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Make the reference data variables local in GetIrTest
2018-01-19
Al
e
ksei Iup
i
n
ov
Make the ref
e
rence d
a
ta variables
local in GetIrTest
commit
|
commitdiff
|
tree
2018-01-18
A
l
eks
e
i Iupinov
Got rid of manu
a
l
memory
m
an
a
gement in
t
he
P
ME overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Re-enable multi-ran
k
PME
t
ests
(
with the
file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Alek
s
ei Iupinov
M
e
rge branch 'r
e
lease-2
0
18' into mast
e
r
commit
|
commitdiff
|
tree
2018-01-16
Aleksei Iupinov
Always write t
h
e input MD
P
f
ile for
testing just before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iup
i
nov
Move OctaneS
a
ndwich
.
mdp an
d
s
p
c2-IMD
.
mdp into string
s
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iu
p
ino
v
Remove unused
al
a
nine
_
vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupinov
Do not pri
n
t
PME counter breakdown if it's
emp
t
y
commit
|
commitdiff
|
tree
2017-12-20
Aleksei
Iu
p
i
n
o
v
Set GMX_G
P
U_A
U
TO to FALSE with
G
MX_GPU defined
commit
|
commitdiff
|
tree
2017-12-20
A
l
eksei Iupinov
Remove
p
o
tentially wron
g
"per us
e
r re
q
uest" not
e
from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Aleksei Iupinov
R
e
l
a
x
e
d precision in spline i
n
t
e
r
p
o
l
a
t
ion tests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei Iupinov
P
r
ovide
d
ummy initializa
t
ion to
s
i
l
ence a
w
arning
commit
|
commitdiff
|
tree
2017-12-05
Aleksei
I
upi
n
ov
Do n
o
t ac
c
ept unsupport
e
d combination "-pme cpu -pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei
Iupinov
Reformulate
PM
E
solving tes
t
s tolerances
commit
|
commitdiff
|
tree
2017-11-28
Aleksei Iupi
n
ov
Replace of pme
G
P
U
variable name with pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Do not fo
r
ce separate PME rank t
o
re
c
omp
u
te recipro
c
al
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Alek
s
ei Iupi
n
ov
Disable failing
s
e
parate PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Add tests for PM
E
t
uning and fix mixed P
M
E mode with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei I
u
pinov
De
s
troy PME GPU context
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
sei Iupinov
Enable separat
e
PME
G
PU ra
n
k
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Do not
c
all mixed
C
PU+GPU PME mode "Hybrid"
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupi
n
ov
A
c
tivate
m
ixed mode of P
M
E on GPU
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei Iupinov
Remove outdated (
a
lready i
m
plement
e
d) pin
n
i
n
g TODO
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei I
u
pin
o
v
Mention gmx_install_headers() in
t
he develop
e
r manua
l
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iupinov
Make FFT re
a
l-space grid use CUDA pinn
i
ng for mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iup
i
no
v
Pin
c
o
ord
i
nates, forces and char
g
e
s f
o
r PME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-21
Al
e
k
sei Iupinov
F
i
x
CUDA release b
u
ild w
a
rning
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupinov
Fix pinned memory status checker
t
ests
commit
|
commitdiff
|
tree
2017-11-18
Aleksei
I
u
pinov
A
synchronous CUDA tra
n
sfers are asserted to a
l
ways
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
A
leksei
I
u
pinov
Ma
k
e
g
p
u_utils-
t
est build
w
ith G
M
X_CLANG_CU
D
A
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iu
p
i
nov
Rename and
expose "ge
n
eric" GPU
memory
t
ransfer func
t
i
o
ns
commit
|
commitdiff
|
tree
2017-11-09
Aleksei
I
upinov
Rename synchronous G
P
U
transfe
r
f
uncti
o
ns t
o
match
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Ale
k
s
ei Iupinov
Re
p
lace math
.
