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Move the PmeGpuSpecific structure into pme-gpu-types-host-impl.h
2018-05-31
Ale
k
se
i
Iupinov
Move
the
P
meGpuSpecif
i
c struc
t
ure into pme-gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iu
p
i
nov
Adde
d
t
h
e b
u
ndled clFFT into
OpenCL bui
l
ds
commit
|
commitdiff
|
tree
2018-05-31
A
leksei
Iupinov
Ad
d
G
puEve
n
t
S
ynchronizer cl
a
s
s
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupino
v
Gat
h
er the PM
E
GPU con
s
tants/macros in
a
sin
g
le
h
eader
commit
|
commitdiff
|
tree
2018-05-30
Aleks
e
i Iupinov
Make PME GPU structures use De
v
iceBuffer
commit
|
commitdiff
|
tree
2018-05-28
Aleksei
Iupinov
Suppor
t
persist
e
nt device context-derived
d
at
a
in
PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iupinov
prepa
r
e
G
p
u
KernelArguments() and launc
h
GpuKernel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei I
u
pi
n
ov
Import clFFT l
i
brary into t
h
e Gromacs sour
c
e
commit
|
commitdiff
|
tree
2018-05-04
Alek
s
ei Iu
p
i
n
ov
Add cl
e
a
r
De
v
iceBuffe
r
Async() for CUDA
/
O
p
e
n
C
L
commit
|
commitdiff
|
tree
2018-05-03
Aleksei Iupinov
Co
p
y
missing GP
U
NB host
deallo
c
ations from O
p
enCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Aleksei
I
upino
v
rep
l
ace cu_c
o
py_* c
a
lls with Devic
e
Buffer func
t
ions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
A
leksei Iupinov
Rename
OpenCL host memory
r
out
i
n
e
s to match the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupi
n
ov
Make asize() a prope
r
t
e
mpl
a
te fu
n
ction
i
n
stead of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
A
l
ek
s
ei Iupinov
Ren
a
me the asize variable
t
o numAlignmentAtoms
commit
|
commitdiff
|
tree
2018-04-26
Aleksei I
u
pinov
Separate PME
GPU ho
s
t-only
a
nd host/d
e
v
ice dat
a
st
r
uctures
commit
|
commitdiff
|
tree
2018-04-26
Ale
k
sei Iu
p
ino
v
Ad
d
c
o
pyFr
o
mDeviceBuffe
r
() CUDA/O
p
e
n
C
L implementations
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iu
p
inov
Removed cu
_
realloc
_
bu
f
fered() i
n
favor of reallocateDevi
c
eB
u
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei
Iup
i
nov
D
e
viceBu
f
fer headers are
a
dded
commit
|
commitdiff
|
tree
2018-04-12
A
leksei Iupinov
Make in-source
Op
e
nCL kernel path a pe
r
-module paramet
e
r
commit
|
commitdiff
|
tree
2018-04-12
Ale
k
sei
I
u
pinov
R
emove CUDA_FUNC
macros f
r
om many functions in P
M
E GPU
commit
|
commitdiff
|
tree
2018-04-12
Al
e
ksei I
u
pinov
Sto
p
PME
G
P
U code f
r
om compiling o
n
non-CUDA builds
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iup
i
n
o
v
Prevent Op
e
nCL timing memory leak
commit
|
commitdiff
|
tree
2018-03-20
A
leksei Iu
p
in
o
v
Clarify the
mdrun GPU options docs
commit
|
commitdiff
|
tree
2018-03-16
Alek
s
ei Iupi
n
ov
Add a basic TPI
sanity test
commit
|
commitdiff
|
tree
2018-03-16
Alek
s
ei
I
u
pinov
Stop
gmx_fe
e
na
b
leexcept() from returning p
r
evious exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
A
le
k
s
e
i Iupin
o
v
Restore the
lost mc
_
temp che
c
k in g
r
ompp
commit
|
commitdiff
|
tree
2018-03-06
Al
e
ksei
I
upino
v
Isolate PME GPU spline parameter indexin
g
in inl
i
ne
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupinov
Stop using
custom Fin
d
OpenCL
.
