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Write lambdas and box to TNG at correct intervals
2018-05-31
Aleksei Iupinov
Merge pme
.
cu
into pme-g
p
u-int
e
rnal
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
A
leksei Iupinov
PME Open
C
L 3D FFT
t
ransfo
r
m
i
s implemented, using cl
F
FT
commit
|
commitdiff
|
tree
2018-05-31
Aleksei I
u
p
i
nov
Move pme-timings
.
cu to pme-gpu-timings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Pr
e
f
e
r l
i
nking to system clFFT rath
e
r
than b
u
n
d
led one
commit
|
commitdiff
|
tree
2018-05-31
Aleks
e
i Iupi
n
ov
Move the PmeGpuSpecific struc
t
ure
i
nto pm
e
-gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
A
d
ded th
e
bun
d
led clFF
T
into OpenCL builds
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei I
u
pinov
Add Gp
u
EventSynchronizer cla
s
s
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Gather the PM
E
GPU constant
s
/
macros in a sin
g
le header
commit
|
commitdiff
|
tree
2018-05-30
A
leksei Iupino
v
Make PME G
P
U st
r
u
c
tures use DeviceBuffer
commit
|
commitdiff
|
tree
2018-05-28
Aleksei Iu
p
inov
Support persistent device context-derived data in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iu
p
inov
prepareGpuKern
e
lA
r
gume
n
ts
(
) and
laun
c
hGp
u
K
ern
e
l()
a
re
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Alekse
i
Iupinov
Import clFFT library into the Gromacs source
commit
|
commitdiff
|
tree
2018-05-04
A
leksei Iupinov
Add clearDeviceBufferAsy
n
c(
)
for CUDA/Ope
n
CL
commit
|
commitdiff
|
tree
2018-05-03
A
lek
s
ei
I
upin
o
v
Copy missing G
P
U NB host
deall
o
ca
t
ions from OpenCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
A
leksei Iup
i
nov
repla
c
e cu_copy_* calls
wi
t
h Dev
i
ceBu
f
fer f
u
nctions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Aleksei
Iupinov
Rename OpenCL h
o
st m
e
mory
r
outines to match the CUD
A
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
A
l
e
kse
i
Iupinov
Make asi
z
e() a proper
t
emplat
e
function instead of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupinov
Rena
m
e th
e
asize variabl
e
t
o
n
u
m
A
lignmentAtoms
commit
|
commitdiff
|
tree
2018-04-26
Aleksei
I
u
p
inov
S
epa
r
ate PM
E
G
PU host-only and host/device data str
u
ctures
commit
|
commitdiff
|
tree
2018-04-26
A
leksei
Iu
p
i
n
ov
Ad
d
c
o
pyFrom
D
e
v
iceBuffer() CUDA/OpenCL impleme
n
ta
t
ions
commit
|
commitdiff
|
tree
2018-04-23
Aleksei
Iupino
v
R
e
moved
c
u
_realloc
_
buffe
r
ed(
)
in fav
o
r of reallocateD
e
vice
B
u
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
DeviceBuffer headers are a
d
ded
commit
|
commitdiff
|
tree
2018-04-12
A
l
eksei Iupinov
M
ake in-sourc
e
OpenCL kernel p
a
th a per-module parameter
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iu
p
inov
Remove
CUDA
_
FUNC macros from man
y
functio
n
s in PME GPU
commit
|
commitdiff
|
tree
2018-04-12
Al
e
ksei
I
u
pinov
Stop
PME GPU code from comp
i
ling on non-
C
UDA b
u
i
l
ds
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
P
revent Op
e
nCL timing memory l
e
ak
commit
|
commitdiff
|
tree
2018-03-20
Al
e
k
se
i
Iup
i
nov
Clarify the
m
drun
GPU option
s
docs
commit
|
commitdiff
|
tree
2018-03-16
Alekse
i
Iupinov
A
d
d a ba
s
ic TPI sanity te
s
t
commit
|
commitdiff
|
tree
2018-03-16
Alekse
i
Iupin
o
v
Stop
gmx_fe
e
n
ab
l
eexcept() from r
e
t
urning
p
revious exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei
I
u
p
inov
Res
t
ore the lost
m
c_temp check in grompp
commit
|
commitdiff
|
tree
2018-03-06
A
l
eksei Iu
p
inov
Is
o
lat
e
PME
GPU s
p
l
i
n
e
pa
r
ameter indexing
i
n inl
i
ne
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupinov
S
t
op usin
g
custo
m
Fi
n
dOpenCL
.
