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Fix erroneous PME GPU "step" namings
2017-11-01
Aleks
e
i Iupinov
Fix
errone
o
us PME GPU
"step" nami
n
gs
commit
|
commitdiff
|
tree
2017-11-01
Mark Abra
h
am
Improve
handling of GPU
I
Ds
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Simplif
y
PME GPU
s
ynchro
n
izati
o
n co
d
e
commit
|
commitdiff
|
tree
2017-10-31
Aleks
e
i
Iu
p
ino
v
R
e
use epbcXY logi
c
commit
|
commitdiff
|
tree
2017-10-31
Szilár
d
Páll
Fix n
s
tlist increa
s
e
w
arn
i
ng print
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Check C
U
DA available/co
m
piled code
c
ompatibility
commit
|
commitdiff
|
tree
2017-10-30
Alek
s
ei Iupi
n
ov
Fix r
e
f
e
rence mode build
unused function war
n
i
n
gs
commit
|
commitdiff
|
tree
2017-10-30
Berk
H
ess
R
e
m
ove
u
nused sign para
m
eter from dih_angl
e
()
commit
|
commitdiff
|
tree
2017-10-30
Rolan
d
Sc
h
ulz
Arr
a
y
Ref: Replac
e
fromVecto
r
with subArray
commit
|
commitdiff
|
tree
2017-10-30
Da
v
id van der Spoel
A
d
de
d
o
p
tion -water tips3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-30
Aleksei I
u
pinov
Bring P
M
E GPU/C
U
D
A
i
nternal structure names to CamelCase
commit
|
commitdiff
|
tree
2017-10-27
Ma
r
k A
b
raham
Fix
hw
detection more
commit
|
commitdiff
|
tree
2017-10-26
M
a
rk Abraham
N
e
w
quot
e
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
Me
r
ge
branch r
e
lease-2016
commit
|
commitdiff
|
tree
2017-10-20
Ber
k
Hess
F
ix warning for confout
with p
e
riodic molecules
commit
|
commitdiff
|
tree
2017-10-16
Mark Abraham
Merge branch rele
a
se
-
201
6
commit
|
commitdiff
|
tree
2017-10-15
Berk Hes
s
Improve vsi
t
e
p
ara
l
lel
c
hecking
commit
|
commitdiff
|
tree
2017-10-13
A
leksei
Iupinov
Relax PME sp
l
in
e
comput
a
tion
tolerance in double precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Mark A
b
raham
Up
d
ate tests fo
r
C+
+
11 compiler and sta
n
dard library
commit
|
commitdiff
|
tree
2017-10-13
R
o
land Schulz
Special
i
z
e A
r
rayRef for SimdReal
commit
|
commitdiff
|
tree
2017-10-11
Ma
r
k Abraham
I
ntroduced header fo
r
commu
n
ication to
/
fr
o
m PME ranks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
Fix clang
w
a
r
nings for
PME
C
UDA kernels
commit
|
commitdiff
|
tree
2017-10-11
Al
e
ksei Iupino
v
Re
l
ax P
M
E
solving test complex grid toleran
c
e
commit
|
commitdiff
|
tree
2017-10-11
Mark
Abraham
Cleaned up ewaldcoeff for PME-only ra
n
ks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
PME solving - CUDA
k
er
n
el
+ unit tests
commit
|
commitdiff
|
tree
2017-10-11
Paul Bauer
Ch
a
ng
e
to modules for build of w
e
b doc
u
mentation
commit
|
commitdiff
|
tree
2017-10-11
Alekse
i
Iupinov
PME force ga
t
hering - CUDA kernel + unit tes
t
s
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
P
ME spline+spread CUDA kernel
a
nd unit tests
commit
|
commitdiff
|
tree
2017-10-11
Mark Abra
h
am
U
se
cla
n
g-5 in J
e
nkins
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
D
i
s
able ARM Neon native rsqr
t
ite
r
ation
commit
|
commitdiff
|
tree
2017-10-09
Al
e
ks
e
i Iupi
n
ov
PME GPU/CUDA data
framewor
k
.
commit
|
commitdiff
|
tree
2017-10-07
M
a
rk Abraha
m
Tell cppcheck that
.
c
p
p
and
.
