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prepareGpuKernelArguments() and launchGpuKernel() are added
2018-05-18
Ale
k
sei Iupi
n
ov
p
r
e
par
e
GpuKernelA
r
gument
s
() and launchGpuKernel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei
I
upinov
I
m
port
c
lFFT lib
r
ary into th
e
G
r
o
macs sourc
e
commit
|
commitdiff
|
tree
2018-05-04
Aleksei
I
upinov
A
d
d
c
le
a
r
DeviceBufferAsync()
for CUDA/OpenC
L
commit
|
commitdiff
|
tree
2018-05-03
Aleksei I
u
pin
o
v
Copy mi
s
sing GPU NB host deallocat
i
o
n
s from OpenCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Al
e
ksei Iu
p
in
o
v
r
epl
a
ce cu_copy_* calls
w
ith
Device
B
uffer functions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Al
e
k
s
ei Iupino
v
Rename OpenCL host memory routines to match the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Alek
s
ei Iupinov
Make asi
z
e() a
p
roper
tem
p
late
function
i
nstead o
f
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupinov
R
e
name the
a
size variable to numAlignmentA
t
o
ms
commit
|
commitdiff
|
tree
2018-04-26
Aleksei
Iupi
n
o
v
Separa
t
e
P
ME GPU
host-on
l
y
a
nd host/device
dat
a
s
t
ructures
commit
|
commitdiff
|
tree
2018-04-26
Aleksei
I
upinov
Add copyFromDe
v
iceBuffer() CUDA/OpenCL implementa
t
ions
commit
|
commitdiff
|
tree
2018-04-23
A
l
e
kse
i
I
upinov
Removed cu_r
e
alloc_bu
f
f
e
red() in
f
a
v
o
r
of reallocateDe
v
ic
e
Bu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei I
u
pinov
DeviceBu
f
fer
headers
a
re
a
d
d
ed
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Make in-sourc
e
O
p
enC
L
ker
n
e
l
path a
p
er-module
p
a
r
ame
t
e
r
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
R
emove CUDA_
F
UNC m
a
cros
from
m
any function
s
in PME GP
U
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Stop PME GPU
c
ode
f
rom com
p
il
i
ng on non-C
U
DA build
s
commit
|
commitdiff
|
tree
2018-04-10
Ale
k
sei
Iu
p
inov
Preve
n
t OpenCL timin
g
m
e
m
ory leak
commit
|
commitdiff
|
tree
2018-03-20
Aleksei I
u
p
i
nov
Clarify the mdrun GPU
o
ptio
n
s docs
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupi
n
ov
Ad
d
a basic TPI san
i
ty test
commit
|
commitdiff
|
tree
2018-03-16
Aleks
e
i Iupinov
Stop gmx_feenableexcept() from
returning previ
o
us ex
c
eption
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Al
e
ksei Iupinov
Restore
the los
t
mc_te
m
p check
i
n
gr
o
mpp
commit
|
commitdiff
|
tree
2018-03-06
A
l
e
ks
e
i
I
upino
v
Isolate PME GPU spline pa
r
amet
e
r indexing in inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupinov
Stop us
i
ng custom Fin
d
OpenCL
.
