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Move the PmeGpuSpecific structure into pme-gpu-types-host-impl.h
2018-05-31
Aleksei Iupinov
Mov
e
t
h
e PmeGpuSpecific structure in
t
o pme-gpu-type
s
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iu
p
inov
Add
e
d the bundled clFF
T
into
OpenCL builds
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupin
o
v
Add
G
puE
v
entSynchronizer cla
s
s
commit
|
commitdiff
|
tree
2018-05-31
Al
e
k
s
e
i Iupi
n
ov
Gather
t
he PME
G
PU co
n
stants/m
a
cr
o
s in a single head
e
r
commit
|
commitdiff
|
tree
2018-05-30
Aleksei Iupinov
Make PME GPU structures u
s
e
D
e
v
iceBuffer
commit
|
commitdiff
|
tree
2018-05-28
Aleksei
I
upinov
Suppo
r
t persisten
t
device context-d
e
rived data in
P
ME
.
.
.
commit
|
commitdiff
|
tree
2018-05-18
A
leksei Iupinov
pre
p
are
G
p
u
KernelArguments()
a
n
d l
a
unch
G
p
u
K
ernel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
A
l
e
k
se
i
I
u
p
inov
Imp
o
rt cl
F
FT l
i
brar
y
i
n
to the Gromacs so
u
rce
commit
|
commitdiff
|
tree
2018-05-04
Aleksei Iupino
v
Add clearDeviceBufferAsync() for CUDA/OpenCL
commit
|
commitdiff
|
tree
2018-05-03
Aleksei Iupinov
Copy missing GPU NB h
o
st deallocations
from OpenCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Al
e
ks
e
i Iupinov
replace cu_co
p
y
_
* calls with DeviceBuf
f
er fun
c
tions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Aleksei Iupino
v
R
e
name OpenCL host
memor
y
ro
u
tines to ma
t
ch the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
A
leksei Iupinov
Mak
e
asize() a
p
rope
r
template f
u
nct
i
on instead of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei I
u
pinov
R
ename the
a
size vari
a
ble to nu
m
A
lignmentAtoms
commit
|
commitdiff
|
tree
2018-04-26
Aleksei Iupinov
Separate PME
G
PU ho
s
t
-
on
l
y and host/
d
evice data
st
r
uctures
commit
|
commitdiff
|
tree
2018-04-26
Aleksei
Iupinov
Ad
d
copyFromDevic
e
Buf
f
er()
CUDA/Open
C
L impl
e
men
t
ations
commit
|
commitdiff
|
tree
2018-04-23
Al
e
k
s
e
i
Iupino
v
Remove
d
cu_re
a
l
loc_
b
uff
e
re
d
()
i
n favor of real
l
o
c
ateDeviceBu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
A
l
eksei Iupinov
DeviceBuffer
headers are added
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Make in-source OpenCL kerne
l
path a per-modul
e
param
e
ter
commit
|
commitdiff
|
tree
2018-04-12
A
l
eksei Iupinov
Remove CUDA_FUN
C
ma
c
ros from m
a
ny functions
in PME
GPU
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupi
n
ov
Sto
p
PME GP
U
code from co
m
p
iling on n
o
n-CUDA builds
commit
|
commitdiff
|
tree
2018-04-10
Aleksei
I
upinov
Pr
e
v
ent Open
C
L
timing memory l
e
ak
commit
|
commitdiff
|
tree
2018-03-20
Aleksei I
u
pinov
Clarify the mdrun GP
U
o
pti
o
ns doc
s
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
Add a basic
T
PI sanity
test
commit
|
commitdiff
|
tree
2018-03-16
A
l
eksei
I
upinov
Stop
g
mx_feen
a
bleexcept() from re
t
urning prev
i
ous
e
xcep
t
ion
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iu
p
i
nov
Restore
t
he lost mc_temp check in grompp
commit
|
commitdiff
|
tree
2018-03-06
Aleksei Iupin
o
v
I
s
o
l
ate PM
E
GPU splin
e
param
e
t
e
r indexin
g
in i
n
l
i
ne
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iup
i
nov
Stop
u
s
ing
c
ustom
F
in
d
OpenCL
.
