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Support pinning in HostAllocator
2017-11-21
Mark Abraham
S
uppo
r
t
pinning
in Ho
s
tAllocator
commit
|
commitdiff
|
tree
2017-11-21
V
iveca L
i
n
d
ahl
Add
force
c
orrela
t
ion to AW
H
mo
d
u
l
e
commit
|
commitdiff
|
tree
2017-11-21
Paul Bauer
Fir
s
t
g
eneral
a
dditions to the d
o
cumentatio
n
commit
|
commitdiff
|
tree
2017-11-19
Vive
c
a
Lindahl
Ad
d
AWH section
to man
u
al
.
commit
|
commitdiff
|
tree
2017-11-19
Viv
e
ca Lind
a
hl
Add
AW
H
biasing modu
l
e
+ tests
commit
|
commitdiff
|
tree
2017-11-17
Mark Abra
h
a
m
Us
e
HostAllocationPolicy for chargeA
commit
|
commitdiff
|
tree
2017-11-17
Ma
r
k Abr
a
ham
Add chec
k
i
ng function for whether
a buffer is p
i
n
ned
commit
|
commitdiff
|
tree
2017-11-17
Mark A
b
raham
Improv
e
h
andling of PME GPU force b
u
ffer
commit
|
commitdiff
|
tree
2017-11-15
A
l
eksei Iupinov
Rename a
n
d expose "generic
"
GP
U
memory tra
n
s
fer functions
commit
|
commitdiff
|
tree
2017-11-10
Mark
A
b
r
aham
Import
c
m
ake Mo
d
ules/FindCUDA
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
Aleksei
Iup
i
nov
Rename synchronous
G
PU tra
n
sfer f
u
nctio
n
s to
m
atch
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Mark Abraham
Prepared t_mdatoms for
using vector
commit
|
commitdiff
|
tree
2017-11-09
Mark
A
braham
In
t
r
o
duce Hos
t
All
o
cationPolicy
commit
|
commitdiff
|
tree
2017-11-09
Rola
n
d Schu
l
z
IC
C
should use ZMM if cod
e
anyhow
u
s
es ZMM
commit
|
commitdiff
|
tree
2017-11-07
M
a
rk
Abraham
Refo
r
m
gmx_pme_pp allo
c
and use ve
c
tor
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Introduce gmxope
n
cl
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abr
a
ham
Test clan
g
on ARM in nightly matrix
commit
|
commitdiff
|
tree
2017-11-07
S
z
i
lárd Páll
A
d
d wal
l
cycle timer f
o
r
the PME GPU F
r
ed
u
ct
i
on
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Split off nbnxn GPU ti
m
ing a
n
d
s
taging reduction
commit
|
commitdiff
|
tree
2017-11-07
Mark
A
braham
I
m
pro
v
e PME includes
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Dedu
p
licat
e
C
UDA and OpenCL t
i
m
er struct
commit
|
commitdiff
|
tree
2017-11-06
David van der Spoel
Fixed chec
k
for water in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
Mar
k
Abraham
Me
r
ge
"
Mer
g
e bran
c
h release-2016"
commit
|
commitdiff
|
tree
2017-11-02
David van d
e
r Spo
e
l
New
m
dp
i
nput fo
r
elec
t
r
ic fields
.
commit
|
commitdiff
|
tree
2017-11-02
A
l
ekse
i
Iupinov
Rep
l
ace m
a
th
.
h by cmat
h
incl
u
des in cpp files
commit
|
commitdiff
|
tree
2017-11-02
Mark Abraham
Merge br
a
nch release-2016
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
Small change t
o
LaT
e
X
m
a
nua
l
generatio
n
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Fix
t
hread-MPI ran
k
choic
e
fo
r
orientati
o
n restraints
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Remove
unused PME GPU d
e
cla
r
a
t
ions
commit
|
commitdiff
|
tree
2017-11-01
Ale
k
sei
I
upinov
Move pme
_
gpu_finish_computat
i
on() do
c
u
m
entatio
n
to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
Fixing missing refere
n
ces in web documentation
commit
|
commitdiff
|
tree
2017-11-01
A
l
e
ksei Iupinov
Fix erroneou
s
PME GPU "step"
namings
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Improve
h
andling of GPU IDs
commit
|
commitdiff
|
tree
2017-11-01
Aleksei
I
upino
v
Simpli
f
y
PM
E
G
P
U
s
y
nchroniz
a
tion code
commit
|
commitdiff
|
tree
2017-10-31
A
l
e
ksei I
u
pinov
Reuse ep
b
cXY
l
ogic
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Fix nstlist incr
e
ase
war
n
ing
pri
n
t
commit
|
commitdiff
|
tree
2017-10-31
S
zilárd Páll
Check CUDA availabl
e
/compiled code
c
o
mpatibility
commit
|
commitdiff
|
tree
2017-10-30
Ale
k
s
e
i I
u
pinov
Fix r
e
ferenc
e
mode buil
d
unused fun
c
t
i
on warn
i
ngs
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remove
unused sign parameter from
di
h
_angle()
commit
|
commitdiff
|
tree
2017-10-30
Roland Sc
h
u
lz
A
r
ray
R
ef: R
e
p
l
ac
e
f
r
omVector
w
it
h
subArray
commit
|
commitdiff
|
tree
2017-10-30
David
v
an der Spoel
Added option -water tips3p t
o
pdb2
g
m
x
.
