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Merge "fixed bug with sd integrator and OpenMP threading" into release-4-6
2013-02-12
Mark
A
b
r
a
ham
Merge "fixed bug
w
it
h
sd in
t
e
g
r
a
tor and O
p
enMP th
r
eading
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Mar
k
A
b
raham
Merge "Fix
CUDA_HOST_
C
OMPILER fl
a
g name"
i
n
to r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-02-09
Roland Schulz
Mer
g
e
"Typo f
i
x" into
rele
a
se-4-6
commit
|
commitdiff
|
tree
2013-02-08
Mark Abraham
Me
r
ge "added back
cuda
.
h inclu
d
es to fix missing CUDA
_
VER
S
IO
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark Ab
r
aham
Merge "Fixed flop counting for generic
c
g/ad
r
e
ss ker
n
els
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
M
ark Abraham
Merge "cm
a
k
e
: fixed typo in templa
t
e C
M
akeLis
t
s
.
t
x
t
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Ch
r
istoph Junghans
Merge
"Docume
n
ted wh
a
t
G
MX_CPU_ACCELERATION
r
e
ally
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Mark Abra
h
am
Merg
e
"impro
v
ed load bal
a
nci
n
g on the GPU" into release-4-6
commit
|
commitdiff
|
tree
2013-01-25
Christoph Jung
h
ans
Merge "Moved a few comments
b
ack into position" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark
A
br
a
h
a
m
Merge "Illegal ac
c
eleration defaulte
d
to QPX" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark Abraham
Me
r
ge "Re-licenc
e
d
F
indGROMACS
.
c
make (was written
by
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Roland Sc
h
u
l
z
Illegal
accelera
t
ion defaulted to QPX
commit
|
commitdiff
|
tree
2013-01-22
Mark Abrah
a
m
Mer
g
e "Fi
x
T
OU
P
PER usage"
i
nto release-4
-
6
commit
|
commitdiff
|
tree
2013-01-22
Mark
Ab
r
aham
Merge "Updated html manual t
o
4
.
6
" int
o
release-4-6
commit
|
commitdiff
|
tree
2013-01-22
Mark Abraha
m
Merge "
a
dded missing cle
a
nup of some nbnxn_cud
a
da
t
a
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
R
oland S
c
hulz
Fix T
O
UPPER u
s
age
commit
|
commitdiff
|
tree
2013-01-22
Roland Sc
h
ulz
U
p
d
ate
d
html
m
anual
t
o 4
.
6
commit
|
commitdiff
|
tree
2013-01-21
C
hrist
o
p
h
Ju
n
ghans
Merge "S
e
t version
i
nfo for 4
.
6
.
x release series"
i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Mark Abr
a
ham
S
et version inf
o
for 4
.
6
.
x re
l
ease se
r
ies
commit
|
commitdiff
|
tree
2013-01-18
Mark Abraham
Ne
w
ma
j
or
r
e
lease: 4
.
6
commit
|
commitdiff
|
tree
2013-01-18
Michael Sh
i
rts
A
ddendum for expanded
e
n
s
emble opt
i
ons plus formatting
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Rola
n
d
S
c
hulz
Fix typo
commit
|
commitdiff
|
tree
2013-01-18
Ro
l
and Schulz
Code beau
t
i
f
i
c
ation with u
n
c
r
ustify
commit
|
commitdiff
|
tree
2013-01-18
Roland Schulz
A
dd colon af
t
e
r macro to help uncrusti
f
y
commit
|
commitdiff
|
tree
2013-01-18
B
e
rk He
s
s
t
hre
a
d
a
ff
i
nity no
w
use
s
som
e
t
o
po
l
og
y
information
commit
|
commitdiff
|
tree
2013-01-18
M
ark Abraham
Fix
i
n
g
copyright
i
ss
u
es and code contribu
t
ors
commit
|
commitdiff
|
tree
2013-01-18
Erik Lindah
l
Merge "remove unn
e
ce
s
sary cm
a
ke messa
g
es"
i
n
to rele
a
se-
4
-
6
commit
|
commitdiff
|
tree
2013-01-18
Erik Lindahl
Merge "fix OpenMP
d
etection on Mac
OS b
r
oken
b
y a6
f
ee0b
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Szilárd
Páll
f
ix
Open
M
P
detection o
n
M
a
c OS brok
e
n
b
y a6
f
ee0b
commit
|
commitdiff
|
tree
2013-01-17
Szilárd
Páll
added m
i
ssing cle
a
nup of
s
ome
nbnxn_cuda data
commit
|
commitdiff
|
tree
2013-01-17
Ma
r
k A
b
raham
Merge
"
R
e
move
unnecessary ICC
f
l
ags
affecting
p
e
r
forman
c
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Merge "improved CUD
A
kernel performa
n
ce
b
y p
r
e
-loading
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Chris
t
oph J
u
nghans
Me
r
g
e "Added
not
e
a
bout
make_
e
di
and fl
o
o
d
i
ng in ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
Merge "use
t
he compiler version provided by CMa
k
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
Merge
"Merge bra
n
c
h
'rel
e
ase-4-5-patches
'
into release
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Szi
l
árd
P
áll
Merge changes I9
3
0b31
6
c,Iea4
2
83e0,I103648
f
8 into r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-01-17
Ma
r
k Ab
r
aham
Merge "Fix trjconv -
s
ub with
.
