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Merge "corrected grompp rvdw charge-group radii check" into release-4-6
2013-04-16
David van de
r
Spoe
l
Mer
g
e
"
c
o
r
rec
t
ed g
r
ompp
rvdw charge-
g
r
o
u
p r
a
dii check
.
.
.
commit
|
commitdiff
|
tree
2013-04-13
David v
a
n d
e
r Spoel
Merge "added
mdr
u
n che
c
k f
o
r Verl
e
t+perturbed atoms
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
Mar
k
Abr
a
h
am
Mer
g
e "removed x86 specifi
c
s from nbnxn SI
M
D
ker
n
e
ls
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
Mark Abr
a
h
am
Merg
e
"correct
e
d lo
g
file wall time b
r
ea
k
down" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
M
ark Abraham
Merge "
m
ade
P
ME w
o
r
k w
i
th a
mix
o
f
1
a
nd mo
r
e threads
.
.
.
commit
|
commitdiff
|
tree
2013-04-10
Teemu Murto
l
a
M
erg
e
"Merge rele
a
se-4-5-pat
c
hes into r
e
lease-4-6"
.
.
.
commit
|
commitdiff
|
tree
2013-03-29
Christoph J
u
nghan
s
M
e
rge "A
d
ded
i
nstall
guide sectio
n
for BL
A
S/LAPACK
.
.
.
commit
|
commitdiff
|
tree
2013-03-19
Christoph Junghan
s
M
er
g
e "Essential dynamics
:
fixed legen
d
in ED
.
xv
g
.
.
.
commit
|
commitdiff
|
tree
2013-03-12
M
a
rk A
b
raham
M
e
rge "fix broke
n
things in mkhtm
l
" into rel
e
a
se-
4
-6
commit
|
commitdiff
|
tree
2013-03-11
M
a
rk Abraham
Mer
g
e "F
i
xes
l
inkage with
F
FTW + MKL f
o
r
B
L
A
S/LAPACK
.
.
.
commit
|
commitdiff
|
tree
2013-03-06
Roland
Sc
h
ulz
Merge "fixed PME
time
p
rint
wi
t
h
-
ntomp_pme != -n
t
omp
.
.
.
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
New patch release 4
.
6
.
1
commit
|
commitdiff
|
tree
2013-03-05
Mark Abra
h
am
Fix au
t
oma
t
ed regressio
n
testing GMX
L
IB value
commit
|
commitdiff
|
tree
2013-03-05
Berk Hess
fixed bug with D
D
cut-off check a
n
d PME DLB
commit
|
commitdiff
|
tree
2013-03-05
Mark Abr
a
ham
Fix regression
t
ests automated download
commit
|
commitdiff
|
tree
2013-03-05
B
erk Hess
fi
x
ed recent
bu
g
with sorti
n
g atoms
for GPUs
commit
|
commitdiff
|
tree
2013-03-05
M
a
rk
Abraham
Updat
e
shell
c
ompletion
s
commit
|
commitdiff
|
tree
2013-03-05
Mark Ab
r
aham
Upd
a
te ou
t
d
a
ted admin th
i
ngs
commit
|
commitdiff
|
tree
2013-03-05
Justin Lem
k
ul
Fi
x
es for install guide page
.
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
U
p
dated in
s
tal
l
guide
commit
|
commitdiff
|
tree
2013-03-02
Chri
s
to
p
h Junghan
s
Me
r
ge "Uncru
s
tified code changes since 4
.
6" into releas
e
-4-6
commit
|
commitdiff
|
tree
2013-02-20
Christoph Jun
g
ha
n
s
Bump
s
hared object version
t
o 8
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
fixed issues with FEP sof
t
-core and cut-off's
commit
|
commitdiff
|
tree
2013-02-18
Berk Hess
fixed GPU
p
article gridding performance issue
commit
|
commitdiff
|
tree
2013-02-18
Cars
t
en Kutzner
Made g_tune_
p
me w
o
rk wi
t
h
4
.
6 if us
e
r
sets "-p" co
m
m
a
nd
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Mark Abraham
Fix C
M
ak
e
nam
e
space
p
ollution
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Merge
"Minor fix
e
s to Verle
t
kernels" into rel
e
a
s
e-
4
-6
commit
|
commitdiff
|
tree
2013-02-15
Mar
k
Abr
a
ham
Merge "impr
o
v
ed PME loa
d
balanc
i
ng re
p
orting" into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Merge "Re-generated group k
e
rnel
s
"
into
rel
e
as
e
-4-6
commit
|
commitdiff
|
tree
2013-02-15
Ma
r
k Abraha
m
Merge "Unwinds flag dependencies in g_ord
e
r
.
