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Partial conversion of gmx_domdec_t to C++
2018-06-07
Aleksei Iupin
o
v
Compile
m
o
s
t
o
f
P
ME GPU host co
d
e
wit
h
OpenCL
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iup
i
nov
Merge
p
me
.
cu in
t
o pme-gpu-int
e
rnal
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-31
Alekse
i
I
upinov
PME OpenC
L
3D FFT t
r
ansf
o
rm is implemented, usin
g
clF
F
T
commit
|
commitdiff
|
tree
2018-05-31
Al
e
kse
i
Iu
p
inov
Mov
e
pme-timings
.
c
u
to pme-gpu-timings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iup
i
n
o
v
Prefer
l
i
nkin
g
t
o sy
s
t
e
m
clFFT rathe
r
t
han
bundled o
n
e
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
up
i
n
ov
Move the P
m
eGpuSpec
i
fic structu
r
e into pme-gpu
-
types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
sei Iupino
v
Added the bundled clFFT into O
p
enCL builds
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei Iupinov
Add
G
p
u
Ev
e
ntSynchronizer cl
a
ss
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
Iup
i
nov
Gather the PME G
P
U
c
onstants/macr
o
s in
a
single header
commit
|
commitdiff
|
tree
2018-05-30
Aleksei Iupinov
Ma
k
e
PME
GPU structures use
D
e
viceBuff
e
r
commit
|
commitdiff
|
tree
2018-05-28
Aleksei Iupinov
Su
p
port
persist
e
nt devi
c
e context-derived data in PM
E
.
.
.
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iupinov
prepar
e
GpuKerne
l
Argu
m
ents() and launchGp
u
Kern
e
l(
)
are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei
I
u
pinov
Im
p
or
t
clF
F
T
library
into the Gromac
s
source
commit
|
commitdiff
|
tree
2018-05-04
Aleks
e
i Iupin
o
v
Ad
d
c
l
earDeviceBu
f
ferAs
y
nc(
)
for CUDA/O
p
en
C
L
commit
|
commitdiff
|
tree
2018-05-03
Aleksei Iupinov
C
opy missing GPU NB
h
ost deallocations fr
o
m
OpenCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Aleksei
Iupinov
replace cu_copy_* calls with D
e
viceBuffer
f
u
nction
s
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Al
e
ksei Iu
p
in
o
v
Rename OpenCL h
o
st memory
r
outines to m
a
tch the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
A
leksei Iupinov
M
a
k
e
a
size()
a p
r
oper template function inst
e
ad
o
f
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei I
u
p
i
no
v
Rename the as
i
ze v
a
r
iable to numAlignm
e
n
tAtoms
commit
|
commitdiff
|
tree
2018-04-26
A
le
k
sei Iupinov
Separate
P
M
E GPU host
-
o
nly and host
/
d
e
vice d
a
ta str
u
ctures
commit
|
commitdiff
|
tree
2018-04-26
Alekse
i
Iupinov
Add copyFromDeviceBuffer(
)
C
UDA/OpenCL implementations
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
Removed cu
_
realloc_buffered(
)
in favor of reallocateDevi
c
eBu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Al
e
ksei I
u
pinov
DeviceBuffer headers
are a
d
ded
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupin
o
v
Mak
e
in-
s
ource OpenCL k
e
rnel p
a
th
a per-module parameter
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Re
m
ove CUDA_FUNC macros
f
rom many
functions in PME GPU
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
S
t
op PME GPU code from compiling on non-CUDA builds
commit
|
commitdiff
|
tree
2018-04-10
Aleksei
Iu
p
inov
Prevent OpenCL timing memory leak
commit
|
commitdiff
|
tree
2018-03-20
Aleksei
Iupinov
Clarify th
e
m
d
run GPU opt
i
ons docs
commit
|
commitdiff
|
tree
2018-03-16
A
leksei
I
up
i
nov
Add
a basic TPI
s
anity test
commit
|
commitdiff
|
tree
2018-03-16
Aleksei I
u
pinov
S
t
op
gmx_feenableexc
e
p
t
()
from returning previous exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleks
e
i Iupinov
Rest
o
r
e the lo
s
t
mc_temp ch
e
ck
i
n
gromp
p
commit
|
commitdiff
|
tree
2018-03-06
A
leksei Iupinov
Is
o
la
t
e PME GPU
s
pl
i
ne parame
t
er i
n
d
e
xin
g
in inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
A
l
eksei I
u
pinov
Stop
u
sing custom FindOpenC
L
.
