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Activate PME on GPUs
2017-11-24
Ma
r
k
A
braham
Activ
a
te PME on G
P
Us
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Remove ou
t
da
t
ed (already implemented) pinning TODO
commit
|
commitdiff
|
tree
2017-11-24
M
a
r
k
Abraham
Add
PME integration test
commit
|
commitdiff
|
tree
2017-11-24
M
ark Abrah
a
m
Ext
e
nd task ass
i
gnment
c
ode
commit
|
commitdiff
|
tree
2017-11-24
A
l
e
k
sei Iupinov
M
e
n
tion gmx_instal
l
_headers()
i
n
the d
e
ve
l
oper
m
anual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupino
v
M
ake FF
T
r
eal-space grid use CUDA pi
n
ning for
m
i
xed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Pin coordin
a
te
s
, forces and charges for PME on GP
U
commit
|
commitdiff
|
tree
2017-11-22
Pascal Merz
Proof
o
f conc
e
pt: Phys
i
c
a
l validation su
i
t
e
commit
|
commitdiff
|
tree
2017-11-21
Erik Lindahl
Sep
a
rate SIMD flag dete
c
t
i
o
n
from m
a
nagemen
t
commit
|
commitdiff
|
tree
2017-11-21
Mark Abraham
Support pinning in HostAllocator
commit
|
commitdiff
|
tree
2017-11-21
Viveca Linda
h
l
A
dd fo
r
ce correlation t
o
AWH modul
e
commit
|
commitdiff
|
tree
2017-11-21
Paul
B
a
uer
First general additions to
t
he documentation
commit
|
commitdiff
|
tree
2017-11-19
Viveca Lindahl
Add
AWH s
e
ctio
n
to manual
.
commit
|
commitdiff
|
tree
2017-11-19
V
i
v
e
ca Lindahl
Add AWH biasing module + tests
commit
|
commitdiff
|
tree
2017-11-17
Mark Abrah
a
m
Use HostAllocationPolicy for
c
hargeA
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
Add checking func
t
ion f
o
r w
h
ether a buffer is
pinned
commit
|
commitdiff
|
tree
2017-11-17
Mar
k
Abraham
Improve handli
n
g of PME GPU f
o
rce buffer
commit
|
commitdiff
|
tree
2017-11-15
Al
e
ksei Iupinov
Ren
a
me and
e
x
p
os
e
"gene
r
ic" GPU memory transfer f
u
n
c
t
ions
commit
|
commitdiff
|
tree
2017-11-10
Mar
k
Abraham
Import cmake Modules
/
F
i
n
d
C
UDA
.
c
m
ake
commit
|
commitdiff
|
tree
2017-11-09
Alek
s
ei Iupin
o
v
Rename syn
c
hronous G
P
U trans
f
er functions to match
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Mar
k
Abra
h
am
Prepared t
_
mdatoms for u
s
ing vector
commit
|
commitdiff
|
tree
2017-11-09
M
ark
A
braham
I
n
tro
d
uce HostAllocationP
o
l
i
cy
commit
|
commitdiff
|
tree
2017-11-09
Roland Sch
u
lz
ICC should use
ZMM if code any
h
ow uses ZMM
commit
|
commitdiff
|
tree
2017-11-07
Ma
r
k Abraham
Refor
m
gmx_pme_pp a
l
loc and use v
e
ctor
commit
|
commitdiff
|
tree
2017-11-07
Mark Ab
r
aham
Intr
o
duce gmxopencl
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
T
e
st
cla
n
g on
A
RM in nightly matrix
commit
|
commitdiff
|
tree
2017-11-07
S
z
ilárd Páll
Add wa
l
l
c
ycle
timer for the PM
E
GPU F
r
e
d
ucti
o
n
commit
|
commitdiff
|
tree
2017-11-07
Szilárd
Páll
Split of
f
nbnxn
GPU
timing and s
t
aging reduct
i
on
commit
|
commitdiff
|
tree
2017-11-07
Mar
k
Abraham
Improv
e
PME includes
commit
|
commitdiff
|
tree
2017-11-07
Szilárd
Pál
l
Ded
u
plic
a
te
C
UDA
and OpenCL timer struct
commit
|
commitdiff
|
tree
2017-11-06
David va
n
der Spoe
l
Fixed c
h
eck fo
r
wa
t
er
i
n gen
_
vsite
.
cp
p
commit
|
commitdiff
|
tree
2017-11-03
Mark Abraham
Me
r
ge "Merge br
a
nch r
e
lea
s
e-2016"
commit
|
commitdiff
|
tree
2017-11-02
D
a
v
i
d van der Spoel
New
mdp in
p
ut for electr
i
c
f
i
e
l
d
s
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei
Iupinov
Replace
m
a
th
.