"
into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
David
v
an der Spoe
l
Merge "Fix
e
d
an
initialization issue
i
n
gm
x
_dipoles
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Me
r
g
e "
u
se legacy CUDA non-bonded kernels
o
nly on Fermi
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mar
k
Abraham
Merge
"
More descriptive Ve
r
let kernel ma
c
ro
pa
r
ameter
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Ber
k
Hess
improved PME load balancing
r
eporting
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Mino
r
fixes to Verlet kernels
commit
|
commitdiff
|
tree
2013-02-15
Ma
r
k Abraham
Merge "F
i
x and
a
d
d Verle
t
ker
n
el e
r
ro
r
m
e
ssages" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Sander Pronk
Merge
"Fix code bug wi
t
h thread-MPI on
P
owe
r
PC wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Roland Schulz
Merge "Fixed th
e
MPI recognition stri
n
g in g
_
tune_pm
e
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
R
o
land Schulz
Me
r
ge "improv
e
setup
o
f
mu
l
tiple
t
f
t
ables" into
release-4
-
6
commit
|
commitdiff
|
tree
2013-02-13
Roland
Schulz
Merge "Upda
t
ed FindGSL
.
cmake to version written
b
y
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Mark Ab
r
aham
Merge "PME-only counters are now reset w
i
th
-
maxh
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Chris
t
o
ph Junghans
Update
d
Find
G
SL
.
cmake to ve
r
sion writt
e
n by me
.
commit
|
commitdiff
|
tree
2013-02-12
Mark Abraham
Merge "
f
ixed bug
w
i
th sd integ
r
ator and
Op
e
nMP t
h
read
i
ng
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Mark Ab
r
aham
Merge "Fix
C
UDA_HOST_COMPI
L
ER flag name" into
r
elease
-
4-6
commit
|
commitdiff
|
tree
2013-02-09
Rol
a
nd Sch
u
l
z
Merge
"Typo fix" int
o
releas
e
-4-6
commit
|
commitdiff
|
tree
2013-02-08
Mark Abraham
M
e
rg
e
"added
b
ack cuda
.
h
inc
l
u
d
e
s
to fix missing CUDA
_
VERSIO
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
M
ark Abraham
Merge
"
Fixed
fl
o
p c
o
u
n
t
ing for generi
c
cg/
a
dres
s
ker
n
els
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark Abraham
M
e
rge "cmake: f
i
xed typo in te
m
plate CMakeLists
.
txt
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Christoph Junghans
Merge "
D
ocume
n
ted what GMX_CPU_ACCELE
R
A
TION really
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Mark Abraha
m
M
erge "improved load
b
alancing on the
G
P
U
" into release-4-6
commit
|
commitdiff
|
tree
2013-02-01
Berk Hess
PME
-
o
n
ly counters are now re
s
et with -maxh -res
e
thway
commit
|
commitdiff
|
tree
2013-01-25
Christoph
Junghans
Merge "Moved a few co
m
ments back into position
"
i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mar
k
Abraham
Merg
e
"Illegal acceleration defaulted
t
o Q
P
X" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark Abraham
Merge
"
Re-
l
i
cenced
FindGROMACS
.
cmake
(was wri
t
ten by
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Roland Schulz
Illegal acceler
a
tion d
e
fa
u
l
t
e
d t
o
QPX
commit
|
commitdiff
|
tree
2013-01-22
Ma
r
k Abraham
Merge "Fix TOUPPER usa
g
e" into release-
4
-6
commit
|
commitdiff
|
tree
2013-01-22
Mark Abraham
Merge "Updated html manual
to 4
.
6" into release-4-6
commit
|
commitdiff
|
tree
2013-01-22
M
ark Abraham
Merge "added missing c
l
ea
n
up
of some nbnxn_cuda data
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Roland Schulz
Fix
T
OUPPER usage
commit
|
commitdiff
|
tree
2013-01-22
R
o
land Schulz
Updat
e
d html manual to 4
.
6
commit
|
commitdiff
|
tree
2013-01-21
Christoph Junghans
Me
r
ge
"
S
e
t ve
r
sion info for
4
.
6
.
x releas
e
series" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Mark
A
braham
Set versi
o
n info f
o
r
4
.
6
.
x release series
commit
|
commitdiff
|
tree
2013-01-18
Mark
Abraham
New major release: 4
.
