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GROMACS 2018 first beta release
2017-11-28
Mark A
b
raham
GROMACS 2018 first beta rel
e
ase
commit
|
commitdiff
|
tree
2017-11-28
Berk
H
ess
Refactor nbnxn exclusion sett
i
ng
commit
|
commitdiff
|
tree
2017-11-28
E
r
ik Lindahl
Imp
r
ove s
t
atus message
s
for
S
IMD checks
commit
|
commitdiff
|
tree
2017-11-27
Szil
á
rd Páll
Time
FFT
/
gathe
r
in mixed mode
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupino
v
Dis
a
ble failing separate PME ra
n
k
tests
commit
|
commitdiff
|
tree
2017-11-27
Paul Bauer
Add GPU task info
r
mation to us
e
r-
g
uide
commit
|
commitdiff
|
tree
2017-11-24
A
l
e
ks
e
i I
u
p
inov
E
nabl
e
separa
t
e PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
A
l
ekse
i
I
upin
o
v
Activat
e
m
i
x
e
d
mode of PM
E
on G
P
U
commit
|
commitdiff
|
tree
2017-11-24
S
z
ilárd Páll
A
d
d G
P
U sharing post-
s
ubmit co
n
fig
commit
|
commitdiff
|
tree
2017-11-24
Mark
Abraha
m
Update
develo
p
er guide
commit
|
commitdiff
|
tree
2017-11-24
Mark
A
braham
Act
i
vate PME o
n
G
PU
s
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Remove outdated (already implement
e
d) pinning TODO
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
Add PM
E
integration t
e
st
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
E
x
tend ta
s
k
assignm
e
n
t cod
e
commit
|
commitdiff
|
tree
2017-11-24
A
le
k
sei Iupinov
M
e
ntion gmx_install_headers() in the de
v
elope
r
manual
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iupi
n
ov
Make FFT real-space
g
rid use
C
UDA pinning f
o
r
mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
P
in coordin
a
tes,
forces and charges f
o
r
PME on G
P
U
commit
|
commitdiff
|
tree
2017-11-22
Pascal Merz
P
ro
o
f
o
f concept: Phys
i
cal va
l
id
a
t
i
on
suite
commit
|
commitdiff
|
tree
2017-11-21
Erik Linda
h
l
Separat
e
SIMD flag detection fr
o
m managem
e
nt
commit
|
commitdiff
|
tree
2017-11-21
Mark Abraham
Support pinning in HostAllo
c
a
t
or
commit
|
commitdiff
|
tree
2017-11-21
Viveca Lin
d
a
h
l
Add force correlation
to AWH mo
d
ule
commit
|
commitdiff
|
tree
2017-11-21
Paul Bauer
First general
a
dditio
n
s to
t
h
e
d
ocume
n
tation
commit
|
commitdiff
|
tree
2017-11-19
Viveca Lindahl
Add A
W
H sec
t
i
o
n to
m
a
nual
.
commit
|
commitdiff
|
tree
2017-11-19
Viveca
Lindahl
Add AWH biasing modu
l
e
+
tests
commit
|
commitdiff
|
tree
2017-11-17
Mark Abr
a
ham
Use
Hos
t
A
llocation
P
olicy for
chargeA
commit
|
commitdiff
|
tree
2017-11-17
M
ar
k
A
b
r
a
h
a
m
A
d
d
c
he
c
king function for whether a buffer is
pinned
commit
|
commitdiff
|
tree
2017-11-17
Mar
k
A
braham
Improve hand
l
ing of PME
GPU fo
r
ce buff
e
r
commit
|
commitdiff
|
tree
2017-11-15
Aleksei I
u
p
i
nov
R
ename and e
x
pose
"generic" GPU mem
o
ry transfer fu
n
ctions
commit
|
commitdiff
|
tree
2017-11-10
M
a
rk Abraham
Import cmake
Modul
e
s/FindCUDA
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupinov
Rename synchr
o
n
o
u
s
G
P
U
tr
a
nsfer fu
n
c
t
ions to ma
t
ch
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Mark Abraha
m
Prepared t_mdatoms for using vector
commit
|
commitdiff
|
tree
2017-11-09
M
ark Ab
r
aham
Introduce H
o
stAllocat
i
onPolicy
commit
|
commitdiff
|
tree
2017-11-09
Roland Sc
h
ulz
ICC should use Z
M
M
i
f code any
h
ow
u
ses ZMM
commit
|
commitdiff
|
tree
2017-11-07
Mark
Ab
r
aham
Reform gmx_pme_pp alloc
and use vecto
r
commit
|
commitdiff
|
tree
2017-11-07
M
ark Abraha
m
Introduce gmxopen
c
l
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Test clang on ARM in nigh
t
ly matri
x
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Add
wallcycle t
i
m
e
r for the PM
E
GPU F r
e
duction
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Split off nbnxn
G
PU
t
i
ming and s
t
aging
r
educ
t
ion
commit
|
commitdiff
|
tree
2017-11-07
Mark Ab
r
aham
Improv
e
P
M
E
i
ncludes
commit
|
commitdiff
|
tree
2017-11-07
Szilá
r
d Páll
Dedupli
c
ate CUDA and OpenCL timer st
r
uct
commit
|
commitdiff
|
tree
2017-11-06
D
a
vi
d
van der
Spoel
Fixed c
h
e
c
k
for wate
r
in g
e
n
_
vsite
.