h by
cmath inc
l
udes in cpp files
commit
|
commitdiff
|
tree
2017-11-02
Mark Abraham
Merge bran
c
h release-2016
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
S
m
a
l
l
ch
a
nge to LaT
e
X manual generation
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraha
m
Fix th
r
ead-MPI rank c
h
oic
e
for or
i
e
n
tati
o
n
r
est
r
a
i
n
t
s
commit
|
commitdiff
|
tree
2017-11-01
A
l
eksei I
u
p
i
n
o
v
Remove unused
P
ME GPU dec
l
a
rations
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Move
pme_gpu_finish
_
compu
t
ati
o
n() documentati
o
n to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
F
ixing
missing r
e
f
e
rences
i
n web
documentation
commit
|
commitdiff
|
tree
2017-11-01
A
leksei Iupinov
Fix
e
r
roneous P
M
E GP
U
"step
"
namings
commit
|
commitdiff
|
tree
2017-11-01
Mark Abr
a
ham
Impr
o
v
e handling of G
P
U IDs
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Simplify PME GPU
synch
r
o
n
ization cod
e
commit
|
commitdiff
|
tree
2017-10-31
Aleksei
I
upinov
Reuse epbcXY logi
c
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Fix nstlist increase warn
i
ng
p
rint
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Check CUDA a
v
a
i
la
b
l
e/compiled
code compatibility
commit
|
commitdiff
|
tree
2017-10-30
Aleks
e
i
Iupinov
F
i
x reference mode build
u
nused funct
i
on warnings
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remov
e
unused
s
ign p
a
rameter from dih_angle()
commit
|
commitdiff
|
tree
2017-10-30
Roland Schu
l
z
ArrayRef: Replace from
V
ector wi
t
h sub
A
rra
y
commit
|
commitdiff
|
tree
2017-10-30
David va
n
der Spoel
Added option -w
a
ter tips3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-30
A
leksei
Iupinov
Bring PME GPU/
C
U
D
A
internal
s
t
ructure names to
Came
l
Case
commit
|
commitdiff
|
tree
2017-10-27
Mark Ab
r
ah
a
m
F
ix h
w
detection more
commit
|
commitdiff
|
tree
2017-10-26
M
a
rk Abraham
New quote
commit
|
commitdiff
|
tree
2017-10-20
Mark
Abraham
Clari
f
y docs for Fmax in EM
commit
|
commitdiff
|
tree
2017-10-20
Ma
r
k Abraham
Mer
g
e b
r
a
n
ch
relea
s
e-2016
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix
w
ar
n
ing for co
n
fout with periodic molecules
commit
|
commitdiff
|
tree
2017-10-16
Mark A
b
raham
Mer
g
e branch release-2016
commit
|
commitdiff
|
tree
2017-10-15
Berk
Hess
I
m
prove v
s
ite
par
a
llel checking
commit
|
commitdiff
|
tree
2017-10-13
A
leksei Iupinov
R
e
lax PME spline computat
i
on tol
e
r
ance in double p
r
ecision
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
M
a
rk A
b
raham
U
pdate t
e
sts
for C++11 co
m
piler and standard library
commit
|
commitdiff
|
tree
2017-10-13
R
o
land Schulz
S
pe
c
ialize Array
R
ef fo
r
S
imdReal
commit
|
commitdiff
|
tree
2017-10-11
Mark
A
b
rah
a
m
Introduced header for
communi
c
ation to/from PME ra
n
ks
commit
|
commitdiff
|
tree
2017-10-11
Al
e
kse
i
Iu
p
inov
Fix clang warn
i
ngs
f
o
r P
M
E
C
UDA kernels
commit
|
commitdiff
|
tree
2017-10-11
Alek
s
e
i Iupinov
Relax PME solving t
e
st
complex gr
i
d to
l
erance
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
C
l
ea
n
ed up ewaldcoeff for PM
E
-only ranks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupi
n
ov
PME
s
olving - C
U
DA kernel +
unit
t
ests
commit
|
commitdiff
|
tree
2017-10-11
Pa
u
l Bauer
Change to modules for build o
f
web doc
u
m
e
ntation
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
PM
E
f
o
rce gather
i
ng - CUDA ker
n
el + uni
t
t
ests
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
PME spline+spread CUDA kernel and
unit tests
commit
|
commitdiff
|
tree
2017-10-11
Mark Ab
r
aham
Use clang-5 in Jenkins
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disab
l
e ARM Neon n
a
tive rsq
r
t iteration
commit
|
commitdiff
|
tree
2017-10-09
Aleksei I
u
p
inov
PME GPU/CUDA
d
a
t
a framewo
r
k
.
