release-5-1
commit
|
commitdiff
|
tree
2016-02-17
Berk Hess
R
enamed nbnxn static
c
onst i
n
ts
commit
|
commitdiff
|
tree
2016-02-05
Be
r
k Hess
Fix incorrect cmap par
s
ing
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Added d
o
cumen
t
at
i
on fo
r
pme g
r
id indexing
commit
|
commitdiff
|
tree
2016-01-29
Berk He
s
s
Fix
T
PI
igno
r
ing PME mesh cont
r
i
b
u
t
ions
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Updat
e
-ntomp_pme -npme check
commit
|
commitdiff
|
tree
2016-01-20
Ansg
a
r E
s
zter
m
ann
Add mi
s
sing initializa
t
ion
i
n nbnxn_pairlis
t
_t
commit
|
commitdiff
|
tree
2015-12-20
B
e
r
k H
e
ss
Merge re
l
ease-5-1 i
n
to
master
commit
|
commitdiff
|
tree
2015-12-19
Berk He
s
s
Bring per
f
ormance estim
a
t
i
on up to
d
ate
commit
|
commitdiff
|
tree
2015-12-11
Berk
Hess
Fix bug with
pull g
r
ou
p
w
ei
g
hts
commit
|
commitdiff
|
tree
2015-12-02
Berk He
s
s
Increa
s
e pdb chain
i
d
s to 62 in
outp
u
t
commit
|
commitdiff
|
tree
2015-12-01
Berk Hess
Pull
gr
o
up count for coords s
t
o
r
ed in tpr
commit
|
commitdiff
|
tree
2015-11-25
M
a
r
k Abra
h
am
Fix logi
c
of dd
_
pri
n
t_missing_inte
r
actions
e
xit
commit
|
commitdiff
|
tree
2015-11-19
B
e
rk Hess
Removed mdrun fatal_error
w
ith
P
3M-AD
commit
|
commitdiff
|
tree
2015-11-18
Berk Hess
Rem
o
v
e
d
R
eaction-Field-nec
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
Fixed
(harm
l
es
s
) fp exception in w
a
llcyc
l
e_sum
commit
|
commitdiff
|
tree
2015-11-09
Berk Hess
Correct
LINCS
dHd
l
contribution
commit
|
commitdiff
|
tree
2015-11-05
V
edran Mileti
ć
Update explanation of replica ex
c
han
g
e
output
commit
|
commitdiff
|
tree
2015-11-03
Mark Ab
r
aha
m
Merge bra
n
ch release-5-1
commit
|
commitdiff
|
tree
2015-09-16
Berk Hess
S
p
l
it nbn
x
n_grid
.
c of
f
from
nbnxn_s
e
arch
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk H
e
ss
Detec
t
incorrect cycle cou
n
t
i
ng
commit
|
commitdiff
|
tree
2015-08-25
Be
r
k He
s
s
Simp
l
ify c
h
an
g
ing the tpx_versio
n
commit
|
commitdiff
|
tree
2015-08-12
Berk Hess
Add
e
d c
o
nst qualifier
s
to c
o
re MD ro
u
tine
s
commit
|
commitdiff
|
tree
2015-06-30
B
e
rk Hess
Fix inconsis
t
ent OpenM
P
aut
o
ma
t
ion
commit
|
commitdiff
|
tree
2015-06-26
Alexey Sh
v
etsov
Fix recent c
o
mpilation issue in
p
ullcode
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Fix g_
e
nerg
y
average/RMSD bug
commit
|
commitdiff
|
tree
2015-05-23
Berk
Hess
Re
m
oved
static from variable
s
in
g
m
x_l
a
pack
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fix
e
d CUD
A
error wit
h
emp
t
y
domains
commit
|
commitdiff
|
tree
2015-05-11
Berk
Hess
Cha
n
ged FFTW warnin
g
from
AVX to no
S
SE
commit
|
commitdiff
|
tree
2015-05-07
Berk Hess
Removed non-ff atomtypes from oplsaa and
c
ha
r
mm27
commit
|
commitdiff
|
tree
2015-05-04
B
e
rk Hess
Fixed GPU non-l
o
cal F copy loca
l
condition
a
l
commit
|
commitdiff
|
tree
2015-04-28
Berk Hess
R
e-enabled F
M
A
for AVX-128-FM
A
commit
|
commitdiff
|
tree
2015-04-22
Berk Hes
s
Merge branch 'release-5-0
'
commit
|
commitdiff
|
tree
2015-04-17
Berk
Hess
Correct
-ntmpi auto f
o
r intel n
e
halem and older
commit
|
commitdiff
|
tree
2015-03-05
Berk H
e
ss
Made DD exclusion processing more efficient
commit
|
commitdiff
|
tree
2015-02-12
Berk Hess
Re-
f
ixed
P
ME bug
with high OpenMP th
r
e
ad count
commit
|
commitdiff