cmake, per TOD
O
commit
|
commitdiff
|
tree
2018-03-05
A
l
eksei
I
upinov
Corre
c
t t
h
e nbnxn_g
p
u
_com
p
i
l
e
_kernels() doc
s
commit
|
commitdiff
|
tree
2018-03-02
Alekse
i
Iu
p
inov
M
a
ke TPI use do
u
ble pr
e
cision exp
commit
|
commitdiff
|
tree
2018-02-27
Ale
k
sei Iupinov
M
e
r
g
e
b
ranch 'release-20
1
8'
commit
|
commitdiff
|
tree
2018-02-26
A
leksei Iupinov
Advice users
on infinite output of TPI
commit
|
commitdiff
|
tree
2018-02-20
Al
e
ksei Iupi
n
ov
R
e
move unus
e
d Open
C
L debug buffer
commit
|
commitdiff
|
tree
2018-02-18
Aleksei Iu
p
inov
Replace *_free_
b
uff
e
red calls
by
f
re
e
D
e
vic
e
Buffer
commit
|
commitdiff
|
tree
2018-02-16
Aleksei
Iupinov
Fix
P
ME for large
systems
with Fermi GP
U
s
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Update
FFTW buil
d
to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Al
e
ksei Iupinov
Add freeDeviceBuffer GPU utility function
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
A
d
d t
h
e mis
s
ing c
o
mm
a
in the quote
commit
|
commitdiff
|
tree
2018-02-14
A
lekse
i
Iu
p
inov
Repla
c
e
t
h
e remaining
EXPECT_DEA
T
H w
i
th EXPEC
T
_DE
A
TH_
I
F_
S
U
P
P
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Add De
v
iceBuffer as a typedef
f
or
c
l
_mem/d
e
vice pont
e
r
commit
|
commitdiff
|
tree
2018-02-13
Al
e
ksei
I
upinov
Mo
v
e GPU trait
s
into separat
e
headers
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iu
p
ino
v
Fi
x
t
he includ
e
guar
d
commit
|
commitdiff
|
tree
2018-02-09
Aleks
e
i Iupi
n
ov
Rev
e
rt
"
E
n
a
ble
debu
g
FP exceptions
w
ithout TPI, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
Always run the essenti
a
l dynamics tests
commit
|
commitdiff
|
tree
2018-02-08
Aleksei
I
u
p
i
nov
Enable
debug
FP
e
x
c
eptions
without TPI, n
o
t with TPI
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
M
e
r
ge branch 'release-2018' into master
commit
|
commitdiff
|
tree
2018-02-06
Alekse
i
Iupino
v
Remove unnece
s
sary includes fro
m
domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iup
i
n
o
v
Zero unused valu
e
s t
o
silence the
w
arning
commit
|
commitdiff
|
tree
2018-02-06
Alek
s
e
i
Iupin
o
v
Only setu
p
Ewald in the generic group
kernel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupinov
Make
n
d
x
files optional in
Simulati
o
nRunner
commit
|
commitdiff
|
tree
2018-02-05
A
l
eksei Iupi
n
ov
Remove
m
dpInputFil
e
N
a
me_ from S
i
m
ulationRunn
e
r, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
Don'
t
p
r
int im
p
ossible CUDA version numbers i
n
ab
s
en
c
e
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Ale
k
sei I
u
pinov
F
i
x
i
n
put
MDP contents for sw
a
p
and
I
MD
tests
commit
|
commitdiff
|
tree
2018-02-01
Aleksei Iupinov
C
h
eck for G
T
EST_
I
S
_THREADSAFE being define
d
commit
|
commitdiff
|
tree
2018-01-24
Aleksei Iupin
o
v
Remove unused fields per TODO
commit
|
commitdiff
|
tree
2018-01-23
A
leksei Iupinov
Test t
h
e mixed mode PME
w
it
h
w
a
l
ls and b
o
x sc
a
ling
commit
|
commitdiff
|
tree
2018-01-23
A
leksei Iu
p
inov
Test PM
E
CPU/GPU
with walls and
b
ox
s
cali
n
g
commit
|
commitdiff
|
tree
2018-01-23
A
l
eks
e
i Iupinov
W
r
a
p the
PME tes
t
ing loop
in a method
for extensib
i
lity
commit
|
commitdiff
|
tree
2018-01-19
Al
e
ksei Iupino
v
Add a death tes
t
for the dup
l
ic
a
te inputrec keys checking
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
R
e
name class
B
iasReader to s
t
ruct BiasOu
t
pu
t
Se
t
u
p
commit
|
commitdiff
|
tree
2018-01-19
Aleksei
I
upinov
Move
t
he temporar
y
fil
e
MPI wo
r
karoun
d
into the base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
A
leksei Iupin
o
v
Mak
e
the reference data
v
ariables local
in GetIr
T
est
commit
|
commitdiff
|
tree
2018-01-19
A
l
eksei Iupinov
Merge branch '
r
e
l
ease-201
8
' into master
commit
|
commitdiff
|
tree
2018-01-18
Aleks
e
i Iupinov
G
o
t
r
id of manual memory management in
the
PME overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iu
p
in
o
v
Re-enable mult
i
-
rank PME
t
ests (with the
f
ile
r
a
c
e
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Fi
x
bo
x
scal
i
ng in PME mixed
mode
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Merge branch 'release-2018' into
m
a
ster
commit
|
commitdiff
|
tree
2018-01-16
A
leksei Iu
p
inov
A
lwa
y
s writ
e
the i
n
pu
t
MDP f
i
le for testing just
b
efor
e
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Alekse
i
I
u
pinov
M
o
ve OctaneSandwic
h
.
