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Added the bundled clFFT into OpenCL builds
2018-05-31
Al
e
ksei Iupinov
Added the bundle
d
clFFT into OpenCL
buil
d
s
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Add GpuEve
n
tSy
n
chroni
z
er cla
s
s
commit
|
commitdiff
|
tree
2018-05-31
Alekse
i
Iupinov
G
ather the
P
ME GPU constants/macro
s
in a sing
l
e header
commit
|
commitdiff
|
tree
2018-05-30
Aleksei Iupinov
Make PME GPU st
r
uctures use DeviceBuffer
commit
|
commitdiff
|
tree
2018-05-28
Aleksei
I
upinov
S
uppo
r
t
p
ersi
s
t
e
nt dev
i
ce contex
t
-deriv
e
d data in P
M
E
.
.
.
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iupinov
p
repareGpuKer
n
el
A
rgum
e
nts(
)
a
nd launchGpuKernel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
A
l
eksei Iupinov
Import
c
lFFT
l
ibrary into the Gromacs source
commit
|
commitdiff
|
tree
2018-05-04
Aleksei Iupinov
Ad
d
clearD
e
v
iceBufferAsync()
f
or CUDA/OpenCL
commit
|
commitdiff
|
tree
2018-05-03
Aleksei Iupino
v
Cop
y
m
i
ssing GPU NB host dea
l
locations fr
o
m
O
penCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
A
lekse
i
Iup
i
nov
re
p
lace
cu_copy_* cal
l
s
with De
v
iceBuffer fu
n
ctions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Aleks
e
i Iupinov
Rename OpenC
L
host
memory rout
i
nes
to match the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Ale
k
sei Iu
p
i
n
ov
Ma
k
e asize() a
p
r
o
per
template function ins
t
ead of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupinov
R
ena
m
e the
asize
v
a
r
i
able to nu
m
Alignmen
t
Atoms
commit
|
commitdiff
|
tree
2018-04-26
Al
e
k
sei Iupinov
Separate PME GP
U
host-
o
nly and
ho
s
t/dev
i
ce
d
ata
structures
commit
|
commitdiff
|
tree
2018-04-26
A
leksei Iupinov
Add copyFromDevi
c
eBuff
e
r() CUDA/OpenCL implement
a
t
ions
commit
|
commitdiff
|
tree
2018-04-23
Aleksei
I
upinov
R
e
moved cu_
r
eall
o
c_
b
uffered() in favor of r
e
allo
c
ateDeviceBu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
DeviceBuffer headers ar
e
added
commit
|
commitdiff
|
tree
2018-04-12
Aleksei
I
u
p
i
nov
Make in-source Op
e
n
C
L
k
ernel path
a per-module parame
t
e
r
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Re
m
o
ve CUDA
_
FUNC macros from
m
any f
u
nctions in PME
G
PU
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Stop PME G
P
U code
from
c
o
m
piling on
non-CUDA bu
i
lds
commit
|
commitdiff
|
tree
2018-04-10
Ale
k
sei Iupinov
Prevent Op
e
nCL ti
m
ing memory leak
commit
|
commitdiff
|
tree
2018-03-20
Aleksei Iupin
o
v
Cl
a
ri
f
y
t
h
e mdr
u
n GPU op
t
ions docs
commit
|
commitdiff
|
tree
2018-03-16
Aleksei I
u
pino
v
Add
a basic
TPI sanity test
commit
|
commitdiff
|
tree
2018-03-16
Aleksei
I
u
p
i
n
o
v
Sto
p
gmx_feenableexcept()
f
r
om retur
n
ing pre
v
io
u
s exc
e
ption
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
Restore the
l
o
st mc_temp check in
g
r
omp
p
commit
|
commitdiff
|
tree
2018-03-06
Aleksei
Iupinov
Isolate PME
GPU spline parameter i
n
de
x
in
g
in inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Alekse
i
Iupinov
Stop usi
n
g custom
F
indOpe
n
CL
.