|
tree
2015-01-21
B
erk Hess
Correct
e
d
R
DTSCP war
n
ing t
e
xt
commit
|
commitdiff
|
tree
2014-12-11
Be
r
k Hess
Add
e
d grompp error for pulling
to
negative distance
commit
|
commitdiff
|
tree
2014-12-09
Berk Hess
Fix recent
b
u
g
with trilinic
1
D
DD
commit
|
commitdiff
|
tree
2014-11-24
D
a
v
i
d
van der Spoel
Add
e
d
war
n
in
g
s for ewald-geometry
a
nd surface-epsilon
commit
|
commitdiff
|
tree
2014-10-07
Berk
H
ess
Fi
x
es
is
s
ue with
v
siten
a
nd
Verlet buffers
commit
|
commitdiff
|
tree
2014-09-09
Berk
H
ess
Fi
x
ed DD state collection iss
u
e
commit
|
commitdiff
|
tree
2014-09-08
Berk Hess
Check for im
p
licit solvent +
V
erle
t
scheme
commit
|
commitdiff
|
tree
2014-08-25
Ber
k
Hess
Fixed bugs in v
s
iteN with OpenMP
commit
|
commitdiff
|
tree
2014-08-02
Berk Hes
s
F
i
x
ed PME bug
w
ith hi
g
h OpenMP thr
e
ad count
commit
|
commitdiff
|
tree
2014-07-31
Berk H
e
ss
Avoid divis
i
o
n
by 0 in nb
n
xn_searc
h
commit
|
commitdiff
|
tree
2014-07-28
Christian
Wennberg
Fix overflow in LJ-P
M
E n
b
nxn
k
ernels
commit
|
commitdiff
|
tree
2014-06-20
Berk Hes
s
Fixe
d
shel
l
s
w
ith particle de
c
omposition
commit
|
commitdiff
|
tree
2014-06-10
Berk
Hess
Repla
c
ed gmx_hostname_n
u
m
by gmx_phys
i
c
a
lno
d
e_
i
d_
h
ash
commit
|
commitdiff
|
tree
2014-06-02
Berk
H
e
ss
Fixed g_
e
nergy Einst
e
in viscosity
commit
|
commitdiff
|
tree
2014-03-24
Be
r
k Hess
Adds cut-off check
s
for tricli
n
ic domain
d
ecomp
o
sition
commit
|
commitdiff
|
tree
2013-12-03
Berk Hess
Removed
r
estrict
i
on of
one ref
e
r
e
nce
p
ul
l
gr
o
up
commit
|
commitdiff
|
tree
2013-11-15
Berk Hess
corrected po
t
ent
i
al nbnxn SI
M
D me
m
ory issue
commit
|
commitdiff
|
tree
2013-11-08
B
erk Hess
f
i
x
nbnxn atom sorting with
dis
t
ant bon
d
eds
commit
|
commitdiff
|
tree
2013-11-06
Szilard Pall
enable GPU shari
n
g among tMPI ranks
commit
|
commitdiff
|
tree
2013-10-31
Berk
Hess
reorgani
z
ed GPU de
t
e
ctio
n
and selection
commit
|
commitdiff
|
tree
2013-10-22
Berk Hess
fi
x
ed
r
ecent bug with CUDA te
x
ture ob
j
ect
s
commit
|
commitdiff
|
tree
2013-10-22
Berk
Hess
fixed Op
e
n
M
P
thread
s
being p
i
nned to
t
he sa
m
e
c
o
r
es
commit
|
commitdiff
|
tree
2013-10-10
Berk Hess
fixed nbnxn 4x8 pair search w
i
tho
u
t AVX
commit
|
commitdiff
|
tree
2013-06-03
Berk
Hess
f
i
x
e
d dead
l
ock with replica exchange
and -
m
ax
h
commit
|
commitdiff
|
tree
2013-05-08
Berk Hess
fixed inco
r
rect s
c
aling of c
o
s
-acceler
a
tion vi
s
cosity
commit
|
commitdiff
|
tree
2013-04-26
Berk Hess
PME load balan
c
ing now
checks
for
P
M
E grid
restrictions
commit
|
commitdiff
|
tree
2013-04-18
B
e
rk Hess
changed
mdrun -nstep
s
to
g
mx_large_int
_
t
commit
|
commitdiff
|
tree
2013-04-12
Berk Hess
imp
r
oved load balancing with
V
e
r
let
c
ut-off scheme
commit
|
commitdiff
|
tree
2013-03-27
Berk H
e
ss
removed
x8
6
specif
i
c
s
from nbn
x
n SIMD ke
r
n
e
l
s
commit
|
commitdiff
|
tree
2013-03-27
Berk
H
ess
correc
t
e
d l
o
g
f
i
le wall time break
d
own
commit
|
commitdiff
|
tree
2013-03-21
Berk H
e
ss
m
a
de
PME w
o
rk with
a
m
i
x of 1 and more threads
commit
|
commitdiff
|
tree
2013-03-14
B
erk Hess
corre
c
t
ed grompp rvdw
c
h
arge-gr
o
up radii c
h
ec
k
commit
|
commitdiff
|
tree
2013-02-26
Berk Hess
fixed
PME time
print
w
ith -ntomp_p
m
e != -ntom
p
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
