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Fix CMake namespace pollution
2013-02-18
M
a
r
k Abraham
F
ix CMake name
s
pace polluti
o
n
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Merge "M
i
n
o
r fixes to V
e
rle
t
kernels" into release-
4
-6
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Merge
"
i
mproved
PM
E
load
bal
a
ncing r
e
porting" i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
M
e
rge "R
e
-g
e
nerat
e
d
g
roup ker
n
els" int
o
rel
e
a
se-4-6
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Merge "Unwinds
f
lag dependenci
e
s
in
g_order
.
" into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
David van der Spoel
Merge
"Fixed an initialization
i
s
sue in
gmx_d
i
poles
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Ma
r
k Abraham
M
erg
e
"us
e
legacy CU
D
A non-bonded
kernels only on
F
e
rmi
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Merge "More
descr
i
pt
i
ve Verlet kerne
l
macr
o
para
m
e
ter
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Berk Hess
impr
o
v
ed PME load balanc
i
ng
r
e
porting
commit
|
commitdiff
|
tree
2013-02-15
Mark Ab
r
aha
m
Minor fixes to Verlet kernels
commit
|
commitdiff
|
tree
2013-02-15
Ma
r
k Abraham
Merge "
F
ix and add Ve
r
let kernel
e
rro
r
mes
s
ages"
into
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Sander
P
ronk
Merg
e
"Fix cod
e
b
u
g
with thr
e
ad-MPI on PowerPC with
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
R
o
l
and Schulz
Merge "
F
ixed the MPI recognition stri
n
g in g_tune_pme
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Roland Schulz
M
e
rg
e
"improv
e
setup of mu
l
tiple
tf tables" into release-
4
-6
commit
|
commitdiff
|
tree
2013-02-13
R
o
land Schul
z
Merge
"Update
d
FindGSL
.
cmak
e
to version written
by
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Mark
Abraham
Merge
"
PME-only
c
ounters are
now reset with -maxh
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Christoph
J
un
g
hans
Updated Find
G
SL
.
cmake to ve
r
sion
written b
y
me
.
commit
|
commitdiff
|
tree
2013-02-12
Mark Abraham
Merge "f
i
xed bug wi
t
h
sd integrato
r
and Op
e
n
MP thre
a
ding
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
M
a
rk Abr
a
ham
Merge "Fix CUDA_HOST_COMPILER flag name" into relea
s
e-4-
6
commit
|
commitdiff
|
tree
2013-02-09
Roland Schulz
Merge "Typo
f
ix"
i
nt
o
release-4-6
commit
|
commitdiff
|
tree
2013-02-08
Mark
A
b
rah
a
m
Merge "a
d
ded back c
u
da
.
h inclu
d
es t
o
fi
x
missi
n
g CUDA_VERS
I
O
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark Ab
r
a
h
a
m
M
e
rg
e
"Fix
e
d flo
p
coun
t
i
n
g for ge
n
er
i
c
c
g
/adress kern
e
l
s
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark Abraham
Merge "
c
make: f
i
x
e
d typo
i
n
template CMakeLists
.
txt
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Christoph Junghans
Mer
g
e
"
D
ocu
m
ented what G
M
X_CPU_A
C
CEL
E
RATION
really
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Mar
k
A
b
raham
M
e
rge "improved lo
a
d
b
a
lancing on
the GPU" int
o
release-4-6
commit
|
commitdiff
|
tree
2013-02-01
Berk H
e
s
s
P
ME-only counters are now reset with -ma
x
h -r
e
sethway
commit
|
commitdiff
|
tree
2013-01-25
Christoph Ju
n
ghans
Merge "Moved a
f
ew comm
e
nts back
i
nt
o
po
s
it
i
on" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark
Abraham
Merge "Illegal acc
e
lerati
o
n
d
efaulted
t
o
Q
P
X"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark Abraha
m
Merg
e
"
R
e-licenced FindGR
O
MACS
.
cmake (was wri
t
ten
b
y
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Rolan
d
Schulz
I
llega
l
accele
r
ation def
a
ulted to QPX
commit
|
commitdiff
|
tree
2013-01-22
Ma
r
k A
b
raham
Merge "Fix
TOUPPER usa
g
e
"
int
o
releas
e
-4-6
commit
|
commitdiff
|
tree
2013-01-22
Mark Abr
a
ham
Merge "
U
pdate
d
html manual to 4
.
6" into release
-
4-6
commit
|
commitdiff
|
tree
2013-01-22
M
a
rk Abrah
a
m
Merge "added missi
n
g cleanup of
s
ome
nbnxn_cuda
d
ata
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Ro
l
and Schul
z
F
ix TOUPPE
R
u
s
age
commit
|
commitdiff
|
tree
2013-01-22
Roland
Schulz
U
p
dated html manual to 4
.