cp
p
commit
|
commitdiff
|
tree
2017-11-03
M
ark Abraham
Mer
g
e "Me
r
ge branch releas
e
-
2
016"
commit
|
commitdiff
|
tree
2017-11-02
Dav
i
d van der Spoel
New mdp in
p
ut for electric fields
.
commit
|
commitdiff
|
tree
2017-11-02
Alek
s
ei Iupino
v
Re
p
lace math
.
h by cmath inclu
d
es in cpp files
commit
|
commitdiff
|
tree
2017-11-02
Mark Abrah
a
m
M
er
g
e branch
r
ele
a
se-2
0
16
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
S
m
a
ll
ch
a
nge to LaTeX manual generat
i
on
commit
|
commitdiff
|
tree
2017-11-01
Mark
Abr
a
ham
Fix threa
d
-
M
PI rank choice
for
ori
e
nta
t
ion restrain
t
s
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Remove unused PME GPU declarati
o
ns
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupi
n
ov
Move p
m
e
_
gpu_finish_computation() documentati
o
n
to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
P
aul Bauer
F
ixing
m
i
ssing references in web d
o
cument
a
t
i
on
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iu
p
inov
Fix er
r
on
e
o
us PM
E
GPU "step"
n
aming
s
commit
|
commitdiff
|
tree
2017-11-01
Ma
r
k Ab
r
aham
Improve
h
a
n
d
l
i
ng of GPU IDs
commit
|
commitdiff
|
tree
2017-11-01
Alekse
i
Iu
p
inov
S
i
mplify PME
GPU synchronization code
commit
|
commitdiff
|
tree
2017-10-31
A
leksei I
u
pinov
Reuse epbcXY logic
commit
|
commitdiff
|
tree
2017-10-31
Szilár
d
P
á
ll
Fix
nst
l
ist increa
s
e
warning
p
rint
commit
|
commitdiff
|
tree
2017-10-31
Szilárd
P
áll
Check CUDA available/compi
l
ed
c
od
e
compatibil
i
ty
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
F
i
x reference m
o
d
e
b
uild unused function warnings
commit
|
commitdiff
|
tree
2017-10-30
Be
r
k
H
e
ss
Remo
v
e un
u
sed sign parameter
f
rom dih_angle()
commit
|
commitdiff
|
tree
2017-10-30
Rola
n
d Schulz
Array
R
ef: R
e
place f
r
omVec
t
o
r
w
i
th
s
u
bArray
commit
|
commitdiff
|
tree
2017-10-30
David va
n
der Spoel
Added option -w
a
t
e
r tips3
p
t
o
pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-30
Aleksei
I
u
pinov
Bring PME
GPU/CUDA inter
n
al structur
e
n
a
me
s
to Ca
m
e
lCase
commit
|
commitdiff
|
tree
2017-10-27
Mark
Abraham
Fix hw dete
c
tio
n
more
commit
|
commitdiff
|
tree
2017-10-26
Mar
k
Abra
h
am
New quote
commit
|
commitdiff
|
tree
2017-10-20
Mark A
b
raham
Cla
r
i
f
y
d
o
cs for
F
m
ax in E
M
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
Merge
b
r
a
n
ch relea
s
e-201
6
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix warning
for
confout wi
t
h pe
r
iodic
m
olecu
l
e
s
commit
|
commitdiff
|
tree
2017-10-16
Mark Abraham
Merge
branch release-2016
commit
|
commitdiff
|
tree
2017-10-15
Berk
Hess
I
m
p
rove vsite pa
r
alle
l
checking
commit
|
commitdiff
|
tree
2017-10-13
A
l
ek
s
e
i Iupinov
Relax PME spline c
o
mputati
o
n tolerance in
d
o
uble precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Mark Abraham
Update tes
t
s
for C++11
c
o
mpiler an
d
standard l
i
br
a
ry
commit
|
commitdiff
|
tree
2017-10-13
R
oland Sch
u
lz
Speciali
z
e
ArrayRef
f
o
r SimdReal