added mdrun check for Verlet+pert
u
rbed atoms
commit
|
commitdiff
|
tree
2013-02-06
Berk
H
ess
fixed bug w
i
th
s
d int
e
grator
a
nd OpenMP threading
commit
|
commitdiff
|
tree
2013-02-05
Berk H
e
s
s
improved l
o
ad balancing on the GPU
commit
|
commitdiff
|
tree
2013-02-04
Ber
k
H
e
s
s
fix
e
d segv in init
_
forc
e
r
e
c with fr
-
>hwi
n
f
o
=
N
U
L
L
commit
|
commitdiff
|
tree
2013-01-17
Berk
H
ess
improv
e
d
C
UDA kernel per
f
ormance
b
y pre-loading cj
commit
|
commitdiff
|
tree
2013-01-16
Ca
r
sten
K
ut
z
ne
r
Made g
_
tune_pme work correctly again
w
i
th thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Berk Hes
s
made SHAKE work again wi
t
h
p
a
rticle decomposti
o
n
commit
|
commitdiff
|
tree
2013-01-10
Berk Hess
fixe
d
bug wi
t
h Verlet + DD + bon
d
ed a
t
om commun
i
cation
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindahl
Revert def
a
ult rlist/rvdw/rcoulo
m
b to valid valu
e
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-02
Be
r
k Hess
m
inor speed-up and code cle
a
n-u
p
in nbnxn kernels
commit
|
commitdiff
|
tree
2012-12-20
Berk Hess
fixed rece
n
t bugs in LINCS f
o
r derivati
v
es
commit
|
commitdiff
|
tree
2012-12-18
B
e
r
k Hess
r
ena
m
ed
gmx_x86
_
simd_macros
.
h to gmx_simd_macros
.
h
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
implem
e
n
ted
n
bnxn
A
VX-256
2
x(N
+
N) kernels
commit
|
commitdiff
|
tree
2012-12-11
B
e
rk
H
e
ss
re
d
uced PLI
N
CS
c
ommu
n
icati
o
n
w
ith H-bond
c
onstraints
commit
|
commitdiff
|
tree
2012-12-07
Berk Hess
fixed GPU pair-s
e
ar
c
h with GMX_CPU_ACCELERATI
O
N=None
commit
|
commitdiff
|
tree
2012-12-05
B
erk
H
es
s
fix
e
d
i
ncorrect
vir
i
a
l
with vi
r
tua
l
sites
and OpenMP
commit
|
commitdiff
|
tree
2012-12-05
Ber
k
Hess
fixed
s
e
gv in
V
erlet
p
air-sea
r
ch with
trilinic DD
commit
|
commitdiff
|
tree
2012-11-30
Be
r
k Hess
f
ixe
d
issue with -multi and GPUs
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
fix
e
d th
r
ead pinning with md
r
un -multi
commit
|
commitdiff
|
tree
2012-11-28
Szilar
d
Pall
ena
b
le
G
PU emulat
i
on without GPU
s
upport
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
e
x
ten
d
ed nb
n
xn x86 SIMD k
e
r
n
el blen
d
v support
commit
|
commitdiff
|
tree
2012-11-27
Berk Hess
fixed
b
u
g in nbnxn Op
e
nMP non-bo
n
ded
f
orce red
u
ct
i
on
commit
|
commitdiff
|
tree
2012-11-26
Be
r
k Hess
m
ade nbn
x
n
analytical Ewald
c
ons
i
s
t
ent
commit
|
commitdiff
|
tree
2012-11-26
Berk Hess
added nbn
x
n analytica
l
Ew
a
ld correction ke
r
nel
s
commit
|
commitdiff
|
tree
2012-11-15
Berk
H
ess
fixed
i
n
c
orrect 1-4 energies wi
t
h
OpenMP +
e
ner
g
y
g
roups
commit
|
commitdiff
|
tree
2012-11-14
Ber
k
Hess
fixed nbnxn
x
86 SIMD non-bonded performance r
e
gress
i
on
commit
|
commitdiff
|
tree
2012-11-12
Berk H
e
ss
nbnxn CPU force buffer reduction
n
o
w uses S
I
MD
commit
|
commitdiff
|
tree
2012-11-05
Berk Hess
updated
s
everal thi
n
gs related with OpenMP t
h
r
e
ad count
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
fixed
i
ncorrect PME load
b
a
lancin
g
lim
i
tation
commit
|
commitdiff
|
tree
2012-10-26
B
erk Hess
set the defau
l
t for
n
stdhdl
t
o 100
commit
|
commitdiff
|
tree
2012-10-26
Be
r
k Hess
fixed
incorre
c
t gro
u
p
energies with nbn
x
n C
P
U ker
n
els
commit
|
commitdiff
|
tree
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