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optimized generic SIMD invsqrt
2013-03-19
C
hri
s
toph Junghans
M
erge "E
s
sential dynamics:
f
ixed le
g
end in ED
.
xvg
.
.
.
commit
|
commitdiff
|
tree
2013-03-12
Mark
A
brah
a
m
Merge
"
fix
broken th
i
ngs
i
n mkht
m
l" into
r
elease-4-6
commit
|
commitdiff
|
tree
2013-03-11
M
a
rk Ab
r
aham
Merge "Fixes linkage w
i
th FFTW + MKL for BL
A
S/L
A
PAC
K
.
.
.
commit
|
commitdiff
|
tree
2013-03-06
Roland
Schulz
Merge "f
i
xe
d
PME time
print with -ntomp_pme != -nto
m
p
.
.
.
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
New pa
t
c
h r
e
l
e
as
e
4
.
6
.
1
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
Fi
x
automated regr
e
ssion
t
esting GMXLIB
v
alue
commit
|
commitdiff
|
tree
2013-03-05
Berk
H
e
ss
fixe
d
bug wit
h
D
D cut-of
f
check and PME DLB
commit
|
commitdiff
|
tree
2013-03-05
M
a
r
k Ab
r
aham
Fix
r
e
gr
e
ssiont
e
sts aut
o
mate
d
d
o
wnload
commit
|
commitdiff
|
tree
2013-03-05
Berk Hess
fi
x
e
d
rec
e
n
t bug with sorting ato
m
s for GPUs
commit
|
commitdiff
|
tree
2013-03-05
Ma
r
k Abraham
Update
s
hell com
p
letio
n
s
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
Update outdated admin things
commit
|
commitdiff
|
tree
2013-03-05
Justin Lemkul
Fixes for
install
gui
d
e p
a
ge
.
commit
|
commitdiff
|
tree
2013-03-05
Mark
A
braham
Up
d
ated install guide
commit
|
commitdiff
|
tree
2013-03-02
C
hris
t
oph Junghans
Merge "Uncrusti
f
ied code change
s
si
n
ce 4
.
6" in
t
o r
e
le
a
se-4-6
commit
|
commitdiff
|
tree
2013-02-20
Ch
r
istoph Junghans
Bump shared
object ver
s
ion to 8
commit
|
commitdiff
|
tree
2013-02-20
Ber
k
Hes
s
fixed issues with
FEP soft-core and cut-off'
s
commit
|
commitdiff
|
tree
2013-02-18
B
er
k
Hess
f
i
xed GPU par
t
icle g
r
idding perform
a
n
ce is
s
ue
commit
|
commitdiff
|
tree
2013-02-18
Ca
r
s
t
en Kutz
n
er
M
a
d
e g
_
t
u
ne_pme work with 4
.
6
if user s
e
ts
"-p" com
m
and
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Mark
Abr
a
ham
Fix CMake
n
amespace pollution
commit
|
commitdiff
|
tree
2013-02-15
Mark Abr
a
ham
Merge "Min
o
r fi
x
e
s to Verle
t
kerne
l
s
"
int
o
release-4-6
commit
|
commitdiff
|
tree
2013-02-15
Mark A
b
raham
Merg
e
"im
p
rov
e
d PME
load balan
c
ing reporting" into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
M
ark Abraham
Merge
"
Re-generated group kernel
s
" into
re
l
e
a
se-4-
6
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Mer
g
e "Unwinds flag depen
d
encies
i
n
g_o
r
der
.
" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
David van der Sp
o
el
Merge
"Fixed an initialization issu
e
in
g
mx_dipo
l
es
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Ma
r
k Abraham
Merge "use legacy CUDA non-bonded kernels
o
nly on Fermi
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark
A
braham
M
e
rg
e
"Mor
e
descri
p
tive Verlet kernel m
a
cro parameter
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Berk
H
ess
impr
o
ved P
M
E load
b
al
a
nci
n
g r
e
porting
commit
|
commitdiff
|
tree
2013-02-15
M
a
r
k Abrah
a
m
M
i
nor fi
x
es to
Ver
l
et
k
ernels
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Merge "Fix an
d
add Verlet kerne
l
error messages" into
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
S
ander Pronk
M
e
rg
e
"Fix code bug w
i
th thread-MP
I
on PowerPC with
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
R
oland Sc
h
ulz
Merg
e
"Fixed
the MPI re
c
ognition string in g_tune_
p
me
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Roland
S
c
h
u
lz
M
e
r
ge
"
improve setup of multiple tf
t
ables" i
n
to rele
a
s
e
-4-6
commit
|
commitdiff
|
tree
2013-02-13
Roland Sc
h
ulz
Merge "Updated FindGSL
.
c
make to version
written by
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Ma
r
k
Ab
r
aham
Merge "PME-only counters
a
r
e
n
o
w r
e
set with -m
a
xh
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Ch
r
istoph Jun
g
hans
U
pdated FindGSL
.
