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Version 2018.1
2017-12-07
Roland
Schulz
Fix
AWH
t
e
s
t ac
c
uracy
commit
|
commitdiff
|
tree
2017-12-07
B
e
rk Hess
Choose fast
e
r
n
bnxn
SIMD kernels on
A
MD Zen
commit
|
commitdiff
|
tree
2017-12-07
Rolan
d
Schulz
Fix
e
x
p
test
for ICC
i
n double
commit
|
commitdiff
|
tree
2017-12-07
Roland Schulz
Fix
RelWithA
s
sert wit
h
ICC
commit
|
commitdiff
|
tree
2017-12-07
Aleksei Iupinov
Relaxed preci
s
i
o
n in splin
e
inte
r
polation tests
commit
|
commitdiff
|
tree
2017-12-06
Szilárd P
á
ll
Implemen
t
alternating GPU
w
ait
commit
|
commitdiff
|
tree
2017-12-05
A
lek
s
ei
Iupi
n
ov
Do not ac
c
ept
unsuppo
r
ted combination "-pme cp
u
-pmeff
t
.
.
.
commit
|
commitdiff
|
tree
2017-12-05
R
o
l
and
Schulz
Fix Arr
a
yRe
f
<SimdDInt32> for SSE/AVX128
commit
|
commitdiff
|
tree
2017-12-05
Ma
r
k Abraham
Update testing
to include
c
make
3
.
10
.
0
commit
|
commitdiff
|
tree
2017-12-05
Magnus
L
und
b
org
SIMD ac
c
eler
a
ted Ur
e
y-
B
r
a
dley
commit
|
commitdiff
|
tree
2017-12-05
B
erk Hess
Fix DD exac
t
cont
i
nuation
bug
commit
|
commitdiff
|
tree
2017-12-04
Mark
A
b
raham
Fix free_gpu
commit
|
commitdiff
|
tree
2017-12-04
Mark A
b
raham
Me
r
ge
bran
c
h release-201
6
i
nto release-
2
018
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Update mdrun signal help text
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Only stop
a
t
nstlist ste
p
s
wit
h
-rep
r
o
d
commit
|
commitdiff
|
tree
2017-12-04
E
r
ik Lin
d
a
hl
Fix
c
ompi
l
ation issues f
o
r
AVX-
5
12
commit
|
commitdiff
|
tree
2017-11-28
M
ark Abrah
a
m
GR
O
MACS 2018 fi
r
st beta release
commit
|
commitdiff
|
tree
2017-11-28
Ber
k
H
es
s
Refactor
n
bnxn exclus
i
on setting
commit
|
commitdiff
|
tree
2017-11-28
Erik Li
n
dahl
Imp
r
ove stat
u
s me
s
sages for SIMD checks
commit
|
commitdiff
|
tree
2017-11-27
Szilárd Páll
Time FFT/
g
ath
e
r in mi
x
ed
mode
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
Iupinov
D
i
sable failing separate PME rank tes
t
s
commit
|
commitdiff
|
tree
2017-11-27
Paul
B
a
ue
r
A
d
d GP
U
task information to use
r
-guide
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupinov
Enable s
e
para
t
e PME GPU ra
n
k
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei I
u
p
inov
Activat
e
mixe
d
mo
d
e o
f
P
M
E on
GPU
commit
|
commitdiff
|
tree
2017-11-24
S
z
ilá
r
d
P
áll
Add GPU sharing post-submit
c
o
nfi
g
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraha
m
U
pdat
e
developer
g
uide
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
Activate PME
o
n GPUs
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iu
p
inov
Remove outdated
(
already imp
l
e
men
t
e
d) pinn
i
ng TODO
commit
|
commitdiff
|
tree
2017-11-24
Mark
Abr
a
ham
Add PME
i
ntegration
t
est
commit
|
commitdiff
|
tree
2017-11-24
M
a
rk Abraham
Extend task assignment code
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
se
i
Iupinov
M
e
ntion gmx_i
n
stall_headers() in the
d
eveloper manual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Make FFT real-space grid use
CUDA p
i
nning for mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i Iupinov
Pin coordinates, for
c
es and charges for
P
ME on GP
U
commit
|
commitdiff
|
tree
2017-11-22
P
a
scal Merz
Pr
o
o
f o
f
co
n
c
ept: Phy
s
i
c
al
validatio
n
suite
commit
|
commitdiff
|
tree
2017-11-21
Erik Lin
d
ahl
Separate SIMD flag dete
c
tion from management
commit
|
commitdiff
|
tree
2017-11-21
M
ark Abraham
S
u
pport pinning in Host
A
l
l
ocator
commit
|
commitdiff
|
tree
2017-11-21
Viveca Li
n
dahl
A
d
d
for
c
e
correlation
to AWH modul
e
commit
|
commitdiff
|
tree
2017-11-21
Pa
u
l
Bauer
Fi
r
st genera
l
a
dditions to the doc
u
mentation
commit
|
commitdiff
|
tree
2017-11-19
Viveca
L
indahl
Add AWH
s
ection t
o
manual
.