cu
files are c
+
+
commit
|
commitdiff
|
tree
2017-10-07
Roland Schul
z
Ref
a
ctor load+SimdLoad*Pro
x
yInternal to reduc
e
duplicatio
n
commit
|
commitdiff
|
tree
2017-10-06
B
e
rk Hess
Add
SI
M
D intri
n
si
c
s
v
ersion of
s
imp
l
e updat
e
commit
|
commitdiff
|
tree
2017-10-06
Berk
H
ess
Impro
v
e Padde
d
RVecVector resizing
commit
|
commitdiff
|
tree
2017-10-06
Ale
k
sei Iupino
v
Add
tim
i
ng accumulation ca
p
ability
into GpuRegionTimer
commit
|
commitdiff
|
tree
2017-10-05
Berk Hess
M
a
ke SIMD amb
i
g
uo
u
s test wo
r
k with float/do
u
ble
o
nly
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Páll
F
i
x pair list
a
rray assertion
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Páll
Av
o
id -
W
mi
s
sing-prototypes
w
arnings i
n
clang CUDA builds
commit
|
commitdiff
|
tree
2017-10-05
R
o
land Schulz
Fi
x
that exp(load(x)) is ambiguous
commit
|
commitdiff
|
tree
2017-10-04
Mark Abraham
Enable group-scheme SIMD w
i
th G
M
X_SIMD
=
A
VX2_
1
28
commit
|
commitdiff
|
tree
2017-10-04
Aleks
e
i Iupinov
Add GpuRegion
T
imer class
commit
|
commitdiff
|
tree
2017-10-03
M
a
rk Abraham
In
t
roduce
a
n
d use
AlignedA
l
lo
c
ationPolicy
commit
|
commitdiff
|
tree
2017-10-02
Be
r
k Hess
Remove h
y
b
r
id gpu+cpu nonbonded mode
commit
|
commitdiff
|
tree
2017-09-26
Aleksei Iup
i
nov
Mo
v
e CUDA text
u
r
e
setup code from
N
B
CUDA m
o
dule to
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
M
a
r
k A
b
raham
Merge branc
h
relea
s
e-2016
commit
|
commitdiff
|
tree
2017-09-15
Berk Hess
Remove nb-parameters
from t_forcerec
commit
|
commitdiff
|
tree
2017-09-15
Ma
r
k Abra
h
am
Express inte
n
t o
f
matrix
r
e
l
e
a
s
e build types e
x
pli
c
i
t
l
y
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
Bumped
p
atch version
f
or nex
t
release
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
V
ersion 2016
.
4
commit
|
commitdiff
|
tree
2017-09-14
Aleks
e
i
Iupi
n
ov
F
ix non-SI
M
D buil
d
f
ailing
commit
|
commitdiff
|
tree
2017-09-14
Szilárd Pá
l
l
CUDA 9/Volta support
f
or t
h
e
p
runi
n
g
k
e
rnel
commit
|
commitdiff
|
tree
2017-09-14
Mark
A
brah
a
m
F
o
rm taskas
s
ig
n
m
en
t
module
commit
|
commitdiff
|
tree
2017-09-14
Mark Abr
a
ham
Fix co
m
pat module d
e
finition
commit
|
commitdiff
|
tree
2017-09-12
Erik Lin
d
ahl
Improve accur
a
cy of SIMD
exp for small args
commit
|
commitdiff
|
tree
2017-09-12
Mark Abraha
m
Merge b
r
a
n
ch
r
elease-2016
commit
|
commitdiff
|
tree
2017-09-12
Berk H
e
s
s
Do not pass state to ini
t
_replica_ex
c
hange
commit
|
commitdiff
|
tree
2017-09-11
Szilárd Páll
N
V
IDIA Volta performan
c
e tweaks
commit
|
commitdiff
|
tree
2017-09-11
Berk Hess
Fi
x
PBC b
u
gs
i
n the swa
p
code
commit
|
commitdiff
|
tree
2017-09-07
M
a
rk A
b
r
a
ham
Introduce t
y
pe-
s
af
e
GPU emulation variables
commit
|
commitdiff
|
tree
2017-09-07
Roland Schul
z
Add isIntegralConstant type trait
commit
|
commitdiff
|
tree
2017-09-07
M
a
r
k Abrah
a
m
Enabl
e
group-scheme SIMD kernel
s
on recent AVX extensions
commit
|
commitdiff
|
tree
2017-09-06
Rol
a
nd Schulz
PME
-
gather: Use templated functor instead of pr
e
proc
e
ss
o
r
commit
|
commitdiff
|
tree
2017-09-05
Christoph Junghans
Supp
o
r
ted qu
i
et
trajectory-handling I/O
commit
|
commitdiff
|
tree
2017-09-05
Mark Abraham
Fixes for Solar
i
s
commit
|
commitdiff
|
tree
2017-09-05
Mark Abraham
Fix
u
se
o
f GPU
in
f
o
rmation fo
r
t
h
r
ead-MPI set
u
p
commit
|
commitdiff
|
tree
2017-09-04
