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Merge "Minor fixes to Verlet kernels" into release-4-6
2013-02-15
Mark Abraham
Mer
g
e
"Minor fixe
s
t
o
Verl
e
t kernels
"
into release
-
4-6
commit
|
commitdiff
|
tree
2013-02-15
Ma
r
k
Abraham
M
erge
"
improved PME load balancing reporting" into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mar
k
Ab
r
aham
Merge
"Re-generated group kernels" into re
l
e
a
se-4-6
commit
|
commitdiff
|
tree
2013-02-15
M
ark
A
braham
Merge "
U
nwinds flag
d
ependencies in g_order
.
"
into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
David van
der Sp
o
el
Me
r
g
e "Fix
e
d
a
n initializ
a
tion issu
e
in gm
x
_dipo
l
e
s
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abra
h
am
Merge "use
lega
c
y
C
UDA non-bonded
k
e
r
nels
o
nl
y
on Fermi
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abra
h
am
Merge "More descriptive
Verlet ker
n
el macro parame
t
er
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Berk H
e
ss
impro
v
e
d PME
load
b
a
l
ancing repo
r
t
i
ng
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Minor
fixe
s
to Verlet k
e
rnels
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraha
m
Mer
g
e "Fix and ad
d
Verlet kernel e
r
ror messag
e
s
" into
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Sander
P
r
o
nk
Merg
e
"Fix code bug with thread-MPI on PowerPC with
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
R
olan
d
Schu
l
z
Merge
"
Fixed t
h
e MPI recognition strin
g
in g_
t
une_p
m
e
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Rolan
d
Schulz
Merge
"i
m
p
r
ove setup of
mul
t
iple tf tables" into re
l
ease-4-6
commit
|
commitdiff
|
tree
2013-02-13
R
o
land S
c
hulz
Merge "Updated Find
G
SL
.
cmake to
v
ersi
o
n
writte
n
by
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
M
a
rk Abrah
a
m
Mer
g
e
"P
M
E-only
counters are
n
ow reset wit
h
-maxh
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
Chri
s
toph Jung
h
ans
U
pd
a
ted Fin
d
GSL
.
c
m
a
ke
to
v
ersion written
b
y me
.
commit
|
commitdiff
|
tree
2013-02-12
Mark Abraha
m
M
e
rge "fixed bug
w
ith sd int
e
grator and O
p
e
nMP threadi
n
g
.
.
.
commit
|
commitdiff
|
tree
2013-02-12
M
a
r
k
Abr
a
h
am
Merge
"Fix CUDA_H
O
ST_COMPILER flag name" int
o
release
-
4
-
6
commit
|
commitdiff
|
tree
2013-02-09
Roland Schulz
Merge "T
y
po fi
x
" into releas
e
-4-6
commit
|
commitdiff
|
tree
2013-02-08
Mark
Abraham
Merge "a
d
de
d
back
cuda
.
h
inc
l
udes to fix mi
s
sing CUDA_VERSIO
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
M
a
rk Abra
h
am
M
e
r
g
e "Fixed
flop counting for gener
i
c
c
g/adress kernels
.
.
.
commit
|
commitdiff
|
tree
2013-02-08
Mark Abraham
Merge "cmake: fixed typo in template CMakeLists
.
txt
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Chr
i
stoph Junghans
Merg
e
"Documen
t
ed
what GMX_CPU_ACC
E
LERATION really
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Mark
A
bra
h
a
m
Merg
e
"improved l
o
ad balancing
on t
h
e
GPU"
int
o
release
-
4-6
commit
|
commitdiff
|
tree
2013-02-01
Berk Hess
PME-only
c
ounters are no
w
reset with -maxh -
r
e
s
ethway
commit
|
commitdiff
|
tree
2013-01-25
Ch
r
ist
o
ph
Jungha
n
s
Me
r
ge "Moved a few comments back in
t
o posi
t
ion"
into
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark Abraham
Mer
g
e "Illegal acceleration def
a
ulted to QPX"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Mark Ab
r
aha
m
Merge
"Re-licenc
e
d FindGROMACS
.
c
m
ake (was wr
i
tten by
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Rol
a
nd Schulz
Illegal a
c
celeration def
a
ulted to QPX
commit
|
commitdiff
|
tree
2013-01-22
Mark
A
braham
Merg
e
"Fix
T
OUPPER usage"
into release-4-6
commit
|
commitdiff
|
tree
2013-01-22
Mark
Abraham
Me
r
ge
"
U
pdated html
manual to 4
.
6" into rel
e
as
e
-4
-
6
commit
|
commitdiff
|
tree
2013-01-22
Mark
Ab
r
aham
Merg
e
"ad
d
ed missing
c
lea
n
up o
f
some nbnx
n
_cu
d
a
data
.
.
.
commit
|
commitdiff
|
tree
2013-01-22
Roland
S
chulz
Fix
T
OUPPER us
a
ge
commit
|
commitdiff
|
tree
2013-01-22
Rola
n
d
Sc
h
ulz
Updated html man
u
al to 4
.