commit
|
commitdiff
|
tree
2017-11-19
Vi
v
eca
L
ind
a
hl
Add AWH bias
i
ng module + tests
commit
|
commitdiff
|
tree
2017-11-17
Mark Ab
r
a
h
am
Use Ho
s
tAllocationPolicy
f
or chargeA
commit
|
commitdiff
|
tree
2017-11-17
Mark A
b
raha
m
Add ch
e
cking function for whether a buf
f
er is
p
inned
commit
|
commitdiff
|
tree
2017-11-17
Ma
r
k Abraham
I
m
p
r
o
ve handling of
PME GPU force bu
f
fer
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iupinov
R
ename and expose "generic" GPU memory
tran
s
fe
r
functions
commit
|
commitdiff
|
tree
2017-11-10
M
a
rk Abra
h
am
Import cmake M
o
dules/Find
C
U
D
A
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
Aleksei
I
u
p
ino
v
Rename
s
y
nc
h
ronous GPU transfer
functi
o
ns to match
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Mark Abraham
Prepared t_md
a
toms for us
i
ng vector
commit
|
commitdiff
|
tree
2017-11-09
Mark Ab
r
aham
I
n
troduce HostAllocationP
o
l
i
c
y
commit
|
commitdiff
|
tree
2017-11-09
Roland Schulz
IC
C
shoul
d
u
s
e ZM
M
if code anyhow uses ZM
M
commit
|
commitdiff
|
tree
2017-11-07
M
a
rk Abra
h
a
m
Reform gmx_
p
me_pp alloc and us
e
v
e
ctor
commit
|
commitdiff
|
tree
2017-11-07
Ma
r
k
Abraha
m
Introdu
c
e gmxo
p
e
n
cl
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark
A
b
r
aham
Te
s
t c
l
a
n
g on ARM in nightly
m
atr
i
x
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Add wall
c
y
c
l
e timer
for
t
h
e
P
M
E GPU F red
u
ction
commit
|
commitdiff
|
tree
2017-11-07
Szilárd
P
áll
Split of
f
nbnxn G
P
U timin
g
a
nd sta
g
ing reduction
commit
|
commitdiff
|
tree
2017-11-07
M
a
rk Abraham
Improv
e
PME incl
u
des
commit
|
commitdiff
|
tree
2017-11-07
Szilá
r
d
Páll
Dedupli
c
ate CUD
A
and
O
penCL timer
str
u
ct
commit
|
commitdiff
|
tree
2017-11-06
Davi
d
van der S
p
oel
F
i
xe
d
check
f
or wat
e
r in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
Mark Abraham
M
e
rge
"
Merge branch release-2016"
commit
|
commitdiff
|
tree
2017-11-02
Dav
i
d van de
r
S
p
o
e
l
Ne
w
mdp inpu
t
for elec
t
ric fields
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei Iupinov
Replace math
.