h by cm
a
t
h
includes in cpp f
i
les
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupi
n
ov
Remove unused PME GPU decl
a
r
ations
commit
|
commitdiff
|
tree
2017-11-01
Alekse
i
Iupi
n
ov
Move pme_gp
u
_finis
h
_computation()
documentation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Fix erroneous PME
GPU "step" na
m
ings
commit
|
commitdiff
|
tree
2017-11-01
Alekse
i
Iup
i
nov
S
i
mpl
i
fy PME GPU s
y
nchronizatio
n
code
commit
|
commitdiff
|
tree
2017-10-31
A
l
eksei I
u
pin
o
v
Reus
e
e
p
bcXY logic
commit
|
commitdiff
|
tree
2017-10-30
Alek
s
ei Iupinov
Fix ref
e
rence mode b
u
ild
u
nused function w
a
rnings
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iu
p
inov
Bring PME GPU/CUDA int
e
rnal structu
r
e
names
to CamelC
a
se
commit
|
commitdiff
|
tree
2017-10-30
Aleksei
Iupinov
Use new/d
e
lete for gmx_pme
_
t
commit
|
commitdiff
|
tree
2017-10-30
Aleks
e
i
I
u
pino
v
Simplify PME data ha
n
dl
i
ng in
runner
commit
|
commitdiff
|
tree
2017-10-29
Aleksei Iup
i
n
o
v
Make
PM
E
tuning logic mo
r
e
r
e
ada
b
le
commit
|
commitdiff
|
tree
2017-10-27
Aleksei
I
upinov
Remove unused PME gr
i
d dump
debug fu
n
ctions
commit
|
commitdiff
|
tree
2017-10-27
Aleksei Iup
i
nov
Replac
e
a few asserts with GMX_
A
SSER
T
's
commit
|
commitdiff
|
tree
2017-10-27
Aleksei Iu
p
inov
R
e
move defunct
P
ME i
n
itial
i
z
a
tion error code return
commit
|
commitdiff
|
tree
2017-10-24
Aleksei Iupinov
Remove duplicate/outda
t
e
d functi
o
n declaration
commit
|
commitdiff
|
tree
2017-10-24
Aleksei Iupinov
M
o
v
e
co
m
mrec duty
checking
i
nto sim
p
le g
e
tte
r
s
commit
|
commitdiff
|
tree
2017-10-23
Alekse
i
Iup
i
no
v
Cor
r
ect the
p
a
ge
a
llocator description
commit
|
commitdiff
|
tree
2017-10-22
Aleksei Iupinov
Ch
a
nge PM
E
G
P
U gather re
d
u
c
t
i
on argument
from boolean
.
.
.
commit
|
commitdiff
|
tree
2017-10-21
A
l
eksei
I
u
p
i
nov
Add calls to the PME GPU
s
tag
e
s
commit
|
commitdiff
|
tree
2017-10-13
Alek
s
ei
I
upino
v
R
elax PME spline compu
t
at
i
o
n tol
e
rance
i
n
doub
l
e precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
Aleksei Iup
i
nov
R
emove useless exte
r
n CU
D
A te
x
ture reference declarations
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
Aleksei I
u
pinov
Rev
e
rt
"Dr
o
p
NB_ from GMX_CUDA_NB_SINGLE
_
COMP
I
L
ATION_
U
NIT
.
.
.
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
Fix
c
l
ang warnin
g
s for
P
M
E CUDA ke
r
nels
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
R
e
l
a
x
PME
solving test
c
om
p
lex grid toleran
c
e
commit
|
commitdiff
|
tree
2017-10-11
Aleks
e
i Iupin
o
v
CUDA 9/Volta su
p
port for PME
commit
|
commitdiff
|
tree
2017-10-11
Ale
k
s
e
i Iupinov
PME solvi
n
g
- CUDA ker
n
el + unit tests
commit
|
commitdiff
|
tree
2017-10-11
Ale
k
s
ei Iupinov
P
M
E
f
o
rce gat
h
ering
- CUDA kernel + u
n
i
t
tes
t
s
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupino
v
Dro
p
NB_ from
GMX_CU
D
A_NB_SIN
G
LE_COMPILATION_UNIT cmake
.
