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Add PME integration test
2017-11-24
Mar
k
Abraham
Add
P
ME int
e
gration tes
t
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
Extend task assig
n
ment code
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei I
u
pinov
Mention gmx_install_headers() i
n
t
he developer manual
commit
|
commitdiff
|
tree
2017-11-24
A
l
ek
s
ei Iupi
n
ov
Make FFT r
e
al-space grid use CUDA pinnin
g
for mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
se
i
Iupino
v
P
i
n
c
oordinate
s
,
f
orces and charg
e
s fo
r
PME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-22
Pa
s
c
al Merz
Pro
o
f
of c
o
ncept
:
P
h
ysic
a
l validat
i
on suite
commit
|
commitdiff
|
tree
2017-11-21
Erik Lindahl
Se
p
ara
t
e
S
IMD
f
lag de
t
e
c
tion from manage
m
en
t
commit
|
commitdiff
|
tree
2017-11-21
Mark Abraham
Support pinn
i
n
g
i
n H
o
s
t
All
o
cator
commit
|
commitdiff
|
tree
2017-11-21
Viveca Lindahl
Add force correlatio
n
to AW
H
module
commit
|
commitdiff
|
tree
2017-11-21
Paul Bauer
First gen
e
ral add
i
tions
to the d
o
cumentation
commit
|
commitdiff
|
tree
2017-11-19
Vi
v
eca
L
indahl
Add AWH
sec
t
i
on to m
a
nual
.
commit
|
commitdiff
|
tree
2017-11-19
Viveca Lindahl
Add
A
WH
b
ia
s
ing
modu
l
e +
t
ests
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
Use HostAllo
c
ation
P
olicy fo
r
char
g
eA
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
Add ch
e
cking func
t
ion f
o
r whe
t
her a buffer i
s
p
i
nned
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
Improve
ha
n
dling of PME G
P
U force buffer
commit
|
commitdiff
|
tree
2017-11-15
A
l
ekse
i
I
upinov
R
e
n
ame and
expose "generic"
GPU me
m
ory transfer functions
commit
|
commitdiff
|
tree
2017-11-10
Mark Abraham
Import cmake Modules/FindCU
D
A
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
Alek
s
ei Iupino
v
Rename synchronous G
P
U transfer fun
c
tions to
match
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Mark Abraham
Prepared t_mdat
o
m
s for using v
e
ctor
commit
|
commitdiff
|
tree
2017-11-09
Mark
A
bra
h
am
Intro
d
uc
e
Host
A
llocatio
n
Policy
commit
|
commitdiff
|
tree
2017-11-09
Roland Schulz
I
C
C should
u
se ZMM
i
f code
anyh
o
w uses
ZM
M
commit
|
commitdiff
|
tree
2017-11-07
Mark
Abraham
Reform g
m
x_pme_pp alloc and
u
s
e vector
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
I
ntrodu
c
e
gmxopen
c
l
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abr
a
ham
Test c
l
ang
on
A
RM
i
n nightly ma
t
rix
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
A
d
d
w
a
l
l
cycle timer for
t
h
e
P
ME GPU F reduction
commit
|
commitdiff
|
tree
2017-11-07
Szil
á
rd Páll
Spli
t
off nbnxn GPU
t
imi
n
g
and
s
t
agi
n
g
r
educ
t
ion
commit
|
commitdiff
|
tree
2017-11-07
Mar
k
Abraham
Improve PME includes
commit
|
commitdiff
|
tree
2017-11-07
Szi
l
árd Páll
D
e
d
upli
c
ate CUDA an
d
Open
C
L
t
imer struct
commit
|
commitdiff
|
tree
2017-11-06
Da
v
id
v
a
n
der Spoel
Fixed ch
e
ck for
w
a
t
er in g
e
n_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
Mark A
b
raham
Mer
g
e
"Merge branch release-
2
016"
commit
|
commitdiff
|
tree
2017-11-02
Da
v
i
d v
a
n der Spoel
New md
p
inpu
t
for elec
t
ric fields
.
commit
|
commitdiff
|
tree
2017-11-02
Alek
s
e
i
Iupinov
Replace m
a
th
.
