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prepareGpuKernelArguments() and launchGpuKernel() are added
2018-05-18
Aleks
e
i Iup
i
nov
prepare
G
puKernelArguments() and
launc
h
GpuKerne
l
()
a
re
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei Iupinov
Import clFFT
l
ibrary into the Gromacs sourc
e
commit
|
commitdiff
|
tree
2018-05-04
Aleks
e
i
I
upinov
Add
c
learDevi
c
e
Buffer
A
s
y
nc()
f
o
r
C
UDA/Ope
n
CL
commit
|
commitdiff
|
tree
2018-05-03
Aleksei Iupinov
C
opy
missi
n
g GPU NB host deal
l
oc
a
t
ions
f
rom OpenCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Alekse
i
I
upi
n
ov
re
p
lace
c
u_copy_
*
c
a
lls with DeviceBuffer functions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Aleksei
I
upinov
Re
n
ame OpenCL
h
ost memo
r
y routines to match the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Alek
s
ei Iupi
n
ov
Make asize(
)
a prop
e
r t
e
mplate function inste
a
d
of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Ale
k
s
e
i Iupinov
Rename the asize var
i
able to nu
m
Align
m
entAtoms
commit
|
commitdiff
|
tree
2018-04-26
Aleksei Iupinov
S
e
p
a
rate PME GPU ho
s
t-onl
y
an
d
host/device da
t
a s
t
r
u
ctures
commit
|
commitdiff
|
tree
2018-04-26
Ale
k
sei Iupinov
Add copyFromDevic
e
B
u
ffer()
C
UDA/OpenCL imple
m
entations
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupin
o
v
Removed cu_re
a
llo
c
_buffered() in favor of re
a
ll
o
cateDeviceBu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
DeviceBu
f
f
er headers are added
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iu
p
inov
M
a
ke in-source
OpenCL k
e
rnel p
a
t
h
a per-modul
e
parameter
commit
|
commitdiff
|
tree
2018-04-12
Ale
k
s
e
i Iupinov
Remo
v
e CU
D
A_
F
UNC macros from ma
n
y f
u
nctions in PME GP
U
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Stop PM
E
GP
U
code from compiling on non-CUDA builds
commit
|
commitdiff
|
tree
2018-04-10
A
leksei Iup
i
nov
Pr
e
vent OpenCL
t
iming memory
leak
commit
|
commitdiff
|
tree
2018-03-20
A
l
eksei Iupinov
Clari
f
y
th
e
mdrun GPU options docs
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
Add a basic TPI
s
a
nity
test
commit
|
commitdiff
|
tree
2018-03-16
Alek
s
ei
I
u
p
inov
Stop
g
mx_
f
ee
n
ableexcept() from ret
u
r
n
ing previous exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iu
p
inov
Restore the lost mc_temp
check in g
r
ompp
commit
|
commitdiff
|
tree
2018-03-06
Aleksei Iu
p
i
nov
Isolate
P
ME GPU spline parameter ind
e
x
i
ng in
i
nline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei
I
upinov
S
top using
custom
F
indOpenC
L
.
c
m
ak
e
,
p
er TODO
commit
|
commitdiff
|
tree
2018-03-05
Aleksei I
u
pinov
Co
r
rect the
n
b
nxn_gpu
_
compile_kernels() docs
commit
|
commitdiff
|
tree
2018-03-02
A
l
e
k
sei Iupinov
Ma
k
e TPI use dou
b
l
e
p
recision exp
commit
|
commitdiff
|
tree
2018-02-27
A
leksei Iu
p
inov
Merge branch '
r
ele
a
se-201
8
'
commit
|
commitdiff
|
tree
2018-02-26
Aleksei
I
upinov
Ad
v
ic
e
users o
n
i
nf
i
ni
t
e outpu
t
of TPI
commit
|
commitdiff
|
tree
2018-02-20
Aleksei Iu
p
i
n
ov
Re
m
ove unused
O
pe
n
CL debug b
u
f
fer
commit
|
commitdiff
|
tree
2018-02-18
A
l
eks
e
i Iupinov
Replac
e
*_
f
ree
_
buffe
r
ed calls by freeDeviceBuffer
commit
|
commitdiff
|
tree
2018-02-16
Aleks
e
i Iupino
v
Fix PM
E
for large s
y
s
t
e
ms with
F
ermi
G
PUs
commit
|
commitdiff
|
tree
2018-02-15
Ale
k
sei
I
u
p
inov
Up
d
ate FFTW
b
uild to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
A
l
eksei
I
upinov
Add
f
reeDeviceBu
f
fer GPU utility fu
n
ct
i
on
commit
|
commitdiff
|
tree
2018-02-15
A
l
ek
s
ei Iupinov
Add t