cmake, per TODO
commit
|
commitdiff
|
tree
2018-03-05
Aleksei I
u
p
inov
C
orrect the n
b
n
x
n
_gpu_compi
l
e_
k
ernels(
)
docs
commit
|
commitdiff
|
tree
2018-03-02
A
l
eksei Iupinov
Make TPI
u
se double
p
recision
e
xp
commit
|
commitdiff
|
tree
2018-02-27
A
leksei Iupino
v
M
e
rge branch 'release-2018'
commit
|
commitdiff
|
tree
2018-02-26
Aleksei
I
upinov
Advice users o
n
infinite output of TPI
commit
|
commitdiff
|
tree
2018-02-20
Aleksei
I
upi
n
ov
Re
m
ove u
n
u
sed Ope
n
CL debug buffer
commit
|
commitdiff
|
tree
2018-02-18
Al
e
k
s
ei Iup
i
nov
Replace *_free_b
u
ffered calls by
f
reeDev
i
ceBuffer
commit
|
commitdiff
|
tree
2018-02-16
Aleksei
I
u
pinov
Fix
P
ME
for l
a
r
ge s
y
stems with Fermi GPUs
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
U
p
d
ate FFT
W
build
to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Ad
d
freeDeviceBuffer GPU utili
t
y
f
unction
commit
|
commitdiff
|
tree
2018-02-15
Alek
s
ei I
u
pinov
A
dd
the missing comm
a
in t
h
e quote
commit
|
commitdiff
|
tree
2018-02-14
Ale
k
sei Iupinov
Repla
c
e the remaining EX
P
ECT_DEATH with EXPECT
_
DEATH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iu
p
inov
A
dd DeviceBuffer as a typ
e
def fo
r
c
l
_mem/device po
n
ter
commit
|
commitdiff
|
tree
2018-02-13
Aleksei
I
u
pinov
Move GPU traits int
o
sep
a
r
ate headers
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iupinov
Fix the include g
u
ard
commit
|
commitdiff
|
tree
2018-02-09
A
leksei Iupinov
Revert "Enable debug FP
e
xceptions wit
h
o
u
t
T
PI, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
A
l
ek
s
ei Iupin
o
v
A
l
ways run
t
he essent
i
al dynamics tes
t
s
commit
|
commitdiff
|
tree
2018-02-08
A
l
e
k
sei
I
upinov
Enab
l
e debug
FP
e
xc
e
p
tions without TPI, not
with T
P
I
commit
|
commitdiff
|
tree
2018-02-08
Aleks
e
i I
u
pinov
Me
r
g
e b
r
anch
'
relea
s
e
-
201
8
' into maste
r
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Remove unnece
s
s
a
ry includes from domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupi
n
o
v
Zero unu
s
ed
v
alues to si
l
en
c
e the warning
commit
|
commitdiff
|
tree
2018-02-06
Al
e
ksei Iupinov
Only setup Ewald in the generi
c
gr
o
u
p
kernel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Ale
k
s
ei Iupin
o
v
Mak
e
ndx files opti
o
nal in SimulationRunner
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupino
v
Re
m
ove mdpInputFileName
_
fr
o
m SimulationRunner, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei I
u
pinov
Don't prin
t
impossi
b
le CUDA version n
u
mbers in
a
bsence
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei I
u
p
i
nov
Fix
i
nput
M
DP contents for
s
wa
p
and IMD tests
commit
|
commitdiff
|
tree
2018-02-01
Al
e
ksei Iupino
v
Check for GTEST_IS_T
H
REA
D
SAFE being
d
e
f
i
ned
commit
|
commitdiff
|
tree
2018-01-24
Alek
s
ei Iupinov
Remov
e
unused field
s
per TODO
commit
|
commitdiff
|
tree
2018-01-23
Aleks
e
i Iupino
v
Test the mixed mode PME with walls and bo
x
sc
a
ling
commit
|
commitdiff
|
tree
2018-01-23
A
leksei Iupinov
T
e
st PME CPU/
G
PU
wi
t
h wal
l
s
and box
s
ca
l
ing
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Wrap the
P
M
E
te
s
ting loop in a method for exten
s
ibility
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Add
a deat
h
test for the duplicate input
r
ec ke
y
s
c
he
c
king
commit
|
commitdiff
|
tree
2018-01-19
Al
e
kse
i
Iupi
n
ov
Rename cla
s
s
BiasReader to struct BiasOutputS
e
tup
commit
|
commitdiff
|
tree
2018-01-19
Alekse
i
Iupin
o
v
Move th
e
temporary fi
l
e
M
P
I workaround
into the base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Make
t
he r
e
f
erence data variables
local in
GetIrTest
commit
|
commitdiff
|
tree
2018-01-19
A
le
k
s
ei
I
u
pino
v
Mer
g
e
branc
h
'release-2018' into
m
aster
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
G
ot rid o
f
m
anual
m
e
mory mana
g
ement in the PM
E
overl
a
p
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Re-en
a
b
le mu
l
ti-rank PME tests (w
i
t
h the fi
l
e race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Alekse
i
Iupinov
Fix box scaling in PM
E
mi
x
ed mo
d
e
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iu
p
inov
M
e
r
g
e branch '
r
e
le
a
se-2018' into master
commit
|
commitdiff
|
tree
2018-01-16
A
l
eks
e
i Iupinov
Always write the input MDP file fo
r
testi
n
g
j
u
st before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Aleksei
Iupinov
Mo
v
e OctaneSandwich
.
