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Compile most of PME GPU host code with OpenCL
2018-06-07
A
l
eksei I
u
p
ino
v
C
om
p
ile most of PME GP
U
host c
o
de
w
i
th Ope
n
CL
commit
|
commitdiff
|
tree
2018-05-31
A
leksei I
u
p
in
o
v
Merge
p
me
.
c
u int
o
pme-gpu-in
t
erna
l
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Alek
s
ei Iupinov
P
ME OpenCL 3
D
FFT transform is imp
l
e
m
ented, using clFFT
commit
|
commitdiff
|
tree
2018-05-31
A
le
k
sei Iupinov
M
o
ve pme-timi
n
gs
.
c
u t
o
p
me-
g
p
u
-t
i
mings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
A
l
e
ksei Iu
p
inov
Prefer l
i
nking to system clFFT rather than bundled
o
ne
commit
|
commitdiff
|
tree
2018-05-31
A
leksei
I
u
p
inov
Move t
h
e PmeGpu
S
pecific stru
c
t
ur
e
i
nt
o
p
me-gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleks
e
i Iupinov
Added the b
u
ndle
d
clFFT
into OpenCL builds
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei Iupino
v
Add
GpuEventSynchronizer c
l
ass
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
upinov
Gather the PME GPU constants/macros in a sing
l
e head
e
r
commit
|
commitdiff
|
tree
2018-05-30
Alek
s
ei I
u
pinov
Make PME GPU s
t
ructur
e
s us
e
DeviceBuffer
commit
|
commitdiff
|
tree
2018-05-28
A
l
eks
e
i Iup
i
nov
Support persistent device context
-
derived
d
ata in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-18
Ale
k
s
ei
I
u
pinov
prepareGpuKernelArguments() and l
a
unchGpuKernel() ar
e
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei Iupinov
I
mport
clFFT library into the
Gromacs sourc
e
commit
|
commitdiff
|
tree
2018-05-04
Aleksei Iupino
v
Add
c
learDevic
e
BufferA
s
ync() for CUDA/OpenCL
commit
|
commitdiff
|
tree
2018-05-03
Aleksei Iupinov
Copy mi
s
sing GPU NB host dea
l
locations from
O
pe
n
CL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Aleksei
Iupinov
r
e
p
lace cu
_
copy_* calls with
D
eviceBuffer functions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
A
l
eksei I
u
pinov
Re
n
ame Ope
n
CL h
o
st m
e
mory routines
to
match the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupino
v
Mak
e
a
s
ize(
)
a
p
roper
templat
e
function inste
a
d
o
f
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupinov
Rename the as
i
ze va
r
iable
t
o
numAli
g
n
m
ent
A
to
m
s
commit
|
commitdiff
|
tree
2018-04-26
Aleksei I
u
pinov
Sepa
r
a
t
e PM
E
G
PU host-only and
host/device dat
a
structure
s
commit
|
commitdiff
|
tree
2018-04-26
Aleks
e
i
I
u
pinov
Add copyFr
o
m
Dev
i
ceB
u
ffer() CU
D
A/OpenCL imp
l
ementations
commit
|
commitdiff
|
tree
2018-04-23
Al
e
ksei Iupinov
Rem
o
ved
c
u_re
a
lloc
_
b
u
ffered(
)
in
favor
o
f r
e
allocateD
e
vice
B
u
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iup
i
nov
DeviceBuffer he
a
der
s
are
a
dded
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Make
in-s
o
urce OpenCL ker
n
e
l path a per-m
o
dule para
m
eter
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Rem
o
ve CUDA
_
FUNC macros f
r
om many functions in PME G
P
U
commit
|
commitdiff
|
tree
2018-04-12
A
leksei Iupinov
S
t
o
p
PME GPU code from compiling on non
-
CUDA builds
commit
|
commitdiff
|
tree
2018-04-10
Ale
k
s
e
i Iupinov
P
revent Op
e
n
CL timing memory leak
commit
|
commitdiff
|
tree
2018-03-20
Aleksei Iu
p
i
n
ov
Clarify t
h
e
mdrun GPU opt
i
o
ns doc
s
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
Add a basi
c
T
P
I
sanity test
commit
|
commitdiff
|
tree
2018-03-16
Al
e
ksei Iu
p
inov
Stop gmx_f
e
e
nableexcept()
f
r
om returni
n
g
p
revious exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
A
l
eksei
Iupinov
Restor
e
the lo
s
t mc_temp che
c
k
i
n g
r
ompp
commit
|
commitdiff
|
tree
2018-03-06
Aleksei Iup
i
nov
Isolate PME
G
PU
spline parameter indexing in inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupinov
S
t
op using custom FindOpenCL
.