mdp and spc2-I
M
D
.
mdp into st
r
i
ngs
commit
|
commitdiff
|
tree
2018-01-11
Alekse
i
I
up
i
nov
Remove unus
e
d alanine_vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupin
o
v
D
o
not print
P
ME counter breakdown
if it's empty
commit
|
commitdiff
|
tree
2017-12-20
Ale
k
s
e
i
Iupi
n
ov
Set GMX_
G
PU_
A
U
TO t
o
FALSE with GMX_GPU de
f
ined
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupino
v
Remove p
o
tentially w
r
ong "per user reque
s
t" note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Al
e
kse
i
Iupinov
Relaxe
d
precision in spline i
n
terpol
a
tion tests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei Iupinov
Provide dummy init
i
alization to silence
a
w
arni
n
g
commit
|
commitdiff
|
tree
2017-12-05
Aleksei
Iupinov
Do not accept unsupp
o
rted
combin
a
t
ion
"-pme
cpu -pm
e
f
f
t
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei Iupinov
R
eformulate PME solvi
n
g te
s
ts t
o
lerances
commit
|
commitdiff
|
tree
2017-11-28
Aleks
e
i
I
upinov
Replace of
p
m
eGPU va
r
iable name
with pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
A
leksei
I
upi
n
ov
Do
not force separate
PM
E
r
ank to r
e
co
m
p
u
t
e
reciproca
l
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
A
leksei I
u
pinov
Di
s
ab
l
e fail
i
n
g
separate
PME rank
t
ests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
A
d
d tests
f
o
r PME tu
n
ing
a
nd fix mixed
PME mod
e
w
i
th
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei Iupinov
Destro
y
PME
G
PU co
n
tex
t
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i Iupinov
E
nable separate PME GP
U
rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iup
i
nov
Do not call mixed
C
PU+GPU
P
M
E
mode "Hy
b
rid"
commit
|
commitdiff
|
tree
2017-11-24
A
leks
e
i Iupinov
Activate mixed mode of PME
o
n GP
U
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupin
o
v
Remove out
d
ate
d
(already
implemented) pinn
i
ng
TODO
commit
|
commitdiff
|
tree
2017-11-24
Aleksei I
u
p
i
n
ov
Mention gmx_install_
h
eaders() in the developer ma
n
ual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
upinov
Make FFT real-spac
e
grid use CU
D
A
pinning fo
r
mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupi
n
o
v
Pin coordinates, f
o
rc
e
s and charges for PME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-21
Alek
s
ei Iup
i
nov
Fix CUDA
r
elease
b
uild warning
commit
|
commitdiff
|
tree
2017-11-21
Al
e
ksei
I
upinov
Fix
p
inn
e
d memory st
a
tus c
h
e
c
ker
t
e
s
ts
commit
|
commitdiff
|
tree
2017-11-18
Aleksei Iu
p
ino
v
As
y
nchronous
C
U
DA t
r
ansfers are
a
s
serted to alwa
y
s
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Alek
s
ei I
u
pino
v
Make gp
u
_uti
l
s-test build with GMX_CL
A
N
G_CUDA
commit
|
commitdiff
|
tree
2017-11-15
Alekse
i
Iupinov
Rename and expose "gener
i
c" G
P
U memory transfer funct
i
ons
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupi
n
ov
Ren
a
me
s
ynchronous
GPU transfer functions to match
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei
I
u
p
inov
Replace math
.
h
b
y cmath inclu
d
e
s
in cpp files
commit
|
commitdiff
|
tree
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