6
commit
|
commitdiff
|
tree
2013-01-21
Christoph J
u
nghan
s
Merge "Set ve
r
sion
i
n
f
o for 4
.
6
.
x release series" int
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Mark A
b
raham
Set version info for
4
.
6
.
x
r
elease series
commit
|
commitdiff
|
tree
2013-01-18
Mark
Abraham
New m
a
jo
r
release: 4
.
6
commit
|
commitdiff
|
tree
2013-01-18
Michael Sh
i
rts
Addendum for expan
d
ed ensembl
e
options
plus
f
orm
a
tt
i
ng
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Rol
a
n
d
Schulz
F
i
x typo
commit
|
commitdiff
|
tree
2013-01-18
Rolan
d
Sc
h
ulz
Code beauti
f
ication wit
h
uncrustify
commit
|
commitdiff
|
tree
2013-01-18
Roland Sc
h
ulz
A
dd col
o
n after
m
a
cro t
o
help uncrusti
f
y
commit
|
commitdiff
|
tree
2013-01-18
Ber
k
Hess
thread affini
t
y now uses some
t
opology informatio
n
commit
|
commitdiff
|
tree
2013-01-18
M
ark
Ab
r
aham
Fi
x
i
ng copyright
i
ssues and code contributo
r
s
commit
|
commitdiff
|
tree
2013-01-18
Erik Lin
d
ah
l
Merge "rem
o
ve unnecessary cmake messag
e
s" int
o
release
-
4-6
commit
|
commitdiff
|
tree
2013-01-18
Erik Lindahl
Mer
g
e "fix OpenMP
detection on Mac OS broken by a6fee0b
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Szilárd Páll
fix OpenMP detection on Mac OS b
r
oken by a6
f
ee0b
commit
|
commitdiff
|
tree
2013-01-17
Szilárd Pál
l
a
dded mis
s
in
g
cleanup of some
nbnxn
_
cuda data
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Merge "Remove unnecessary ICC
f
lags affecting p
e
r
f
ormanc
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark A
b
raham
Merge
"improve
d
CUD
A
kernel performa
n
c
e by pre-loading
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph Jungh
a
ns
Merge "Added note ab
o
ut
m
a
k
e_ed
i
and flooding in
E
D
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Ch
r
ist
o
p
h Junghans
M
erge "use the c
o
mpiler
version provide
d
by CMake
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Rol
a
nd Schulz
Merge "
M
erg
e
bran
c
h 'r
e
lease-
4
-5-patches'
i
nto relea
s
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
S
zilárd
P
á
ll
Merge changes I930b
3
1
6c,Iea4
2
83
e
0,I103
6
48f8 into rel
e
a
se-4-6
commit
|
commitdiff
|
tree
2013-01-17
M
a
rk Abraham
Merge "F
i
x trj
c
onv -sub with
.
trr files
"
into
r
e
leas
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Ma
r
k Abraham
BlueGe
n
e
/
Q installa
t
ion notes
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
Merge "note the reason
f
or a
u
to-disabling GP
U
support
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Ab
r
aham
M
e
rge
"
Adde
d
md
p
o
ption 'calc-lambda-neighb
o
rs'
.
" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland S
c
hulz
Merge "clarify wording of
GPU driver-rel
a
ted no
t
es
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Rol
a
n
d
S
ch
u
l
z
Merge "A
d
d
ed check for valid w
a
ll_
a
tomtype in
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark
A
braham
Fix trjconv
-sub w
i
th
.
t
r
r fil
e
s
commit
|
commitdiff
|
tree
2013-01-17
Berk
H
e
s
s
f
i
xed SD+BD integra
t
ion slowing
down with OpenMP threads
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
Run
r
e
gress
i
o
n
tests
f
ro
m
build
commit
|
commitdiff
|
tree
2013-01-17
Sande
r
Pron
k
A
dde
d
mdp optio
n
'
c
alc-lambda-neighbor
s
'
.
commit
|
commitdiff
|
tree
2013-01-17
M
a
rk
A
b
raha
m
Finally
mov
e
OpenMM to contrib
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
Fix
c
on
f
using gmx_header_config
.
h
include
commit
|
commitdiff
|
tree
2013-01-17
Szilard Pall
don
'
t
use polling with new driver
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
clean up fo
r
tran name mangl
i
ng
commit
|
commitdiff
|
tree
2013-01-17
Berk
H
ess
fixed nb
n
xn hyb
r
id mode with Op
e
nMP
commit
|
commitdiff
|
tree
2013-01-17
Berk
H
ess
made
P
M
E lo
a
d balanci
n
g + DD
DLB m
o
re efficient
commit
|
commitdiff
|
tree
2013-01-16
Christoph J
u
nghans
Remove de
b
ug statm
e
nt
commit
|
commitdiff
|
tree
2013-01-15
Mark
Abraham
Merge "Hid
n
bnxn
k
ernel names
behind
a
lookup
function
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Chr
i
s
toph Ju
n
ghans
Merge "
A
dded fatal error
for
c
onstraints
+ L-BFGS minimizer
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Christoph J
u
nghans
Mer
g
e "
d
isabl
e
OpenMP with
a
ll OS
X
gcc
4
.