h by c
m
a
t
h includ
e
s in cp
p
files
commit
|
commitdiff
|
tree
2017-11-02
Mark Abr
a
ham
Merge branch
release-2016
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
Small change t
o
LaTeX manual genera
t
ion
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Fix thread-MPI rank choice fo
r
orien
t
a
tion restraints
commit
|
commitdiff
|
tree
2017-11-01
Ale
k
sei Iupinov
Remov
e
unuse
d
P
M
E GPU declarations
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iup
i
nov
Move pme_gpu_finish_computation() documentat
i
o
n
to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
P
aul Bauer
Fixing missin
g
references in
web
documentatio
n
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iup
i
nov
Fi
x
erroneous PME
G
P
U "step" naming
s
commit
|
commitdiff
|
tree
2017-11-01
Ma
r
k Abraham
Improve handling
of GPU IDs
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iu
p
inov
Simplify PME
G
P
U
synchr
o
nizatio
n
code
commit
|
commitdiff
|
tree
2017-10-31
Ale
k
sei Iup
i
n
o
v
Reuse epbc
X
Y logic
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Pá
l
l
Fix nstlis
t
inc
r
ease warning prin
t
commit
|
commitdiff
|
tree
2017-10-31
Szi
l
árd Páll
Check
C
UDA av
a
ilable/com
p
iled co
d
e
compatibility
commit
|
commitdiff
|
tree
2017-10-30
Aleksei I
u
pinov
Fix
refe
r
ence mode build unused function warn
i
ngs
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remove unused sign para
m
eter from dih_
a
ngle()
commit
|
commitdiff
|
tree
2017-10-30
Roland Schulz
ArrayRef: Replace
fromVector with sub
A
rray
commit
|
commitdiff
|
tree
2017-10-30
David van der S
p
oel
Adde
d
option -water ti
p
s
3p to
p
db2gmx
.
commit
|
commitdiff
|
tree
2017-10-30
Aleksei I
u
pinov
B
r
in
g
PME GP
U
/C
U
DA internal stru
c
ture
n
ames to Came
l
Case
commit
|
commitdiff
|
tree
2017-10-27
Mark Abraham
Fix hw detection more
commit
|
commitdiff
|
tree
2017-10-26
Mark Abraham
New quot
e
commit
|
commitdiff
|
tree
2017-10-20
Mark Abrah
a
m
Clarify d
o
c
s
for Fmax in EM
commit
|
commitdiff
|
tree
2017-10-20
Mark
A
b
rah
a
m
Merge branch rel
e
ase-2016
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix warning for confout wi
t
h
p
e
riodic
m
o
lec
u
l
e
s
commit
|
commitdiff
|
tree
2017-10-16
Mark Ab
r
aham
Merge
b
r
anch
r
elease-201
6
commit
|
commitdiff
|
tree
2017-10-15
B
e
rk Hess
Im
p
rove vsite paralle
l
che
c
king
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iu
p
ino
v
R
elax PME
s
pline c
o
m
putat
i
on to
l
e
r
ance
i
n double precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Mark Abraham
Update tests for C++1
1
compiler and
s
tandard
library
commit
|
commitdiff
|
tree
2017-10-13
Roland
S
c
h
u
lz
S
p
eci
a
liz
e
Arra
y
Ref for SimdReal
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Introd
u
ced head
e
r for commun
i
cation
t
o
/
from
P
ME ranks
commit
|
commitdiff
|
tree
2017-10-11
Al
e
ksei
Iupinov
Fix clang warn
i
ngs for PME CUDA k
e
rnels
commit
|
commitdiff
|
tree
2017-10-11
Alekse
i
Iupi
n
ov
R
ela
x
PM
E
sol
v
ing test complex grid toleranc
e
commit
|
commitdiff
|
tree
2017-10-11
Mark
A
b
raham
Cleaned up ewaldcoef
f
for PM
E
-only ranks
commit
|
commitdiff
|
tree
2017-10-11
Ale
k
sei
I
upinov
P
M
E solv
i
ng - CUDA k
e
rnel
+
unit
tests
commit
|
commitdiff
|
tree
2017-10-11
Paul
B
auer
Change t
o
modu
l
es f
o
r build of web documentation
commit
|
commitdiff
|
tree
2017-10-11
Al
e
k
s
ei Iupinov
PME
force g
a
thering - CUDA kernel + uni
t
test
s
commit
|
commitdiff
|
tree
2017-10-11
A
leksei Iupinov
PME spline+sprea
d
CU
D
A
k
e
rnel and unit tests
commit
|
commitdiff
|
tree
2017-10-11
Mark A
b
r
aha
m
Use cl
a
ng-
5
i
n Jen
k
ins
commit
|
commitdiff
|
tree
2017-10-11
Berk
H
ess
Disable ARM N
e
on native rs
q
r
t i
t
e
ration
commit
|
commitdiff
|
tree
2017-10-09
Aleksei Iupinov
PM
E
GPU/CUDA
d
ata framew
o
rk
.
