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Change image conversion to only be build once
2018-04-23
Aleksei Iupinov
R
emove
d
cu_re
a
lloc_buffered()
i
n favor
of
r
e
alloca
t
eDev
i
ceBu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
A
l
e
ksei Iupinov
DeviceBuffer headers are added
commit
|
commitdiff
|
tree
2018-04-12
Alekse
i
Iu
p
in
o
v
Make in-
s
ource
Op
e
n
CL kern
e
l
path a per-module param
e
te
r
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Remove CUDA_FUNC
m
ac
r
os from
m
a
n
y
functions in PME GPU
commit
|
commitdiff
|
tree
2018-04-12
A
leksei Iupinov
Stop PME GPU code from
c
o
mpiling on non-CUDA bui
l
ds
commit
|
commitdiff
|
tree
2018-04-10
Alek
s
ei Iupinov
Preve
n
t O
p
enCL
ti
m
ing memory lea
k
commit
|
commitdiff
|
tree
2018-03-20
Aleksei Iu
p
inov
Clari
f
y
the mdrun GPU optio
n
s docs
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupin
o
v
Add
a
basic TPI sanity t
e
st
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupi
n
ov
Stop gmx_feenabl
e
except() from returning pre
v
iou
s
exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
R
estore th
e
lost mc_temp
check
i
n grompp
commit
|
commitdiff
|
tree
2018-03-06
Aleksei Iup
i
nov
Isolate
PME GPU spline pa
r
ameter inde
x
ing in inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei
I
upinov
Stop using cust
o
m FindOpenCL
.
cmake, per TODO
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupino
v
Correct the nbnxn_gpu_comp
i
le_kernels() d
o
cs
commit
|
commitdiff
|
tree
2018-03-02
A
leksei Iupino
v
Make
TPI use double pr
e
cision exp
commit
|
commitdiff
|
tree
2018-02-27
Alek
s
e
i Iu
p
i
nov
Mer
g
e branc
h
're
l
e
a
se-2
0
18
'
commit
|
commitdiff
|
tree
2018-02-26
Al
e
k
s
ei Iup
i
nov
Ad
v
ice users on infin
i
te output of
TPI
commit
|
commitdiff
|
tree
2018-02-20
Alek
s
ei I
u
pino
v
Remove unused Op
e
nCL debug bu
f
fer
commit
|
commitdiff
|
tree
2018-02-18
Aleks
e
i Iupinov
Replac
e
*_
f
ree_b
u
ffere
d
calls by
freeDev
i
ceBuffer
commit
|
commitdiff
|
tree
2018-02-16
Aleksei
I
upinov
Fix
PME for large
sy
s
t
e
m
s with Fermi
G
P
Us
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupi
n
ov
Update F
F
TW build to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei
I
upinov
Add freeDeviceBu
f
fer G
P
U
utili
t
y functi
o
n
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Add
t
h
e missing comma in the quot
e
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
R
eplace the remaining EXPECT_DEATH with EXPECT_DE
A
TH
_
IF_S
U
PP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Add DeviceBuffe
r
as
a t
y
pedef for cl_mem/device p
o
nter
commit
|
commitdiff
|
tree
2018-02-13
A
l
eksei Iu
p
inov
Move GP
U
tra
i
ts int
o
sepa
r
ate hea
d
ers
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iupinov
F
ix the
i
nclude guard
commit
|
commitdiff
|
tree
2018-02-09
Aleksei Iup
i
n
o
v
Revert "
E
nable debug FP
e
xceptio
n
s wit
h
out TPI, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupi
n
ov
Alw
a
ys run th
e
es
s
ential dynamics t
e
sts
commit
|
commitdiff
|
tree
2018-02-08
Ale
k
sei Iupinov
Enable debu
g
FP exceptions wit
h
out T
P
I, not wit
h
TPI
commit
|
commitdiff
|
tree
2018-02-08
Ale
k
sei
Iupinov
Merge branch 'release-2018'
into master
commit
|
commitdiff
|
tree
2018-02-06
A
leksei Iup
i
nov
Remove unnecessary includes f
r
o
m
do
m
d
ec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Ale
k
s
ei Iupinov
Zero u
n
used va
l
u
e
s
t
o si
l
e
n
ce
t
he warning
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Only setup Ewald in the generic gro
u
p kernel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Al
e
ksei Iupinov
Make n
d
x files optional in Simula
t
ion
R
unner