cmake, per TODO
commit
|
commitdiff
|
tree
2018-03-05
Al
e
ksei Iupinov
C
orre
c
t the nbnxn_gpu_compile
_
kernels() doc
s
commit
|
commitdiff
|
tree
2018-03-02
Aleksei
I
upinov
Make TPI use do
u
ble precision
e
xp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei Iupino
v
Merge branch
'rel
e
ase-2018'
commit
|
commitdiff
|
tree
2018-02-26
Aleksei
I
upino
v
A
dvice users on infi
n
ite ou
t
put o
f
TPI
commit
|
commitdiff
|
tree
2018-02-20
A
l
eks
e
i
Iupinov
Remove unused OpenCL debug
buffer
commit
|
commitdiff
|
tree
2018-02-18
Al
e
ks
e
i Iupinov
Replace *_free_buff
e
r
e
d calls by f
r
eeDe
v
ic
e
Bu
f
fer
commit
|
commitdiff
|
tree
2018-02-16
A
leksei Iupinov
F
ix PME for large systems with F
e
rmi
G
PUs
commit
|
commitdiff
|
tree
2018-02-15
Aleksei
Iupinov
Upda
t
e F
F
TW b
u
ild to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
A
l
e
k
s
ei Iupino
v
Add freeDevi
c
eBuffer GPU utilit
y
function
commit
|
commitdiff
|
tree
2018-02-15
Aleksei I
u
pino
v
Add t
h
e missing comma in the quote
commit
|
commitdiff
|
tree
2018-02-14
A
l
eks
e
i Iupinov
Replace the remaining EXPECT_DEATH with
EXPECT_DEATH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Add Device
B
uffe
r
as a typedef
for cl_mem/devic
e
ponter
commit
|
commitdiff
|
tree
2018-02-13
Aleksei Iupinov
Move
G
P
U
traits into separate he
a
ders
commit
|
commitdiff
|
tree
2018-02-12
Al
e
ksei Iupinov
Fix
the include guard
commit
|
commitdiff
|
tree
2018-02-09
Al
e
ksei Iu
p
inov
Revert "Enable debug FP exceptio
n
s wi
t
h
ou
t
TPI, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupin
o
v
Always run the es
s
ential
d
ynam
i
cs t
e
sts
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupi
n
ov
Enable debug
FP exceptions wi
t
hout TPI, not with TPI
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
M
e
rge branch 'release-2018'
i
nto mast
e
r
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Remove unnecessary incl
u
des fr
o
m do
m
dec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupi
n
o
v
Zero unus
e
d
values to silenc
e
the w
a
rning
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Only setup Ew
a
ld
i
n the gen
e
ric gr
o
up kernel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Aleksei
I
upinov
Make
n
d
x
files optional in Si
m
ulation
R
un
n
e
r
commit
|
commitdiff
|
tree
2018-02-05
Aleksei
I
upinov
Remove
mdpInp
u
tFileNam
e
_ from Simulatio
n
R
u
nne
r
,
per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
l
e
ks
e
i Iupino
v
Don't p
r
i
n
t im
p
ossible CUD
A
version numbers i
n
absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
l
ek
s
ei Iu
p
inov
Fi
x
in
p
ut MDP con
t
ents for s
w
a
p
an
d
IMD tests
commit
|
commitdiff
|
tree
2018-02-01
Alek
s
ei Iup
i
nov
Check for G
T
EST_IS_T
H
READS
A
FE bei
n
g define
d
commit
|
commitdiff
|
tree
2018-01-24
Aleksei Iup
i
n
o
v
Remove unused fields pe
r
T
O
DO
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Te
s
t the
m
ixed mode PME with walls and
b
ox sca
l
ing
commit
|
commitdiff
|
tree
2018-01-23
Aleksei
Iupi
n
ov
Test PME C
P
U/G
P
U with
walls and box scal
i
n
g
commit
|
commitdiff
|
tree
2018-01-23
Alek
s
ei
Iupinov
Wrap t
h
e PME
te
s
ting loop in a method f
o
r extensibility
commit
|
commitdiff
|
tree
2018-01-19
A
l
eksei Iupinov
A
dd a death test for the duplicate
i
n
p
utrec keys checking
commit
|
commitdiff
|
tree
2018-01-19
A
l
e
k
se
i
Iupinov
Rename cl
a
s
s
B
iasReader t
o
struct Bia
s
Outpu
t
Setu
p
commit
|
commitdiff
|
tree
2018-01-19
A
leksei Iupinov
Move the temporar
y
file MP
I
workaroun
d
into the
b
ase
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
A
l
e
ks
e
i Iu
p
inov
M
ake the refere
n
ce data variables local in GetIrTest
commit
|
commitdiff
|
tree
2018-01-19
A
l
eksei Iupinov
Merge branch 're
l
ease-2018'
i
nt
o
master
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Got
r
i
d o
f
ma
n
ual memo
r
y man
a
g
e
m
ent
i
n the PME o
v
erla
p
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei
Iupinov
Re-enable multi-rank PME tests (wi
t
h the f
i
le race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Alek
s
ei Iupinov
Fix
b
ox scaling
in
PME
m
ixed mode
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Merge br
a
nch 'release-2
0
18'
in
t
o master
commit
|
commitdiff
|
tree
2018-01-16
Aleksei Iupinov
Al
w
a
y
s
wri
t
e th
e
inpu
t
MDP file for t
e
s
t
in
g
j
ust before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Ale
k
sei Iup
i
nov
Move Octane
S
andwich
.
m
dp and spc2
-
IMD
.
