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GROMACS 2018 first beta release
2017-11-28
M
a
r
k Abraham
GRO
M
AC
S
2018 first beta release
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
R
e
f
actor nbnxn exclusion setting
commit
|
commitdiff
|
tree
2017-11-28
Erik Lindahl
Imp
r
o
ve s
t
atu
s
mess
a
ges for SIMD checks
commit
|
commitdiff
|
tree
2017-11-27
Szilárd
Páll
Time F
F
T/g
a
ther in
mix
e
d mode
commit
|
commitdiff
|
tree
2017-11-27
Ale
k
sei Iupinov
Disable failing sepa
r
ate PME rank
tests
commit
|
commitdiff
|
tree
2017-11-27
Pau
l
Bauer
Add
G
PU tas
k
information to use
r
-guide
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
En
a
ble separate PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
upinov
A
c
t
i
vat
e
mixed mode o
f
PME on GPU
commit
|
commitdiff
|
tree
2017-11-24
Sz
i
lárd Pá
l
l
Add
G
PU sharing
post-su
b
mit confi
g
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
Update de
v
eloper guide
commit
|
commitdiff
|
tree
2017-11-24
M
ark
A
braham
Acti
v
at
e
P
M
E on GPUs
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Remov
e
outda
t
ed (already
i
m
p
leme
n
ted) p
i
n
n
i
n
g TODO
commit
|
commitdiff
|
tree
2017-11-24
M
a
r
k
Abraham
Add PM
E
integration test
commit
|
commitdiff
|
tree
2017-11-24
Mark
A
braham
Exte
n
d t
a
sk
a
ssignment code
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Ment
i
o
n
gmx_i
n
stall_head
e
rs
(
) in the d
e
veloper manual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Make FFT real
-
s
pace grid us
e
CU
D
A
pinning for mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Pin co
o
rdinates
,
forces and
c
harge
s
for
P
ME
o
n GPU
commit
|
commitdiff
|
tree
2017-11-22
Pascal
Merz
Proof of
conce
p
t: Physical validation suite
commit
|
commitdiff
|
tree
2017-11-21
Erik Lin
d
ahl
Sep
a
rate
S
IMD flag detection from manage
m
e
n
t
commit
|
commitdiff
|
tree
2017-11-21
Mark Abrah
a
m
Support pinning in
H
o
s
t
All
o
cator
commit
|
commitdiff
|
tree
2017-11-21
Viveca L
i
ndahl
Add for
c
e correlation
t
o AWH
m
odule
commit
|
commitdiff
|
tree
2017-11-21
P
a
u
l
Bauer
First g
e
n
eral additions to t
h
e documen
t
ation
commit
|
commitdiff
|
tree
2017-11-19
V
i
v
e
c
a
Li
n
dahl
Add
AWH section
to manual
.
commit
|
commitdiff
|
tree
2017-11-19
Viveca
L
ind
a
hl
Add
A
WH biasing m
o
dule
+ tests
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
Use HostAllocati
o
nPolicy
for
charg
e
A
commit
|
commitdiff
|
tree
2017-11-17
Mark
Abraham
Add checking function fo
r
whether a b
u
ffer
is
p
i
nned
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
I
m
pr
o
ve handling of PME GPU for
c
e
buffer
commit
|
commitdiff
|
tree
2017-11-15
Aleks
e
i Iupino
v
R
en
a
me and
expo
s
e "generic" GP
U
m
em
o
ry t
r
an
s
fer
f
u
nctions
commit
|
commitdiff
|
tree
2017-11-10
M
a
r
k Abr
a
ham
I
m
port c
m
a
k
e Modules/FindCUDA
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
Al
e
k
s
e
i Iupinov
Rename s
y
nchr
o
nous
G
PU transfe
r
functions to mat
c
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Mark Abraham
Pr
e
pared t_mdatoms for usin
g
v
ector
commit
|
commitdiff
|
tree
2017-11-09
Ma
r
k
A
braham
In
t
roduc
e
HostAllo
c
atio
n
Polic
y
commit
|
commitdiff
|
tree
2017-11-09
Roland Schulz
I
C
C should
u
se ZMM if code anyhow uses
Z
MM
commit
|
commitdiff
|
tree
2017-11-07
Mar
k
Abraham
Refo
r
m gmx_pme_p
p
alloc and
use vector
commit
|
commitdiff
|
tree
2017-11-07
M
ark Abraham
Introd
u
ce gmxopen
c
l
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Test clang on ARM in nightly m
a
trix
commit
|
commitdiff
|
tree
2017-11-07
Sz
i
lárd
Pá
l
l
Add wa
l
lcycle timer
f
or t
h
e PME GPU F re
d
uction
commit
|
commitdiff
|
tree
2017-11-07
S
z
il
á
rd P
á
ll
Split off nbnxn
G
PU
timing
and
st
a
ging
reduction
commit
|
commitdiff
|
tree
2017-11-07
Mark Abra
h
am
Improve
P
ME inc
l
ude
s
commit
|
commitdiff
|
tree
2017-11-07
Szil
á
rd Páll
Deduplicat
e
CUDA
and Op
e
n
CL timer s
t
r
u
ct
commit
|
commitdiff
|
tree
2017-11-06
David
v
a
n
der
Spoel
Fixed c
h
eck fo
r
water in gen_vs
i
te
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
Mark Ab
r
ah
a
m
Merge "Merge branch
release-2016"
commit
|
commitdiff
|
tree
2017-11-02
David van der Spoel
N
e
w
mdp i
n
put for electric fields
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei Iu
p
in
o
v
Rep
l
a
ce m
a
th
.