cmake, p
e
r TODO
commit
|
commitdiff
|
tree
2018-03-05
Al
e
kse
i
Iupinov
Cor
r
ect the nbnxn_gpu_com
p
ile_kernels
(
)
docs
commit
|
commitdiff
|
tree
2018-03-02
Aleksei
Iupinov
M
ake TPI use dou
b
le prec
i
s
ion exp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei Iupinov
M
e
r
g
e
branch 'rele
a
se-2018'
commit
|
commitdiff
|
tree
2018-02-26
A
l
eksei Iupinov
Ad
v
ice users
o
n in
f
i
n
ite
o
u
t
put
o
f TPI
commit
|
commitdiff
|
tree
2018-02-20
Ale
k
sei Iup
i
no
v
R
emove u
n
used OpenCL debug buffer
commit
|
commitdiff
|
tree
2018-02-18
A
l
eksei Iupinov
Replace *_free_buffered cal
l
s
by freeDevi
c
eBuffer
commit
|
commitdiff
|
tree
2018-02-16
Aleksei Iupinov
Fix PME for
large
sy
s
t
e
m
s with Fermi GPUs
commit
|
commitdiff
|
tree
2018-02-15
A
l
e
k
sei Iupinov
Upda
t
e FFTW build to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei I
u
pinov
Add freeDeviceBu
f
fer GP
U
utility fun
c
tion
commit
|
commitdiff
|
tree
2018-02-15
Ale
k
sei Iupin
o
v
Add
the mis
s
ing comma in the quot
e
commit
|
commitdiff
|
tree
2018-02-14
Ale
k
sei Iupinov
Replace t
h
e
r
e
main
i
ng EXPECT_DEATH wi
t
h
E
X
PEC
T
_D
E
ATH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
A
leksei Iupinov
Add DeviceBuf
f
er as
a
ty
p
ed
e
f
f
or
cl
_
mem/device ponter
commit
|
commitdiff
|
tree
2018-02-13
Alekse
i
I
u
p
inov
M
o
ve G
P
U
traits i
n
to se
p
arate
headers
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iupinov
Fix the includ
e
guard
commit
|
commitdiff
|
tree
2018-02-09
Alekse
i
Iupinov
Rever
t
"E
n
able debug FP exceptions w
i
tho
u
t TPI,
not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
A
leksei Iupinov
Alwa
y
s run t
h
e
e
sse
n
tial dynamics tests
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupino
v
Enable debug FP
exceptions without TPI,
not with TPI
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
Merge b
r
anch
'release-2018' into maste
r
commit
|
commitdiff
|
tree
2018-02-06
A
l
e
k
sei
Iupinov
Remove unneces
s
ary includes
f
rom domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Alek
s
ei Iu
p
in
o
v
Ze
r
o u
n
use
d
values to silen
c
e
the
warning
commit
|
commitdiff
|
tree
2018-02-06
A
l
eksei
I
u
pinov
Only setup
Ewald in the gene
r
ic grou
p
kernel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Alekse
i
I
u
pinov
Ma
k
e ndx
files optional in SimulationRunner
commit
|
commitdiff
|
tree
2018-02-05
A
l
e
ks
e
i I
u
pinov
Remove md
p
In
p
utFileName_
f
rom SimulationRun
n
er
,
per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Al
e
ksei Iupinov
Don't pri
n
t impossib
l
e CUDA ve
r
s
ion numbers in ab
s
e
n
ce
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
l
eks
e
i
I
u
pi
n
ov
Fix in
p
ut MD
P
contents for swap
a
n
d
IMD te
s
ts
commit
|
commitdiff
|
tree
2018-02-01
Alekse
i
I
up
i
nov
Check
f
or GTEST
_
IS_THREADSA
F
E being defined
commit
|
commitdiff
|
tree
2018-01-24
Aleksei Iupi
n
o
v
Remove unused
fields per TODO
commit
|
commitdiff
|
tree
2018-01-23
Ale
k
sei Iu
p
inov
Te
s
t the mixed mode PM
E
with walls and box
s
caling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei
Iupinov
T
e
st PME CP
U
/GPU wit
h
walls and
box scaling
commit
|
commitdiff
|
tree
2018-01-23
Ale
k
sei Iupinov
Wrap
t
he PME testing loop in a method for extensibility
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iup
i
nov
Add a
d
ea
t
h
tes
t
f
o
r the
duplicat
e
input
r
ec keys checking
commit
|
commitdiff
|
tree
2018-01-19
Aleksei
Iupinov
Rename
class BiasR
e
ader to stru
c
t BiasOu
t
putSetup
commit
|
commitdiff
|
tree
2018-01-19
Aleksei
I
upinov
Mov
e
the tempora
r
y file
MPI
wor
k
aro
u
n
d
i
nto t
h
e base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Aleksei I
u
pinov
M
a
ke
the reference data
variable
s
lo
c
a
l in GetIrTes
t
commit
|
commitdiff
|
tree
2018-01-19
Al
e
ksei I
u
pinov
Merge branch 'relea
s
e
-
2018' in
t
o
m
a
s
ter
commit
|
commitdiff
|
tree
2018-01-18
Aleks
e
i
Iu
p
inov
Got rid of manual memory man
a
gement in t
h
e PME overl
a
p
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Ale
k
sei I
u
pinov
Re-enable multi-ra
n
k PME t
e
sts
(
with
t
h
e file r
a
ce
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Alek
s
ei Iup
i
nov
F
ix box scaling in PME mixed mode
commit
|
commitdiff
|
tree
2018-01-17
Aleksei
I
upinov
M
erge
bra
n
ch 'release-2018' into master
commit
|
commitdiff
|
tree
2018-01-16
Aleksei
Iupinov
Always w
r
ite the input
M
DP file for testing just before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
A
l
eksei
I
upin
o
v
Move OctaneSandwic
h
.
