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GROMACS 2018 first beta release
2017-11-28
Mark Abraham
GROMACS 2018
first
beta relea
s
e
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Refactor nbnxn exclusion sett
i
n
g
commit
|
commitdiff
|
tree
2017-11-28
Er
i
k Lindah
l
I
m
prove statu
s
messages for S
I
MD checks
commit
|
commitdiff
|
tree
2017-11-27
Szilárd Páll
Ti
m
e
FFT
/
gather in mixed m
o
de
commit
|
commitdiff
|
tree
2017-11-27
A
l
eksei Iupino
v
Disab
l
e
failing separate PME
r
ank tests
commit
|
commitdiff
|
tree
2017-11-27
Paul
B
auer
Add GPU task infor
m
ation
t
o user-guide
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
sei Iupinov
Ena
b
le
separate PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei Iupinov
Activ
a
te mixed
mode of PME on
G
PU
commit
|
commitdiff
|
tree
2017-11-24
Szilárd P
á
ll
Add GPU sha
r
ing p
o
st-submi
t
config
commit
|
commitdiff
|
tree
2017-11-24
M
a
rk
A
b
r
aham
Update
developer guide
commit
|
commitdiff
|
tree
2017-11-24
Mark Ab
r
aham
Act
i
vat
e
PME on GPUs
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Remove outdate
d
(
a
lrea
d
y
i
mpleme
n
ted) pinning TODO
commit
|
commitdiff
|
tree
2017-11-24
Mar
k
Abra
h
a
m
A
d
d PME
i
n
tegration t
e
st
commit
|
commitdiff
|
tree
2017-11-24
Mark A
b
raham
Extend
task assig
n
m
e
nt cod
e
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei Iupinov
M
e
ntion g
m
x_install_hea
d
ers() in
t
he developer manual
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iupinov
Mak
e
F
F
T
real
-
s
p
ace grid use CUDA pinnin
g
f
or mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupin
o
v
Pin coordi
n
ate
s
, forces and
charg
e
s fo
r
PME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-22
P
a
scal Merz
Proof of conc
e
p
t: Physical
v
alida
t
ion suite
commit
|
commitdiff
|
tree
2017-11-21
Erik Lind
a
hl
Sepa
r
ate SIMD fl
a
g detection from mana
g
e
ment
commit
|
commitdiff
|
tree
2017-11-21
Mark Abraham
Support pin
n
ing in HostAll
o
c
ator
commit
|
commitdiff
|
tree
2017-11-21
Viveca L
i
n
dahl
Add
f
orce
c
orrelation to AWH module
commit
|
commitdiff
|
tree
2017-11-21
Pa
u
l Ba
u
er
Fi
r
st
g
eneral add
i
tions to t
h
e docu
m
entati
o
n
commit
|
commitdiff
|
tree
2017-11-19
V
i
veca Linda
h
l
Add
A
WH section to manual
.
commit
|
commitdiff
|
tree
2017-11-19
V
iveca Lindahl
Add AWH biasin
g
module + tests
commit
|
commitdiff
|
tree
2017-11-17
M
ark Ab
r
ah
a
m
Use Hos
t
AllocationPolicy
f
or chargeA
commit
|
commitdiff
|
tree
2017-11-17
Mark Abra
h
a
m
Add ch
e
cking function
for wh
e
ther
a buffer is
pinned
commit
|
commitdiff
|
tree
2017-11-17
Mark Abr
a
h
am
I
m
prov
e
han
d
ling of PME
G
PU force buffer
commit
|
commitdiff
|
tree
2017-11-15
A
l
eksei Iupinov
Rename and expose "generic" GPU mem
o
ry transfer functions
commit
|
commitdiff
|
tree
2017-11-10
M
ark
A
braham
Import cmake Modules/FindCUDA
.