commit
|
commitdiff
|
tree
2017-10-30
A
l
eksei Iupinov
Bring PM
E
GPU/CUDA
i
nternal structure
n
a
m
es t
o
CamelCase
commit
|
commitdiff
|
tree
2017-10-27
Mark
A
b
r
a
ha
m
Fix hw
d
e
t
ection
m
ore
commit
|
commitdiff
|
tree
2017-10-26
Mark
Abraham
New quote
commit
|
commitdiff
|
tree
2017-10-20
Mark Abr
a
ha
m
Clar
i
fy docs
for Fma
x
in EM
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
Merge branch release-2016
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix war
n
ing f
o
r confout with p
e
riodic molecules
commit
|
commitdiff
|
tree
2017-10-16
Mar
k
Abraham
Merge branch r
e
lease-2016
commit
|
commitdiff
|
tree
2017-10-15
B
erk Hess
Im
p
ro
v
e vsite pa
r
all
e
l
checking
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iup
i
nov
Relax
P
M
E sp
l
ine computa
t
io
n
tolerance
i
n
double precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Mark Abra
h
a
m
Update tests
for C++11 compiler and st
a
ndard l
i
brary
commit
|
commitdiff
|
tree
2017-10-13
Roland Sch
u
lz
S
p
ec
i
alize ArrayRef
for SimdRe
a
l
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
In
t
roduce
d
h
ea
d
er for communication to/from
P
ME
ranks
commit
|
commitdiff
|
tree
2017-10-11
A
leksei Iupi
n
ov
Fi
x
c
l
ang wa
r
nings for PME CUDA
k
e
r
nels
commit
|
commitdiff
|
tree
2017-10-11
Al
e
ksei
Iupinov
Relax PME solving te
s
t c
o
mplex grid tolerance
commit
|
commitdiff
|
tree
2017-10-11
Mar
k
Abraham
Cleaned up ewaldcoeff for
P
ME-only ranks
commit
|
commitdiff
|
tree
2017-10-11
A
le
k
sei Iupinov
PME solving - CUDA
kernel +
unit test
s
commit
|
commitdiff
|
tree
2017-10-11
Paul B
a
uer
Change to modules for
b
u
ild of web documentati
o
n
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iup
i
n
o
v
PM
E
force gathering -
CUDA kernel + unit tests
commit
|
commitdiff
|
tree
2017-10-11
Aleks
e
i Iupinov
P
M
E spline+s
p
read CUDA ker
n
el and unit t
e
s
t
s
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Use clang-5 in Jenk
i
ns
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disable
ARM Neon
na
t
ive
r
sqrt ite
r
ation
commit
|
commitdiff
|
tree
2017-10-09
Aleksei Iupinov
PME G
P
U/CUDA data f
r
amework
.
commit
|
commitdiff
|
tree
2017-10-07
Mark Ab
r
aham
T
ell cpp
c
heck t
h
at
.
c
p
p
and
.