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupin
o
v
Remove mdpInp
u
t
F
ileName_
f
rom Simul
a
tionRunner, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Alekse
i
Iupi
n
o
v
Don't print i
m
p
o
ssible CU
D
A versi
o
n numbers in
a
bsence
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei
Iupinov
Fix
i
n
put MDP contents for swap
a
nd IM
D
tests
commit
|
commitdiff
|
tree
2018-02-01
A
l
e
k
sei Iupi
n
ov
Check for GTEST_IS_THRE
A
D
SAFE being defined
commit
|
commitdiff
|
tree
2018-01-24
A
l
eksei Iu
p
inov
Remov
e
unu
s
ed fiel
d
s
per TODO
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Test the mixed mode
PME with walls and b
o
x scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iup
i
nov
Test
PME
CPU
/
G
P
U with wal
l
s and box scaling
commit
|
commitdiff
|
tree
2018-01-23
A
lekse
i
Iupinov
Wrap the PME
testing loop in a
method for ex
t
ensibi
l
i
t
y
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iu
p
inov
Add
a death test for the d
u
plicate
i
n
p
utr
e
c
k
e
y
s
checking
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupi
n
ov
Rename c
l
a
s
s BiasRead
e
r to s
t
ruct Bi
a
sOutputSetup
commit
|
commitdiff
|
tree
2018-01-19
A
leksei Iu
p
inov
M
o
ve t
h
e tempora
r
y
file MPI workar
o
und
i
n
to
t
he base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
sei Iupinov
Make
t
he ref
e
rence data variable
s
loc
a
l
i
n GetIrTest
commit
|
commitdiff
|
tree
2018-01-19
A
l
e
k
sei Iupino
v
Merge
b
ranch 'release-2018' into ma
s
ter
commit
|
commitdiff
|
tree
2018-01-18
Aleksei
I
upinov
Go
t
rid of man
u
al memory manag
e
me
n
t
i
n the
PME over
l
a
p
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei I
u
p
inov
Re-enable multi-rank PME t
e
st
s
(with th
e
file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Ale
k
sei I
u
pinov
F
i
x box scal
i
ng in PME mixed mode
commit
|
commitdiff
|
tree
2018-01-17
Ale
k
sei
I
upino
v
Merge
branch
'
r
elea
s
e-2018' into ma
s
t
e
r
commit
|
commitdiff
|
tree
2018-01-16
Alekse
i
I
upinov
Always write the inp
u
t
M
D
P fi
l
e for testing
j
u
s
t befo
r
e
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
A
leksei Iupinov
Move Octan
e
S
a
n
d
wich
.
mdp an
d
spc2-IMD
.
mdp
i
nto str
i
ngs
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupinov
Remove unused ala
n
in
e
_vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupi
n
ov
Do n
o
t pri
n
t P
M
E coun
t
er b
r
eakdown if it'
s
empty
commit
|
commitdiff
|
tree
2017-12-20
Aleksei
I
upinov
S
et
G
MX
_
GPU
_
A
U
TO t
o
FALSE with GMX_GPU
d
efined
commit
|
commitdiff
|
tree
2017-12-20
Ale
k
s
ei
I
upin
o
v
Remov
e
po
t
ent
i
ally wr
o
ng "per user
r
e
q
ues
t
" note
f
rom
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Aleksei I
u
pin
o
v
R
e
laxed
precision in spli
n
e interpolation
t
est
s
commit
|
commitdiff
|
tree
2017-12-06
Alek
s
ei Iupinov
Provide
d
ummy initi
a
lization to silenc
e
a warning
commit
|
commitdiff
|
tree
2017-12-05
Aleksei Iupinov
Do not accep
t
unsuppor
t
ed combination "-
p
m
e
cpu -pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleks
e
i Iupinov
Ref
o
rmulate PME solvi
n
g test
s
to
l
erances
commit
|
commitdiff
|
tree
2017-11-28
Aleks
e
i I
u
pinov
Re
p
lace of pme
G
PU v
a
r
iable name w
i
th pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Do
n
o
t force separate PM
E
rank
t
o recompute reciprocal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Disable failing separate PME
r
ank tests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
I
up
i
nov
Ad
d
tests f
o
r PME tun
i
ng
a
nd fix mixed PME mode with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i I
u
pi
n
ov
Destroy PME GPU context
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iu
p
inov