c
make, p
e
r TODO
commit
|
commitdiff
|
tree
2018-03-05
A
l
e
ks
e
i Iupi
n
o
v
Correct
t
he nbnxn_gpu_co
m
pil
e
_kernels() docs
commit
|
commitdiff
|
tree
2018-03-02
A
l
eks
e
i Iupino
v
Ma
k
e
TPI us
e
double precision exp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei Iupinov
Me
r
g
e branch 'release-2018'
commit
|
commitdiff
|
tree
2018-02-26
A
leks
e
i Iup
i
nov
Advice user
s
on infinit
e
output of TPI
commit
|
commitdiff
|
tree
2018-02-20
Aleksei Iupinov
Remove unused O
p
enCL debug buffer
commit
|
commitdiff
|
tree
2018-02-18
A
l
e
k
sei Iupinov
Repl
a
c
e
*
_
f
r
ee_buff
e
red calls by freeDev
i
c
eBuffer
commit
|
commitdiff
|
tree
2018-02-16
A
l
e
ksei
I
u
p
inov
Fi
x
PME
for
large system
s
with Fermi GPUs
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iup
i
nov
Update FFTW build to
3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Add freeDe
v
i
ceB
u
ffer GPU
u
tility function
commit
|
commitdiff
|
tree
2018-02-15
Aleksei
I
up
i
nov
Add the missing comma
in the quote
commit
|
commitdiff
|
tree
2018-02-14
Ale
k
sei Iupinov
Rep
l
ace the remain
i
ng EXP
E
CT_DEATH with
E
XPECT_DE
A
TH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Alekse
i
Iupinov
Add DeviceBuffer
a
s a typedef for cl_m
e
m
/
d
evice ponter
commit
|
commitdiff
|
tree
2018-02-13
Alekse
i
Iu
p
inov
Move
GPU
t
raits i
n
to separate
h
eaders
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iupin
o
v
Fix the include guard
commit
|
commitdiff
|
tree
2018-02-09
Ale
k
sei Iupin
o
v
Revert "Enable debug FP e
x
cep
t
i
o
n
s
wi
t
ho
u
t T
P
I
, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Ale
k
sei
Iupinov
Always ru
n
t
he e
s
sential dynamics tests
commit
|
commitdiff
|
tree
2018-02-08
A
leksei Iu
p
in
o
v
Enabl
e
debug FP
except
i
ons
without TPI,
n
ot with TPI
commit
|
commitdiff
|
tree
2018-02-08
Ale
k
sei Iupinov
Merg
e
branch 'release-
2
018' into master
commit
|
commitdiff
|
tree
2018-02-06
A
l
e
k
s
ei I
u
pinov
Remove
u
nnecessar
y
in
c
ludes from domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Zero
u
n
used values to silence the warnin
g
commit
|
commitdiff
|
tree
2018-02-06
Alekse
i
Iupinov
Onl
y
setup Ewald in
t
he gen
e
ric group
k
er
n
el
if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Al
e
ksei Iupinov
Make ndx files optiona
l
in SimulationR
u
n
n
er
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupinov
Re
m
ove md
p
InputFileName_ from Simulation
R
unner, p
e
r
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
l
eksei
I
upinov
Don'
t
p
rint impossible CUDA version
num
b
ers
i
n
a
b
s
e
n
ce
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei I
u
pinov
Fix input
M
DP cont
e
nts for swa
p
and IMD t
e
sts
commit
|
commitdiff
|
tree
2018-02-01
Aleksei Iu
p
inov
Check for GTEST_I
S
_TH
R
E
A
DSAFE
b
eing
d
efined
commit
|
commitdiff
|
tree
2018-01-24
Aleksei Iupinov
Remove unused fields per TODO
commit
|
commitdiff
|
tree
2018-01-23
Alekse
i
Iupinov
Test the mixed
m
o
d
e PME with
walls and box scal
i
ng
commit
|
commitdiff
|
tree
2018-01-23
Al
e
ksei Iupinov
Test PME CP
U
/GPU
w
i
th walls and bo
x
sc
a
ling
commit
|
commitdiff
|
tree
2018-01-23
A
l
ek
s
ei Iupinov
W
r
a
p the PME testing loop in a method
f
or extensibility
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
se
i
Iu
p
ino
v
A
dd a death test for t
h
e duplicate inpu
t
rec keys checking
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i Iupi
n
ov
Rename class
BiasR
e
ader
to st
r
u
c
t Bia
s
O
u
tputSetup
commit
|
commitdiff
|
tree
2018-01-19
A
lekse
i
Iupinov
Move the tem
p
orary file MPI w
o
rkaroun
d
int
o
the base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
A
leksei Iupin
o
v
Make the refere
n
ce data vari
a
bles
loca
l
in GetIrTest
commit
|
commitdiff
|
tree
2018-01-19
Aleksei I
u
p
i
n
ov
Merge b
r
anc
h
'r
e
l
e
ase-201
8
'
into m
a
s
t
er
commit
|
commitdiff
|
tree
2018-01-18
Alek
s
ei Iupinov
Go
t
rid of manual memory manag
e
ment in the P
M
E overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei
I
upinov
R
e-enabl
e
multi-rank PME tests (w
i
th the file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Aleksei I
u
pinov
Fix box
scaling in PME mixed mode
commit
|
commitdiff
|
tree
2018-01-17
Alek
s
ei Iu
p
i
nov
Merge branch
'
release-2018' into master
commit
|
commitdiff
|
tree
2018-01-16
Aleksei Iupinov
A
lways write
the input MDP file for
t
esting just before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Alekse
i
Iup
i
nov
Move O
c
taneSa
n
dw
i
ch
.
