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GROMACS 2018 first beta release
2017-11-28
Mark Abraham
GROMACS 2018 fir
s
t beta release
commit
|
commitdiff
|
tree
2017-11-28
Berk H
e
ss
Re
f
ac
t
or nbnxn exclusion se
t
t
ing
commit
|
commitdiff
|
tree
2017-11-28
Er
i
k
Lind
a
hl
Improve statu
s
messages for SIMD checks
commit
|
commitdiff
|
tree
2017-11-27
Szilárd Páll
Time FFT/
g
ather i
n
mixed mode
commit
|
commitdiff
|
tree
2017-11-27
Alek
s
ei Iupinov
Disable
f
ailing
s
e
parate PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Paul B
a
uer
Add GPU ta
s
k informati
o
n to user-guide
commit
|
commitdiff
|
tree
2017-11-24
A
l
e
ksei I
u
p
inov
E
na
b
le separ
a
te PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
sei I
u
pinov
A
c
t
ivat
e
mixed
mode of PME on
G
PU
commit
|
commitdiff
|
tree
2017-11-24
Szilárd Pá
l
l
Add
G
PU sharing
p
ost-submit con
f
ig
commit
|
commitdiff
|
tree
2017-11-24
M
a
rk Abraha
m
Upd
a
te de
v
eloper guide
commit
|
commitdiff
|
tree
2017-11-24
Mark Abr
a
ham
Act
i
vate PME on G
P
Us
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei
I
upin
o
v
Remove outd
a
ted (a
l
re
a
dy imple
m
ented) pinning TOD
O
commit
|
commitdiff
|
tree
2017-11-24
M
ar
k
Abraham
Add P
M
E inte
g
ration test
commit
|
commitdiff
|
tree
2017-11-24
Mark
Ab
r
ah
a
m
Exten
d
tas
k
a
ssignment code
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
s
e
i Iupinov
Mention g
m
x_install_headers() in the developer
m
anual
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei I
u
pi
n
ov
Ma
k
e
F
FT rea
l
-space grid
u
se CUDA pi
n
n
ing for m
i
xed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupinov
Pin coordinates, forc
e
s and
c
harges for
P
ME on
GPU
commit
|
commitdiff
|
tree
2017-11-22
Pas
c
al Mer
z
Proof of conc
e
pt:
P
h
y
s
ical v
a
l
i
datio
n
suite
commit
|
commitdiff
|
tree
2017-11-21
E
rik Lindahl
Separa
t
e SIMD flag detection from
management
commit
|
commitdiff
|
tree
2017-11-21
Mark Abraham
Support pinning in HostAllocator
commit
|
commitdiff
|
tree
2017-11-21
Viveca Lin
d
ah
l
Add f
o
rce
corre
l
ation to AWH module
commit
|
commitdiff
|
tree
2017-11-21
Paul Bauer
First general additions to t
h
e d
o
cu
m
en
t
ation
commit
|
commitdiff
|
tree
2017-11-19
Viveca Lindahl
Add A
W
H
secti
o
n
to manual
.
commit
|
commitdiff
|
tree
2017-11-19
Viveca
L
i
n
dahl
Add A
W
H
biasing modu
l
e
+ te
s
ts
commit
|
commitdiff
|
tree
2017-11-17
M
ark
A
braham
Use HostA
l
location
P
olicy for ch
a
rgeA
commit
|
commitdiff
|
tree
2017-11-17
Mar
k
Abraham
Add ch
e
cking function for w
h
et
h
er a buffer
is pinned
commit
|
commitdiff
|
tree
2017-11-17
Ma
r
k Abrah
a
m
Im
p
ro
v
e hand
l
i
n
g of
P
M
E GPU force buffer
commit
|
commitdiff
|
tree
2017-11-15
A
l
eksei
I
upinov
Renam
e
and expose "generic
"
GP
U
m
e
mory transfer functions
commit
|
commitdiff
|
tree
2017-11-10
Mark Abr
a
ham
Im
p
ort cmake Modules/FindC
U
DA
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupi
n
ov
R
ename syn
c
hron
o
us
G
PU tra
n
sfe
r
functions t
o
mat
c
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
M
ark Abraham
Pre
p
ared
t
_m
d
atoms for
u
si
n
g vector
commit
|
commitdiff
|
tree
2017-11-09
Mark Abraham
Introduc
e
HostAll
o
c
a
tionPolicy
commit
|
commitdiff
|
tree
2017-11-09
Rola
n
d Schulz
ICC shoul
d
u
s
e
ZMM
if code anyh
o
w uses ZMM
commit
|
commitdiff
|
tree
2017-11-07
Mark A
b
raham
Reform gmx_pme_pp alloc and us
e
vec
t
or
commit
|
commitdiff
|
tree
2017-11-07
Mark A
b
raham
Intr
o
duce gmxopencl
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mar
k
Abraham
Test
c
lang on ARM in
nigh
t
ly matrix
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Add wallcycle
timer for the
PME
G
P
U F red
u
ction
commit
|
commitdiff
|
tree
2017-11-07
Szil
á
r
d
Páll
S
pli
t
off nbnxn
G
PU timin
g
and staging reduction
commit
|
commitdiff
|
tree
2017-11-07
Mark
A
braham
Improve
PME in
c
ludes
commit
|
commitdiff
|
tree
2017-11-07
S
z
ilárd
Páll
Dedup
l
icate CUDA a
n
d O
p
enCL timer
s
truct
commit
|
commitdiff
|
tree
2017-11-06
David
v
a
n der Spoel
Fix
e
d
check f
o
r wa
t
er i
n
g
e
n_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
Mark Abraham
Merg
e
"Merge
branch releas
e
-2016"
commit
|
commitdiff
|
tree
2017-11-02
David
v
an d
e
r Spoel
N
e
w
mdp
i
n
pu
t
fo
r
electric
fields
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei I
u
pinov
Replace math
.
