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Added new testing code for normal mode analysis.
2018-10-13
Al
e
ksei Iupinov
Add
a
nd enable
P
ME Open
C
L
commit
|
commitdiff
|
tree
2018-08-27
Alekse
i
Iupino
v
P
repare
pme-gpu-
t
ypes
.
h for OpenCL
commit
|
commitdiff
|
tree
2018-07-30
Alek
s
e
i
Iu
p
inov
Remo
v
e hardcoded wa
r
p_s
i
ze == 32 assump
t
i
o
n from PME G
P
U
commit
|
commitdiff
|
tree
2018-06-25
Aleks
e
i Iupinov
Move vectype_ops
.
c
l
h into gpu_u
t
ils
commit
|
commitdiff
|
tree
2018-06-25
A
l
eksei Iupinov
Move the PME GPU ker
n
el laun
c
h functions into pme-
g
pu
.
.
.
commit
|
commitdiff
|
tree
2018-06-14
Aleksei Iupinov
Ens
u
re PME
with OpenCL does not attempt to pin
commit
|
commitdiff
|
tree
2018-06-07
Aleksei Iupinov
Co
m
pil
e
most of PME
GPU hos
t
code with O
p
enCL
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei Iupi
n
o
v
Merge pme
.
c
u
into
p
me-g
p
u-i
n
t
ernal
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
Iupinov
PME Open
C
L 3D
F
F
T
tra
n
s
f
orm is impleme
n
ted, using c
l
FFT
commit
|
commitdiff
|
tree
2018-05-31
Alek
s
e
i
Iupinov
Mo
v
e
pme-timings
.
cu to pm
e
-gpu-timings
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupin
o
v
Prefer
l
in
k
ing to system
c
lFFT rat
h
er than bundled o
n
e
commit
|
commitdiff
|
tree
2018-05-31
Al
e
ksei I
u
pinov
M
ove the Pme
G
puSpecific structu
r
e into pme-gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
up
i
nov
Added the bundled c
l
FFT into OpenCL builds
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Add Gpu
E
v
e
ntSyn
c
hronizer class
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
u
pinov
Gather the
PME GPU con
s
tan
t
s/
m
acros in a s
i
ngle h
e
ader
commit
|
commitdiff
|
tree
2018-05-30
Aleksei Iupinov
Make PME GPU
struc
t
ures
use DeviceBuffer
commit
|
commitdiff
|
tree
2018-05-28
Alekse
i
Iupinov
Support per
s
istent
device contex
t
-derived data in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-22
Alek
s
ei Iupinov
Remove unused
res
u
lt
s
of cudaStream
Q
u
ery()
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iupinov
prepareGpuKernelArgum
e
nt
s
()
a
nd launch
G
puKernel() ar
e
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Al
e
k
s
ei
I
u
pinov
Impo
r
t clFFT library into
t
he Gromacs sou
r
ce
commit
|
commitdiff
|
tree
2018-05-04
Aleksei Iupinov
Add clearDe
v
iceBuffe
r
Async(
)
for CUDA/O
p
enCL
commit
|
commitdiff
|
tree
2018-05-03
Aleksei Iupi
n
o
v
Co
p
y m
i
ss
i
n
g
GPU NB host deallocati
o
ns from OpenCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Aleksei
I
upi
n
ov
replace
cu_co
p
y
_* calls with DeviceBuffer functions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Al
e
k
s
ei Iupinov
Rename OpenCL hos
t
m
emory
r
outines to matc
h
the
C
UDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei
I
upinov
Make asiz
e
() a
proper t
e
mplate function i
n
stead of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Ale
k
s
ei Iupino
v
Rename
the asize variable to
numAlignmentAtoms
commit
|
commitdiff
|
tree
2018-04-26
Alek
s
ei Iupinov
Sep
a
rate
P
M
E GPU host-only and h
o
st/devi
c
e
data structures
commit
|
commitdiff
|
tree
2018-04-26
Al
e
k
s
ei Iupino
v
Add copyFrom
D
ev
i
ceBuffe
r
() CUDA/OpenCL implementations
commit
|
commitdiff
|
tree
2018-04-23
Alek
s
e
i
Iupinov
R
emo
v
ed cu_
r
ealloc_bu
f
fere
d
()
in
f
avor o
f
reallocateDeviceBu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
Devic
e
B
u
ffer
he
a
d
ers ar
e
a
dded
commit
|
commitdiff
|
tree
2018-04-12
Ale
k
sei Iup
i
nov
Make in-source OpenCL kerne
l
p
a
th
a per-mod
u
le para
m
eter
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
R
e
move CUDA
_
FUNC macros fr
o
m many functio
n
s
in PME GPU
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
S
top PME
G
PU code from
compiling on n
o
n-CUD
A
builds
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iu
p
ino
v
Prevent Op
e
n
C
L tim
i
n
g
m
emory leak
commit
|
commitdiff
|
tree
2018-03-20
Al
e
ksei Iupinov
C
la
r
ify the mdrun GPU options docs
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
A
d
d
a basic TPI sanity t
e
st
commit
|
commitdiff
|
tree
2018-03-16
Aleksei
Iup
i
nov
Stop gmx
_
feenableexcep
t
(
)
from retu
r
ning p
r
e
vious ex
c
eptio
n
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleks
e
i I
u
p
i
nov
Re
s
tore the l
o
st mc_temp chec
k
in g
r
o
mpp
commit
|
commitdiff
|
tree
2018-03-06
Aleksei Iupinov
Is
o
late P
M
E GPU
s
p
l
ine
p
ar
a
m
e
t
er i
n
dexing in inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupinov
S
t
o
p
using custom Fi
n
d
Ope
n
CL
.