mdp
and spc2-I
M
D
.
mdp in
t
o str
i
ngs
commit
|
commitdiff
|
tree
2018-01-11
Ale
k
s
ei Iupinov
Remove unused
a
l
a
nine_vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupinov
Do not
p
r
i
nt PME counter b
r
eakdown i
f
it's
empty
commit
|
commitdiff
|
tree
2017-12-20
Alekse
i
I
u
pinov
Set
G
MX_GPU_A
U
TO to FALSE with G
M
X_GPU
defin
e
d
commit
|
commitdiff
|
tree
2017-12-20
A
lek
s
ei Iupinov
Re
m
ove p
o
tentiall
y
wrong "per
u
ser request" no
t
e from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Aleksei Iupinov
Relax
e
d precision
i
n spli
n
e int
e
rpolation tests
commit
|
commitdiff
|
tree
2017-12-06
Alek
s
ei
I
up
i
nov
Pr
o
v
i
de dummy i
n
itialization
to s
i
lence
a w
a
rni
n
g
commit
|
commitdiff
|
tree
2017-12-05
Ale
k
sei Iupinov
Do
not a
c
ce
p
t unsupported combination "-pme cpu -pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei Iupinov
R
efo
r
mul
a
te
P
M
E
s
olvin
g
tests tol
e
rances
commit
|
commitdiff
|
tree
2017-11-28
Aleksei Iupinov
Replace
o
f
pmeGPU
v
ariab
l
e name with pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Do not force separate PME rank to recompute rec
i
procal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Alekse
i
Iupi
n
ov
D
i
s
able failing separate PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
I
upinov
Add tests for PME tun
i
n
g
and fix mixed PME mode with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupinov
Destroy PME GPU context
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei I
u
pinov
Enable separate P
M
E G
P
U rank
commit
|
commitdiff
|
tree
2017-11-24
A
leksei Iupinov
Do not call mixed
C
PU+G
P
U PME mode
"
Hybrid"
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei Iupino
v
Activate mixed
m
o
de of PM
E
o
n
G
PU
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei Iupino
v
Remove outdated (alr
e
ady
i
mplemented) pinn
i
ng TODO
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i Iu
p
inov
M
ention gm
x
_
i
nstall_headers()
i
n t
h
e developer man
u
a
l
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
M
ake FFT real-space g
r
id use CUDA pin
n
ing for m
i
xed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupinov
Pin
co
o
rdin
a
tes, forces and
ch
a
rges f
o
r
PME on
GPU
commit
|
commitdiff
|
tree
2017-11-21
Aleksei
Iupinov
Fi
x
CUDA
rel
e
ase build warni
n
g
commit
|
commitdiff
|
tree
2017-11-21
A
leksei Iupinov
Fix pinned me
m
ory statu
s
checke
r
tes
t
s
commit
|
commitdiff
|
tree
2017-11-18
Al
e
k
sei Iupino
v
Asynchro
n
ous
CUDA transfers are asser
t
ed to always
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Aleksei Iupinov
Make gpu
_
utils-test b
u
ild with GMX_CL
A
N
G
_
C
UDA
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iupinov
Rename
a
n
d
expose "generic" GPU
m
emory
transfer functio
n
s
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupinov
Ren
a
me syn
c
hr
o
nous GPU transfer functions to m
a
tch
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei I
u
pinov
R
e
pla
c
e
math
.
h by cmath includes in
c
pp files
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupi
n
ov
R
e
move
unused PME G
P
U dec
l
aration
s
commit
|
commitdiff
|
tree
2017-11-01
A
le
k
s
e
i Iupinov
Move pme_g
p
u_f
i
ni
s
h_computatio
n
()
documentati
o
n to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Fix erroneous PME GP
U
"step" nami
n
g
s
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Sim
p
l
ify PME G
P
U synch
r
onizat
i
on cod
e
commit
|
commitdiff
|
tree
2017-10-31
Aleksei I
u
pi
n
ov
Reus
e
epbcXY logic
commit
|
commitdiff
|
tree
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