trr files" into
releas
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Ma
r
k Abra
h
am
BlueGene/Q installation notes
commit
|
commitdiff
|
tree
2013-01-17
Chr
i
stoph J
u
nghans
Merge "note the reason
for aut
o
-disabling GPU su
p
port
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Ma
r
k Abra
h
am
Merge "Ad
d
ed mdp option 'calc-la
m
bda-neighbors'
.
" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Rola
n
d Schulz
Merge "clarify wording of
G
PU
driver-related no
t
es
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
R
o
land Schu
l
z
M
e
rge "Added check for v
a
lid wa
l
l
_
ato
m
type in
.
md
p
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abr
a
ham
Fix trjcon
v
-sub
w
ith
.
trr
f
iles
commit
|
commitdiff
|
tree
2013-01-17
B
e
rk Hess
f
i
xed SD+BD integrati
o
n slowing down
w
ith
O
p
e
n
MP t
h
r
e
ads
commit
|
commitdiff
|
tree
2013-01-17
R
o
land
Sc
h
ulz
Run reg
r
essiont
e
sts from build
commit
|
commitdiff
|
tree
2013-01-17
San
d
er Pronk
Added mdp option 'calc-lambd
a
-neig
h
bors'
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Finally move
OpenMM to
contrib
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
Fix confusing gmx_header_co
n
fig
.
h
include
commit
|
commitdiff
|
tree
2013-01-17
Szi
l
ard Pall
don't
u
se
poll
i
ng with ne
w
driver
commit
|
commitdiff
|
tree
2013-01-17
Christop
h
Junghans
clean up fortran name mang
l
ing
commit
|
commitdiff
|
tree
2013-01-17
Be
r
k Hess
fixed nbnxn hybrid mod
e
with O
p
enMP
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
m
a
de PME load bal
a
ncing +
DD DL
B
more
e
ff
i
cie
n
t
commit
|
commitdiff
|
tree
2013-01-16
Ch
r
istoph
Junghans
Remo
v
e deb
u
g
s
tat
m
e
n
t
commit
|
commitdiff
|
tree
2013-01-15
Mark Abraham
Merge
"
Hid n
b
nxn kernel
n
ames
b
ehind a lookup
f
unction
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Christoph Junghans
Merge "Ad
d
e
d
f
atal err
o
r
f
o
r
c
onstraints
+ L-BFGS minimizer
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Christoph Junghans
Merge "disable OpenMP w
i
th
a
ll OS
X
gcc 4
.
2-bas
e
d co
m
pilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Sander
P
ron
k
Me
r
ge "Continuation of docum
e
ntation for expanded ensemble
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Mar
k
A
bra
h
a
m
Velo
c
ity-
v
erle
t
integra
t
ors and v-
r
esca
l
e are br
o
ken
commit
|
commitdiff
|
tree
2013-01-14
Carst
e
n
K
u
tzner
Essen
t
i
a
l dyn
a
m
ics o
u
tput fi
l
e
now in
.
xv
g
format
commit
|
commitdiff
|
tree
2013-01-14
David van der Spoel
Merge "Fixing trjconv -sub" into
r
elease-4-5-
p
a
t
c
hes
commit
|
commitdiff
|
tree
2013-01-14
David van
d
e
r Spoel
Merge "Noting that
a
n
d why
gmxdu
m
p -s -sys is broken
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Ro
l
an
d
Schu
l
z
Merge "Fixes fo
r
md-vv a
n
d rerun"
i
nto release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Rol
a
nd Schulz
Merge "fixed res
e
t
t
ing
states wit
h
parallel Verlet
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Rol
a
n
d Schulz
Pr
o
per fix for c
o
py
r
i
te
c
uda d
e
pendence
commit
|
commitdiff
|
tree
2013-01-13
Michael Shirts
Fixe
s
for md
-
vv and rerun
commit
|
commitdiff
|
tree
2013-01-13
Berk Hess
fi
x
ed r
e
setting st
a
tes with parallel
Verlet
s
che
m
e
commit
|
commitdiff
|
tree
2013-01-13
Chri
s
toph Junghans
M
e
r
ge "Rem
o
ve unused b
f
unc
.
h
.