6
commit
|
commitdiff
|
tree
2013-01-21
C
h
ristoph Junghans
Merge "Set versi
o
n in
f
o for 4
.
6
.
x release series" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Mark
A
braham
Se
t
version i
n
fo f
o
r 4
.
6
.
x re
l
e
a
s
e
series
commit
|
commitdiff
|
tree
2013-01-18
Mark Ab
r
aham
Ne
w
major
r
el
e
ase
:
4
.
6
commit
|
commitdiff
|
tree
2013-01-18
Michae
l
Shirts
Adde
n
du
m
f
o
r e
x
panded ense
m
b
le opti
o
ns plus formatting
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Rola
n
d Schulz
Fix
t
ypo
commit
|
commitdiff
|
tree
2013-01-18
Roland Sch
u
lz
Code beautification with uncrustify
commit
|
commitdiff
|
tree
2013-01-18
Roland
S
c
hulz
A
dd
colon aft
e
r
ma
c
ro t
o
help
un
c
ru
s
tify
commit
|
commitdiff
|
tree
2013-01-18
B
e
rk Hess
t
hread af
f
i
nity now
u
ses some
t
opol
o
gy i
n
formation
commit
|
commitdiff
|
tree
2013-01-18
Mark Abraham
Fixing c
o
pyri
g
ht issues an
d
code contributors
commit
|
commitdiff
|
tree
2013-01-18
Erik Lindahl
Me
r
ge "remove unnec
e
ssary cmake mes
s
ages
"
i
n
to r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-01-18
Erik
L
i
ndahl
Merge "fix
O
penMP detect
i
on on Mac O
S
b
r
o
ken by a6fee0b
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Szilárd Páll
fix
O
pe
n
MP detection on Mac OS broken
by
a6fee0b
commit
|
commitdiff
|
tree
2013-01-17
Sz
i
lárd Páll
added missing
c
lean
u
p
of some nb
n
xn_cuda data
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
M
e
rge "Remov
e
unnece
s
sa
r
y
I
C
C flags af
f
e
cti
n
g performance
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
M
ark Abraham
Me
r
ge
"
improved CUDA
kernel performanc
e
by pre-loading
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christoph Ju
n
ghans
M
erge "Add
e
d note about
m
ake_e
d
i and flooding in ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Christo
p
h Junghans
Me
r
g
e "use
t
he compi
l
er v
e
rsion provided
b
y CMake
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
M
erge
"Merge branch 'release-4-
5
-patches' into relea
s
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
S
z
ilárd P
á
ll
Merge chan
g
es I930b316c,Iea4283e
0
,I103648f8 into release-4-6
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Mer
g
e "Fix
trjconv
-
s
u
b
w
ith
.
t
rr files
"
into release
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
M
a
r
k Abraham
BlueGene/Q installation notes
commit
|
commitdiff
|
tree
2013-01-17
Christ
o
ph Junghans
Merge "note t
h
e reason
f
or auto-di
s
abl
i
n
g G
P
U support
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
M
a
rk Abr
a
ham
M
erge "Added md
p
option 'calc-lambd
a
-neighbors
'
.
"
into
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
Me
r
ge "
c
l
arify wording of GPU drive
r
-relate
d
notes
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
R
oland Schulz
Merge "Added check for v
a
lid wall
_
a
t
o
mtype
i
n
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark
Abraham
Fix trjconv -su
b
w
ith
.
tr
r
files
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
fixed
S
D
+BD integration slowing down wit
h
O
p
e
nMP
t
hreads
commit
|
commitdiff
|
tree
2013-01-17
R
oland Schulz
Run
r
e
g
ressiontest
s
from
b
uild
commit
|
commitdiff
|
tree
2013-01-17
Sander Pronk
A
dded mdp option 'calc
-
lam
b
da-neighbors
'
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Finally move Ope
n
MM to contrib
commit
|
commitdiff
|
tree
2013-01-17
Roland Sch
u
lz
Fix con
f
usin
g
gmx_head
e
r_
c
onfig
.
h
i
n
c
l
u
d
e
commit
|
commitdiff
|
tree
2013-01-17
Szilard Pall
don't u
s
e
polling with n
e
w driver
commit
|
commitdiff
|
tree
2013-01-17
Ch
r
i
stoph
Jungha
n
s
c
l
ean up fortran nam
e
mangling
commit
|
commitdiff
|
tree
2013-01-17
B
erk Hes
s
f
ixe
d
nbn
x
n hybrid mo
d
e with OpenMP
commit
|
commitdiff
|
tree
2013-01-17
B
erk Hess
m
a
de PME
l
oad balan
c
ing + DD DLB
more effici
e
n
t
commit
|
commitdiff
|
tree
2013-01-16
Christoph Jungh
a
ns
Re
m
ove deb
u
g
statment
commit
|
commitdiff
|
tree
2013-01-15
Mar
k
Abraham
M
e
rge "Hid nbnxn
k
er
n
e
l
n
ames behind a lo
o
kup function
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
C
h
rist
o
ph Junghans
Merge "Added
fatal erro
r
for cons
t
ra
i
nt
s
+
L-BFGS m
i
nimize
r
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Ch
r
istop
h
Jung
h
ans
Me
r
ge "disable
OpenMP with al
l
OS X gcc 4
.
