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Support pinning in HostAllocator
2017-11-21
Mar
k
Ab
r
aha
m
Su
p
port pinni
n
g in HostAllocator
commit
|
commitdiff
|
tree
2017-11-21
Viveca Lindahl
Add force
c
orrelati
o
n to AWH mod
u
le
commit
|
commitdiff
|
tree
2017-11-21
Paul Bauer
First
general additions to t
h
e documentation
commit
|
commitdiff
|
tree
2017-11-19
Viveca Li
n
d
ahl
A
d
d AWH
secti
o
n to manua
l
.
commit
|
commitdiff
|
tree
2017-11-19
Viveca Lindahl
Add AWH biasi
n
g
m
o
d
ule
+
t
ests
commit
|
commitdiff
|
tree
2017-11-17
M
ark Abraham
Use H
o
stAlloc
a
ti
o
n
P
o
licy for charge
A
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
A
dd
c
hecking
f
unction
for wheth
e
r a b
u
ff
e
r is
pinned
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
Impr
o
v
e
h
a
ndling of PME GPU force buffe
r
commit
|
commitdiff
|
tree
2017-11-15
Aleksei I
u
pinov
Re
n
ame and expose
"gen
e
ric" GPU memory transfer functions
commit
|
commitdiff
|
tree
2017-11-10
Mark
A
b
raham
I
m
port cmak
e
Modules/Fi
n
dCUDA
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
Ale
k
sei Iup
i
nov
Rename synchrono
u
s GPU transfer
functions t
o
match
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Ma
r
k
Abr
a
ham
Prepared t_mdatoms fo
r
using vect
o
r
commit
|
commitdiff
|
tree
2017-11-09
Mar
k
Abr
a
ham
Introduce HostA
l
locationPol
i
cy
commit
|
commitdiff
|
tree
2017-11-09
Roland Schulz
ICC s
h
ould u
s
e ZMM if co
d
e
a
nyhow u
s
es ZMM
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Re
f
orm gmx_pme_pp alloc an
d
use vec
t
o
r
commit
|
commitdiff
|
tree
2017-11-07
Mark
Abraham
Introduce gmxopencl
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abr
a
ham
Test clang on
A
RM in
n
ightl
y
ma
t
r
ix
commit
|
commitdiff
|
tree
2017-11-07
S
zilárd Páll
Add wall
c
ycle time
r
for the PME GPU F reduction
commit
|
commitdiff
|
tree
2017-11-07
Sz
i
lárd
Páll
S
plit
o
ff nbnxn GPU timing a
n
d staging reduction
commit
|
commitdiff
|
tree
2017-11-07
Mar
k
Abraham
Improve
P
ME includes
commit
|
commitdiff
|
tree
2017-11-07
S
zilárd Páll
Deduplicate
C
U
DA and OpenCL t
i
m
e
r st
r
uct
commit
|
commitdiff
|
tree
2017-11-06
David v
a
n
d
er Spoel
Fixed
c
h
eck for water in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
Mark Abraham
Mer
g
e "Merge br
a
nc
h
re
l
ease-2016"
commit
|
commitdiff
|
tree
2017-11-02
David van der Spoel
New mdp input for electric fields
.
commit
|
commitdiff
|
tree
2017-11-02
A
l
eksei Iu
p
inov
Replace
m
ath
.
