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Activate PME on GPUs
2017-11-24
Mark Abraham
Activate
P
ME on GPU
s
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Remove
o
utd
a
ted (alr
e
ady implemented) pinning TODO
commit
|
commitdiff
|
tree
2017-11-24
M
a
rk Abraham
Ad
d
PME in
t
egrati
o
n t
e
s
t
commit
|
commitdiff
|
tree
2017-11-24
M
a
rk Abraham
E
x
tend
task assignment cod
e
commit
|
commitdiff
|
tree
2017-11-24
A
leksei Iupino
v
Mention gmx_install_headers() in t
h
e
d
e
ve
l
oper
manual
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
e
i
Iup
i
nov
Ma
k
e FFT real-space grid use CU
D
A pinning
f
or
m
ixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iupinov
Pin co
o
rd
i
nates, forces and
c
harges for PME on
GPU
commit
|
commitdiff
|
tree
2017-11-22
Pascal Merz
Proof of
concept: Phy
s
ical validation suite
commit
|
commitdiff
|
tree
2017-11-21
E
r
ik
L
indahl
S
e
parate SIMD flag detection
f
rom m
a
nagement
commit
|
commitdiff
|
tree
2017-11-21
Mark Abr
a
ham
S
u
pport pinni
n
g in HostA
l
locat
o
r
commit
|
commitdiff
|
tree
2017-11-21
V
iveca L
i
ndahl
Add force c
o
r
r
elation to AWH m
o
du
l
e
commit
|
commitdiff
|
tree
2017-11-21
Paul Bauer
Fi
r
s
t general additio
n
s t
o
t
he
documentation
commit
|
commitdiff
|
tree
2017-11-19
Viveca Lindahl
Add AWH sect
i
o
n to manual
.
commit
|
commitdiff
|
tree
2017-11-19
Viveca Lindahl
Add
AWH b
i
asing
m
odule
+ tests
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
Us
e
H
o
stAllocat
i
onPolic
y
f
or chargeA
commit
|
commitdiff
|
tree
2017-11-17
Ma
r
k Abraha
m
Add checking function
f
or whether a buffer is pinned
commit
|
commitdiff
|
tree
2017-11-17
M
ark Abraham
Improve
handling
of
P
ME GPU for
c
e bu
f
fer
commit
|
commitdiff
|
tree
2017-11-15
Al
e
ksei Iupi
n
ov
R
e
name and
e
xpose "generic
"
GPU memory trans
f
er fu
n
ctions
commit
|
commitdiff
|
tree
2017-11-10
Mark Abraham
Impo
r
t cmake Mod
u
les/FindCUDA
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
A
leksei Iupinov
Re
n
ame synch
r
onou
s
GPU tra
n
sfe
r
f
unc
t
ions
t
o m
a
tc
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Mark Ab
r
a
h
am
P
repared t_mda
t
o
m
s fo
r
usi
n
g vector
commit
|
commitdiff
|
tree
2017-11-09
Mark Abraham
Int
r
oduc
e
Host
A
llocationP
o
licy
commit
|
commitdiff
|
tree
2017-11-09
Roland Sc
h
ulz
ICC s
h
ould use
ZMM if code
a
nyho
w
uses Z
M
M
commit
|
commitdiff
|
tree
2017-11-07
Mark Abrah
a
m
Re
f
or
m
gmx_pme_pp al
l
oc and u
s
e
vector
commit
|
commitdiff
|
tree
2017-11-07
M
a
rk Ab
r
aha
m
Introdu
c
e
g
m
xopencl
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Test clang on ARM
i
n nig
h
tly matrix
commit
|
commitdiff
|
tree
2017-11-07
S
z
ilárd Páll
Ad
d
wallcycle timer for the
PME
G
PU F
r
eduction
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Split of
f
n
b
nxn
G
PU timing and stagin
g
reducti
o
n
commit
|
commitdiff
|
tree
2017-11-07
M
a
rk Ab
r
aham
Improve PM
E
includes
commit
|
commitdiff
|
tree
2017-11-07
S
zilárd P
á
l
l
Deduplic
a
t
e CUDA and OpenCL
t
i
me
r
struct
commit
|
commitdiff
|
tree
2017-11-06
David
v
an
de
r
Spoel
F
i
x
ed
check for water in
g
en_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
M
ark Abra
h
am
Merge
"Merge branch release-2016"
commit
|
commitdiff
|
tree
2017-11-02
D
a
vid van der Spoel
N
e
w
mdp
input for electric
fields
.
commit
|
commitdiff
|
tree
2017-11-02
Aleks
e
i Iu
p
i
n
ov
Repla
c
e m
a
th
.
