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Fix CPU detection and SIMD on modern Mac/cmake combos
2018-12-22
Aleksei
I
u
pinov
Ad
d
a sanity
c
hec
k
f
o
r
OpenCL devices
commit
|
commitdiff
|
tree
2018-10-13
Aleksei I
u
p
i
nov
Add and e
n
a
ble PME OpenCL
commit
|
commitdiff
|
tree
2018-08-27
Aleksei Iupinov
Prep
a
re
p
m
e
-gpu-typ
e
s
.
h for OpenCL
commit
|
commitdiff
|
tree
2018-07-30
Aleksei Iupinov
Remove
h
ardc
o
ded war
p
_size == 32 assumption from
PME GP
U
commit
|
commitdiff
|
tree
2018-06-25
Aleksei Iu
p
inov
Move vect
y
pe_ops
.
clh into gpu_utils
commit
|
commitdiff
|
tree
2018-06-25
Aleksei
Iup
i
n
o
v
Move the
P
ME
G
PU kernel launch
functi
o
ns into pme-gpu
.
.
.
commit
|
commitdiff
|
tree
2018-06-14
Aleks
e
i Iupino
v
En
s
ure PME
w
ith Op
e
nCL
does
n
ot atte
m
pt to pin
commit
|
commitdiff
|
tree
2018-06-07
Alekse
i
Iupinov
Compile m
o
st of PME GPU host code
with
OpenCL
commit
|
commitdiff
|
tree
2018-05-31
Al
e
kse
i
Iup
i
nov
M
e
rg
e
pm
e
.
cu into pme-g
p
u-internal
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-31
A
lek
s
ei Iupino
v
PME OpenCL
3
D
FFT
t
ransform
i
s implemented,
u
s
i
ng clFFT
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupi
n
o
v
Move pme-ti
m
ings
.
cu to pme-gpu-timings
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupin
o
v
Prefe
r
li
n
king to system
c
lFFT rather than
bundled one
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupi
n
o
v
Mo
v
e
the PmeGpuSpecifi
c
structure into pm
e
-gpu-type
s
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleks
e
i Iupinov
Added
t
he bundled clFFT into OpenCL bu
i
lds
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupino
v
Add GpuEventSynchronizer cl
a
s
s
commit
|
commitdiff
|
tree
2018-05-31
Alek
s
ei Iup
i
nov
Gat
h
er the PME GPU
c
onstants/macros in a singl
e
header
commit
|
commitdiff
|
tree
2018-05-30
A
le
k
s
ei Iupinov
Mak
e
PME GPU structures use Devi
c
eBuff
e
r
commit
|
commitdiff
|
tree
2018-05-28
Aleks
e
i Iupinov
S
u
ppor
t
persistent device
c
ontext-
d
e
rived data
i
n PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-22
Al
e
ksei Iupinov
Remove
unuse
d
results of cudaS
t
reamQuery()
commit
|
commitdiff
|
tree
2018-05-18
Aleksei I
u
pinov
prepa
r
eGpuKerne
l
Arguments() and l
a
unchGpuKernel
(
)
a
re
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei Iupinov
Im
p
ort c
l
FFT library
i
nto the Gromacs source
commit
|
commitdiff
|
tree
2018-05-04
Alek
s
ei Iupin
o
v
A
d
d
clearDe
v
iceB
u
ffe
r
Async() for CUDA/OpenCL
commit
|
commitdiff
|
tree
2018-05-03
Aleks
e
i Iupinov
Copy missin
g
GPU NB
host d
e
a
l
lo
c
a
t
io
n
s f
r
om Op
e
nCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Ale
k
sei I
u
pinov
replace cu_copy_* calls with DeviceBuffer functions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Al
e
kse
i
Iupinov
Rename
Op
e
nCL hos
t
memory rou
t
ines t
o
match the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupi
n
ov
Make asize() a proper t
e
m
p
la
t
e fu
n
c
tion inst
e
ad of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei I
u
pi
n
ov
Rename the asiz
e
variab
l
e to numAlign
m
entAt
o
ms
commit
|
commitdiff
|
tree
2018-04-26
Aleksei Iupinov
S
e
parate PME GPU host-o
n
ly and host
/
device data st
r
uctures
commit
|
commitdiff
|
tree
2018-04-26
Ale
k
sei I
u
p
i
nov
Add copy
F
romDevi
c
eBuffer
(
) CUD
A
/OpenCL implementations
commit
|
commitdiff
|
tree
2018-04-23
Aleksei
I
upino
v
Removed cu_realloc_buffer
e
d() in favor of rea
l
locateDevi
c
e
B
u
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei I
u
p
i
nov
DeviceBuffer headers are added
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iu
p
inov
Make in-sour
c
e
O
p
en
C
L kernel pa
t
h a
per-module para
m
e
t
er
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Remove CUDA_FUNC mac
r
os
f
rom
m
a
n
y functi
o
ns in PME GPU
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupin
o
v
Stop PME GPU code from compiling
o
n non-CUDA builds
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
Pr
e
vent OpenCL timing memory l
e
a
k
commit
|
commitdiff
|
tree
2018-03-20
A
l
e
ksei Iupin
o
v
Cl
a
r
i
fy the mdrun GPU options
docs
commit
|
commitdiff
|
tree
2018-03-16
Aleksei I
u
p
i
n
o
v
A
d
d a basic TPI sa
n
ity
test
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
Stop gmx_
f
eenableexc
e
pt() from retur
n
in
g
previ
o
u
s exce
p
t
i
on
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei
Iupi
n
ov
Res
t
ore the lost mc_temp che
c
k in grompp
commit
|
commitdiff
|
tree
2018-03-06
Aleksei
Iupinov
Iso
l
a
te PM
E
G
PU
s
pline p
a
ramete
r
inde
x
ing
i
n inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Alekse
i
Iupinov
S
t
op usi
n
g c
u
s
t
om FindO
p
e
n
CL
.
