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Break apart update_constraints
2018-04-12
Aleksei Iupino
v
Make in-source OpenCL kernel path a per
-
modu
l
e parameter
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupin
o
v
Remove
C
U
DA_FUNC macros
fr
o
m many fun
c
tions in PM
E
G
PU
commit
|
commitdiff
|
tree
2018-04-12
Ale
k
sei
I
u
p
i
nov
S
top PME GPU code fro
m
compiling on non-CUDA build
s
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
P
r
even
t
Op
e
nCL timing m
e
mor
y
leak
commit
|
commitdiff
|
tree
2018-03-20
Aleksei Iupinov
Clarify the mdrun GPU
o
pt
i
o
n
s docs
commit
|
commitdiff
|
tree
2018-03-16
Al
e
ksei
Iu
p
inov
Add a ba
s
ic T
P
I sanity test
commit
|
commitdiff
|
tree
2018-03-16
Al
e
ksei
I
upinov
Stop gmx_feenablee
x
cept() fro
m
returning previous exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Al
e
ksei
I
upinov
Restore t
h
e l
o
s
t
m
c_temp chec
k
i
n
grompp
commit
|
commitdiff
|
tree
2018-03-06
Al
e
ksei Iupinov
Isolate PME GPU spline parameter indexing in inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Al
e
ksei Iupinov
Stop using custom Find
O
p
enCL
.
cma
k
e,
p
e
r T
O
DO
commit
|
commitdiff
|
tree
2018-03-05
Alekse
i
Iupino
v
C
orre
c
t the nbnxn_gpu_compile_
k
ernels() docs
commit
|
commitdiff
|
tree
2018-03-02
Aleks
e
i Iupinov
Make TPI use double p
r
ecision exp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei Iupinov
Mer
g
e branch 're
l
ease-2018'
commit
|
commitdiff
|
tree
2018-02-26
A
leksei Iupi
n
ov
Advice us
e
rs on i
n
finite
o
u
tput
o
f TPI
commit
|
commitdiff
|
tree
2018-02-20
Aleksei
I
upinov
Remove un
u
sed
OpenCL debug buffer
commit
|
commitdiff
|
tree
2018-02-18
Aleksei Iu
p
inov
Replace *
_
free_buffered calls by f
r
eeDev
i
ceBuffer
commit
|
commitdiff
|
tree
2018-02-16
A
l
eks
e
i Iupinov
Fix PME for larg
e
systems with Fermi GPUs
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iup
i
nov
Up
d
ate
F
FTW
build to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Add
f
reeD
e
viceBuffer G
P
U util
i
ty functi
o
n
commit
|
commitdiff
|
tree
2018-02-15
A
leksei Iupinov
Add the missin
g
co
m
ma in th
e
q
uote
commit
|
commitdiff
|
tree
2018-02-14
Alekse
i
Iupi
n
ov
Rep
l
ac
e
t
h
e re
m
aining EXPECT_
D
E
A
T
H with EXPEC
T
_DEATH_I
F
_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei
Iupinov
Add
DeviceBuffe
r
a
s
a
t
y
pedef
f
or cl_mem/device ponter
commit
|
commitdiff
|
tree
2018-02-13
Aleksei Iupinov
Move GPU tr
a
its into s
e
parate h
e
ade
r
s
commit
|
commitdiff
|
tree
2018-02-12
Alek
s
e
i
I
upinov
Fix
t
he include gu
a
rd
commit
|
commitdiff
|
tree
2018-02-09
Aleksei I
u
pinov
Revert "Enabl
e
debug FP
exceptions without
T
PI,
n
o
t
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
A
l
eksei Iup
i
n
ov
A
lways run the esse
n
ti
a
l dynam
i
c
s tests
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iu
p
ino
v
Enabl
e
debug FP exc
e
ptions without
TPI, not with TPI
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iup
i
nov
Merge branch 'rele
a
se
-
2
01
8
' i
n
to master
commit
|
commitdiff
|
tree
2018-02-06
Alekse
i
Iupi
n
ov
Re
m
ove
unnecessary inclu
d
es from d
o
mdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Zero unused v
a
lues to silence the
warning
commit
|
commitdiff
|
tree
2018-02-06
A
l
eksei Iupinov
Only set
u
p
E
wald
in the ge
n
eric group kernel if i
t
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupinov
M
a
k
e ndx file
s
optional in Simul
a
t
i
o
nRunner
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupinov
Remove mdpInputF
i
leName_
from Simul
a
tionR
u
nne
r
, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
leksei Iupinov
Don't print
i
m
p
ossib
l
e CUDA ver
s
ion numbers in
a
bsence
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei
I
upi
n
o
v
Fix input MDP contents for sw
a
p and
IMD tests
commit
|
commitdiff
|
tree
2018-02-01
A
leksei Iupi
n
ov
Check for
GTEST_IS_THREADSAFE being defin
e
d
commit
|
commitdiff
|
tree
2018-01-24
Aleks
e
i I
u
pi
n
ov
Remove unused f
i
elds per TODO
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Test the mixe
d
mode PME with walls and box
s
cal
i
n
g
commit
|
commitdiff
|
tree
2018-01-23
A
l
eksei Iupinov
T
e
s
t PME
C
PU/GPU with walls and box
s
caling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupi
n
o
v
Wrap the PME testing loop in a