2-based
compilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Sande
r
Pron
k
Merge "Cont
i
nuation of docu
m
entation for expand
e
d
e
n
semble
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Ma
r
k
Abrah
a
m
Velocity-verlet
i
ntegrators a
n
d v-rescale are broken
commit
|
commitdiff
|
tree
2013-01-14
C
a
rst
e
n Kut
z
ner
E
s
sential dyna
m
i
cs out
p
ut file now in
.
x
vg
f
ormat
commit
|
commitdiff
|
tree
2013-01-14
David van der S
p
oel
Merge "Fixi
n
g trjconv
-
sub
"
into releas
e
-
4
-5-patches
commit
|
commitdiff
|
tree
2013-01-14
David van der Spoel
M
erge "
N
oting that and why
g
mxdum
p
-s -sys is broken
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Roland Schulz
Me
r
g
e "Fixes for md-vv and rerun" into re
l
ease-4-6
commit
|
commitdiff
|
tree
2013-01-13
Roland Schulz
Me
r
ge "
f
ixed resett
i
ng s
t
a
t
es with
p
aral
l
e
l
Verlet
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
R
o
land Sc
h
ulz
Prope
r
fix for
c
o
p
y
rite cuda dependence
commit
|
commitdiff
|
tree
2013-01-13
Michael Shirts
F
i
x
es for md-vv and rerun
commit
|
commitdiff
|
tree
2013-01-13
B
e
rk Hes
s
fixed resetting s
t
ates w
i
t
h parallel Verl
e
t s
c
heme
commit
|
commitdiff
|
tree
2013-01-13
Chris
t
oph Jung
h
ans
Merge "Remove unused bf
u
nc
.
h
.
" into
rele
a
se-4-6
commit
|
commitdiff
|
tree
2013-01-13
C
hr
i
stop
h
Junghans
Merge
"
C
l
a
r
ifie
d
som
e
com
m
e
n
ts & warn
i
ngs about thread
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Chri
s
toph Jungha
n
s
Me
r
ge "
M
anag
e
Blue
G
e
n
e/Q
c
onf
i
guration"
i
nto release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph Ju
n
ghans
Merge "Re-organ
i
ze
BlueGene toolchain
files" i
n
to
release-4-6
commit
|
commitdiff
|
tree
2013-01-13
Chr
i
st
o
ph Junghans
Me
r
ge "Changed default
s
for
b
u
ild
i
ng
s
h
ared l
i
bra
r
ies
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Mar
k
A
braham
Clarified some comments
&
warnings a
b
out
thread pinning
commit
|
commitdiff
|
tree
2013-01-13
R
oland Schulz
Merge "pr
e
pared the nbn
x
n code for non-x86 SIMD" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
M
a
rk Abr
a
ham
Me
r
ge "Added basic CPU topo
l
ogy inf
o
rm
a
t
i
on
t
o
cpuid
.
.
.
commit
|
commitdiff
|
tree
2013-01-12
Berk Hess
p
r
epar
e
d the nb
n
xn code fo
r
non-x86 SIMD
commit
|
commitdiff
|
tree
2013-01-12
Christ
o
p
h Junghans
Mer
g
e "
A
dded missing e
x
port" into release-4-6
commit
|
commitdiff
|
tree
2013-01-11
Er
i
k Lindahl
Merge "made SHAKE w
o
rk
a
g
a
in w
i
t
h
particle d
e
co
m
postion
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Ro
l
an
d
Schul
z
Merge "tim
e
the GPU force cl
e
a
r
in
g
async lau
n
ch overhead
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Chris
t
oph
Jun
g
h
ans
Merge "console
a
nd log output i
m
p
ro
v
ements" into rele
a
s
e
-4-6
commit
|
commitdiff
|
tree
2013-01-11
Chris
t
oph Junghans
Merg
e
"Fix C
U
DA
bein
g
quiet and mark all CUDA_*
a
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
E
r
ik Lin
d
ahl
A
d
d
e
d bas
i
c CPU topolog
y
information to cp
u
id co
d
e
commit
|
commitdiff
|
tree
2013-01-11
E
rik Lindahl
Merge "fixed
nbnxn
n
o L
J
comb
.
rule AVX25
6
P
ME kern
e
l
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Rol
a
nd Schulz
M
erge
"
Ha
n
d
l
e com
p
iler flags more
flexi
b
ly" into rele
a
se-4-6
commit
|
commitdiff
|
tree
next