cmake, per TODO
commit
|
commitdiff
|
tree
2018-03-05
A
l
ek
s
ei I
u
pino
v
C
o
rrect t
h
e nbnxn_
g
pu_comp
i
le_kernels
(
)
d
o
c
s
commit
|
commitdiff
|
tree
2018-03-02
A
l
eksei Iupinov
Make TPI
use double precision exp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei Iupi
n
ov
Mer
g
e branch 'r
e
l
e
a
se-2018'
commit
|
commitdiff
|
tree
2018-02-26
Aleksei Iupinov
Advice users on infinite
o
utp
u
t
of
T
PI
commit
|
commitdiff
|
tree
2018-02-20
Al
e
ksei Iupinov
Remove unus
e
d OpenCL deb
u
g
buffer
commit
|
commitdiff
|
tree
2018-02-18
Alekse
i
I
upinov
Replace *_fr
e
e_buff
e
red
c
a
lls by freeDeviceB
u
ffer
commit
|
commitdiff
|
tree
2018-02-16
Aleksei Iupi
n
ov
Fix PME for large systems w
i
th
Fermi GPU
s
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
U
p
date FFTW build to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Add
f
re
e
Dev
i
c
e
B
uffer GPU utility fu
n
c
t
i
o
n
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iu
p
inov
Ad
d
the missing comma in the
quote
commit
|
commitdiff
|
tree
2018-02-14
Aleks
e
i I
u
pinov
Replac
e
t
he remain
i
ng
E
XPEC
T
_DEAT
H
wit
h
EXPECT_DEATH_I
F
_S
U
PP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleks
e
i Iupinov
Add DeviceBuffer
a
s a typede
f
for cl
_
mem/device ponter
commit
|
commitdiff
|
tree
2018-02-13
Alekse
i
Iupinov
Move G
P
U t
r
aits in
t
o separate h
e
aders
commit
|
commitdiff
|
tree
2018-02-12
A
lekse
i
I
upinov
Fix the inc
l
ude guar
d
commit
|
commitdiff
|
tree
2018-02-09
Alekse
i
I
upinov
Reve
r
t
"Enable d
e
bug FP exceptio
n
s without T
P
I
,
n
o
t
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
A
l
eksei
I
u
pinov
Always run
t
he
e
ssenti
a
l dyna
m
ics tests
commit
|
commitdiff
|
tree
2018-02-08
Alek
s
e
i
Iupinov
En
a
ble debug FP ex
c
e
p
tions
w
ithout TPI, not with
T
PI
commit
|
commitdiff
|
tree
2018-02-08
A
l
eksei Iupino
v
Merge
b
ranch 'release
-
201
8
'
i
nto
m
aster
commit
|
commitdiff
|
tree
2018-02-06
Alek
s
ei Iupinov
Remo
v
e unneces
s
ary
includes
f
r
o
m domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
A
leksei Iupinov
Zero
u
n
u
s
ed va
l
ues to silence the warning
commit
|
commitdiff
|
tree
2018-02-06
A
l
e
k
s
e
i
Iupinov
Only setup Ewald
in the generic group kernel if
it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupi
n
ov
Make n
d
x fi
l
es optio
n
al in Sim
u
lationRunne
r
commit
|
commitdiff
|
tree
2018-02-05
A
le
k
se
i
Iupinov
Remove mdpI
n
put
F
il
e
Name_
from Simulat
i
onRunner,
per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Al
e
ksei Iu
p
inov
Don't p
r
in
t
im
p
ossible CUDA version n
u
m
b
ers
i
n a
b
s
ence
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei
Iupinov
Fix input MDP
contents for swap and IMD tests
commit
|
commitdiff
|
tree
2018-02-01
Aleksei Iupinov
Check
f
or GTE
S
T_IS_THREADSAFE being de
f
i
ned
commit
|
commitdiff
|
tree
2018-01-24
A
leksei Iu
p
inov
Remove unused fields per TODO
commit
|
commitdiff
|
tree
2018-01-23
A
l
eks
e
i Iupinov
T
e
st
t
he mix
e
d
m
od
e
PME with walls an
d
box scal
i
ng
commit
|
commitdiff
|
tree
2018-01-23
A
leksei Iup
i
nov
Test P
M
E
C
PU/GP
U
with wa
l
ls a
n
d box scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleks
e
i
I
upinov
Wrap the PME testing loop in a method for extensibi
l
ity
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
sei Iupi
n
ov
Add a death
t
e
st for
the duplicate inputrec keys check
i
n
g
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
sei Iupinov
Rename class
B
ias
R
eader to struct BiasOutputSetup
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Move th
e
t
e
mporary
file MPI wo
r
k
around into the
b
ase
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupi
n
ov
Make the
reference data variab
l
e
s
lo
c
al
in G
e
tIrTe
s
t
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Me
r
g
e
branch 'releas
e
-2018' into
m
aster
commit
|
commitdiff
|
tree
2018-01-18
Aleksei
I
upi
n
ov
G
o
t ri
d
of
ma
n
ual memory manageme
n
t
in
t
he PM
E
overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
A
leks
e
i Iupinov
Re-enable multi-rank PME tes
t
s
(with
t
h
e f
i
le ra
c
e
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Fix
box scaling in
P
ME mix
e
d mode
commit
|
commitdiff
|
tree
2018-01-17
A
l
e
ksei Iupinov
Merge b
r
anch
'releas
e
-2018' into mast
e
r
commit
|
commitdiff
|
tree
2018-01-16
A
leksei Iupinov
Always write the input MDP file for
testing just b
e
fore
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupinov
M
o
ve Oct
a
ne
S
an
d
wic
h
.