" into release-4-
6
commit
|
commitdiff
|
tree
2013-01-13
C
hristoph Jung
h
ans
Merge "
C
larifi
e
d s
o
me c
o
mments & warnin
g
s
abo
u
t thread
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Christoph J
u
nghans
Merg
e
"Manage BlueGene/Q config
u
rat
i
on" into release-4-6
commit
|
commitdiff
|
tree
2013-01-13
C
hristo
p
h Ju
n
ghans
Merge
"
Re-org
a
nize BlueGene toolch
a
in
fi
l
es" into
r
el
e
ase
-
4
-
6
commit
|
commitdiff
|
tree
2013-01-13
C
hristoph Jungh
a
ns
M
erge "Changed default
s
for building shar
e
d
libraries
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Ma
r
k Abraham
Clarif
i
ed some comments & warning
s
a
b
o
ut thread pin
n
ing
commit
|
commitdiff
|
tree
2013-01-13
Roland
Schulz
Merge
"
prepared
t
he nb
n
xn cod
e
for
n
on-x86 SIMD" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Mark A
b
raham
M
e
rge "
A
dded ba
s
i
c
CPU topolog
y
information to c
p
uid
.
.
.
commit
|
commitdiff
|
tree
2013-01-12
B
e
rk Hess
prepared the n
b
nxn cod
e
for
non
-
x86 SIMD
commit
|
commitdiff
|
tree
2013-01-12
Chr
i
sto
p
h
Jungha
n
s
Merge "Ad
d
ed m
i
ssing exp
o
r
t
" into
r
elease-4-6
commit
|
commitdiff
|
tree
2013-01-11
Erik Lindahl
Merge "made SHAKE work aga
i
n wi
t
h particle
decompostion
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Roland S
c
hulz
Merge "time the
G
PU force clearin
g
async launch overhea
d
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Chr
i
stoph Junghans
Merg
e
"console and log output im
p
rovements" into release-
4
-6
commit
|
commitdiff
|
tree
2013-01-11
Ch
r
isto
p
h
J
u
ng
h
ans
M
er
g
e "
F
ix
C
UDA bein
g
quiet and m
a
rk al
l
CUDA_* as
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Erik Lin
d
ahl
Adde
d
basic C
P
U topology information to cpuid
c
o
d
e
commit
|
commitdiff
|
tree
2013-01-11
E
r
ik Lindahl
Merge
"fixed nbnxn n
o
L
J
co
m
b
.
rule AVX
2
56 PME k
e
rnel
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
R
o
l
a
nd Schulz
Merge
"
Handle compiler flags more f
l
exibly" into
r
elease
-
4-6
commit
|
commitdiff
|
tree
2013-01-11
Ch
r
i
stoph
Jun
g
hans
Merge "Remove incorrect assert add
e
d
by
0
5f9a740" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Berk Hess
fixed nbnxn no
LJ comb
.
rule AVX256 P
M
E ker
n
el
commit
|
commitdiff
|
tree
2013-01-10
E
r
i
k
L
inda
h
l
F
i
xed f
l
op-ac
c
ounting for
p
eriodic improper dihedrals
commit
|
commitdiff
|
tree
2013-01-10
Mark
Ab
r
aham
M
erge "
R
evert def
a
ult rlist/rvd
w
/rcoulomb to val
i
d
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Mark
A
bra
h
am
Merge "fixed bug w
i
th V
e
rlet + DD +
bonded atom co
m
municatio
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
R
o
l
and Schulz
Handle compiler flags more
f
lexibly
commit
|
commitdiff
|
tree
2013-01-10
Erik Lin
d
ahl
Dis
a
l
l
ow the use
o
f Cl
a
ng t
o
com
p
ile AVX
_
128_FMA
commit
|
commitdiff
|
tree
2013-01-10
Roland Sch
u
lz
Merge "Move Windows
shared/static op
t
ions to late
r
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Roland S
c
hulz
Merge "Remove work
a
round" into release-4-6
commit
|
commitdiff
|
tree
2013-01-10
R
ol
a
nd S
c
hul
z
M
o
v
e Windows sh
a
red/static
o
ptions to
l
a
ter poin
t
commit
|
commitdiff
|
tree
2013-01-10
Rolan
d
S
ch
u
lz
R
emove workaround
commit
|
commitdiff
|
tree
2013-01-10
Erik
L
indahl
Remove bro
k
en g_dih tool
commit
|
commitdiff
|
tree
2013-01-10
Ma
r
k
A
b
raham
Merge "Fixes SSE/AVX
c
ompi
l
atio
n
u
nder Windows" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
E
rik Lindah
l
Merg
e
"Correct
e
d gm
x
che
c
k
o
utput f
o
r Gromos96 bo
n
d
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
R
o
l
a
nd Schulz
M
e
rge "Ad
d
ed work-aro
u
nd for gcc bug
i
n AVX intrinsi
n
cs
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Ro
l
a
n
d
S
chul
z
Merge "Add check to remove
zero
C
ha
r
mm dihedrals" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
R
oland Schulz
Mer
g
e "[tools] g_sans
- add trajectory avereging" into
.
.
.
commit
|
commitdiff
|
tree
next