mdp and
spc
2
-IMD
.
mdp into strings
commit
|
commitdiff
|
tree
2018-01-11
A
leksei Iupinov
R
emove unused alan
i
ne_vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupinov
D
o
n
o
t p
r
int PME counter breakdow
n
i
f
it's empt
y
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupino
v
Set
G
MX_GPU_AUTO to FALSE with G
M
X_GPU
defined
commit
|
commitdiff
|
tree
2017-12-20
Alekse
i
I
upinov
Remove po
t
entially wrong "
p
er user r
e
quest
"
note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
A
l
e
ksei Iupinov
Rel
a
xed pr
e
cision in spli
n
e
i
nterpo
l
ation tests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei
Iupin
o
v
Pro
v
ide d
u
mmy initialization to silence a warning
commit
|
commitdiff
|
tree
2017-12-05
Aleksei
Iupi
n
ov
D
o n
o
t
acce
p
t
u
n
s
upported combinati
o
n "-pme
cpu
-p
m
efft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Alek
s
ei Iupinov
Reformulate PME
solving tests tol
e
ranc
e
s
commit
|
commitdiff
|
tree
2017-11-28
Aleksei Iupinov
Repl
a
ce of pme
G
PU
v
ariable name w
i
t
h pmeGp
u
commit
|
commitdiff
|
tree
2017-11-27
Alek
s
ei Iupinov
D
o
n
o
t force
separ
a
te
PME rank to rec
o
mpute
r
ecipro
c
al
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
A
lek
s
ei
Iupin
o
v
Disable
failin
g
sepa
r
ate PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
Iu
p
inov
Add
t
ests for PM
E
t
uning and fix mixed PME
mode with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei Iupino
v
D
estro
y
PME GPU
c
ontext
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
E
nable separate PME
GPU rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei I
u
pinov
D
o
no
t
ca
l
l mixed C
P
U+GPU
P
ME mo
d
e "Hybri
d
"
commit
|
commitdiff
|
tree
2017-11-24
A
leksei Iupinov
A
c
tivat
e
mixed mode
o
f PME on
G
PU
commit
|
commitdiff
|
tree
2017-11-24
A
leks
e
i I
u
pinov
Remo
v
e outdated (alre
a
dy implemented)
p
inn
i
ng
TODO
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i Iupin
o
v
Menti
o
n
gmx_ins
t
all_head
e
rs() in the developer manual
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iupinov
Make F
F
T
real-space grid use
C
UDA pinning for
m
ixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
P
i
n coordin
a
tes,
forces an
d
charges for PME on
GP
U
commit
|
commitdiff
|
tree
2017-11-21
A
l
eksei Iupinov
Fix CUDA release build war
n
ing
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupinov
F
i
x pinned memo
r
y sta
t
us checker tests
commit
|
commitdiff
|
tree
2017-11-18
Al
e
ksei Iupinov
Asy
n
chr
o
n
ous CUDA
t
ransfer
s
are asserted t
o
always
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Aleksei Iupi
n
ov
M
ake gpu_utils-test bu
i
l
d with GM
X
_CLANG_CUDA
commit
|
commitdiff
|
tree
2017-11-15
Alekse
i
Iupinov
Renam
e
a
n
d e
x
pos
e
"gener
i
c" GPU memory tr
a
nsfer functions
commit
|
commitdiff
|
tree
2017-11-09
Ale
k
sei I
u
p
ino
v
Rename s
y
nchronous GPU tr
a
ns
f
e
r functions
to match
.
.
.
commit
|
commitdiff
|
tree
next