cmake, per TOD
O
commit
|
commitdiff
|
tree
2018-03-05
Aleksei
I
upinov
Correct the nbnxn_gpu_compile_kernels()
docs
commit
|
commitdiff
|
tree
2018-03-02
Aleksei Iupinov
Ma
k
e TPI use dou
b
le precision exp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei Iup
i
no
v
Merge
b
ranch 'release
-
2
018'
commit
|
commitdiff
|
tree
2018-02-26
Aleks
e
i Iupinov
Adv
i
ce users on infi
n
ite outpu
t
of TPI
commit
|
commitdiff
|
tree
2018-02-20
A
leksei I
u
pino
v
R
emove u
n
use
d
Op
e
n
C
L d
e
bug buffer
commit
|
commitdiff
|
tree
2018-02-18
Alekse
i
I
u
pinov
Replace
*_fre
e
_buff
e
r
ed calls by
freeDevice
B
u
f
fer
commit
|
commitdiff
|
tree
2018-02-16
Aleksei Iupinov
Fix
P
ME for large syste
m
s with Fermi GPUs
commit
|
commitdiff
|
tree
2018-02-15
Aleksei
I
u
pinov
Update FFTW
b
u
i
ld t
o
3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Add freeDeviceB
u
f
fer GPU
u
t
i
lity f
u
n
c
tio
n
commit
|
commitdiff
|
tree
2018-02-15
Alekse
i
Iupinov
Add the missing comm
a
in
the
qu
o
te
commit
|
commitdiff
|
tree
2018-02-14
Ale
k
se
i
I
u
pi
n
ov
Replace the r
e
maining EXPECT
_
DE
A
TH with EXPEC
T
_D
E
A
T
H_IF_SUP
P
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
A
leksei Iupin
o
v
A
d
d DeviceBuffer as a
t
y
pede
f
fo
r
cl_mem/d
e
vi
c
e
po
n
ter
commit
|
commitdiff
|
tree
2018-02-13
Aleksei Iupino
v
Move GPU traits into
s
eparate
headers
commit
|
commitdiff
|
tree
2018-02-12
Al
e
kse
i
Iupinov
F
ix the include guard
commit
|
commitdiff
|
tree
2018-02-09
Aleksei Iupinov
Rev
e
rt "En
a
ble debug FP excepti
o
ns
wit
h
ou
t
T
PI, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Alek
s
ei Iupinov
A
lwa
y
s
run the essentia
l
dynamics tests
commit
|
commitdiff
|
tree
2018-02-08
Aleksei I
u
pi
n
ov
Enable
d
ebug FP exc
e
ptions with
o
ut TPI, not
w
ith T
P
I
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupin
o
v
Merg
e
branc
h
'releas
e
-2018' in
t
o master
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Remove un
n
ecessary
i
ncludes from domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Zero unused valu
e
s t
o
s
il
e
n
ce th
e
wa
r
ning
commit
|
commitdiff
|
tree
2018-02-06
Aleksei I
u
pinov
Only setup Ewald
in the generic grou
p
kernel if
it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Alek
s
ei I
u
pinov
Make
ndx
files optional in SimulationRu
n
ner
commit
|
commitdiff
|
tree
2018-02-05
Alek
s
ei Iupinov
Remove mdpInputFileName
_
from SimulationRunner, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei I
u
pi
n
ov
Don't print impossib
l
e CUD
A
version numbers in absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
leksei Iupi
n
ov
Fix in
p
ut
MDP con
t
ents for s
w
ap and
I
MD tests
commit
|
commitdiff
|
tree
2018-02-01
Alek
s
ei I
u
pinov
C
heck for GTES
T
_IS_
T
HR
E
A
D
SAFE being defined
commit
|
commitdiff
|
tree
2018-01-24
Ale
k
sei Iupinov
Remove unused
fields per TODO
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Test the mixed mode PME w
i
t
h walls and box
s
caling
commit
|
commitdiff
|
tree
2018-01-23
Ale
k
sei Iupi
n
o
v
Test
PME
C
P
U
/
GPU with
walls an
d
box scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Wrap the PME te
s
ting loo
p
in a method for extensi
b
il
i
ty
commit
|
commitdiff
|
tree
2018-01-19
A
l
e
ksei Iupinov
Add a death test for t
h
e dupl
i
cate
i
nputre
c
keys che
c
ki
n
g
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupin
o
v
R
ename class Bia
s
Reader to struct BiasOutputSetu
p
commit
|
commitdiff
|
tree
2018-01-19
A
l
eksei Iupinov
M
ove t
h
e t
e
mp
o
rary fi
l
e MPI
work
a
round
i
n
to
the bas
e
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Mak
e
th
e
referen
c
e d
a
ta var
i
abl
e
s local in GetI
r
Test
commit
|
commitdiff
|
tree
2018-01-19
Al
e
ksei Iupinov
Merge branch
'
release-2018' into master
commit
|
commitdiff
|
tree
2018-01-18
Al
e
k
sei Iupinov
Go
t
rid of manual me
m
o
ry management in the
P
ME overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
A
l
eksei Iupinov
R
e-enable multi-rank
P
ME tests
(
with the fi
l
e
race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Aleksei
Iupinov
Fix box s
c
aling in PME mix
e
d m
o
de
commit
|
commitdiff
|
tree
2018-01-17
Ale
k
sei Iupinov
Merg
e
branch 're
l
ea
s
e-2018' into master
commit
|
commitdiff
|
tree
2018-01-16
A
leksei Iupinov
Always
write the i
n
p
ut
M
DP file for testing just before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Alek
s
ei Iupinov
Move
Oct
a
neSand
w
ich
.