cmake
,
p
e
r TODO
commit
|
commitdiff
|
tree
2018-03-05
Alek
s
ei Iupinov
Correct the nbnxn_g
p
u_com
p
ile_kernels() docs
commit
|
commitdiff
|
tree
2018-03-02
Aleksei Iupinov
Ma
k
e TPI us
e
d
ouble preci
s
ion ex
p
commit
|
commitdiff
|
tree
2018-02-27
A
l
eksei Iupinov
Merge bran
c
h
'
re
l
ease-2018'
commit
|
commitdiff
|
tree
2018-02-26
Aleksei Iupinov
Advice us
e
rs on infinite out
p
ut of TPI
commit
|
commitdiff
|
tree
2018-02-20
Aleksei Iupino
v
Remove unus
e
d OpenCL de
b
ug buffe
r
commit
|
commitdiff
|
tree
2018-02-18
Aleksei Iupinov
Replace
*
_free_buffered calls by
f
reeD
e
vice
B
u
ffe
r
commit
|
commitdiff
|
tree
2018-02-16
Aleksei Iupino
v
Fix PME for l
a
rge systems with Fer
m
i
GPUs
commit
|
commitdiff
|
tree
2018-02-15
Alek
s
ei I
u
pinov
Update FFTW build t
o
3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Al
e
ksei I
u
pinov
Ad
d
f
r
eeDeviceBu
f
fer GPU utili
t
y function
commit
|
commitdiff
|
tree
2018-02-15
Al
e
ksei Iupi
n
ov
Ad
d
the missing comma in the quote
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iu
p
inov
Rep
l
ace the remaining EXPECT_DEATH wit
h
EXP
E
CT_DEATH
_
IF
_
SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
A
d
d DeviceBuffer a
s
a typed
e
f
for cl_mem/de
v
ice po
n
ter
commit
|
commitdiff
|
tree
2018-02-13
Ale
k
sei Iup
i
nov
Move G
P
U
traits into separ
a
te head
e
rs
commit
|
commitdiff
|
tree
2018-02-12
Alek
s
e
i
Iup
i
nov
Fix the include g
u
ard
commit
|
commitdiff
|
tree
2018-02-09
Aleksei Iupi
n
ov
Rev
e
rt "
E
nable debug FP ex
c
ep
t
ions
with
o
ut TPI, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
A
leksei Iupin
o
v
Alw
a
ys
r
un th
e
esse
n
tial dynamics
tests
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iup
i
n
o
v
Enable d
e
bug FP exceptions without TPI, n
o
t
with TPI
commit
|
commitdiff
|
tree
2018-02-08
Ale
k
sei
Iupinov
Merg
e
bra
n
ch 're
l
ease-
2
018' into ma
s
ter
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iu
p
i
nov
Re
m
ove un
n
e
c
ess
a
r
y
includes
from dom
d
ec
.