cu files are c++
commit
|
commitdiff
|
tree
2017-10-07
Roland Schulz
R
e
factor load+SimdL
o
ad*ProxyInternal to
redu
c
e duplicat
i
on
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Add SIMD in
t
ri
n
sic
s
v
er
s
ion of simpl
e
upda
t
e
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
I
mpr
o
v
e
Padded
R
V
e
cVec
t
or
resizi
n
g
commit
|
commitdiff
|
tree
2017-10-06
Alekse
i
I
u
pinov
Add tim
i
ng acc
u
mulation capability
i
nto GpuRe
g
ionT
i
mer
commit
|
commitdiff
|
tree
2017-10-05
Berk
Hess
Make SIM
D
a
m
biguous t
e
st wor
k
wit
h
float/
d
oubl
e
only
commit
|
commitdiff
|
tree
2017-10-05
Szilá
r
d Páll
Fix pair list
a
rray assertion
commit
|
commitdiff
|
tree
2017-10-05
Sz
i
l
árd Pá
l
l
Avo
i
d
-Wmissing-prototypes warnings in clan
g
CU
D
A
builds
commit
|
commitdiff
|
tree
2017-10-05
Roland Schulz
Fix that ex
p
(l
o
a
d
(x
)
) is ambiguous
commit
|
commitdiff
|
tree
2017-10-04
M
ark A
b
raham
Ena
b
le group-schem
e
SI
M
D with
GMX_SIMD=AVX
2
_128
commit
|
commitdiff
|
tree
2017-10-04
Aleksei I
u
p
i
nov
Add GpuR
e
gionTimer class
commit
|
commitdiff
|
tree
2017-10-03
Mark Abraham
Introduce and use Al
i
gne
d
A
l
locati
o
nPolicy
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
R
emove hybrid gpu+
c
pu nonbon
d
e
d mode
commit
|
commitdiff
|
tree
2017-09-26
Aleksei Iupinov
Mov
e
CUDA texture s
e
tup co
d
e fr
o
m NB CUD
A
m
odule to
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
M
a
r
k
Abr
a
ha
m
Merge branch relea
s
e-2016
commit
|
commitdiff
|
tree
2017-09-15
Berk Hes
s
Remove nb-pa
r
a
m
e
ters from t_
f
orcerec
commit
|
commitdiff
|
tree
2017-09-15
Mark
Abraham
Express intent of matrix release
b
uild types
e
xpli
c
itl
y
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
Bum
p
ed patch version fo
r
next release
commit
|
commitdiff
|
tree
2017-09-15
Mark Abrah
a
m
Version 2016
.
4
commit
|
commitdiff
|
tree
2017-09-14
Aleksei Iupinov
Fix non-SIMD
b
ui
l
d
failing
commit
|
commitdiff
|
tree
2017-09-14
Szi
l
á
rd Páll
CU
D
A
9/
V
olta support for the
p
run
i
ng
k
ernel
commit
|
commitdiff
|
tree
2017-09-14
Mark Abraham
Form tas
k
a
ssig
n
me
n
t module
commit
|
commitdiff
|
tree
2017-09-14
M
a
rk Abraha
m
Fix compat module definiti
o
n
commit
|
commitdiff
|
tree
2017-09-12
Erik L
i
ndahl
Improve ac
c
uracy
o
f SIMD exp for small
args
commit
|
commitdiff
|
tree
2017-09-12
Mark Abraha
m
Merge branch re
l
ease-2016
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Do not pass
stat
e
to init_replic
a
_exchang
e
commit
|
commitdiff
|
tree
2017-09-11
S
z
ilá
r
d
P
á
ll
NVI
D
IA Vol
t
a performa
n
ce tweaks
commit
|
commitdiff
|
tree
2017-09-11
Berk Hess
F
i
x PBC bugs
in th
e
s
wap
c
ode
commit
|
commitdiff
|
tree
2017-09-07
Mark Abraham
Introduce type-safe
G
PU emulat
i
on
variab
l
e
s
commit
|
commitdiff
|
tree
2017-09-07
Roland
S
c
hulz
Add isIntegralConstant type tr
a
it
commit
|
commitdiff
|
tree
2017-09-07
Mark
Abraham
Enable gro
u
p-scheme SIMD ke
r
nels
o
n recent
A
V
X extensions
commit
|
commitdiff
|
tree
2017-09-06
Roland Schulz
PME-
g
ather: Use tem
p
lated functor instead of prepro
c
essor
commit
|
commitdiff
|
tree
2017-09-05
Christ
o
ph J
u
nghans
Suppo
r
ted
quiet traj
e
ctory-handl
i
ng I/O
commit
|
commitdiff
|
tree
2017-09-05
Mark Abraham
F
ixes for Solaris
commit
|
commitdiff
|
tree
2017-09-05
Ma
r
k
A
b
r
aham
Fix use of GPU information for
thread-MPI setup
commit
|
commitdiff
|
tree
2017-09-04
Ber
k
Hess
F
i
x
two
nbnxn search indexing b
u
gs
commit
|
commitdiff
|
tree
2017-09-04
Rolan
d
Schulz
Fi
x
accuracy for cvtDouble
2
F
loat/cprod
commit
|
commitdiff
|
tree
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