m
dp
and s
p
c2-
I
MD
.
m
dp int
o
stri
n
gs
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupinov
Remove unused al
a
nine_vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Ale
k
sei
I
u
p
inov
Do not
p
rint
PME counter break
d
own
if it's
e
m
pty
commit
|
commitdiff
|
tree
2017-12-20
A
leksei Iupinov
Se
t
GMX_GPU_AUTO to FALSE with GMX_GPU de
f
ined
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupinov
Rem
o
ve pot
e
nt
i
ally wrong "p
e
r user request" note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Alek
s
e
i
Iup
i
nov
Relax
e
d p
r
eci
s
ion
i
n spline int
e
r
pola
t
i
on tests
commit
|
commitdiff
|
tree
2017-12-06
Al
e
ksei Iupinov
Provide dummy in
i
tialization
to
si
l
en
c
e
a
warning
commit
|
commitdiff
|
tree
2017-12-05
A
leksei Iupinov
D
o
n
o
t ac
c
ept uns
u
pported co
m
bination "-pme
c
pu -pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Ale
k
sei Iupinov
Reformulate PME solving tests tol
e
r
a
nces
commit
|
commitdiff
|
tree
2017-11-28
Aleksei Iupinov
Replace
o
f
pmeGPU variable name
with pme
G
pu
commit
|
commitdiff
|
tree
2017-11-27
A
leksei Iupinov
Do no
t
force sepa
r
ate PME r
a
n
k
to
rec
o
mpute reci
p
roca
l
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iu
p
inov
Di
s
able failing separ
a
t
e
PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
A
leksei Iupinov
Add
t
e
s
ts f
o
r
P
M
E
tuning and fix mixed
P
ME mod
e
with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
se
i
Iupinov
Dest
r
oy PME
G
PU c
o
ntext
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iu
p
inov
Enable s
e
parate
P
ME G
P
U ra
n
k
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iu
p
inov
Do
n
o
t c
a
ll mixed CPU
+
G
P
U PME mode "Hybrid"
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupi
n
ov
Acti
v
ate mixed m
o
de of PME
o
n G
P
U
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Remove outda
t
e
d
(already implemented) pinn
i
ng TODO
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei Iupinov
Mention gmx_install_headers
(
)
in t
h
e developer manual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
upinov
Make FFT r
e
al-space
grid
u
s
e CUDA pinning
f
or mixe
d
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
upinov
P
in coordinates, for
c
es
and charges f
o
r PME on GPU
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupin
o
v
Fi
x
CUDA rel
e
a
s
e build
warning
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupinov
F
i
x
pinned memor
y
status
checker tests
commit
|
commitdiff
|
tree
2017-11-18
Aleksei Iupinov
Asynchronous CUDA
trans
f
ers are asserted to always
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Aleks
e
i I
u
p
inov
M
a
ke gpu_utils-tes
t
bu
i
ld with
GMX_CLANG_CUDA
commit
|
commitdiff
|
tree
2017-11-15
Al
e
ks
e
i I
u
pinov
R
ename
a
nd exp
o
s
e
"
generic" GPU
memory transfer functio
n
s
commit
|
commitdiff
|
tree
2017-11-09
Alekse
i
Iupi
n
ov
Rename s
y
nchronous G
P
U transfer functions to match
.
.
.
commit
|
commitdiff
|
tree
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