6
commit
|
commitdiff
|
tree
2013-01-18
Michael Shirts
Addendum
f
o
r e
x
panded
e
nsemble options
p
lus formatting
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Roland Schu
l
z
Fix typo
commit
|
commitdiff
|
tree
2013-01-18
Roland Schulz
C
o
de beaut
i
fication w
i
th u
n
c
r
us
t
ify
commit
|
commitdiff
|
tree
2013-01-18
Roland Schulz
A
d
d
colon a
f
ter macro
t
o help
u
ncrustify
commit
|
commitdiff
|
tree
2013-01-18
B
erk He
s
s
thread affinity
now use
s
som
e
topology informa
t
ion
commit
|
commitdiff
|
tree
2013-01-18
Mark
Abraham
Fixing copyright issu
e
s and code contribu
t
ors
commit
|
commitdiff
|
tree
2013-01-18
Erik L
i
n
da
h
l
Merge
"remove unnecessary cma
k
e m
e
ssa
g
es" in
t
o release-4-6
commit
|
commitdiff
|
tree
2013-01-18
Erik Lindahl
Merge "fix OpenMP detection on Mac
OS broke
n
by a6fee0b
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Szilárd Páll
fi
x
OpenMP
d
etection on Mac OS
bro
k
en b
y
a6fee0b
commit
|
commitdiff
|
tree
2013-01-17
S
z
ilárd Páll
a
d
d
e
d
m
i
ssi
n
g cleanup of
s
ome
nbnxn_cuda data
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Merg
e
"Rem
o
ve unnecessa
r
y ICC flags
affecting performance
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Merg
e
"improved CUDA kernel performance by pre-loading
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph Jun
g
han
s
Merge "Added
n
ote abou
t
make_e
d
i
and flooding in ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christ
o
ph Junghans
Merge "use the c
o
mp
i
ler version provided
by
C
Mak
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Rol
a
nd Sc
h
u
lz
Mer
g
e
"
Merg
e
branch 'release-4-5-patc
h
es' i
n
t
o release
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Szi
l
árd Páll
Merge changes I9
3
0b
3
16c,Iea42
8
3e0,I1036
4
8f8 i
n
to release-4-6
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraha
m
Merge "Fix tr
j
conv -s
u
b
with
.
trr fil
e
s" into releas
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abra
h
am
BlueG
e
ne/Q insta
l
lation
notes
commit
|
commitdiff
|
tree
2013-01-17
Chri
s
t
o
ph Jungha
n
s
Merge "not
e
the
rea
s
on for
a
uto-disabling GPU su
p
por
t
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abra
h
a
m
Merge "Adde
d
mdp o
p
tion '
c
alc-l
a
mbda-neigh
b
ors'
.
" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
Merge
"
clarify w
o
rding
o
f GPU driver-rel
a
ted
n
o
t
es
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Ro
l
a
nd Sc
h
ulz
Merge "Ad
d
ed check for val
i
d wal
l
_atomtyp
e
in
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Fix trjconv -sub w
i
th
.
trr files
commit
|
commitdiff
|
tree
2013-01-17
B
e
rk Hess
fix
e
d
SD+BD integ
r
a
t
ion slowing do
w
n
wit
h
OpenMP
t
hread
s
commit
|
commitdiff
|
tree
2013-01-17
Rolan
d
Sc
h
ulz
Run regre
s
s
iont
e
sts
f
rom
b
uild
commit
|
commitdiff
|
tree
2013-01-17
Sander
P
ronk
Added mdp opti
o
n
'c
a
lc-lambda-neighbors'
.
commit
|
commitdiff
|
tree
2013-01-17
Mark
Abraham
Fina
l
ly
m
ove OpenMM to co
n
tri
b
commit
|
commitdiff
|
tree
2013-01-17
Ro
l
and
Schulz
Fix conf
u
sing gmx
_
header_con
f
i
g
.
h in
c
lude
commit
|
commitdiff
|
tree
2013-01-17
Szil
a
r
d
P
a
ll
don't use po
l
ling
wi
t
h n
e
w dr
i
ver
commit
|
commitdiff
|
tree
2013-01-17
Christoph Jung
h
an
s
c
lean up fo
r
tr
a
n name mangling
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
fixe
d
nbnxn hybrid mode with OpenMP
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
made PME
l
oad balancing + DD DLB more efficient
commit
|
commitdiff
|
tree
2013-01-16
Chr
i
stoph Ju
n
ghans
R
e
move
d
e
b
u
g
s
t
atme
n
t
commit
|
commitdiff
|
tree
2013-01-15
Mark Ab
r
ah
a
m
Merge "Hid nbnxn kerne
l
n
ames be
h
ind a lookup
f
un
c
t
i
on
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Christ
o
ph
J
u
nghans
Merge "
A
dded fa
t
al error for c
o
ns
t
raints + L-BF
G
S
m
inimizer
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Christoph
J
u
ngha
n
s
Merge "di
s
a
b
le
Op
e
nMP with a
l
l
OS
X gcc
4
.
2
-
b
a
sed compilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Sa
n
d
e
r Pronk
Merge "
C
o
ntinuati
o
n of documentation
for expanded ense
m
b
le
.
.
.
commit
|
commitdiff
|
tree
next