2
-
based
c
o
m
p
ilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Sand
e
r Pr
o
nk
Me
r
ge "Continuatio
n
of d
o
c
umentation for
expanded ensem
b
le
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Mark Abraham
Velocity-verlet integrators
a
n
d
v-rescale ar
e
b
r
o
k
e
n
commit
|
commitdiff
|
tree
2013-01-14
Ca
r
sten Kutzn
e
r
Ess
e
ntial dynamics output fi
l
e no
w
in
.
x
vg format
commit
|
commitdiff
|
tree
2013-01-14
David van der Spoel
Merge "Fixing trjconv -sub"
into rele
a
se
-
4-5-patches
commit
|
commitdiff
|
tree
2013-01-14
David
van der S
p
o
el
M
e
r
ge "No
t
ing th
a
t and w
h
y gmxdump -
s
-sys is
b
roken
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Rol
a
nd Schul
z
M
e
rge "Fixes for md-vv and
rerun" into release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Rol
a
nd
S
chulz
Merge
"
fixed resetti
n
g
s
tates
w
i
th
p
aralle
l
Verlet
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Roland S
c
hulz
Proper fix
for copyrite
cu
d
a dependence
commit
|
commitdiff
|
tree
2013-01-13
Michael
S
hirts
Fixes for md-vv and r
e
run
commit
|
commitdiff
|
tree
2013-01-13
B
erk Hess
fixed resetting st
a
te
s
wi
t
h paralle
l
Ve
r
let s
c
heme
commit
|
commitdiff
|
tree
2013-01-13
C
hr
i
stoph Junghan
s
Merge "Remove unu
s
ed bfunc
.
h
.
"
i
n
t
o
r
elease-4-6
commit
|
commitdiff
|
tree
2013-01-13
Ch
r
ist
o
ph
J
ung
h
ans
Mer
g
e "Clar
i
f
i
ed som
e
comments & warnings abo
u
t
thread
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Christoph Junghans
Merge "Manage Blue
G
ene/Q configura
t
ion" into
r
elease-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph Junghans
Merg
e
"Re-organiz
e
BlueGene to
o
lcha
i
n
f
i
l
es
"
i
n
to
release
-
4
-
6
commit
|
commitdiff
|
tree
2013-01-13
Christoph Junghans
Merge
"
Changed defaults
for
b
uildi
n
g shared libraries
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraham
Clarified some comme
n
ts &
w
ar
n
i
ngs abo
u
t thread
pinning
commit
|
commitdiff
|
tree
2013-01-13
Roland
Schulz
Merge "pr
e
par
e
d the nbnxn
c
o
d
e for non-x86 SIMD" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Mar
k
Abraha
m
Merge
"
Adde
d
basic CPU topology in
f
ormation to cpuid
.
.
.
commit
|
commitdiff
|
tree
2013-01-12
Berk Hess
p
repare
d
the nbn
x
n
code fo
r
n
o
n
-x86 SIMD
commit
|
commitdiff
|
tree
2013-01-12
Ch
r
istoph
J
unghans
Merge
"
A
d
d
e
d mi
s
sing export"
i
nto release-4-6
commit
|
commitdiff
|
tree
2013-01-11
Erik Lindahl
Merge
"made SHAKE
work
a
g
ain wi
t
h par
t
ic
l
e deco
m
posti
o
n
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Rol
a
n
d
S
ch
u
l
z
M
e
r
ge "time t
h
e GPU force clea
r
i
ng
a
sync launch overhead
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Ch
r
i
s
toph
J
u
n
ghans
Merge "console
a
nd
l
og
output impr
o
vements" into release-4-6
commit
|
commitdiff
|
tree
2013-01-11
Chri
s
to
p
h
Junghans
Merge "Fix CUDA bein
g
q
ui
e
t and
ma
r
k all CUD
A
_* as
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Er
i
k Lind
a
hl
Added
basi
c
CPU topology information to cpuid code
commit
|
commitdiff
|
tree
2013-01-11
Erik Lindahl
Merg
e
"fix
e
d nbnxn no LJ comb
.
r
ule AVX25
6
PM
E
ker
n
e
l
.
.
.
commit
|
commitdiff
|
tree
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