h by
cma
t
h i
n
clud
e
s in cpp fi
l
es
commit
|
commitdiff
|
tree
2017-11-02
Ma
r
k Abraham
M
erge branch re
l
ease-2016
commit
|
commitdiff
|
tree
2017-11-01
P
a
u
l Bauer
S
m
all c
h
ange to L
a
TeX manu
a
l
gene
r
at
i
o
n
commit
|
commitdiff
|
tree
2017-11-01
M
ark Abra
h
am
F
i
x t
h
rea
d
-
MPI rank cho
i
c
e for
orien
t
a
t
ion restraint
s
commit
|
commitdiff
|
tree
2017-11-01
A
l
e
ksei Iupino
v
Remove u
n
used PME GPU decla
r
ations
commit
|
commitdiff
|
tree
2017-11-01
Alek
s
ei Iup
i
nov
M
o
ve pme_
g
p
u
_
finish
_
c
omputation
(
) documentation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
P
a
ul Ba
u
er
Fixing missing references in web documentation
commit
|
commitdiff
|
tree
2017-11-01
Aleksei
Iupi
n
ov
Fix erroneo
u
s PME GP
U
"step" namings
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Improve handli
n
g of
G
PU IDs
commit
|
commitdiff
|
tree
2017-11-01
Aleksei
Iup
i
nov
Simplify PM
E
GPU synchr
o
niz
a
tion cod
e
commit
|
commitdiff
|
tree
2017-10-31
Aleksei Iupinov
Reuse ep
b
cXY
logic
commit
|
commitdiff
|
tree
2017-10-31
S
z
i
lárd Páll
Fix nstli
s
t i
n
crease
w
arning print
commit
|
commitdiff
|
tree
2017-10-31
Szil
á
r
d
P
áll
Check CUDA available/co
m
piled code com
p
a
tibility
commit
|
commitdiff
|
tree
2017-10-30
A
l
eksei
I
upinov
F
ix reference
m
ode
build unu
s
ed function w
a
rning
s
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
R
em
o
ve unused sig
n
parameter from dih_angle(
)
commit
|
commitdiff
|
tree
2017-10-30
R
o
l
a
nd Schulz
ArrayRef: R
e
pla
c
e fro
m
V
ect
o
r with subArray
commit
|
commitdiff
|
tree
2017-10-30
David van de
r
Spoel
Add
e
d option -
w
ater tips3p to pd
b
2g
m
x
.