Enable separate PM
E
GP
U
r
a
nk
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Do not call
mixed CPU+GPU PM
E
mode "Hybrid"
commit
|
commitdiff
|
tree
2017-11-24
A
le
k
sei
I
up
i
nov
Activate
mixed mode of
P
ME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i
I
upinov
Remove outdated (already
i
mplem
e
nted)
p
inning
T
ODO
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Mention gmx_i
n
s
tall_headers() i
n
t
he devel
o
per
manual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iu
p
inov
M
ak
e
FF
T
r
e
al-s
p
ace grid use CU
D
A pin
n
i
n
g for mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
kse
i
Iupi
n
ov
Pin c
o
o
r
dinates, forces and charges for PME on GPU
commit
|
commitdiff
|
tree
2017-11-21
Aleksei
I
u
p
i
nov
Fix CUDA rel
e
ase build warning
commit
|
commitdiff
|
tree
2017-11-21
Alek
s
ei Iupi
n
ov
Fix
pinned
memory status checke
r
t
e
s
t
s
commit
|
commitdiff
|
tree
2017-11-18
A
l
eksei Iupinov
A
synchronous CUDA tr
a
nsf
e
rs are as
s
e
r
t
e
d to always
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
A
le
k
sei
Iupinov
Make g
p
u_utils-test build w
i
th GMX_CLANG_CUDA
commit
|
commitdiff
|
tree
2017-11-15
Alek
s
ei Iupinov
R
ename a
n
d expose "g
e
neric"
GPU
memor
y
tr
a
ns
f
er functio
n
s
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupin
o
v
R
e
name s
y
nchr
o
nous GPU transfer fu
n
ctions to
m
atch
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Alek
s
ei Iupi
n
ov
Replace math
.
h
by cmath
i
n
c
ludes in cpp files
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iu
p
inov
R
emove unused PM
E
GPU declarations
commit
|
commitdiff
|
tree
2017-11-01
A
l
eksei
I
u
pinov
M
o
ve pme_g
p
u_finish_computation(
)
documentation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Fix erroneous P
M
E GP
U
"step" na
m
ings
commit
|
commitdiff
|
tree
2017-11-01
Aleksei
Iupinov
Simplify PME GP
U
s
y
nchro
n
i
z
ation code
commit
|
commitdiff
|
tree
2017-10-31
A
leksei Iupinov
Reuse epbcXY logic
commit
|
commitdiff
|
tree
2017-10-30
A
l
e
ksei Iupinov
F
i
x
reference
m
ode build
u
n
used functio
n
warnings
commit
|
commitdiff
|
tree
2017-10-30
A
l
e
k
sei I
u
pi
n
ov
Bring
PM
E
GPU/CUDA internal structure names to CamelCase
commit
|
commitdiff
|
tree
2017-10-30
Alek
s
ei Iupinov
Use new/delete
for gmx_pme_t
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
S
implif
y
PM
E
data han
d
ling in runner
commit
|
commitdiff
|
tree
2017-10-29
Aleksei Iupinov
M
a
ke PME tuning l
o
gic more readable
commit
|
commitdiff
|
tree
2017-10-27
Alek
s
ei Iupinov
Rem
o
ve unused PME grid dum
p
d
ebug functions
commit
|
commitdiff
|
tree
2017-10-27
Aleksei Iupi
n
ov
Rep
l
ace a f
e
w
a
ssert
s
with GMX_ASSER
T
's
commit
|
commitdiff
|
tree
2017-10-27
Aleksei I
u
p
inov
R
emove defunct PME
i
nitialization error code return
commit
|
commitdiff
|
tree
2017-10-24
Aleksei I
u
pinov
Remo
v
e d
u
pli
c
a
t
e/ou
t
d
a
t
e
d fu
n
ct
i
on declarati
o
n
commit
|
commitdiff
|
tree
2017-10-24
Aleksei Iupinov
Move co
m
m
r
ec dut
y
checking into si
m
pl
e
getters
commit
|
commitdiff
|
tree
2017-10-23
Aleksei Iupinov
Correct t
h
e page
a
llo
c
ator descriptio
n
commit
|
commitdiff
|
tree
2017-10-22
Aleksei I
u
pinov
Change P
M
E GPU gather reduction argu
m
ent from boole
a
n
.
.
.
commit
|
commitdiff
|
tree
2017-10-21
Aleksei Iupinov
Add calls to the PME GPU stage
s
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iu
p
inov
Relax PME spline
c
ompu
t
ation
t
o
lerance
i
n double precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
A
l
ek
s
ei Iupinov
Remove useless ex
t
ern
C
UDA te
x
ture
reference decl
a
rat
i
ons
.
.
.
commit
|
commitdiff
|
tree
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