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Make PME GPU structures use DeviceBuffer
2018-05-30
Aleksei Iupinov
Make
PME GPU s
t
r
u
ctur
e
s use D
e
v
i
ceBuffer
commit
|
commitdiff
|
tree
2018-05-28
A
l
eksei Iupinov
Su
p
port
persiste
n
t device c
o
n
t
ext-derived data
in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-18
Ale
k
sei Iupin
o
v
prepar
e
GpuKernelArguments() and launchGpuKernel(
)
are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei Iupinov
Im
p
ort clFFT library int
o
the Gr
o
mac
s
sourc
e
commit
|
commitdiff
|
tree
2018-05-04
Aleks
e
i Iup
i
nov
Add clearDev
i
ceBufferAsync() f
o
r CUDA/OpenCL
commit
|
commitdiff
|
tree
2018-05-03
Aleksei I
u
p
inov
C
o
py m
i
ssing GP
U
N
B host de
a
l
l
o
cations from Ope
n
CL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Aleks
e
i I
u
pinov
replace cu_c
o
py_* calls w
i
t
h D
e
vi
c
e
B
uffer functio
n
s
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
A
leksei Iupinov
R
e
nam
e
OpenCL
hos
t
memory
r
out
i
nes to m
a
tch
the CUD
A
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupin
o
v
Make asize()
a
proper
t
emplate fun
c
ti
o
n instead
o
f
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Ale
k
sei I
u
pinov
Rename the asiz
e
va
r
iable to numAlignmentAtoms
commit
|
commitdiff
|
tree
2018-04-26
Al
e
ksei Iup
i
nov
Se
p
arate PME
GPU host-only and h
o
st/
d
evice data st
r
u
ctures
commit
|
commitdiff
|
tree
2018-04-26
Alekse
i
I
u
pinov
Add copyFromD
e
viceBuffer() CUDA/O
p
enCL implementa
t
i
ons
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
Removed cu_real
l
oc_buffered()
i
n
favor of reallocate
D
e
v
iceBu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
De
v
iceBuffer headers ar
e
added
commit
|
commitdiff
|
tree
2018-04-12
Ale
k
sei Iupinov
Make
in-so
u
rce OpenCL kernel pa
t
h a per-module
p
aramete
r
commit
|
commitdiff
|
tree
2018-04-12
Aleksei
I
u
p
inov
Re
m
ove
C
UDA_FUNC macros from many f
u
n
c
t
ions in PM
E
GPU
commit
|
commitdiff
|
tree
2018-04-12
Al
e
ksei I
u
pinov
Stop
PME
G
P
U c
o
de from co
m
pil
i
ng on no
n
-CUDA b
u
i
lds
commit
|
commitdiff
|
tree
2018-04-10
Aleksei
Iupinov
P
revent Op
e
n
C
L
timing memor
y
lea
k
commit
|
commitdiff
|
tree
2018-03-20
A
leksei Iupinov
Cla
r
ify the mdrun GPU options docs
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupino
v
Ad
d
a basic TPI sanit
y
te
s
t
commit
|
commitdiff
|
tree
2018-03-16
A
l
eksei Iupin
o
v
Stop
g
mx_feenab
l
ee
x
c
e
p
t
(
) from returnin
g
p
r
evi
o
us exceptio
n
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
Restore the lost mc
_
temp check
in gr
o
mpp
commit
|
commitdiff
|
tree
2018-03-06
A
l
eksei Iup
i
nov
Isolate PME GPU spline
p
ar
a
me
t
er index
i
ng in inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
A
l
e
ksei Iupin
o
v
S
top
u
sing
c
ustom FindOpenCL
.