cm
a
ke
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupino
v
Rename
synchronous GPU tra
n
sfe
r
functions to match
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Ma
r
k
Ab
r
ah
a
m
Prepared t_mdatoms for using vect
o
r
commit
|
commitdiff
|
tree
2017-11-09
Mark Abraham
Int
r
oduce
H
ostAlloca
t
io
n
Po
l
icy
commit
|
commitdiff
|
tree
2017-11-09
Rola
n
d
S
chulz
ICC should use ZMM
i
f
code anyhow
uses ZMM
commit
|
commitdiff
|
tree
2017-11-07
M
a
r
k
Abraham
Reform gmx_p
m
e_pp alloc and use
v
ect
o
r
commit
|
commitdiff
|
tree
2017-11-07
M
ark Abraham
Introduce gmx
o
p
encl
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Test cla
n
g o
n
ARM in nigh
t
ly matrix
commit
|
commitdiff
|
tree
2017-11-07
Szil
á
rd P
á
ll
Add wa
l
l
c
yc
l
e timer for th
e
P
M
E GPU F r
e
duction
commit
|
commitdiff
|
tree
2017-11-07
Szi
l
á
r
d
P
áll
Split off n
b
nxn GPU timin
g
and stag
i
ng
red
u
ction
commit
|
commitdiff
|
tree
2017-11-07
Mark
A
b
raham
Improve
P
ME
i
ncludes
commit
|
commitdiff
|
tree
2017-11-07
Szi
l
árd Páll
De
d
uplic
a
te CU
D
A and O
p
en
C
L timer struct
commit
|
commitdiff
|
tree
2017-11-06
David van der Spoel
Fixed check for water in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
Mar
k
Abraham
Merge "Merge branch r
e
l
e
ase-2
0
16"
commit
|
commitdiff
|
tree
2017-11-02
D
av
i
d van
d
er Spoel
New mdp input
fo
r
el
e
ctri
c
fie
l
d
s
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei Iupino
v
Rep
l
a
ce
m
ath
.
h by cmath include
s
in cpp files
commit
|
commitdiff
|
tree
2017-11-02
Mark Abrah
a
m
Merge branch re
l
ease-2016
commit
|
commitdiff
|
tree
2017-11-01
Paul Baue
r
Small
c
ha
n
ge to LaTeX
m
a
n
u
al generation
commit
|
commitdiff
|
tree
2017-11-01
M
ark Abraham
Fix thread-
M
P
I
rank choice for ori
e
ntation res
t
raints
commit
|
commitdiff
|
tree
2017-11-01
A
lek
s
ei
I
u
p
inov
R
emove unused P
M
E GPU declarations
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Move pme_g
p
u_finish_computation() documentation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Paul B
a
uer
Fixing missing ref
e
rence
s
i
n
w
e
b
do
c
umentation
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iup
i
nov
Fix errone
o
u
s
P
M
E GPU "step" namings
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Improv
e
handling o
f
GPU IDs
commit
|
commitdiff
|
tree
2017-11-01
Al
e
ksei Iupinov
Simplify
P
M
E GPU synchr
o
nizatio
n
code
commit
|
commitdiff
|
tree
2017-10-31
Alek
s
ei Iupinov
R
e
use epbcXY lo
g
ic
commit
|
commitdiff
|
tree
2017-10-31
Szilárd
P
áll
Fix nstlist in
c
rease warning p
r
int
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Check CUDA
available/compi
l
e
d
code compatibility
commit
|
commitdiff
|
tree
2017-10-30
Alekse
i
Iupinov
Fix ref
e
r
ence m
o
de
build unused
f
unction wa
r
ni
n
g
s
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remove unused si
g
n param
e
ter from dih_
a
ngle()
commit
|
commitdiff
|
tree
2017-10-30
Roland Schul
z
ArrayRe
f
: Replace fromVector wi
t
h subArray
commit
|
commitdiff
|
tree
2017-10-30
David
v
a
n d
e
r Spoel
Added option -water tip
s
3p
t
o
p
db2gmx
.