h
e missing
c
o
mma i
n
th
e
q
u
ote
commit
|
commitdiff
|
tree
2018-02-14
A
l
eksei Iupino
v
Re
p
lace the remainin
g
EXP
E
CT_D
E
ATH with
E
XPECT_DEATH
_
IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei
Iupinov
Add
DeviceB
u
ff
e
r as a typedef fo
r
cl
_
mem/device
p
onter
commit
|
commitdiff
|
tree
2018-02-13
Aleksei Iupinov
Move GPU
tra
i
ts into se
p
arate h
e
a
ders
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iup
i
nov
Fix the
i
n
c
lude guard
commit
|
commitdiff
|
tree
2018-02-09
Al
e
ksei Iupinov
Revert "E
n
a
bl
e
debug FP except
i
ons wi
t
hout
T
P
I
, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iup
i
no
v
Always run the essential dynamics tests
commit
|
commitdiff
|
tree
2018-02-08
Aleksei
I
upinov
Enable
d
e
bu
g
FP e
x
ceptions without TPI, not with
T
PI
commit
|
commitdiff
|
tree
2018-02-08
Al
e
k
sei Iupi
n
ov
Merge branch 'release-2018' in
t
o master
commit
|
commitdiff
|
tree
2018-02-06
Al
e
ksei Iupinov
Remove
un
n
ecessa
r
y
includes from d
o
mdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Alekse
i
Iupi
n
ov
Zero
unused
v
alues to silen
c
e
the warning
commit
|
commitdiff
|
tree
2018-02-06
A
leksei Iupinov
Onl
y
setup Ewald in
t
he
g
eneric group kerne
l
if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Alek
s
e
i
Iu
p
i
nov
Ma
k
e ndx
files op
t
i
onal in
S
im
u
lati
o
nRunner
commit
|
commitdiff
|
tree
2018-02-05
A
leksei Iu
p
inov
Remove
m
dpInputFileName_ from Simula
t
ion
R
u
n
ner,
pe
r
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei
Iupin
o
v
Don't prin
t
impo
s
s
i
ble
C
U
DA
version numbe
r
s in a
b
sence
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupin
o
v
F
i
x in
p
ut M
D
P co
n
tents
for swap
a
nd I
M
D tests
commit
|
commitdiff
|
tree
2018-02-01
Aleksei Iupi
n
ov
Check for
GTE
S
T_IS_THR
E
ADSA
F
E
being
d
efined
commit
|
commitdiff
|
tree
2018-01-24
Ale
k
sei Iupinov
Remove
unused
fields
p
er
T
O
DO
commit
|
commitdiff
|
tree
2018-01-23
A
leksei
I
upinov
Test th
e
mix
e
d m
o
de
P
ME with walls and box scal
i
ng
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
T
est PME CPU/GP
U
with w
a
lls and bo
x
scaling
commit
|
commitdiff
|
tree
2018-01-23
A
l
eks
e
i Iup
i
nov
Wrap the PME
t
esting loop in a method
f
or extensibility
commit
|
commitdiff
|
tree
2018-01-19
Alekse
i
Iupino
v
Add a death
t
est
f
or t
h
e duplicate inputrec key
s
checki
n
g
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
sei Iupinov
Re
n
ame c
l
a
ss
B
iasReader to stru
c
t BiasOu
t
putSetup
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Move the t
e
mpora
r
y file MPI workaround into t
h
e base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
M
a
ke the reference data variab
l
es
local in
Ge
t
I
r
Tes
t
commit
|
commitdiff
|
tree
2018-01-19
Al
e
ksei Iupin
o
v
M
e
rge b
r
anch 'rel
e
ase
-
2018' into m
a
ster
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupi
n
ov
Got rid of man
u
al memory m
a
nage
m
e
n
t in th
e
PME over
l
ap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Re-enable multi-rank PME tests (with the file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Fix box
scali
n
g
i
n PME mixed mode
commit
|
commitdiff
|
tree
2018-01-17
Al
e
kse
i
Iupin
o
v
Merge branch 'release-2018' into master
commit
|
commitdiff
|
tree
2018-01-16
Aleksei Iupin
o
v
Always
write the input M
D
P file for test
i
ng jus
t
b
e
fore
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupinov
Move O
c
taneS
a
ndwi
c
h
.
mdp a
n
d
spc2-IMD
.
mdp into stri
n
g
s
commit
|
commitdiff
|
tree
2018-01-11
Alek
s
ei Iupinov
Rem
o
ve unused a
l
anine_
v
s
ite
.