cmake
,
per TODO
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupin
o
v
Correct the nbnxn_
g
p
u
_
compil
e
_kernels() docs
commit
|
commitdiff
|
tree
2018-03-02
Aleksei Iupinov
Make TPI use doubl
e
precision exp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei Iupino
v
Merge
branc
h
'rele
a
s
e
-2018'
commit
|
commitdiff
|
tree
2018-02-26
A
leks
e
i Iupinov
A
d
vice us
e
rs on infinite output of TPI
commit
|
commitdiff
|
tree
2018-02-20
Aleksei Iupinov
Remove unus
e
d
Open
C
L
debu
g
buffer
commit
|
commitdiff
|
tree
2018-02-18
Aleksei Iup
i
nov
Replace *_free
_
buf
f
ered calls
by freeDe
v
i
c
eB
u
ffer
commit
|
commitdiff
|
tree
2018-02-16
A
l
e
ksei Iupino
v
Fix PME for
larg
e
syst
e
m
s
with F
e
rmi GPUs
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iup
i
nov
Updat
e
FFTW build t
o
3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Add
freeDeviceBuffer
GPU u
t
ility f
u
nct
i
o
n
commit
|
commitdiff
|
tree
2018-02-15
Ale
k
sei Iu
p
i
nov
Add the missin
g
com
m
a
in
t
he
quo
t
e
commit
|
commitdiff
|
tree
2018-02-14
A
l
eksei Iupinov
Repla
c
e
the rem
a
ining EXPECT_DEA
T
H wit
h
E
X
PECT_DEATH_IF_
S
UPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Alekse
i
Iupinov
Add Dev
i
c
e
Buffer as
a
typ
e
d
e
f for c
l
_mem/device pon
t
er
commit
|
commitdiff
|
tree
2018-02-13
Aleksei Iupinov
Move GPU trait
s
into
separate he
a
ders
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iupi
n
ov
F
ix t
h
e include guard
commit
|
commitdiff
|
tree
2018-02-09
Alekse
i
Iupinov
Revert
"Enable debug FP exc
e
ptions without TPI
,
n
o
t
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Al
e
k
s
e
i
Iupi
n
ov
A
lways run the essential dynamics t
e
st
s
commit
|
commitdiff
|
tree
2018-02-08
Al
e
ksei
Iup
i
nov
Enable
deb
u
g FP exceptions w
i
thout TPI, not with TPI
commit
|
commitdiff
|
tree
2018-02-08
Al
e
ksei Iupinov
Merge branch
'release-2018'
i
n
to master
commit
|
commitdiff
|
tree
2018-02-06
A
l
eksei Iupinov
Remove unneces
s
ary includes from d
o
mdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Alek
s
ei Iupinov
Zero unused v
a
lue
s
to silence the warning
commit
|
commitdiff
|
tree
2018-02-06
Aleks
e
i
Iupinov
Only
setup Ewald in th
e
generic
group ke
r
nel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Ale
k
sei Iupinov
Make n
d
x
files optional in SimulationRun
n
e
r
commit
|
commitdiff
|
tree
2018-02-05
A
l
e
ksei Iupin
o
v
Remove mdpIn
p
u
tFileN
a
me_ from Simulati
o
n
R
un
n
er, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
leksei Iupi
n
o
v
Do
n
't print impossible CUDA
version nu
m
bers
i
n abs
e
nc
e
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei
Iupinov
Fix input MDP
c
ontents for swap and IMD tests
commit
|
commitdiff
|
tree
2018-02-01
Aleksei I
u
pinov
C
h
eck
fo
r
GTEST
_
IS_T
H
READSAFE being
defined
commit
|
commitdiff
|
tree
2018-01-24
Aleksei
I
upinov
Remove unused field
s
per TO
D
O
commit
|
commitdiff
|
tree
2018-01-23
Al
e
ksei
Iupinov
Tes
t
the mixed mode PME w
i
th w
a
lls and box sc
a
ling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Test
P
M
E CPU/GPU with
wal
l
s and box sca
l
ing
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
W
rap
t
h
e
P
ME testing lo
o
p in a metho
d
for extensibility
commit
|
commitdiff
|
tree
2018-01-19
A
l
eksei Iupinov
A
dd a
d
ea
t
h test for
the duplicate
i
npu
t
rec k
e
y
s ch
e
cking
commit
|
commitdiff
|
tree
2018-01-19
Aleksei I
u
p
i
nov
Rename class
B
iasRead
e
r to struct Bias
O
utput
S
e
t
up
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i
I
u
p
ino
v
Move th
e
temporary file MPI workaround into the
base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
A
l
eks
e
i
I
upinov
Make the reference
d
ata varia
b
les
local i
n
G
e
tIrTest
commit
|
commitdiff
|
tree
2018-01-19
A
l
e
k
sei Iupinov
Merge
br
a
nch 'releas
e
-2018' in
t
o maste
r
commit
|
commitdiff
|
tree
2018-01-18
Al
e
ksei I
u
pinov
Got rid of manua
l
memory manag
e
ment in th
e
PME ov
e
r
lap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Al
e
ksei Iupinov
Re-enable multi-ra
n
k P
M
E
tests (
w
ith the file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Ale
k
s
e
i Iupinov
Fix box
scal
i
ng in PME m
i
x
ed m
o
de
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Merge branch 'release-2018
'
into master
commit
|
commitdiff
|
tree
2018-01-16
Aleksei Iupinov
Al
w
a
ys write
th
e
input MDP fil
e
for testing just before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupinov
Move Octan
e
San
d
wich
.
mdp and spc2-I
M
D
.