method for extensibility
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
A
d
d a death test for
t
he d
u
plicate
inputre
c
k
e
ys checking
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupin
o
v
Re
n
ame class Bia
s
Reader t
o
struct BiasOutputSetup
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Mov
e
t
h
e
t
empora
r
y fil
e
MPI workaround
into the base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i Iupinov
Mak
e
t
h
e
r
e
ferenc
e
data
v
ari
a
b
l
es local in Get
I
r
Test
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i I
u
pinov
Merge branch 'release-201
8
' into master
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Got
rid of manual m
e
mory management i
n
the PME overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Alek
s
e
i
Iupinov
Re-enab
l
e mu
l
ti-ra
n
k PME
tes
t
s (with the file rac
e
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
A
l
ek
s
ei Iupinov
Fi
x
box scaling in PME mixed m
o
de
commit
|
commitdiff
|
tree
2018-01-17
A
l
eksei Iupinov
M
erge branch
'
release-2018'
i
nto ma
s
ter
commit
|
commitdiff
|
tree
2018-01-16
Aleksei I
u
pinov
Always write
t
he
input M
D
P
f
i
le fo
r
testing just
b
e
f
o
r
e
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
A
leksei Iupinov
M
ove Oc
t
an
e
Sandwich
.
mdp
a
nd s
p
c
2-IMD
.
mdp int
o
str
i
ngs
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupinov
Remove unused alanin
e
_
vsi
t
e
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Aleks
e
i Iupino
v
Do n
o
t pr
i
nt PME c
o
unter breakdown if it
'
s empty
commit
|
commitdiff
|
tree
2017-12-20
A
leksei Iupinov
Set GM
X
_
GPU_AUTO to
FALS
E
w
i
th GMX_GPU
d
e
f
i
n
e
d
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupino
v
Remove potentially wrong
"per user request" not
e
fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Ale
k
sei
I
upinov
Rela
x
ed precision in s
p
l
i
ne
interpolat
i
on tes
t
s
commit
|
commitdiff
|
tree
2017-12-06
Ale
k
s
e
i Iupinov
P
rovide du
m
my initial
i
zatio
n
to silence a w
a
rning
commit
|
commitdiff
|
tree
2017-12-05
Aleksei Iupinov
D
o
not a
c
cept unsu
p
ported combinati
o
n "-pm
e
cpu -
p
mefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei Iu
p
i
nov
Refor
m
ulat
e
PME
s
olving tests
tolerances
commit
|
commitdiff
|
tree
2017-11-28
A
leksei Iupinov
Re
p
lace of pmeGPU vari
a
b
l
e nam
e
with pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupi
n
ov
Do not f
o
rc
e
separate
PME rank
to re
c
o
m
pute reciprocal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleks
e
i Iupinov
Disable failing separa
t
e PME ran
k
t
e
st
s
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
A
d
d tests for PM
E
tuning and fix mixed PME mode
with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Destroy
PME GPU cont
e
xt
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i Iupinov
Enable sep
a
r
a
te PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
D
o
not ca
l
l mixed CPU+
G
P
U PME mode
"
H
ybr
i
d"
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i I
u
pinov
Act
i
vate mi
x
ed
mode of PME
o
n
GPU
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei Iupin
o
v
Remov
e
ou
t
dated (alrea
d
y
implemented
)
pi
n
ning T
O
DO
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
se
i
Iupinov
Mention gmx_in
s
ta
l
l_headers()
i
n
the devel
o
per manu
a
l
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iupinov
Make
FFT re
a
l-space
grid use CUDA pinning for mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
sei I
u
p
i
nov
Pin coor
d
i
n
ates, f
o
rces
and
charges for P
M
E on GPU
commit
|
commitdiff
|
tree
2017-11-21
Alek
s
ei Iupinov
Fix
CUDA r
e
lea
s
e build warn
i
n
g
commit
|
commitdiff
|
tree
2017-11-21
Alek
s
ei Iupinov
Fix p
i
n
ned me
m
ory status
c
hecker
t
ests
commit
|
commitdiff
|
tree
2017-11-18
Aleksei Iupin
o
v
A
s
ynchronou
s
C
U
DA t
r
ansfers are asserted to
a
lways
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Aleksei
I
upinov
Make gp
u
_utils-test build w
i
th GMX_CLANG_CU
D
A
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iupin
o
v
Rename and expose "generi
c
" GPU mem
o
ry tran
s
f
e
r functions
commit
|
commitdiff
|
tree
2017-11-09
Al
e
k
sei Iup
i
nov
Rename
s
yn
c
hronous
GP
U
transfe
r
f
unctions to
m
at
c
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei Iupi
n
ov
R
ep
l
ac
e
math
.