commit
|
commitdiff
|
tree
2017-10-30
A
l
e
ksei
I
u
pino
v
Bring
PME GPU/CUDA inte
r
n
a
l st
r
uctu
r
e name
s
to CamelCase
commit
|
commitdiff
|
tree
2017-10-27
M
ark Abrah
a
m
Fix hw detectio
n
m
o
re
commit
|
commitdiff
|
tree
2017-10-26
M
ark Abraham
New quote
commit
|
commitdiff
|
tree
2017-10-20
Mark A
b
raham
Clarify docs for
F
max in
E
M
commit
|
commitdiff
|
tree
2017-10-20
M
a
rk Abraham
Me
r
ge branc
h
r
el
e
ase-2016
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix
w
a
rn
i
ng fo
r
c
o
nfout wit
h
periodic molecules
commit
|
commitdiff
|
tree
2017-10-16
M
a
r
k
A
bra
h
am
Merge branch release-2
0
16
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
Improv
e
vsite parall
e
l checking
commit
|
commitdiff
|
tree
2017-10-13
Alekse
i
Iupinov
Relax PME spline computatio
n
tolerance in
double pr
e
c
i
sion
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Mark Abraham
Update
tests for C++11 compiler and standard lib
r
a
ry
commit
|
commitdiff
|
tree
2017-10-13
Roland
S
chulz
Specialize ArrayRef for SimdRe
a
l
commit
|
commitdiff
|
tree
2017-10-11
Ma
r
k Ab
r
aham
In
t
roduc
e
d
hea
d
er for comm
u
nication to/from PME ranks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei
Iupino
v
F
ix clang
w
arni
n
gs for PME
C
U
D
A k
e
rnels
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iu
p
inov
R
e
lax PME solving test co
m
plex grid tolerance
commit
|
commitdiff
|
tree
2017-10-11
Mark Abr
a
h
a
m
C
l
eaned up ew
a
l
d
coeff for PME-only
r
a
n
ks
commit
|
commitdiff
|
tree
2017-10-11
A
l
e
ksei Iupinov
P
ME solv
i
ng - CUDA
k
erne
l
+ u
n
i
t
tests
commit
|
commitdiff
|
tree
2017-10-11
Paul Bauer
Ch
a
nge to modules fo
r
b
uil
d
of web documentat
i
on
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
PME forc
e
ga
t
he
r
in
g
- CUDA kernel + unit tes
t
s
commit
|
commitdiff
|
tree
2017-10-11
Alekse
i
Iu
p
in
o
v
PME spline+spr
e
ad
C
UDA kernel and unit test
s
commit
|
commitdiff
|
tree
2017-10-11
Ma
r
k Abraham
U
s
e cla
n
g
-
5
in J
e
nki
n
s
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disabl
e
ARM Neon nati
v
e
rsqrt iter
a
tion
commit
|
commitdiff
|
tree
2017-10-09
Al
e
ksei I
u
pinov
PME GPU/CUDA dat
a
fram
e
work
.
commit
|
commitdiff
|
tree
2017-10-07
Mark Abra
h
am
Tell cppch
e
ck
that
.
cpp and
.
cu files are c++
commit
|
commitdiff
|
tree
2017-10-07
Roland Schulz
R
e
f
a
ctor lo
a
d+SimdLoad*ProxyInternal to reduce duplication
commit
|
commitdiff
|
tree
2017-10-06
B
e
rk
H
e
ss
Add SIMD
i
ntrinsics vers
i
on of simple update
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Improve Padd
e
dRVe
c
Vector res
i
zing
commit
|
commitdiff
|
tree
2017-10-06
Al
e
ksei Iupinov
A
dd timing accumulati
o
n capability into GpuRegion
T
i
m
er
commit
|
commitdiff
|
tree
2017-10-05
Berk Hess
Make S
I
MD amb
i
guous test
work with
float/double onl
y
commit
|
commitdiff
|
tree
2017-10-05
S
zilárd Páll
Fi
x
pair list array assertion
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Páll
Avo
i
d -W
m
issing-pro
t
otype
s
wa
r
nings in c
l
ang CUDA builds
commit
|
commitdiff
|
tree
2017-10-05
Roland Sch
u
lz
Fix that exp(load(x)) is
ambiguo
u
s
commit
|
commitdiff
|
tree
2017-10-04
Ma
r
k Abraham
Enable group-
s
cheme SIMD
w
ith
G
M
X
_S
I
MD=A
V
X
2
_128
commit
|
commitdiff
|
tree
2017-10-04
Alekse
i
I
u
pi
n
ov
A
d
d GpuRegionTimer class
commit
|
commitdiff
|
tree
2017-10-03
Ma
r
k A
b
raham
Introduce
and
use AlignedAllocationP
o
licy
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
Rem
o
ve hybrid gpu+cpu nonbonde
d
mode
commit
|
commitdiff
|
tree
2017-09-26
Aleksei Iup
i
no
v
Move CUDA
t
extur
e
setup code f
r
om NB CUDA module t
o
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
Mark
A
braham
Merge branch r
e
lease-2016
commit
|
commitdiff
|
tree
2017-09-15
Berk Hess
Remove
n
b-parameters from t_force
r
ec
commit
|
commitdiff
|
tree
2017-09-15
Mark Ab
r
aham
Ex
p
r
ess inten
t
of m
a
tri
x
releas
e
build types explicitly
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
Bumped patch version fo
r
next r
e
l
ease
commit
|
commitdiff
|
tree
next