mdp in
t
o stri
n
gs
commit
|
commitdiff
|
tree
2018-01-11
A
l
e
ksei Iupinov
Re
m
ove unused
a
lanine_vs
i
te
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Alekse
i
Iu
p
inov
Do not print PME counter breakdow
n
if it's e
m
pty
commit
|
commitdiff
|
tree
2017-12-20
A
l
e
ksei Iupi
n
ov
S
et GMX_GPU_AUTO to FALS
E
with GMX_GPU defined
commit
|
commitdiff
|
tree
2017-12-20
Aleks
e
i I
u
pinov
Remove potential
l
y wrong "per user request"
n
ote from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Alekse
i
I
upinov
Re
l
axed pr
e
cis
i
on in
spline
i
nterpol
a
tion tests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei Iupinov
Provide dummy init
i
alization to silence a warn
i
ng
commit
|
commitdiff
|
tree
2017-12-05
Aleksei Iup
i
nov
Do not accept
unsupporte
d
combination "-pme cpu
-pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei
I
u
pino
v
Reformulate PME so
l
vi
n
g te
s
ts t
o
lerances
commit
|
commitdiff
|
tree
2017-11-28
Aleksei
I
u
p
inov
Re
p
lace of pmeGPU
va
r
ia
b
le name with pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
Al
e
ksei Iupin
o
v
Do not forc
e
separate PME rank t
o
r
ecompute
r
ecipr
o
cal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Disable
f
a
iling separate
PME rank
t
e
sts
commit
|
commitdiff
|
tree
2017-11-27
Aleks
e
i Iupinov
A
dd tests for P
M
E
tuning and fix
mixed PME mode
w
it
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iup
i
nov
Destroy PME G
P
U
context
commit
|
commitdiff
|
tree
2017-11-24
Al
e
k
se
i
Iupinov
Enab
l
e separa
t
e
P
ME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iu
p
in
o
v
Do not ca
l
l
m
ixed CPU+GPU PME mode "
H
yb
r
id"
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Activa
t
e mixed mo
d
e of PME on G
P
U
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iu
p
in
o
v
Remove outdated (already impleme
n
ted)
p
inning TODO
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iup
i
n
o
v
Men
t
ion g
m
x_inst
a
ll_headers() i
n
the developer ma
n
ual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Make FFT real-space
gri
d
use
CUDA pin
n
i
n
g f
o
r
m
ixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupi
n
ov
Pin c
o
ordina
t
es, forces an
d
charges for PME on GP
U
commit
|
commitdiff
|
tree
2017-11-21
Al
e
k
sei Iupinov
Fix CUDA r
e
lease bu
i
ld warn
i
ng
commit
|
commitdiff
|
tree
2017-11-21
Aleks
e
i
Iupinov
Fix
p
inned
m
emo
r
y
status checke
r
tests
commit
|
commitdiff
|
tree
2017-11-18
Aleksei I
u
pinov
Asynchronous
CUDA
transfer
s
are
asserted to a
l
way
s
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Alek
s
ei Iup
i
nov
Make
g
pu_utils-test
b
u
ild with GMX_C
L
ANG_CUDA
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iupinov
Re
n
ame and ex
p
ose
"generic" GPU me
m
ory
t
ran
s
fe
r
functio
n
s
commit
|
commitdiff
|
tree
2017-11-09
Ale
k
sei Iupinov
Rename synchronous GPU tra
n
sfer functions to
m
atch
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Alekse
i
Iupin
o
v
R
e
pla
c
e math
.
h by cmath
i
ncludes in cpp file
s
commit
|
commitdiff
|
tree
2017-11-01
Aleks
e
i Iupinov
R
emove unused PME GPU
declarations
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iup
i
nov
Move pme_
g
pu_finish_computation(
)
documentat
i
on to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
A
leksei
Iupinov
F
ix
e
rroneous PME GPU "s
t
e
p"
n
a
m
ings
commit
|
commitdiff
|
tree
2017-11-01
A
l
eksei Iupinov
Simplify PME GPU synchronization
c
ode
commit
|
commitdiff
|
tree
2017-10-31
Al
e
ksei Iu
p
inov
R
euse epbcXY logic
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Fix refe
r
ence mode
b
u
i
ld unu
s
ed function wa
r
nings
commit
|
commitdiff
|
tree
2017-10-30
Alekse
i
Iupinov
Bring PME
GPU/CUDA
i
ntern
a
l structure n
a
mes to C
a
melCase
commit
|
commitdiff
|
tree
2017-10-30
A
leksei
Iupinov
Use new/delet
e
for gmx_pme_t
commit
|
commitdiff
|
tree
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