md
p
commit
|
commitdiff
|
tree
2018-01-10
Aleksei I
u
p
i
nov
D
o
not print PME
c
ounter
b
reakdown if
i
t
'
s empty
commit
|
commitdiff
|
tree
2017-12-20
Ale
k
sei
I
upin
o
v
S
e
t GMX_GPU_AU
T
O to FAL
S
E
w
ith GMX_GPU
d
efin
e
d
commit
|
commitdiff
|
tree
2017-12-20
A
l
eksei Iupinov
Remove po
t
entially
wrong "per u
s
er request" n
o
t
e
from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Al
e
ksei Iupinov
Relax
e
d preci
s
ion i
n
spli
n
e inter
p
olation tests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei Iupinov
Provide dummy initi
a
liza
t
i
on to
s
ilen
c
e a
w
arning
commit
|
commitdiff
|
tree
2017-12-05
A
l
eksei Iupinov
Do
n
ot
a
ccept
u
ns
u
pported
c
ombination
"
-pme
c
pu
-p
m
e
fft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
A
leksei Iupinov
Re
f
ormulate P
M
E solving t
e
s
t
s
tolerances
commit
|
commitdiff
|
tree
2017-11-28
Aleksei Iu
p
i
n
ov
Replace of
p
m
e
GP
U
variable name
with pme
G
pu
commit
|
commitdiff
|
tree
2017-11-27
Aleks
e
i Iup
i
n
o
v
Do not force separate P
M
E rank to recomp
u
te recipr
o
cal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Alekse
i
Iupinov
Disab
l
e failing sepa
r
ate PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Add t
e
sts for PME tuning and fi
x
mixed PME
m
od
e
with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
A
l
ekse
i
Iup
i
nov
D
e
stroy PME GP
U
c
o
ntext
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
sei Iupino
v
Enable
separate PME
G
PU rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
u
pinov
Do
not call mixed CPU+GPU PME mode "Hybrid"
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
u
pi
n
ov
Activate mixed
mode of P
M
E on
G
PU
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
R
e
m
o
ve outdated (alread
y
implemente
d
)
pinning
T
ODO
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iu
p
inov
Mention
g
mx_install_headers()
i
n t
h
e develo
p
er
manua
l
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iupin
o
v
Make FFT real-space gr
i
d use CUDA
pinning
f
or
m
i
x
ed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
P
i
n co
o
rdinates,
f
orces and charges
for PM
E
on G
P
U
commit
|
commitdiff
|
tree
2017-11-21
A
l
e
kse
i
Iupinov
Fix CUDA re
l
ease b
u
ild warning
commit
|
commitdiff
|
tree
2017-11-21
A
l
eksei Iupinov
F
ix pinned memory statu
s
checker tes
t
s
commit
|
commitdiff
|
tree
2017-11-18
Ale
k
s
ei I
u
pinov
Asynchronous CUD
A
t
r
an
s
fers are asserted to always
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Al
e
ksei Iup
i
nov
M
a
ke
gpu_utils-test build with GMX
_
CLANG_CUDA
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iu
p
inov
Rena
m
e
a
nd exp
o
se "generi
c
" GPU m
e
mory
t
r
a
nsfe
r
functions
commit
|
commitdiff
|
tree
2017-11-09
A
l
eksei Iupinov
Renam
e
synchronous G
P
U transfer fu
n
c
t
ions to
m
at
c
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Ale
k
s
e
i Iupinov
R
e
place math
.
h by cmath includes in cpp f
i
l
e
s
commit
|
commitdiff
|
tree
2017-11-01
Aleksei
I
upinov
Remove
unused PME
GPU de
c
larat
i
o
n
s
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Move
p
me_gpu_f
i
nis
h
_
c
omputati
o
n() docume
n
tation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
A
leks
e
i Iupinov
Fi
x
erroneous PME G
P
U "step" na
m
ings
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Si
m
pl
i
fy PME GPU
s
y
nc
h
r
o
n
izatio
n
cod
e
commit
|
commitdiff
|
tree
2017-10-31
A
lekse
i
Iupi
n
ov
Reuse epbcXY logic
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Fix ref
e
rence mode bui
l
d
unus
e
d fun
c
t
ion w
a
rnings
commit
|
commitdiff
|
tree
2017-10-30
A
lek
s
ei Iupinov
B
r
i
ng PME G
P
U/CUDA internal struct
u
r
e
n
ames to Ca
m
elCase
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Use ne
w
/
d
elete f
o
r gmx_pme_t
commit
|
commitdiff
|
tree
2017-10-30
Al
e
ksei
I
upinov
Simplif
y
PM
E
data ha
n
dlin
g
in
run
n
e
r
commit
|
commitdiff
|
tree
2017-10-29
Aleksei Iup
i
nov
Make P
M
E
tuning logic more readable
commit
|
commitdiff
|
tree
next