cm
a
ke, per TODO
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupin
o
v
Correct th
e
nbnxn_gpu_compile_ker
n
els()
d
ocs
commit
|
commitdiff
|
tree
2018-03-02
Aleksei Iupinov
Ma
k
e TPI use d
o
uble
preci
s
ion
e
xp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei Iupinov
Merge bra
n
c
h 'release-2018
'
commit
|
commitdiff
|
tree
2018-02-26
Al
e
ksei Iupinov
Advice use
r
s on
i
nfinit
e
outpu
t
of TPI
commit
|
commitdiff
|
tree
2018-02-20
Al
e
kse
i
Iupinov
Remo
v
e unused OpenC
L
d
e
b
u
g
buffer
commit
|
commitdiff
|
tree
2018-02-18
A
leksei Iupinov
R
e
p
l
ace *_free_buffered ca
l
ls by fr
e
eDeviceB
u
ffer
commit
|
commitdiff
|
tree
2018-02-16
A
l
ek
s
ei Iupinov
Fi
x
PME for la
r
ge systems
w
ith Fermi GPUs
commit
|
commitdiff
|
tree
2018-02-15
Al
e
ksei
I
upinov
Update
F
FTW bu
i
ld to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Alekse
i
Iupin
o
v
A
dd freeDeviceBuffer GPU utility function
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Add the missin
g
comma in the
quote
commit
|
commitdiff
|
tree
2018-02-14
Al
e
ksei
I
upinov
Replace the
r
e
mainin
g
EXPE
C
T_DEATH with EXPECT_
D
E
A
TH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Add
D
eviceBuffer a
s
a typedef for cl_me
m
/device
p
onter
commit
|
commitdiff
|
tree
2018-02-13
Aleksei
I
u
pinov
Move GPU traits
i
nto
s
e
p
arate
headers
commit
|
commitdiff
|
tree
2018-02-12
A
leksei Iupinov
Fix the include
g
uard
commit
|
commitdiff
|
tree
2018-02-09
Ale
k
sei
I
upinov
Revert "Enable debug FP exceptions
w
ithout TPI,
not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
Always run the
e
s
sential dy
n
amics tes
t
s
commit
|
commitdiff
|
tree
2018-02-08
A
l
eksei
I
upinov
Enable debug F
P
exce
p
tions w
i
thout TPI
,
not with T
P
I
commit
|
commitdiff
|
tree
2018-02-08
Al
e
ks
e
i Iupinov
Merge branch
'
r
elea
s
e-2
0
18'
into maste
r
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iu
p
inov
Remove u
n
nec
e
ssary includes f
r
om domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
A
lek
s
ei Iu
p
inov
Z
e
ro
unused v
a
lues to silenc
e
the warni
n
g
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iup
i
nov
Only setup Ewal
d
in t
h
e
g
eneric group kernel if i
t
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
A
leksei Iupinov
Mak
e
ndx files optional in
S
imul
a
tionRunne
r
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupinov
Remove mdpI
n
putFile
N
ame_ from Simul
a
tionRunner, pe
r
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iu
p
inov
Don't print
i
mpossible CUDA version number
s
in absen
c
e
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
F
i
x input MDP conten
t
s for swap and IMD t
e
s
t
s
commit
|
commitdiff
|
tree
2018-02-01
Aleksei Iupinov
C
h
eck for
G
TES
T
_IS_
T
HREADSAFE being defined
commit
|
commitdiff
|
tree
2018-01-24
Aleksei
Iupinov
Rem
o
v
e unused fi
e
lds pe
r
T
ODO
commit
|
commitdiff
|
tree
2018-01-23
Alekse
i
Iupin
o
v
T
e
st th
e
mixed mode P
M
E with wall
s
and
box scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei
Iupi
n
ov
Test PME CPU/GPU
with
w
a
l
l
s
a
nd box scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupi
n
o
v
W
r
a
p the PME test
i
ng loop in
a method for extensibility
commit
|
commitdiff
|
tree
2018-01-19
A
leksei Iupinov
Add a death t
e
st for the
duplicate inputrec keys