h
by
c
ma
t
h inc
l
udes in cpp files
commit
|
commitdiff
|
tree
2017-11-02
Mark
A
braham
Merge branc
h
release-2016
commit
|
commitdiff
|
tree
2017-11-01
Pau
l
B
a
u
e
r
Small change
to LaTeX man
u
al generation
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Fix thr
e
ad-MP
I
rank choice for orientation
res
t
r
aints
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Remove unus
e
d PME GPU declar
a
tions
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iup
i
nov
Move pm
e
_g
p
u_finish_computation()
d
ocumen
t
ation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
Fixin
g
missing references in web d
o
cumentation
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
F
i
x
erroneous PME G
P
U "step" n
a
mings
commit
|
commitdiff
|
tree
2017-11-01
Mark
Abraham
Impr
o
ve han
d
li
n
g of
GPU IDs
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Simplify PM
E
GPU syn
c
hron
i
zation code
commit
|
commitdiff
|
tree
2017-10-31
Aleksei
I
u
pinov
Reuse epbcXY logic
commit
|
commitdiff
|
tree
2017-10-31
Szilárd
P
áll
Fix nstlis
t
increase warni
n
g
print
commit
|
commitdiff
|
tree
2017-10-31
Sz
i
lárd
P
á
l
l
Check CUDA availabl
e
/
c
ompiled code compatibility
commit
|
commitdiff
|
tree
2017-10-30
Aleks
e
i
I
upinov
Fix refe
r
ence
mode build unused function
w
arn
i
ng
s
commit
|
commitdiff
|
tree
2017-10-30
Berk
Hess
Remove
u
nu
s
ed sign parameter
f
rom dih_angle()
commit
|
commitdiff
|
tree
2017-10-30
Ro
l
and
S
chulz
ArrayRef:
Re
p
lac
e
fromVector with subArray
commit
|
commitdiff
|
tree
2017-10-30
D
avid van der Sp
o
el
A
d
ded
o
ption -wate
r
tips3p to pd
b
2
gmx
.
commit
|
commitdiff
|
tree
2017-10-30
Alekse
i
Iupin
o
v
Bring P
M
E
G
PU/CUDA inte
r
n
a
l
structu
r
e names
t
o CamelC
a
se
commit
|
commitdiff
|
tree
2017-10-27
M
a
r
k Abraham
Fix hw detection more
commit
|
commitdiff
|
tree
2017-10-26
M
a
rk Abraham
N
ew qu
o
t
e
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
Clarify docs for Fm
a
x
in EM
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
Me
r
g
e branch
r
elease-201
6
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fi
x
warning f
o
r
confout with pe
r
iodic
m
olecu
l
es
commit
|
commitdiff
|
tree
2017-10-16
Mark Abraham
Merge branc
h
rele
a
se-2016
commit
|
commitdiff
|
tree
2017-10-15
B
erk Hess
Improve vsite parallel chec
k
ing
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iupinov
Relax PME
s
pline
c
omputation
t
oler
a
nc
e
i
n d
o
u
b
le p
r
ecision
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Mark
A
braham
Updat
e
tests for C++
1
1 comp
i
l
e
r a
n
d
s
ta
n
d
ard li
b
r
a
ry
commit
|
commitdiff
|
tree
2017-10-13
Rol
a
nd
S
chulz
Specialize
A
rrayRef fo
r
SimdR
e
al
commit
|
commitdiff
|
tree
2017-10-11
Mark Ab
r
ah
a
m
I
n
tr
o
duced hea
d
e
r
fo
r
com
m
uni
c
a
ti
o
n to/fro
m
P
M
E ranks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
Fix clang warnings for PME CUDA kernels
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
Relax PME solving te
s
t compl
e
x
grid tol
e
ranc
e
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Cle
a
ned up
e
waldcoeff f
o
r PME-only rank
s
commit
|
commitdiff
|
tree
2017-10-11
Alekse
i
Iupinov
PM
E
solving - CU
D
A
ker
n
el + unit tests
commit
|
commitdiff
|
tree
2017-10-11
Pa
u
l Bauer
Change to modul
e
s
for build of web do
c
umen
t
ation
commit
|
commitdiff
|
tree
2017-10-11
Al
e
k
s
ei I
u
pinov
PME for
c
e gathering
- C
U
D
A
k
e
r
n
el +
u
nit tests
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
PME spline+sprea
d
CUDA k
e
r
n
el
a
nd unit tests
commit
|
commitdiff
|
tree
2017-10-11
Mar
k
Abraham
Use clang-5 in Jenkin
s
commit
|
commitdiff
|
tree
2017-10-11
B
e
rk Hess
Disable A
R
M Neon na
t
ive rsqrt
iterat
i
on
commit
|
commitdiff
|
tree
2017-10-09
Ale
k
s
e
i Iupinov
P
ME GPU/CUDA data
f
ramework
.
commit
|
commitdiff
|
tree
2017-10-07
M
a
r
k
A
bra
h
a
m
T
ell
c
p
p
check
t
hat
.
cpp and
.
cu fi
l
e
s are c++
commit
|
commitdiff
|
tree
2017-10-07
Rol
a
nd Schulz
Refactor load+SimdLoad*ProxyInte
r
nal to reduce d
u
p
licat
i
on
commit
|
commitdiff
|
tree
next