mdp and spc2-IMD
.
mdp into str
i
n
g
s
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iu
p
in
o
v
Remove
unuse
d
ala
n
i
n
e
_
vsi
t
e
.
m
dp
commit
|
commitdiff
|
tree
2018-01-10
Aleksei I
u
p
inov
Do
n
ot print PME counter bre
a
kdown if
it's e
m
pty
commit
|
commitdiff
|
tree
2017-12-20
Aleksei
I
upi
n
o
v
Set GMX_
G
PU_AU
T
O to FALSE with GM
X
_GP
U
d
e
f
i
n
ed
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupinov
R
emove potentially wr
o
n
g
"per use
r
request" note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Aleksei
I
u
p
i
nov
Relaxed precision in s
p
line interpol
a
tion tests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei Iupinov
Provi
d
e dummy initializa
t
ion
to
s
ilence a war
n
ing
commit
|
commitdiff
|
tree
2017-12-05
Alekse
i
Iupinov
Do n
o
t
ac
c
ept unsu
p
ported combination "-p
m
e cpu
-
pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Ale
k
sei Iupinov
Reformulate PME solving
test
s
t
oleranc
e
s
commit
|
commitdiff
|
tree
2017-11-28
A
l
ek
s
ei Iupino
v
Replac
e
of pmeGPU variable na
m
e w
i
th pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
A
leksei Iupinov
Do not force s
e
parate
PME rank to reco
m
pute
reciprocal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Dis
a
bl
e
failing
s
eparate PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupino
v
Add tests fo
r
P
M
E tuning and
fix mixed
PME mode with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei Iu
p
inov
D
estroy PME GPU
context
commit
|
commitdiff
|
tree
2017-11-24
A
leksei Iupinov
Enable separate PM
E
GPU ran
k
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iup
i
n
o
v
Do
n
ot call
m
i
xed CPU+
G
PU PME mode
"
H
y
bri
d
"
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iup
i
nov
Activate mixed
m
ode
o
f
PME on GPU
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Remove
o
utd
a
te
d
(alrea
d
y imp
l
emented) pinning T
O
D
O
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i I
u
pinov
M
e
ntion gmx_i
n
stall_headers() i
n
th
e
developer
m
anual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
M
a
ke FFT real-space grid use CUDA pinn
i
ng for mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
A
le
k
sei
Iupinov
P
i
n
c
oordinates, forces and charges for PME
o
n G
P
U
commit
|
commitdiff
|
tree
2017-11-21
Al
e
ksei Iupino
v
Fix CUDA release build warning
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupin
o
v
Fix pinned memory status checker tests
commit
|
commitdiff
|
tree
2017-11-18
A
l
eksei Iupinov
Asynchron
o
u
s
CUDA tr
a
nsfers are asser
t
ed to always
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Aleksei I
u
pinov
Make gpu_utils-tes
t
build wit
h
GM
X
_CLANG_CUDA
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iupinov
Rename
a
nd exp
o
s
e
"generic" G
P
U
memory tran
s
fer f
u
nc
t
ions
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iup
i
nov
Re
n
am
e
synchrono
u
s
G
PU tr
a
nsfer functions to match
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei Iupinov
Replace m
a
th
.
h by cmath in
c
ludes
i
n cpp f
i
les
commit
|
commitdiff
|
tree
2017-11-01
Aleks
e
i
I
u
p
inov
R
em
o
ve unused
P
ME GPU declar
a
t
i
ons
commit
|
commitdiff
|
tree
2017-11-01
Alekse
i
Iu
p
inov
M
o
ve pme_gpu_finish_
c
om
p
utation()
doc
u
men
t
ation
t
o
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
A
l
ekse
i
Iupinov
Fix erron
e
ous PME GPU
"
st
e
p" namings
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupin
o
v
Simplify P
M
E GPU synchr
o
nization code
commit
|
commitdiff
|
tree
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