h
b
y cmath includes in cp
p
files
commit
|
commitdiff
|
tree
2017-11-02
Mark A
b
r
a
ham
Merge branch release-2016
commit
|
commitdiff
|
tree
2017-11-01
Paul Baue
r
Small
change
to
L
a
TeX
m
anual generation
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Fix thread-MPI r
a
nk choice
f
or ori
e
ntation
r
e
strain
t
s
commit
|
commitdiff
|
tree
2017-11-01
Al
e
ks
e
i Iupinov
R
emove un
u
sed PME GPU de
c
laration
s
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupi
n
ov
Mo
v
e pme
_
gp
u
_finish
_
c
o
mputation() documentation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
P
a
ul Bauer
Fixing
missin
g
referenc
e
s in web documen
t
ation
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
F
i
x erroneous PME
G
PU "ste
p
" namings
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Impro
v
e ha
n
d
l
ing of GPU IDs
commit
|
commitdiff
|
tree
2017-11-01
Al
e
ksei
I
upinov
S
im
p
lify PME
GPU
s
ynchronization
c
ode
commit
|
commitdiff
|
tree
2017-10-31
Aleksei
Iupi
n
ov
R
eus
e
epbcXY l
o
gic
commit
|
commitdiff
|
tree
2017-10-31
Szilárd
P
áll
Fix ns
t
list in
c
rease
w
arn
i
ng
print
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Che
c
k CUDA avail
a
bl
e
/compi
l
ed code compatibility
commit
|
commitdiff
|
tree
2017-10-30
Al
e
ks
e
i
Iupin
o
v
Fix refe
r
ence mode bui
l
d
unused
f
unc
t
io
n
wa
r
ning
s
commit
|
commitdiff
|
tree
2017-10-30
Berk
H
ess
Remo
v
e
unus
e
d
sign parameter
f
r
o
m dih_angl
e
()
commit
|
commitdiff
|
tree
2017-10-30
Rola
n
d S
c
hulz
A
rrayRe
f
: Repl
a
c
e
fromVector with
s
ubArra
y
commit
|
commitdiff
|
tree
2017-10-30
D
a
vi
d
van der Spoel
Added optio
n
-water
t
i
p
s
3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iu
p
inov
Bring PME GPU/CUDA inter
n
al structure names to Camel
C
a
s
e
commit
|
commitdiff
|
tree
2017-10-27
Mark
Abraham
F
i
x
h
w
d
etec
t
ion mo
r
e
commit
|
commitdiff
|
tree
2017-10-26
Mark Abraham
N
ew
q
uote
commit
|
commitdiff
|
tree
2017-10-20
Mar
k
A
brah
a
m
Clarify docs
f
o
r Fmax in EM
commit
|
commitdiff
|
tree
2017-10-20
Mark Abrah
a
m
M
e
rge branch release-2016
commit
|
commitdiff
|
tree
2017-10-20
Ber
k
Hess
F
ix warni
n
g for confout wit
h
periodic molecules
commit
|
commitdiff
|
tree
2017-10-16
M
a
r
k Abraham
Me
r
ge branc
h
release-2016
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
Improve
v
s
ite p
a
rallel checkin
g
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iupino
v
Relax PME spline com
p
u
t
ation tolerance in
d
o
uble precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
M
ark Ab
r
aham
Update te
s
ts
for C++11
c
ompiler
and standar
d
library
commit
|
commitdiff
|
tree
2017-10-13
Rol
a
nd
Schulz
Specialize
A
rrayRef f
o
r Si
m
dReal
commit
|
commitdiff
|
tree
2017-10-11
Mark
A
bra
h
a
m
I
n
t
roduced
header for communication to/from PME rank
s
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iup
i
nov
Fix clang wa
r
nings for PME C
U
DA kern
e
l
s
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iu
p
inov
Relax PME solving test co
m
plex grid tolerance
commit
|
commitdiff
|
tree
2017-10-11
Ma
r
k Abra
h
am
Cleaned up
e
waldcoeff for
P
ME
-
o
nly ranks
commit
|
commitdiff
|
tree
2017-10-11
A
l
e
ksei Iu
p
inov
P
M
E
solving - C
U
DA kernel + unit tests
commit
|
commitdiff
|
tree
2017-10-11
Paul
B
auer
C
h
ange to mod
u
les
f
or build of web docum
e
ntation
commit
|
commitdiff
|
tree
2017-10-11
A
l
e
k
s
ei I
u
pinov
PME force gathering
-
CUDA kernel +
u
n
it te
s
ts
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupin
o
v
PME spline+spread CUDA kernel and unit tests
commit
|
commitdiff
|
tree
2017-10-11
M
ark Abraham
Use cla
n
g-5 in Je
n
kins
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disable AR
M
Neon native
rsqrt iteration
commit
|
commitdiff
|
tree
2017-10-09
Aleksei Iupinov
P
M
E GPU/CU
D
A data framework
.
commit
|
commitdiff
|
tree
2017-10-07
Mark Abraham
Tell c
p
pcheck tha
t
.
c
p
p and
.