h by cm
a
th includes in cpp files
commit
|
commitdiff
|
tree
2017-11-02
Mark Ab
r
aham
Merge branch release-
2
01
6
commit
|
commitdiff
|
tree
2017-11-01
P
a
ul
B
a
u
e
r
Small change to LaTeX
m
anu
a
l generation
commit
|
commitdiff
|
tree
2017-11-01
Ma
r
k
Abraham
Fix threa
d
-MPI rank choice for or
i
e
nt
a
t
i
on restraints
commit
|
commitdiff
|
tree
2017-11-01
Alek
s
ei Iupinov
Remove unu
s
ed PME
G
PU declarations
commit
|
commitdiff
|
tree
2017-11-01
Aleksei I
u
pi
n
o
v
Mov
e
pme_gpu_
f
inis
h
_
c
ompu
t
ati
o
n() d
o
cumentatio
n
to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
Fixing missing
r
efer
e
nces in web documentation
commit
|
commitdiff
|
tree
2017-11-01
Al
e
ksei
Iup
i
no
v
F
i
x er
r
oneou
s
PME GPU "step" namings
commit
|
commitdiff
|
tree
2017-11-01
M
ark Abr
a
ham
Improve han
d
l
i
n
g
o
f
GP
U
IDs
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupin
o
v
S
i
m
plify PME
GPU synchronizatio
n
code
commit
|
commitdiff
|
tree
2017-10-31
A
leksei I
u
pinov
Reuse epbcXY logic
commit
|
commitdiff
|
tree
2017-10-31
S
z
ilárd Pál
l
Fix n
s
tlist
i
ncrease
w
arning print
commit
|
commitdiff
|
tree
2017-10-31
Szilár
d
Pál
l
Check CU
D
A available/com
p
il
e
d cod
e
compatib
i
l
i
ty
commit
|
commitdiff
|
tree
2017-10-30
A
l
eksei Iupinov
Fix reference mode bui
l
d
unused
func
t
io
n
warnin
g
s
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remo
v
e
unused
s
ign parameter from d
i
h_angle()
commit
|
commitdiff
|
tree
2017-10-30
R
o
land Schulz
Arra
y
Ref: Replace fr
o
mVect
o
r with subAr
r
ay
commit
|
commitdiff
|
tree
2017-10-30
David van de
r
Spoel
Adde
d
option -wate
r
tips3p t
o
pdb
2
gmx
.
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Bring PME GPU/CU
D
A internal structure names to CamelCase
commit
|
commitdiff
|
tree
2017-10-27
Mar
k
Abraham
F
i
x hw detection more
commit
|
commitdiff
|
tree
2017-10-26
Mark Abraham
Ne
w
q
u
ote
commit
|
commitdiff
|
tree
2017-10-20
Mark Ab
r
aham
Clarify docs for
Fma
x
in EM
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
Merge branch
r
e
l
ease-
2
0
1
6
commit
|
commitdiff
|
tree
2017-10-20
B
e
rk Hess
Fi
x
warning for
c
o
n
fout
w
it
h
peri
o
di
c
mol
e
cules
commit
|
commitdiff
|
tree
2017-10-16
M
a
rk Abr
a
ha
m
Merge
b
r
anch
r
elease-
2
016
commit
|
commitdiff
|
tree
2017-10-15
Berk He
s
s
Impr
o
ve vs
i
te paralle
l
checking
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iupinov
Relax PME spline c
o
mp
u
tation t
o
ler
a
nce in double precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Ma
r
k Abraham
Update te
s
ts for C++11
c
ompiler and
standa
r
d library
commit
|
commitdiff
|
tree
2017-10-13
Rol
a
nd Sc
h
ulz
Specialize
ArrayRef for S
i
md
R
eal
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Introduced header for
c
o
m
munication to/from PME ra
n
ks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupin
o
v
Fix clang warnings for PM
E
CUDA
k
e
rnels
commit
|
commitdiff
|
tree
2017-10-11
A
leks
e
i
I
up
i
nov
R
elax PME solving test complex grid
tol
e
r
ance
commit
|
commitdiff
|
tree
2017-10-11
Mark Abra
h
am
Cleaned
u
p
ewal
d
coeff
f
o
r
P
ME-only r
a
nk
s
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
PME
solving
- C
U
DA ker
n
el +
unit
t
ests
commit
|
commitdiff
|
tree
2017-10-11
Paul Bauer
Change t
o
mo
d
ules f
o
r build of web doc
u
mentation
commit
|
commitdiff
|
tree
2017-10-11
A
l
eksei Iupinov
PME
f
o
rce gatheri
n
g
- CUDA ker
n
e
l + u
n
it tests
commit
|
commitdiff
|
tree
2017-10-11
Al
e
ksei I
u
pinov
PME spline+
s
pread
C
UDA k
e
rnel and unit tests
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
U
se clang-5
in
Jenkins
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disabl
e
ARM Neon
n
ativ
e
r
s
qrt
i
t
e
ration
commit
|
commitdiff
|
tree
2017-10-09
Aleksei Iupi
n
ov
P
M
E
G
PU/CUDA dat
a
fr
a
mew
o
rk
.