mdp
i
n
t
o strings
commit
|
commitdiff
|
tree
2018-01-11
Ale
k
sei Iupino
v
Remove unused alanine_vs
i
te
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupinov
Do not p
r
int
P
M
E counter breakdown
if
it's empty
commit
|
commitdiff
|
tree
2017-12-20
Alekse
i
Iupinov
Set GMX_GPU_AUTO to F
A
LSE
wit
h
G
MX_G
P
U d
e
fined
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupinov
Remove potentia
l
ly wrong "per user reques
t
" note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Aleksei Iupinov
Re
l
axed pr
e
cision in spline inter
p
olation tests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei Iupinov
Provide d
u
mmy initialization to silence
a warnin
g
commit
|
commitdiff
|
tree
2017-12-05
Alekse
i
Iupinov
Do
not ac
c
ept un
s
u
pported combina
t
ion "-pme
c
pu -p
m
efft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
A
lekse
i
Iup
i
n
o
v
R
efo
r
mulate PME solving
t
ests
t
o
l
erances
commit
|
commitdiff
|
tree
2017-11-28
Aleksei
Iupi
n
ov
R
e
pla
c
e of pme
G
PU
v
ariable name with pme
G
p
u
commit
|
commitdiff
|
tree
2017-11-27
Alek
s
ei Iupinov
D
o
n
o
t force separat
e
PM
E
r
a
nk to recompute re
c
iprocal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
A
l
eksei Iup
i
no
v
Disable failing s
e
parat
e
PME rank t
e
s
ts
commit
|
commitdiff
|
tree
2017-11-27
A
l
e
ksei Iupinov
Add tests for PME tuning and fix mixed PME mode
with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei I
u
pi
n
ov
Destroy PME GPU
c
ontext
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
E
n
able separate
PM
E
GPU rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Do not ca
l
l mixed CPU+G
P
U
P
M
E mode "
H
ybri
d
"
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei Iu
p
inov
A
c
tivate mixe
d
mode of PME on GPU
commit
|
commitdiff
|
tree
2017-11-24
A
lek
s
ei Iupinov
R
em
o
ve outdate
d
(already imp
l
emented
)
pinning TODO
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei
Iupinov
Mention
gm
x
_
i
nstall_headers()
in t
h
e develop
e
r
man
u
al
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Mak
e
FFT real-space grid
u
se CUDA pinning
f
or mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Pin coordinat
e
s, force
s
and charges
for PME on GPU
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iu
p
inov
F
i
x
C
UDA r
e
leas
e
build
warning
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupi
n
ov
Fix
pinned me
m
or
y
status checker test
s
commit
|
commitdiff
|
tree
2017-11-18
A
l
eksei Iupinov
Asynchronous CUDA transfers
a
re a
s
serted
t
o alw
a
ys
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Aleksei Iupinov
M
a
ke gpu_ut
i
ls-test bu
i
ld wi
t
h GMX_CLANG_CUDA
commit
|
commitdiff
|
tree
2017-11-15
Ale
k
sei Iupinov
Re
n
ame and expose "generic
"
GPU
memory
t
r
a
nsfer fu
n
ctions
commit
|
commitdiff
|
tree
2017-11-09
Aleksei
Iupinov
Rename synchronous GPU transfer function
s
to match
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
A
l
eksei I
u
pinov
Replace mat
h
.
h
by cmath inc
l
udes
i
n
cpp files
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Remove
unu
s
ed PME GPU
d
ec
l
arations
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iup
i
nov
Move pme_gpu_fin
i
s
h
_compu
t
ation()
d
o
c
um
e
nta
t
ion to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Aleksei
I
upinov
Fix er
r
one
o
u
s
PME
G
P
U "step
"
namings
commit
|
commitdiff
|
tree
2017-11-01
Al
e
ksei Iup
i
nov
Simp
l
ify
PME GPU synchronization co
d
e
commit
|
commitdiff
|
tree
2017-10-31
Aleksei
Iupin
o
v
Reuse epbc
X
Y l
o
gic
commit
|
commitdiff
|
tree
2017-10-30
Alekse
i
I
u
pinov
Fix
referen
c
e mo
d
e build u
n
used function war
n
ings
commit
|
commitdiff
|
tree
2017-10-30
Aleks
e
i Iu
p
i
nov
Bring PME GPU/CUDA
inte
r
nal st
r
ucture
names to CamelCase
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Us
e
new/delete for gmx_pme_
t
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iu
p
inov
Si
m
plify PME data ha
n
dling in runner
commit
|
commitdiff
|
tree
2017-10-29
A
lekse
i
Iupinov
Make PME tun
i
ng logi
c
more readable
commit
|
commitdiff
|
tree
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