cmak
e
to ve
r
s
i
o
n
writt
e
n by me
.
commit
|
commitdiff
|
tree
2013-02-12
Mar
k
Abra
h
am
Merg
e
"fixed
bug
with sd integrat
o
r and Open
M
P
thread
i
ng
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Mark Abrah
a
m
Merge "Fix CUDA
_
HO
S
T_COM
P
ILER flag name"
into release-4
-
6
commit
|
commitdiff
|
tree
2013-02-09
Ro
l
and Schu
l
z
Mer
g
e
"Typo fix
"
int
o
release-4-6
commit
|
commitdiff
|
tree
2013-02-08
Mark
A
brah
a
m
Mer
g
e "added back cuda
.
h inc
l
udes to fix missing CUDA_VERSIO
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark Abr
a
h
am
Merge "Fixed flop counti
n
g for generi
c
cg/ad
r
ess
kernels
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark
Abraham
Merge "
c
make: fix
e
d typo in templat
e
CMakeL
i
sts
.
txt
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
C
hristoph J
u
n
g
hans
M
erge "Documen
t
ed what
G
MX_
C
PU_ACCELE
R
ATION really
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Mark
Abr
a
h
am
Mer
g
e
"improved load balancing o
n
the GPU"
i
nt
o
r
e
le
a
s
e-4-6
commit
|
commitdiff
|
tree
2013-02-01
Be
r
k
Hess
PME-only count
e
rs are now reset w
i
th -maxh
-
resethwa
y
commit
|
commitdiff
|
tree
2013-01-25
C
h
r
istoph Junghans
Merge
"
Moved a few comment
s
bac
k
into position"
into
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
M
a
rk Abr
a
ham
Merge "I
l
legal acceleration d
e
faul
t
e
d
to QPX
"
into
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Ma
r
k
Abra
h
am
Merge "R
e
-licenced Fi
n
dGROMACS
.
cmake (w
a
s written by
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Roland
Sc
h
ulz
Illegal ac
c
el
e
ration defaulted to QPX
commit
|
commitdiff
|
tree
2013-01-22
Mar
k
Abraham
Merge "F
i
x TOU
P
PER usage"
i
nto rel
e
a
s
e-4-
6
commit
|
commitdiff
|
tree
2013-01-22
Mark Abraham
Merge "Upda
t
ed html manu
a
l
to 4
.
6" into
re
l
ease-4-6
commit
|
commitdiff
|
tree
2013-01-22
M
a
rk
Abra
h
am
Me
r
ge "added missing clea
n
u
p
of
some nbnxn_cuda
data
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Roland Schulz
Fix
T
OUPPER usage
commit
|
commitdiff
|
tree
2013-01-22
Roland
Schulz
Upda
t
ed ht
m
l manual to
4
.
6
commit
|
commitdiff
|
tree
2013-01-21
Christoph Junghan
s
Merge "Set version info for 4
.
6
.
x
release series" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Ma
r
k
Abraham
Set ve
r
s
i
on info fo
r
4
.
6
.
x
release
s
eries
commit
|
commitdiff
|
tree
2013-01-18
Mark Abraham
New major
r
elease: 4
.
6
commit
|
commitdiff
|
tree
2013-01-18
Mic
h
a
e
l
Shirts
Addend
u
m for expande
d
ens
e
mble options p
l
us formatt
i
ng
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Roland Schulz
Fix ty
p
o
commit
|
commitdiff
|
tree
2013-01-18
Roland
Sc
h
ulz
Code beaut
i
fication with uncrustify
commit
|
commitdiff
|
tree
2013-01-18
R
oland Schulz
Add colon after macro to
h
elp uncrustify
commit
|
commitdiff
|
tree
2013-01-18
Berk Hess
thread affin
i
ty
now uses
s
o
m
e
t
opol
o
gy
informa
t
ion
commit
|
commitdiff
|
tree
2013-01-18
Mark Abraham
F
i
xing
copyright
i
ssues
an
d
code
c
ontrib
u
tors
commit
|
commitdiff
|
tree
2013-01-18
Er
i
k Linda
h
l
Merge
"remove unnecessary c
m
ak
e
m
e
ssages" in
t
o r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-01-18
Erik Lind
a
hl
Merge
"
f
ix OpenMP d
e
t
e
ction on Mac OS bro
k
en by a6fee0b
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Szilárd Páll
fi
x
OpenM
P
de
t
ection
o
n
Mac OS b
r
oken by a6fee0b
commit
|
commitdiff
|
tree
2013-01-17
Szilár
d
Páll
a
dded missi
n
g cl
e
anup of some nbnxn_cuda data
commit
|
commitdiff
|
tree
2013-01-17
Mark
A
b
r
a
h
am
Me
r
ge "
R
emove
u
nnecessary ICC fla
g
s affe
c
ting p
e
r
formance
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraha
m
Merge "impr
o
v
e
d
CUDA kernel performan
c
e by pre-loading
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
M
e
rg
e
"A
d
ded note abou
t
m
ake_edi
a
nd f
l
ooding in ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
C
h
ristoph Jung
h
ans
M
erge "use
t
he com
p
iler ve
r
s
ion pr
o
vided b
y
C
Ma
k
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
R
o
land Schulz
Merge "Me
r
ge bran
c
h
'r
e
lease-4-5-patc
h
es
'
into
r
elea
s
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Szilárd
Páll
Mer
g
e changes
I930b316c,Iea42
8
3e0,I
1
03648f8 in
t
o
r
e
l
e
ase-4-
6
commit
|
commitdiff
|
tree
2013-01-17
M
a
rk Ab
r
aham
Merge
"
Fix trjc
o
nv -sub
with
.