mdp and spc
2
-IMD
.
m
dp into st
r
ings
commit
|
commitdiff
|
tree
2018-01-11
Aleksei I
u
pin
o
v
Remove unus
e
d alanine_vsite
.
m
d
p
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iu
p
inov
Do not prin
t
P
M
E co
u
nter bre
a
kdown
if it's empty
commit
|
commitdiff
|
tree
2017-12-20
Ale
k
sei Iup
i
nov
Se
t
GMX_GP
U
_AUTO
to
FALSE with GMX_GPU defined
commit
|
commitdiff
|
tree
2017-12-20
Aleksei
I
upinov
R
e
m
ove
poten
t
ially wro
n
g "per user request" note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Aleksei Iupinov
Relaxed precision in spline inte
r
pol
a
t
i
on tests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei Iupinov
Prov
i
d
e
dummy ini
t
ializatio
n
to
silen
c
e a warning
commit
|
commitdiff
|
tree
2017-12-05
Aleksei Iupi
n
ov
Do not accept u
n
s
u
p
p
orted
c
ombination "-pm
e
cpu -pmef
f
t
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Al
e
kse
i
Iupi
n
o
v
Reformulate PME so
l
ving tests t
o
leran
c
e
s
commit
|
commitdiff
|
tree
2017-11-28
Aleksei Iupinov
R
eplace
o
f pmeGPU v
a
ri
a
b
le
n
ame wi
t
h pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Do
not force
separate P
M
E
rank to rec
o
mpute r
e
ciprocal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupi
n
ov
Di
s
able fail
i
ng separate PME r
a
n
k
tests
commit
|
commitdiff
|
tree
2017-11-27
Alek
s
e
i
Iupin
o
v
Add te
s
ts for
P
ME tun
i
ng and fix mixed PME mode w
i
th
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iupinov
D
es
t
r
o
y PME GPU
c
ontext
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iupinov
E
nable
s
eparate
PME G
P
U rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iupinov
Do
no
t
call mix
e
d CPU
+
GPU PME mod
e
"H
y
brid
"
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
upinov
Activate mi
x
ed m
o
de of PME on GPU
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
sei Iupinov
Remove outdated (already
i
m
pleme
n
ted) pinning TOD
O
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Mention gmx_ins
t
all_head
e
rs() i
n
t
he develop
e
r
manual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iu
p
inov
Make FFT real-space
g
rid use CUDA pinning f
o
r mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
P
i
n coordinates, for
c
es and charges f
o
r
P
ME on GPU
commit
|
commitdiff
|
tree
2017-11-21
Alek
s
ei
I
upi
n
ov
Fix CUDA release build warnin
g
commit
|
commitdiff
|
tree
2017-11-21
Al
e
ks
e
i Iu
p
i
nov
Fix pinne
d
mem
o
r
y
statu
s
ch
e
cke
r
test
s
commit
|
commitdiff
|
tree
2017-11-18
Aleksei Iupinov
A
synchronous CUDA transfers are asserted to a
l
ways
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Ale
k
sei Iu
p
inov
Make gpu_utils
-
test
b
u
i
ld
w
ith GMX_C
L
A
N
G_CUD
A
commit
|
commitdiff
|
tree
2017-11-15
Al
e
ksei Iup
i
nov
Re
n
ame
a
nd e
x
pose "generic" GP
U
memory transfer functions
commit
|
commitdiff
|
tree
2017-11-09
A
l
eksei Iupi
n
ov
Rename sy
n
c
hrono
u
s GPU transfer f
u
nctions to match
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
A
lekse
i
I
upinov
Replace
mat
h
.
h b
y
c
math inc
l
udes in cpp f
i
les
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
R
emove unused
PME
G
P
U declarations
commit
|
commitdiff
|
tree
2017-11-01
Aleks
e
i I
u
pinov
Mo
v
e pme_gpu_finis
h
_computation() documentation
to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Fi
x
erroneous PME
G
PU "s
t
ep" namings
commit
|
commitdiff
|
tree
2017-11-01
A
lek
s
ei Iup
i
n
ov
Si
m
plify PME GPU sy
n
chroniza
t
ion code
commit
|
commitdiff
|
tree
next