h b
y
cmath in
c
ludes in cpp file
s
commit
|
commitdiff
|
tree
2017-11-02
Mark Abraham
Merge branch release
-
20
1
6
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
Small change to LaTe
X
m
a
n
ual generation
commit
|
commitdiff
|
tree
2017-11-01
M
a
rk
A
braham
F
i
x
t
h
r
e
ad-MP
I
rank choice fo
r
orienta
t
i
on re
s
t
r
aints
commit
|
commitdiff
|
tree
2017-11-01
Alek
s
ei Iu
p
inov
Re
m
ove unuse
d
P
M
E GPU
declarations
commit
|
commitdiff
|
tree
2017-11-01
A
lek
s
ei Iupinov
Move pme_gp
u
_fin
i
sh
_
computatio
n
() documentation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
F
ixi
n
g missing refe
r
e
nc
e
s
in web document
a
tion
commit
|
commitdiff
|
tree
2017-11-01
Aleksei I
u
pi
n
o
v
Fix erroneou
s
PME GPU
"step" nam
i
ngs
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Improve handling of GPU ID
s
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupin
o
v
Si
m
plify PME
GP
U
synchronization cod
e
commit
|
commitdiff
|
tree
2017-10-31
Al
e
ksei
I
upinov
Reus
e
epbcXY l
o
gic
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Fix nstlist increa
s
e
w
arning print
commit
|
commitdiff
|
tree
2017-10-31
Szilárd
Páll
Check
CUDA avai
l
able/compile
d
c
o
d
e compatibility
commit
|
commitdiff
|
tree
2017-10-30
Aleksei
Iupinov
Fix referen
c
e mode build
unused function
warn
i
ngs
commit
|
commitdiff
|
tree
2017-10-30
Ber
k
Hess
Remove unused sign par
a
m
e
ter from dih_angle()
commit
|
commitdiff
|
tree
2017-10-30
Roland Schulz
ArrayRef: Re
p
lace fromVector
with
subA
r
ray
commit
|
commitdiff
|
tree
2017-10-30
David van de
r
S
poel
Ad
d
ed option -
w
ater t
i
ps3p to pd
b
2gmx
.