trr files" i
n
t
o r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark
A
braham
BlueGen
e
/Q ins
t
allati
o
n n
o
tes
commit
|
commitdiff
|
tree
2013-01-17
C
h
r
i
s
t
o
ph
J
unghans
M
e
rge
"no
t
e
t
h
e reas
o
n for auto-d
i
sabling
G
PU support
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
M
erg
e
"Added mdp opti
o
n 'cal
c
-lambda-neighbors'
.
" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Rol
a
nd Schulz
Merge "clarify
wording of
GPU driver-related note
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland Sch
u
lz
Merge "A
d
ded check for
v
a
lid
w
all_a
t
o
m
type
in
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
M
ark Abraham
F
i
x trjc
o
nv -sub with
.
t
rr f
i
les
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
fix
e
d SD+BD int
e
gr
a
tion s
l
owi
n
g down with OpenMP threads
commit
|
commitdiff
|
tree
2013-01-17
Rola
n
d Schulz
Run regressionte
s
ts from
bu
i
ld
commit
|
commitdiff
|
tree
2013-01-17
S
a
nd
e
r Pr
o
nk
Added mdp option 'calc-lambda-neig
h
bor
s
'
.
commit
|
commitdiff
|
tree
2013-01-17
Mar
k
Abrah
a
m
Final
l
y move OpenMM to contrib
commit
|
commitdiff
|
tree
2013-01-17
R
oland Schulz
F
i
x
confusing gmx_header_config
.
h
in
c
lud
e
commit
|
commitdiff
|
tree
2013-01-17
Szilard Pa
l
l
don't use polli
n
g
with n
e
w drive
r
commit
|
commitdiff
|
tree
2013-01-17
Christoph
J
ung
h
a
n
s
cle
a
n
u
p fortran nam
e
mangling
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
f
ixed nbnxn hybr
i
d
mod
e
with Op
e
n
M
P
commit
|
commitdiff
|
tree
2013-01-17
Berk
H
ess
made
PME load balanc
i
ng + D
D
DL
B
more
e
fficie
n
t
commit
|
commitdiff
|
tree
2013-01-16
Christoph Jun
g
hans
Re
m
ove debug statm
e
nt
commit
|
commitdiff
|
tree
2013-01-15
Ma
r
k Abraham
Mer
g
e "Hid
n
b
n
xn
k
er
n
el n
a
mes behind a lookup function
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Christoph Jungh
a
ns
Merge "Add
e
d fatal
erro
r
for constraints + L-BFGS minimiz
e
r
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Chri
s
toph
J
u
n
ghans
M
e
rge "disable Op
e
nMP with all
O
S X
g
cc 4
.
2-
b
ased co
m
pilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Sander Pronk
Merg
e
"Co
n
tinuatio
n
o
f documentati
o
n for expanded ensemble
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Mark Abraham
V
e
locity
-
v
e
rlet in
t
egrators and v-re
s
cal
e
are broken
commit
|
commitdiff
|
tree
2013-01-14
C
arst
e
n Kutzne
r
E
s
s
e
n
ti
a
l dynamics
o
ut
p
u
t file
n
ow in
.
x
vg
f
o
r
mat
commit
|
commitdiff
|
tree
2013-01-14
David van der Spoel
Merge "Fixing trjconv -sub" into
r
e
lease-4
-
5-patches
commit
|
commitdiff
|
tree
2013-01-14
D
avid van
der Spoel
Mer
g
e "Notin
g
that and
why
gm
x
dump -s -sys is b
r
oken
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Roland
Schulz
Merg
e
"Fixes for md-v
v
a
nd
r
erun" into release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Roland S
c
hu
l
z
Merge
"f
i
xed res
e
tting
states w
i
th p
a
rallel Verlet
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Rol
a
nd
S
chulz
Proper fix for copyrite cuda
de
p
endence
commit
|
commitdiff
|
tree
next