commit
|
commitdiff
|
tree
2017-10-07
Mark Abraham
T
e
ll
cpp
c
heck
that
.
cpp
and
.
cu
f
ile
s
are c++
commit
|
commitdiff
|
tree
2017-10-07
Rol
a
n
d
S
c
hulz
Re
f
actor load+Si
m
dLoad*P
r
o
x
yInternal to reduc
e
d
uplication
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Add SIMD int
r
insics version of simpl
e
updat
e
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Improv
e
PaddedRVecVector resizing
commit
|
commitdiff
|
tree
2017-10-06
Aleksei
Iupi
n
ov
Add timing accu
m
ulatio
n
c
a
pability into GpuRegionTimer
commit
|
commitdiff
|
tree
2017-10-05
Be
r
k
H
ess
M
a
k
e
SIMD
ambiguous
t
est wor
k
wit
h
floa
t
/double only
commit
|
commitdiff
|
tree
2017-10-05
Szi
l
árd Pál
l
Fix pair list
ar
r
ay as
s
er
t
io
n
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Páll
Avoid -Wm
i
ssi
n
g-prototypes war
n
i
ngs in c
l
ang CUD
A
build
s
commit
|
commitdiff
|
tree
2017-10-05
Roland Sc
h
ulz
Fix t
h
at exp(l
o
a
d(x)
)
is
a
m
biguous
commit
|
commitdiff
|
tree
2017-10-04
Ma
r
k Abraham
E
n
able gro
u
p-scheme
S
I
MD with GMX_S
I
M
D=AVX2_128
commit
|
commitdiff
|
tree
2017-10-04
Aleksei Iupinov
A
dd GpuR
e
g
i
onTimer clas
s
commit
|
commitdiff
|
tree
2017-10-03
Mark Abraha
m
I
n
t
roduce and use AlignedAllocationPolicy
commit
|
commitdiff
|
tree
2017-10-02
Berk Hes
s
Remove hybrid gpu+cpu nonbonded mode
commit
|
commitdiff
|
tree
2017-09-26
Aleksei
I
upi
n
o
v
Move CUDA texture s
e
tup code from NB CUD
A
module to
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
Mark Abraham
Merge branch release-2016
commit
|
commitdiff
|
tree
2017-09-15
Berk
Hess
Remove n
b
-parameters from
t
_f
o
rc
e
r
ec
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
Exp
r
e
ss int
e
nt
o
f mat
r
ix release bui
l
d
typ
e
s explic
i
tly
commit
|
commitdiff
|
tree
2017-09-15
M
a
r
k
Abraham
Bumped patch version for next release
commit
|
commitdiff
|
tree
2017-09-15
Ma
r
k Abraham
Version 201
6
.
4
commit
|
commitdiff
|
tree
2017-09-14
Al
e
ksei
I
up
i
nov
Fix
non-SIMD build
f
a
il
i
ng
commit
|
commitdiff
|
tree
2017-09-14
Szilárd Pá
l
l
CUDA 9
/
Volta suppo
r
t for
the
pruning kernel
commit
|
commitdiff
|
tree
2017-09-14
M
a
r
k
Abraha
m
For
m
t
askassi
g
nment module
commit
|
commitdiff
|
tree
2017-09-14
M
ark
Abraham
Fix compat module definition
commit
|
commitdiff
|
tree
2017-09-12
Erik Lindahl
Improve acc
u
racy
o
f
SIMD
exp
for small arg
s
commit
|
commitdiff
|
tree
2017-09-12
Mark Ab
r
a
h
am
Merge branch
r
e
le
a
se
-
2016
commit
|
commitdiff
|
tree
2017-09-12
B
erk He
s
s
Do not
p
ass s
t
ate
to
i
nit_
r
eplica_excha
n
g
e
commit
|
commitdiff
|
tree
2017-09-11
Szil
á
rd Páll
NV
I
DIA Vol
t
a performance tweaks
commit
|
commitdiff
|
tree
2017-09-11
Berk Hess
Fix PBC bugs in the swap co
d
e
commit
|
commitdiff
|
tree
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