B
e
rk Hess
F
i
x two nbnxn sear
c
h indexing bugs
commit
|
commitdiff
|
tree
2017-09-04
R
oland Schu
l
z
Fix accuracy
for cvtDou
b
le2Floa
t
/cprod
commit
|
commitdiff
|
tree
2017-09-04
Be
r
k H
e
ss
Con
s
olidate architecture b
o
olean
s
commit
|
commitdiff
|
tree
2017-09-03
Mark Abraham
Fix
c
ompiler flags f
o
r using MKL
commit
|
commitdiff
|
tree
2017-09-03
Mark
A
b
raham
Merge branch release-5-1
i
nto
release-2
0
1
6
commit
|
commitdiff
|
tree
2017-08-25
Mark Abra
h
am
Fix flat-b
o
ttomed p
o
sition
restraints with multipl
e
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
M
a
rk A
b
raham
Run G
P
U detect
i
on e
v
en
f
or mdrun
-
nb cpu
commit
|
commitdiff
|
tree
2017-08-22
Mar
k
A
braham
F
ixe
d
threa
d
-MPI with n
o
n-def
a
ult -np
m
e
commit
|
commitdiff
|
tree
2017-08-22
Mark A
b
raham
Fix missing
d
eclaration
o
f
GMX_UNU
S
ED_VA
L
UE
commit
|
commitdiff
|
tree
2017-08-22
A
l
ekse
i
Iupinov
S
e
parate P
M
E sprea
d
and gather wal
l
cycle
counters
commit
|
commitdiff
|
tree
2017-08-22
Berk Hess
Enable d
y
namic pair list pruning
commit
|
commitdiff
|
tree
2017-08-22
M
ark
Abr
a
ham
Merge branch re
l
ease-
2
0
16
commit
|
commitdiff
|
tree
2017-08-21
Teemu Mu
r
tol
a
Simple union-find s
t
ructure
commit
|
commitdiff
|
tree
2017-08-21
M
a
rk Abraham
Mo
v
ed increas
e
_
nstlist
(
) to nbnxn_tuni
n
g
.
h
commit
|
commitdiff
|
tree
2017-08-21
Mark Abraha
m
Fix compilation
i
ssue
s
with
A
RM SIMD
commit
|
commitdiff
|
tree
2017-08-21
Szilárd P
á
ll
A
dd OpenCL pruning
kernels and launch/timing
l
ogic
commit
|
commitdiff
|
tree
2017-08-18
S
z
ilárd Pá
l
l
Imp
r
o
v
e aw
k
ward handling of GMX
_
CUDA_TARGET* help
commit
|
commitdiff
|
tree
2017-08-18
Vedran Milet
i
ć
Improve the
"
files n
o
t present" error me
s
s
age
commit
|
commitdiff
|
tree
2017-08-18
Szilárd Páll
A
dd CUDA
pruning k
e
r
n
els and
lau
n
ch/timing
l
o
g
ic
commit
|
commitdiff
|
tree
2017-08-18
Berk Hess
Add CPU reference and S
I
M
D pruning kernels
commit
|
commitdiff
|
tree
2017-08-17
M
ark Abrah
a
m
Repl
a
ce
cons
i
stency c
h
eck
i
ng w
i
t
h
a
s
se
r
tion
commit
|
commitdiff
|
tree
2017-08-16
Berk He
s
s
Add dy
n
amic pair-li
s
t prun
i
ng framework
commit
|
commitdiff
|
tree
2017-08-16
B
erk Hess
Clean up nbnxn clus
t
er
p
air addition
c
ode
commit
|
commitdiff
|
tree
2017-08-16
Mark Abraham
Parse us
e
r-supplied GPU task
a
ssig
n
m
e
nt only when needed
commit
|
commitdiff
|
tree
2017-08-15
David van der Spoel
Worked around m
i
ssin
g
O
penMP
i
mpleme
n
t
at
i
on in orires
.
commit
|
commitdiff
|
tree
2017-08-15
M
ark Abraha
m
Merge branch rel
e
ase-5-1 into
release-2016
commit
|
commitdiff
|
tree
2017-08-15
Jiri Kraus
CUDA
9/Volta s
u
p
port for the nonbond
e
d
m
o
dule
commit
|
commitdiff
|
tree
2017-08-15
Mark
A
braham
Fi
x
value o
f
Ewald shift
commit
|
commitdiff
|
tree
2017-08-07
Mark Abraham
Fix
i
n
c
lud
e
dependency for getenv
commit
|
commitdiff
|
tree
2017-08-06
Mark Abraham
Simp
l
ify reso
u
r
ce-
d
ivision efficie
n
cy che
c
k
commit
|
commitdiff
|
tree
2017-08-06
Mark Abraham
Decouple task assign
m
ent from
t
ask execution
commit
|
commitdiff
|
tree
2017-08-06
Mark A
b
raham
Re
m
o
v
ed unused host-side allocatio
n
code
commit
|
commitdiff
|
tree
2017-08-04
Mark Abraham
Stop usin
g
hwin
f
o_g for r
e
por
t
ing c
o
de
commit
|
commitdiff
|
tree
2017-08-03
M
ar
k
A
b
ra
h
am
Removed unus
e
d i
n
c
l
ud
e
stateme
n
ts
commit
|
commitdiff
|
tree
next