commit
|
commitdiff
|
tree
2017-10-30
A
leksei Iu
p
in
o
v
Bri
n
g PM
E
GPU
/
CU
D
A i
n
te
r
na
l
structure
n
ames to
C
amelC
a
se
commit
|
commitdiff
|
tree
2017-10-27
Mark
Abraham
F
i
x
hw detection more
commit
|
commitdiff
|
tree
2017-10-26
M
ark Abraha
m
New quote
commit
|
commitdiff
|
tree
2017-10-20
Ma
r
k Abraham
Clarify doc
s
f
or Fmax in EM
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
Merg
e
branch release-2016
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
F
i
x
warning fo
r
confout with pe
r
iodi
c
mole
c
ules
commit
|
commitdiff
|
tree
2017-10-16
M
a
rk Abraham
Merge branc
h
release
-
2016
commit
|
commitdiff
|
tree
2017-10-15
Be
r
k Hess
Improve vsi
t
e pa
r
a
l
lel checking
commit
|
commitdiff
|
tree
2017-10-13
A
leksei Iupinov
Relax PME splin
e
compu
t
a
t
ion tolerance in double precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Mark
A
br
a
ham
Update tests
f
or
C++11 compiler an
d
standard library
commit
|
commitdiff
|
tree
2017-10-13
R
olan
d
Schulz
Specia
l
ize Arr
a
y
Ref
f
o
r
S
i
mdReal
commit
|
commitdiff
|
tree
2017-10-11
Mark Ab
r
aham
In
t
roduced he
a
der for communicat
i
on to/from PME ranks
commit
|
commitdiff
|
tree
2017-10-11
Alekse
i
Iupinov
F
ix clang warnin
g
s for PME
CU
D
A kern
e
l
s
commit
|
commitdiff
|
tree
2017-10-11
Aleks
e
i Iupino
v
Relax PME solving test complex grid t
o
lerance
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraha
m
Cleane
d
up
e
w
a
l
d
c
oeff
for PME-only ranks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei
I
upinov
P
M
E solvin
g
-
C
U
DA
k
er
n
e
l
+ u
n
it tests
commit
|
commitdiff
|
tree
2017-10-11
Pa
u
l
B
auer
Ch
a
nge to
mod
u
les for build of
w
eb documentation
commit
|
commitdiff
|
tree
2017-10-11
Al
e
k
sei Iupi
n
ov
PME force
gathering - CUDA
kernel
+ uni
t
te
s
ts
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
P
M
E spline
+
spre
a
d CUDA kernel a
n
d unit tests
commit
|
commitdiff
|
tree
2017-10-11
Mark Abrah
a
m
U
s
e
clang-5 in J
e
nkins
commit
|
commitdiff
|
tree
2017-10-11
B
e
rk
H
e
ss
Disable ARM Neon nat
i
v
e
rsqrt
i
teration
commit
|
commitdiff
|
tree
2017-10-09
Aleksei Iupinov
PME GPU
/
C
UDA data frame
w
or
k
.
commit
|
commitdiff
|
tree
2017-10-07
Mark Abraha
m
Tell cppcheck that
.
cpp
a
nd
.
cu files a
r
e c++
commit
|
commitdiff
|
tree
2017-10-07
Ro
l
a
nd S
c
hul
z
Refact
o
r load+
S
imdLoad*
P
roxyIntern
a
l to reduc
e
duplicat
i
o
n
commit
|
commitdiff
|
tree
2017-10-06
B
erk
Hess
Add
S
IMD intrinsics version of s
i
m
p
l
e update
commit
|
commitdiff
|
tree
2017-10-06
Ber
k
H
e
ss
Improve Pa
d
dedRVec
V
ector resizing
commit
|
commitdiff
|
tree
2017-10-06
Al
e
ksei Iupinov
Add timing acc
u
mulat
i
o
n
c
apability into GpuR
e
gionTimer
commit
|
commitdiff
|
tree
2017-10-05
Berk Hess
M
a
ke SIMD ambiguous test work wit
h
float/double only
commit
|
commitdiff
|
tree
2017-10-05
Szi
l
ár
d
Páll
F
ix pair
l
i
s
t array assertion
commit
|
commitdiff
|
tree
2017-10-05
Szilárd
Páll
Avoid
-Wmiss
i
ng-prototypes warnings
in clang C
U
DA
builds
commit
|
commitdiff
|
tree
2017-10-05
Roland Schul
z
Fix that exp(load(x)) is
a
m
biguou
s
commit
|
commitdiff
|
tree
2017-10-04
Mark Abraham
Enable group-sch
e
me
S
IMD with GMX_SIMD=AVX2_
1
28
commit
|
commitdiff
|
tree
2017-10-04
Aleks
e
i
Iupinov
A
d
d GpuRegionTimer
cl
a
ss
commit
|
commitdiff
|
tree
2017-10-03
Mark Abr
a
h
am
Introduce and use AlignedAlloc
a
t
i
o
nPolicy
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
Remove hybrid gpu+c
p
u
non
b
onded
m
ode
commit
|
commitdiff
|
tree
2017-09-26
Aleksei Iupinov
Move CUDA texture setu
p
c
o
de fr
o
m NB CU
D
A mod
u
le to
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
Mark Abraham
Merg
e
branc
h
r
e
lease-2016
commit
|
commitdiff
|
tree
2017-09-15
Ber
k
Hess
Remove nb-param
e
ters from t
_
f
o
rcer
e
c
commit
|
commitdiff
|
tree
2017-09-15
Mark
A
brah
a
m
Ex
p
ress in
t
ent of ma
t
rix
release buil
d
types explicit
l
y
commit
|
commitdiff
|
tree
2017-09-15
Mark A
b
raham
Bumped
p
atch version
f
or next
r
e
l
e
ase
commit
|
commitdiff
|
tree
next