commit
|
commitdiff
|
tree
2017-10-07
Mark Abr
a
h
a
m
Tell cppche
c
k th
a
t
.
cpp and
.
cu files
are c++
commit
|
commitdiff
|
tree
2017-10-07
Roland Schulz
Refac
t
or loa
d
+SimdLoad*Pro
x
yInternal
t
o redu
c
e d
u
pli
c
a
t
i
o
n
commit
|
commitdiff
|
tree
2017-10-06
B
erk
Hess
Add SIMD
i
ntrinsi
c
s
version of simple update
commit
|
commitdiff
|
tree
2017-10-06
Berk Hes
s
Improve PaddedRVecVector resiz
i
ng
commit
|
commitdiff
|
tree
2017-10-06
Aleksei
I
u
p
inov
Add timing
a
ccumulation
c
apabilit
y
into GpuRegionT
i
mer
commit
|
commitdiff
|
tree
2017-10-05
Berk Hess
Make SI
M
D ambi
g
uous test work
w
ith
f
l
o
at/double only
commit
|
commitdiff
|
tree
2017-10-05
Szilá
r
d
Pá
l
l
F
i
x pair list array assertion
commit
|
commitdiff
|
tree
2017-10-05
S
zil
á
rd Páll
Avo
i
d -W
m
issi
n
g-
p
rototypes warnings in
clang CUDA builds
commit
|
commitdiff
|
tree
2017-10-05
Roland Schulz
Fix
tha
t
e
x
p
(load(
x
)) is ambiguou
s
commit
|
commitdiff
|
tree
2017-10-04
M
a
r
k Abraham
Enab
l
e
group-sc
h
eme
SIMD wi
t
h GMX_SIMD=AVX
2
_12
8
commit
|
commitdiff
|
tree
2017-10-04
A
leksei Iupinov
Add GpuRegion
T
imer class
commit
|
commitdiff
|
tree
2017-10-03
Mar
k
Abraha
m
I
n
trod
u
ce and use
A
lignedAllocat
i
onP
o
l
i
cy
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
Remove hybrid gpu+cpu nonb
o
nded mode
commit
|
commitdiff
|
tree
2017-09-26
A
l
eksei Iupinov
Move CUDA t
e
xture
setup
c
ode fr
o
m N
B
CUDA m
o
dule to
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
Mark Abraha
m
M
erg
e
branch r
e
lease
-
2
0
1
6
commit
|
commitdiff
|
tree
2017-09-15
Berk Hess
Remove nb-par
a
meters from t_forcerec
commit
|
commitdiff
|
tree
2017-09-15
Mark Abr
a
ham
E
x
pres
s
i
n
tent of m
a
t
r
ix re
l
e
as
e
b
u
i
ld types exp
l
icitly
commit
|
commitdiff
|
tree
2017-09-15
M
ark Abraham
Bumped patch version f
o
r nex
t
r
e
lease
commit
|
commitdiff
|
tree
2017-09-15
M
a
rk Abraham
Version 2016
.
4
commit
|
commitdiff
|
tree
2017-09-14
A
lek
s
ei Iupinov
Fix non-SIMD buil
d
fai
l
ing
commit
|
commitdiff
|
tree
2017-09-14
S
zilár
d
Páll
C
UDA 9/Volta support for
t
he p
r
u
n
ing kern
e
l
commit
|
commitdiff
|
tree
2017-09-14
M
ark Abr
a
ham
Form taskassignment
m
odule
commit
|
commitdiff
|
tree
2017-09-14
M
ark Abraham
Fix compat module de
f
ini
t
ion
commit
|
commitdiff
|
tree
2017-09-12
Erik Lindahl
Im
p
rove accuracy of
SIMD exp for sma
l
l args
commit
|
commitdiff
|
tree
2017-09-12
M
a
rk
A
braham
Mer
g
e bran
c
h
release-2016
commit
|
commitdiff
|
tree
2017-09-12
Berk H
e
ss
Do not pass st
a
te to init_replica_exchange
commit
|
commitdiff
|
tree
2017-09-11
Szilárd Páll
N
V
IDIA
V
o
lta performance twe
a
ks
commit
|
commitdiff
|
tree
2017-09-11
Berk
H
ess
F
i
x
PBC b
u
gs in the swap code
commit
|
commitdiff
|
tree
next