c
hecking
commit
|
commitdiff
|
tree
2018-01-19
Alek
s
ei I
u
pinov
Rename class BiasReader to struct BiasOut
p
utSetup
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Move the temporary file MPI work
a
roun
d
into the b
a
se
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Al
e
ksei
Iupinov
M
ak
e
the reference
data variables local
i
n GetIrTest
commit
|
commitdiff
|
tree
2018-01-19
A
leksei Iup
i
nov
Merge b
r
anch 'release-2018' into mast
e
r
commit
|
commitdiff
|
tree
2018-01-18
Ale
k
se
i
Iupinov
Got rid
of manual memory management in the
P
M
E
overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Re-enable multi-rank PME tests (with
t
h
e file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Al
e
kse
i
Iupinov
Fix
b
ox scaling in PME mix
e
d mode
commit
|
commitdiff
|
tree
2018-01-17
A
leks
e
i
Iu
p
inov
Merge
bra
n
c
h
're
l
ease-2018' into m
a
s
t
e
r
commit
|
commitdiff
|
tree
2018-01-16
Aleks
e
i Iupinov
Always write the input MDP file fo
r
testi
n
g jus
t
b
e
fore
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
A
l
ekse
i
Iupinov
M
ove
Octane
S
andwich
.
mdp and sp
c
2-IM
D
.
mdp into
s
trings
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupinov
Remove unu
s
ed alanine_vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Alekse
i
I
upin
o
v
Do not
print P
M
E counter b
r
e
akdown if
i
t'
s
empty
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupinov
Se
t
GMX_GPU_
A
UT
O
t
o FALSE w
i
th GMX_GPU d
e
fined
commit
|
commitdiff
|
tree
2017-12-20
A
leksei Iu
p
inov
Remove potentially wro
n
g "per user
r
eque
s
t" note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Alekse
i
Iupinov
Re
l
axed precis
i
on in spline interpolati
o
n
te
s
ts
commit
|
commitdiff
|
tree
2017-12-06
Alek
s
ei I
u
pino
v
P
r
ovide dummy
initializ
a
tion to
sil
e
nce a warni
n
g
commit
|
commitdiff
|
tree
2017-12-05
A
l
eksei Iupin
o
v
Do not ac
c
ept unsuppor
t
ed c
o
mbination "-pme cpu -pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Alek
s
ei
I
up
i
nov
Reformulate PME solving test
s
t
olera
n
ces
commit
|
commitdiff
|
tree
2017-11-28
A
leksei Iupinov
Replace of pmeGPU variab
l
e name wi
t
h pm
e
Gpu
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
Iupino
v
Do not force separ
a
te PME
r
ank to
recompute reciprocal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
A
l
eks
e
i
I
u
pinov
Disable f
a
iling separate PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Add tests
f
or PM
E
tuning a
n
d fix mi
x
ed PME mode
w
i
th
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
D
es
t
roy PME GPU context
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Enable se
p
ar
a
t
e PME
G
P
U
rank
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
se
i
Iupinov
Do not ca
l
l mixed CPU+GPU PME mode "Hybrid"
commit
|
commitdiff
|
tree
2017-11-24
A
leksei Iu
p
i
n
ov
Activate
m
i
x
ed mode of PME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupinov
R
emove outdat
e
d
(already impl
e
mented)
p
inning TODO
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iup
i
no
v
Me
n
tion gmx
_
install_he
a
d
ers() in the d
e
velo
p
er manual
commit
|
commitdiff
|
tree
2017-11-24
A
leks
e
i Iupinov
Make FFT real-space grid
use CUDA pinn
i
ng f
o
r
mi
x
ed
.
.
.
commit
|
commitdiff
|
tree
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