cu files are c
+
+
commit
|
commitdiff
|
tree
2017-10-07
Roland Sc
h
ulz
Refactor load+Sim
d
Lo
a
d*ProxyInterna
l
t
o
reduce duplicati
o
n
commit
|
commitdiff
|
tree
2017-10-06
Be
r
k H
e
s
s
A
dd
S
IMD intrins
i
cs
v
e
rsion
o
f si
m
p
l
e up
d
ate
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Impr
o
ve PaddedRVecVector resi
z
ing
commit
|
commitdiff
|
tree
2017-10-06
Aleksei Iup
i
nov
Add timing accumulation capabili
t
y into GpuRegi
o
n
T
imer
commit
|
commitdiff
|
tree
2017-10-05
B
erk Hess
M
a
ke
S
I
M
D
ambiguous test wo
r
k with floa
t
/
d
ouble
o
n
l
y
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Pál
l
Fix pair list array assertion
commit
|
commitdiff
|
tree
2017-10-05
Szilár
d
P
á
ll
Av
o
id -
W
mi
s
sing-pr
o
totype
s
war
n
ings in cl
a
ng
C
UD
A
builds
commit
|
commitdiff
|
tree
2017-10-05
Roland Sc
h
ulz
Fix that exp(load(x)
)
is ambiguous
commit
|
commitdiff
|
tree
2017-10-04
Mark Abraham
Enab
l
e gr
o
up-scheme SIMD wi
t
h GMX_
S
IMD=AVX2
_
128
commit
|
commitdiff
|
tree
2017-10-04
Aleksei
Iupinov
Add GpuR
e
gionTimer cla
s
s
commit
|
commitdiff
|
tree
2017-10-03
M
a
rk Abra
h
a
m
Introduce and
us
e
Al
i
g
nedAllo
c
a
tio
n
Policy
commit
|
commitdiff
|
tree
2017-10-02
B
e
rk He
s
s
Remo
v
e hybrid gpu+cpu nonbonded
m
o
de
commit
|
commitdiff
|
tree
2017-09-26
Aleksei
I
u
pinov
Move C
U
DA tex
t
ure s
e
tup code from NB C
U
DA
module to
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
M
a
rk Abraham
Merge br
a
nc
h
release-
2
016
commit
|
commitdiff
|
tree
2017-09-15
Berk Hess
Remove
nb-
p
arameters fr
o
m
t_forc
e
rec
commit
|
commitdiff
|
tree
2017-09-15
Mark
A
br
a
ham
Ex
p
ress i
n
tent of matrix rel
e
ase b
u
ild typ
e
s expli
c
itly
commit
|
commitdiff
|
tree
2017-09-15
M
a
rk Abraham
Bu
m
ped patch version for
next
r
e
l
e
a
se
commit
|
commitdiff
|
tree
2017-09-15
Ma
r
k Abraham
Vers
i
on 2016
.
4
commit
|
commitdiff
|
tree
2017-09-14
Al
e
ks
e
i
Iupinov
F
ix no
n
-S
I
MD b
u
i
l
d fa
i
l
i
ng
commit
|
commitdiff
|
tree
2017-09-14
Szilárd Páll
CUDA 9
/
Volt
a
support for the
pru
n
ing kernel
commit
|
commitdiff
|
tree
2017-09-14
Mark
A
brah
a
m
Form taskassignment module
commit
|
commitdiff
|
tree
2017-09-14
Mark Ab
r
ah
a
m
Fix c
o
mpat module definition
commit
|
commitdiff
|
tree
2017-09-12
Erik
Lindahl
Impr
o
ve
accuracy of S
I
MD exp for smal
l
args
commit
|
commitdiff
|
tree
2017-09-12
Mar
k
A
b
r
a
ham
Merge
b
r
a
nc
h
rele
a
s
e
-2016
commit
|
commitdiff
|
tree
2017-09-12
Be
r
k Hess
D
o no
t
pa
s
s stat
e
to in
i
t_replica_ex
c
hange
commit
|
commitdiff
|
tree
2017-09-11
Szilárd Páll
NVIDIA V
o
lta pe
r
forman
c
e
t
w
eaks
commit
|
commitdiff
|
tree
2017-09-11
Berk Hess
F
i
x PBC bugs in the swa
p
code
commit
|
commitdiff
|
tree
2017-09-07
Mark Abraham
Intro
d
uce typ
e
-
s
afe
G
PU
e
mulation variables
commit
|
commitdiff
|
tree
2017-09-07
Roland Schulz
Add isIntegralConsta
n
t type
tr
a
it
commit
|
commitdiff
|
tree
2017-09-07
Mark Abraham
Enable group-scheme
SIMD
kerne
l
s
on
r
e
c
ent
A
V
X extensions
commit
|
commitdiff
|
tree
2017-09-06
Roland Schulz
PME-
g
ather: U
s
e t
e
mpla
t
ed func
t
or in
s
tead of preprocessor
commit
|
commitdiff
|
tree
2017-09-05
Chri
s
toph Junghans
Suppor
t
ed quiet tr
a
jectory-handling I/O
commit
|
commitdiff
|
tree
2017-09-05
Mark Abraha
m
Fixes for Solaris
commit
|
commitdiff
|
tree
2017-09-05
Mark Abraham
Fix
u
se of
G
PU
i
nf
o
r
m
ation for thr
e
ad-MPI setup
commit
|
commitdiff
|
tree
2017-09-04
Be
r
k Hess
F
ix two n
b
nxn search index
i
n
g bugs
commit
|
commitdiff
|
tree
2017-09-04
R
o
land
S
ch
u
lz
Fix a
c
curacy
f
or cvtDoubl
e
2Flo
a
t/
c
pro
d
commit
|
commitdiff
|
tree
next