h
commit
|
commitdiff
|
tree
2018-02-06
A
le
k
se
i
Iupinov
Ze
r
o un
u
sed v
a
lues to silence
t
he warning
commit
|
commitdiff
|
tree
2018-02-06
Al
e
kse
i
I
upinov
Only setup Ewald in
t
he ge
n
er
i
c gro
u
p
kernel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupinov
Make
n
dx files optional in Simulati
o
nRunner
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iup
i
nov
Re
m
ov
e
md
p
InputFileName_ f
r
om SimulationRunner, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
Don'
t
p
r
int
im
p
o
ss
i
ble CUDA version
n
u
mb
e
rs in absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
l
ekse
i
Iupino
v
F
ix i
n
put MDP
c
ontents
f
or
s
wap
a
nd IM
D
tests
commit
|
commitdiff
|
tree
2018-02-01
A
le
k
sei Iupinov
C
heck for GTE
S
T_IS_THREADS
A
FE bei
n
g def
i
n
e
d
commit
|
commitdiff
|
tree
2018-01-24
Aleksei Iup
i
no
v
Re
m
ove unus
e
d
fi
e
l
ds per
TODO
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iup
i
nov
T
e
st t
h
e
mixed mode
PME with walls a
n
d
box scal
i
n
g
commit
|
commitdiff
|
tree
2018-01-23
A
l
eksei Iupinov
T
est PME CPU/GPU
with
w
al
l
s
a
nd b
o
x scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei
Iupinov
Wrap the PME testing l
o
op in a
me
t
h
od f
o
r
e
x
tensibil
i
ty
commit
|
commitdiff
|
tree
2018-01-19
A
l
e
ksei Iupinov
Add a deat
h
test for t
h
e
duplicate
i
nput
r
e
c keys ch
e
ckin
g
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iup
i
nov
Re
n
ame
c
lass BiasRea
d
er to struct B
i
asOu
t
putS
e
tu
p
commit
|
commitdiff
|
tree
2018-01-19
Alekse
i
Iupino
v
M
o
ve the temporary file
M
PI workaro
u
nd in
t
o the base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Mak
e
the
reference data varia
b
les
loca
l
i
n
GetIrTe
s
t
commit
|
commitdiff
|
tree
2018-01-19
Aleksei
I
upinov
Merge bran
c
h 'release-2
0
18'
into master
commit
|
commitdiff
|
tree
2018-01-18
Aleksei
Iupinov
Got
r
id of m
a
nual mem
o
ry management in th
e
PME overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei
Iupinov
Re-enabl
e
m
u
lti-rank PME tes
t
s (with t
h
e file
r
ace
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
A
leksei Iupinov
Fix
box scaling in PME mixed
m
od
e
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Me
r
ge b
r
anch 'relea
s
e
-
2
018' into
maste
r
commit
|
commitdiff
|
tree
2018-01-16
Aleksei
Iupinov
Always write the input
MDP file for tes
t
ing just before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Ale
k
sei Iupin
o
v
Move
O
ctaneSand
w
ich
.
mdp
and spc2-IMD
.
md
p
into st
r
ings
commit
|
commitdiff
|
tree
2018-01-11
A
leksei I
u
p
inov
Remove unused alanine_
v
site
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Aleksei
I
upinov
Do not
p
rint PME
c
o
u
n
t
er br
e
akdown if it'
s
empty
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupinov
Set GMX_G
P
U_AUTO to
F
A
L
S
E with GMX_GPU defined
commit
|
commitdiff
|
tree
2017-12-20
Alek
s
ei
I
upinov
Remove pote
n
tiall
y
wrong "per user request" note f
r
om
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
A
l
ek
s
e
i
Iup
i
n
ov
Relaxed precisi
o
n in s
p
l
ine interpolation tests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei I
u
pinov
Provi
d
e dumm
y
initia
l
ization to
s
ilence a warning
commit
|
commitdiff
|
tree
2017-12-05
Al
e
ksei Iupin
o
v
Do
not accept unsupported com
b
inati
o
n "-pme cpu -pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei Iup
i
nov
Reformula
t
e PME solving te
s
ts toleran
c
e
s
commit
|
commitdiff
|
tree
2017-11-28
Ale
k
sei Iupinov
Replac
e
o
f
pmeGPU v
a
riabl
e
nam
e
with
pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
A
leksei Iupinov
Do not force separat
e
PME rank to rec
o
mpute recip
r
o
c
al
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iup
i
nov
Disa
b
le failing separat
e
PME
r
ank tests
commit
|
commitdiff
|
tree
2017-11-27
Al
e
ksei Iupinov
Add test
s
for
P
ME tuni
n
g and fix mixe
d
P
M
E mode with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupin
o
v
Des
t
roy
PME GP
U
context
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iu
p
inov
Enable separ
a
te
PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Do not call mixed CPU+GPU
PME mode "
H
ybri
d
"
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
sei Iupinov
Activate m
i
xe
d
mode of
P
ME on GPU
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
up
i
nov
Remove
o
utda
t
ed (alre
a
d
y
imple
m
ented) pinni
n
g
T
ODO
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
I
upinov
M
ention
g
mx
_
install_headers() in the developer manua
l
commit
|
commitdiff
|
tree
next