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Intro
d
uced
header for communi
c
atio
n
t
o
/fr
o
m
P
M
E ranks
commit
|
commitdiff
|
tree
2017-10-11
Alek
s
ei
I
upino
v
Fix clang w
a
rning
s
for PME CUDA kerne
l
s
commit
|
commitdiff
|
tree
2017-10-11
Aleksei
I
u
p
inov
Rela
x
PME s
o
lving test compl
e
x grid tolerance
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Cleaned up
e
wa
l
dcoeff f
o
r PME-only
r
anks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupi
n
o
v
PME
s
olving - CUD
A
kernel + unit te
s
ts
commit
|
commitdiff
|
tree
2017-10-11
Paul B
a
uer
Change to
m
od
u
l
e
s for bu
i
ld of web
d
ocumenta
t
ion
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iu
p
inov
PME force gathering - CUDA kernel + u
n
it tests
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
P
ME
spline+spread CUDA kernel and unit tests
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Use clan
g
-
5
i
n
J
enkins
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disa
b
le A
R
M Neon native
rsqrt i
t
eration
commit
|
commitdiff
|
tree
2017-10-09
Aleksei Iupino
v
PME GP
U
/
CUDA dat
a
framework
.
commit
|
commitdiff
|
tree
2017-10-07
M
a
rk Abraham
Tell
c
pp
c
heck that
.
cp
p
and
.
c
u
f
i
les ar
e
c++
commit
|
commitdiff
|
tree
2017-10-07
Rola
n
d Schu
l
z
Re
f
a
cto
r
l
o
ad
+
SimdLoad*ProxyInternal to reduce d
u
p
licati
o
n
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Add SIM
D
intrinsics version of simple update
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Improve
P
adde
d
RVecVector resizing
commit
|
commitdiff
|
tree
2017-10-06
Alek
s
ei Iupinov
A
dd timi
n
g accumulation cap
a
bility into G
p
u
R
egion
T
i
m
er
commit
|
commitdiff
|
tree
2017-10-05
B
e
rk Hess
Make SIM
D
ambiguous test wor
k
w
i
th float/doubl
e
only
commit
|
commitdiff
|
tree
2017-10-05
Szil
á
rd P
á
ll
Fix
pair list arra
y
asserti
o
n
commit
|
commitdiff
|
tree
2017-10-05
Szilárd
P
áll
Avoid -W
m
issing-prototyp
e
s
warnings in clan
g
C
U
DA bui
l
d
s
commit
|
commitdiff
|
tree
2017-10-05
Rola
n
d
Schul
z
F
i
x
that exp(load(x)) is
a
mbiguou
s
commit
|
commitdiff
|
tree
2017-10-04
Ma
r
k Abraham
E
nable gro
u
p
-
schem
e
SIM
D
with GMX_SIMD=AVX2_128
commit
|
commitdiff
|
tree
2017-10-04
A
l
eksei I
u
pi
n
ov
Add GpuR
e
gionTimer class
commit
|
commitdiff
|
tree
2017-10-03
M
a
r
k
A
b
r
a
ha
m
Introduc
e
and use
Align
e
d
Allo
c
ationPo
l
icy
commit
|
commitdiff
|
tree
2017-10-02
Be
r
k Hess
Remove h
y
brid gpu+cpu non
b
onded mode
commit
|
commitdiff
|
tree
2017-09-26
Aleksei
I
upi
n
ov
Mov
e
CUDA texture s
e
tup code from
N
B CUDA module to
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
Mark Abraham
Merg
e
branch release-20
1
6
commit
|
commitdiff
|
tree
2017-09-15
Berk Hess
Remove nb-par
a
meter
s
from
t
_
for
c
erec
commit
|
commitdiff
|
tree
2017-09-15
M
a
rk
A
braham
Express intent of m
a
t
rix release build t
y
pes exp
l
icitly
commit
|
commitdiff
|
tree
2017-09-15
Ma
r
k Abrah
a
m
Bumped pat
c
h versio
n
for next
r
elease
commit
|
commitdiff
|
tree
next