commit
|
commitdiff
|
tree
2017-10-07
Mark Abr
a
ham
Tell cppcheck that
.
cpp and
.
cu fil
e
s
a
re c++
commit
|
commitdiff
|
tree
2017-10-07
Ro
l
and
S
chul
z
R
e
fac
t
or load+SimdLoad*ProxyI
n
ternal
to r
e
duce duplica
t
ion
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Ad
d
SIM
D
intrinsics version of s
i
m
ple update
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Impro
v
e
PaddedRVe
c
Vector
r
esizing
commit
|
commitdiff
|
tree
2017-10-06
Aleksei Iupi
n
ov
Add tim
i
n
g
acc
u
mulation capability i
n
to GpuR
e
g
ionTimer
commit
|
commitdiff
|
tree
2017-10-05
Berk Hess
Make S
I
MD ambiguou
s
test work with floa
t
/
do
u
ble only
commit
|
commitdiff
|
tree
2017-10-05
Szilárd
P
áll
Fix pair list array assertion
commit
|
commitdiff
|
tree
2017-10-05
Sz
i
lárd Páll
A
v
oid
-
Wmissing-prototypes warnings
i
n clan
g
CUDA bu
i
l
ds
commit
|
commitdiff
|
tree
2017-10-05
Ro
l
a
n
d
S
chulz
F
i
x that exp(load(x)) is ambiguous
commit
|
commitdiff
|
tree
2017-10-04
Mark Ab
r
aham
Enable group-scheme SIMD
w
ith GMX_
S
IMD=AVX2_
1
2
8
commit
|
commitdiff
|
tree
2017-10-04
A
l
eksei Iup
i
nov
Add GpuRegionT
i
mer cla
s
s
commit
|
commitdiff
|
tree
2017-10-03
Mark
Abrah
a
m
Introduce and u
s
e A
l
ignedAll
o
c
a
t
i
o
n
P
o
licy
commit
|
commitdiff
|
tree
2017-10-02
Berk
He
s
s
Remove hybrid gp
u
+cpu nonb
o
nde
d
mode
commit
|
commitdiff
|
tree
2017-09-26
A
l
ekse
i
Iupinov
Move
C
U
DA te
x
ture se
t
u
p code
from NB CUDA mod
u
le to
.
.
.
commit
|
commitdiff
|
tree
2017-09-17
Mark Ab
r
a
h
a
m
Merge
branch rele
a
se-2016
commit
|
commitdiff
|
tree
2017-09-15
Be
r
k Hess
R
e
move nb-parameters f
r
om t_f
o
rcerec
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
Express
i
ntent of ma
t
rix release
b
uild type
s
e
x
pli
c
itl
y
commit
|
commitdiff
|
tree
2017-09-15
Mark Abra
h
a
m
B
u
mped p
a
tch vers
i
on for
next rel
e
a
s
e
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
Version
2016
.
4
commit
|
commitdiff
|
tree
2017-09-14
Aleksei Iupinov
Fix
non-SIMD bui
l
d fa
i
ling
commit
|
commitdiff
|
tree
2017-09-14
Sz
i
l
á
rd Páll
CUDA 9
/
Volta support for the pruning
k
ernel
commit
|
commitdiff
|
tree
2017-09-14
Ma
r
k A
b
raham
Form t
a
skassignment module
commit
|
commitdiff
|
tree
2017-09-14
Mark
A
bra
h
am
F
ix comp
a
t
module definitio
n
commit
|
commitdiff
|
tree
2017-09-12
Eri
k
L
indahl
Improv
e
accuracy of S
I
MD exp for small args
commit
|
commitdiff
|
tree
2017-09-12
M
ark Abra
h
am
M
e
rg
e
br
a
nch release-
2
016
commit
|
commitdiff
|
tree
2017-09-12
Be
r
k Hess
Do
not pass
s
t
ate to in
i
t
_
replica_exchange
commit
|
commitdiff
|
tree
2017-09-11
Szi
l
árd Páll
NVID
I
A Volta performance
tweak
s
commit
|
commitdiff
|
tree
2017-09-11
Be
r
k
Hess
Fix
P
BC
bug
s
in the swap
c
ode
commit
|
commitdiff
|
tree
2017-09-07
Mark
A
braham
I
ntro
d
uce type-safe GPU
em
u
latio
n
v
ariables
commit
|
commitdiff
|
tree
2017-09-07
R
oland Schulz
Add isInteg
r
alC
o
nstant t
y
pe
tra
i
t
commit
|
commitdiff
|
tree
next