h by cma
t
h includes in cpp files
commit
|
commitdiff
|
tree
2017-11-01
Aleksei
Iupinov
Remove
unuse
d
PME
GPU dec
l
ara
t
ions
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupi
n
ov
Move pme_gpu_finish_
c
omputati
o
n() documentation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupin
o
v
Fix
e
rroneous PME GPU "ste
p
"
namings
commit
|
commitdiff
|
tree
2017-11-01
Ale
k
sei Iupinov
Si
m
plify PME GPU
sy
n
c
h
ro
n
ization code
commit
|
commitdiff
|
tree
2017-10-31
Aleks
e
i Iupino
v
Re
u
se epbcXY l
o
gi
c
commit
|
commitdiff
|
tree
2017-10-30
Alekse
i
Iu
p
inov
Fix referen
c
e
m
ode b
u
ild
unused function warnings
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Bring PME G
P
U
/CUDA internal
structure
na
m
es to
C
a
m
e
lCase
commit
|
commitdiff
|
tree
2017-10-30
A
l
eksei Iupinov
Use new/d
e
lete for gmx_pme_t
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Simp
l
ify
P
ME dat
a
handling i
n
runner
commit
|
commitdiff
|
tree
2017-10-29
A
lekse
i
Iupinov
M
ake
PM
E
tuning logic mo
r
e readable
commit
|
commitdiff
|
tree
2017-10-27
Aleksei I
u
pin
o
v
Remo
v
e unused PME gri
d
dump d
e
bug fu
n
c
t
ions
commit
|
commitdiff
|
tree
2017-10-27
Aleksei Iupi
n
ov
R
e
place a few as
s
erts
w
ith GMX_ASSE
R
T
'
s
commit
|
commitdiff
|
tree
2017-10-27
Ale
k
sei Iupinov
Remove def
u
nct PME initialization er
r
or
c
ode r
e
turn
commit
|
commitdiff
|
tree
2017-10-24
Ale
k
s
e
i
Iupinov
Remo
v
e du
p
lica
t
e/outdated functio
n
declaration
commit
|
commitdiff
|
tree
2017-10-24
Aleksei Iupinov
Mo
v
e c
o
mm
r
e
c dut
y
checking into simp
l
e getter
s
commit
|
commitdiff
|
tree
2017-10-23
Aleksei Iupinov
Correct the page allo
c
ator descr
i
ption
commit
|
commitdiff
|
tree
2017-10-22
Alekse
i
Iupinov
Change PME
GPU gather r
e
d
u
ction argum
e
nt fr
o
m
b
oo
l
ean
.
.
.
commit
|
commitdiff
|
tree
2017-10-21
Aleksei Iupi
n
o
v
Add calls
to the PME GPU s
t
ages
commit
|
commitdiff
|
tree
2017-10-13
Alekse
i
Iup
i
nov
Rela
x
PM
E
spline computation
t
o
l
e
ranc
e
i
n
double precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
Alekse
i
Iupinov
R
e
move useless extern CUDA t
e
xture refere
n
ce decla
r
ations
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
Aleksei Iupin
o
v
Revert "Drop NB_ f
r
om GMX_CUD
A
_NB
_
SIN
G
LE_COMPILATION_UNIT
.
.
.
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
Fi
x
clang
w
arnings for PME CUDA kernels
commit
|
commitdiff
|
tree
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