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Bring PME
G
PU/CUDA
i
n
t
e
rn
a
l
s
tructure names to CamelCase
commit
|
commitdiff
|
tree
2017-10-27
M
ark A
b
raham
Fix hw detect
i
on m
o
re
commit
|
commitdiff
|
tree
2017-10-26
M
ar
k
Abraham
New q
u
ote
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
Clarify doc
s
f
or Fmax
in
E
M
commit
|
commitdiff
|
tree
2017-10-20
Mar
k
Ab
r
aham
M
e
rge br
a
n
c
h release-2016
commit
|
commitdiff
|
tree
2017-10-20
Ber
k
He
s
s
Fix
warning
f
or confout wi
t
h periodic mo
l
ecules
commit
|
commitdiff
|
tree
2017-10-16
Mark Ab
r
aham
Merge branch
release
-
2016
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
I
m
p
rov
e
vs
i
t
e
parallel checking
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iupino
v
Relax PME
spl
i
ne computation tolerance in d
o
u
b
le preci
s
ion
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Mark Abraham
Update t
e
sts for C+
+
11 c
o
mpiler and standa
r
d library
commit
|
commitdiff
|
tree
2017-10-13
Roland
Schu
l
z
Specialize A
r
rayRef
f
or Simd
R
eal
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
In
t
roduced
h
ea
d
er f
o
r commun
i
c
ati
o
n to/fro
m
PME
ran
k
s
commit
|
commitdiff
|
tree
2017-10-11
Ale
k
s
ei Iupinov
Fix cl
a
ng warnings for
PM
E
CUDA kern
e
l
s
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iu
p
ino
v
R
e
lax PM
E
solving test complex
grid to
l
erance
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Cleaned up ewald
c
oeff
f
or PME-only
r
anks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
P
M
E
s
o
lving - CUDA ke
r
nel + unit tests
commit
|
commitdiff
|
tree
2017-10-11
Paul Bauer
Change to
modules for build
o
f
we
b
docume
n
tati
o
n
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupino
v
PME f
o
rce gathering
-
C
U
DA kernel
+ unit tests
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iup
i
nov
PME spline+
s
pread CU
D
A kernel and unit tests
commit
|
commitdiff
|
tree
2017-10-11
M
ark Ab
r
aha
m
U
se clang-5 in Jenkins
commit
|
commitdiff
|
tree
2017-10-11
Berk He
s
s
Disable ARM
N
eon nat
i
ve rsqrt iteration
commit
|
commitdiff
|
tree
2017-10-09
Aleksei Iupinov
PM
E
GPU/CUDA
data framework
.
commit
|
commitdiff
|
tree
2017-10-07
Mark
A
b
raham
Tell cppcheck that
.
cpp and
.
cu
f
i
l
es are c++
commit
|
commitdiff
|
tree
2017-10-07
Roland Schulz
Ref
a
ctor
l
o
ad+Sim
d
L
oad*ProxyI
n
t
ernal to r
e
duce duplicatio
n
commit
|
commitdiff
|
tree
2017-10-06
Berk He
s
s
A
d
d S
I
MD intrinsic
s
v
e
r
s
ion of simple
u
p
date
commit
|
commitdiff
|
tree
2017-10-06
Berk
H
ess
Improve P
a
ddedRVec
V
ector res
i
zi
n
g
commit
|
commitdiff
|
tree
2017-10-06
Aleksei Iupinov
Add timi
n
g ac
c
umulatio
n
capa
b
i
lity into
G
p
u
Regio
n
Ti
m
e
r
commit
|
commitdiff
|
tree
2017-10-05
B
e
rk
H
ess
Make SIMD ambiguous test w
o
rk wi
t
h
f
loat/
d
ouble only
commit
|
commitdiff
|
tree
2017-10-05
Szilár
d
Páll
Fix pair li
s
t array assertion
commit
|
commitdiff
|
tree
2017-10-05
Szilárd
P
áll
Avoid
-
Wmissing-proto
t
ypes warn
i
n
g
s
in clan
g
CUDA builds
commit
|
commitdiff
|
tree
2017-10-05
Roland Schulz
Fix that exp(load(x
)
) is
am
b
igu
o
us
commit
|
commitdiff
|
tree
2017-10-04
Mark
A
brah
a
m
Enable group-scheme
S
I
MD with
G
MX_SIMD=A
V
X2_128
commit
|
commitdiff
|
tree
2017-10-04
Alek
s
e
i
Iupinov
Add GpuRegi
o
nTime
r
class
commit
|
commitdiff
|
tree
2017-10-03
Mark Abraham
Introduce and use Al
i
g
n
edAllocationP
o
licy
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
R
emove hyb
r
i
d gpu+cp
u
nonbonded mode
commit
|
commitdiff
|
tree
2017-09-26
Alekse
i
I
u
pino
v
Move CUD
A
te
x
t
u
re set
u
p co
d
e
f
r
om
NB CUDA module to
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
Mark Abraham
Merge
b
ranch release-2016
commit
|
commitdiff
|
tree
2017-09-15
Ber
k
Hess
Remove nb-parameters from
t_forcerec
commit
|
commitdiff
|
tree
2017-09-15
Ma
r
k Abraham
E
xpress intent of
m
atrix release bu
i
l
d
types explicitly
commit
|
commitdiff
|
tree
2017-09-15
Mark Abr
a
ham
Bumpe
d
patch version for nex
t
relea
s
e
commit
|
commitdiff
|
tree
next