.
.
commit
|
commitdiff
|
tree
2017-10-11
Aleks
e
i Iupinov
PM
E
spline+spread
C
U
D
A
kernel and
u
nit tests
commit
|
commitdiff
|
tree
2017-10-09
Al
e
ksei Iupinov
R
e
mov
e
some unnecessary includes
f
r
om PME
commit
|
commitdiff
|
tree
2017-10-09
Ale
k
sei Iupinov
PME GPU
/
CUDA data fra
m
e
w
ork
.
commit
|
commitdiff
|
tree
2017-10-06
Aleksei I
u
pinov
Ad
d
timin
g
a
c
cumulation capa
b
ilit
y
into GpuRe
g
io
n
Ti
m
er
commit
|
commitdiff
|
tree
2017-10-04
Aleksei
I
u
pinov
Remov
e
G
P
U
timing functions
s
up
e
rsed
e
d by G
p
uRe
g
ionTimer
commit
|
commitdiff
|
tree
2017-10-04
Al
e
ksei I
u
p
i
nov
Add GpuRegion
T
i
mer c
l
ass
commit
|
commitdiff
|
tree
2017-10-03
Aleksei Iupinov
Bring
CU
D
A te
x
t
ur
e
g
e
t
ters documenta
t
ion up-to-da
t
e
commit
|
commitdiff
|
tree
2017-10-03
Al
e
ksei
I
up
i
no
v
T
empl
a
t
e/move CUDA texture
clean
u
p
code
from NB CUD
A
.
.
.
commit
|
commitdiff
|
tree
2017-10-03
A
l
ekse
i
Iupinov
A
d
d W
i
nAP
I
pag
e
siz
e
q
uery for allocato
r
purposes
commit
|
commitdiff
|
tree
2017-09-26
Aleksei
Iupi
n
ov
M
o
ve CUDA
t
extu
r
e set
u
p code from NB
C
UDA module t
o
.
.
.
commit
|
commitdiff
|
tree
2017-09-22
Aleksei Iupinov
Template the CUD
A
text
u
re setup code on raw value t
y
pe T
commit
|
commitdiff
|
tree
2017-09-21
A
l
eks
e
i Iu
p
inov
Eliminate unus
e
d Coulomb correction table size
c
oulomb
_
tab_size
commit
|
commitdiff
|
tree
2017-09-21
Aleksei Iupinov
El
i
minat
e
d
u
plicate CUDA texture setup code
commit
|
commitdiff
|
tree
2017-09-18
Aleksei Iu
p
inov
Sk
i
p GPU rea
l
l
o
cation of
a
n empty no
n
-local pairlist
commit
|
commitdiff
|
tree
2017-09-14
Aleksei I
u
pi
n
ov
Fix non-
S
I
M
D build f
a
ilin
g
commit
|
commitdiff
|
tree
2017-09-12
Aleksei
I
upinov
P
r
event r
e
fere
n
ce XML
r
eader
s
e
g
fault o
n
nullp
t
r error
.
.
.
commit
|
commitdiff
|
tree
2017-09-04
Aleksei Iupinov
Mer
g
e "Mer
g
e
branch release-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Aleksei
I
upinov
Bring b
a
ck space los
t
in commit e43e83bf
commit
|
commitdiff
|
tree
2017-08-29
Aleks
e
i Iup
i
nov
Remove lefto
v
er function
declar
a
t
ion
commit
|
commitdiff
|
tree
2017-08-29
Aleksei Iupino
v
Fix typo
commit
|
commitdiff
|
tree
2017-08-29
A
l
eksei Iupinov
A
l
low pas
s
ing optional
w
idth
argument into CUDA shuffle
.
.
.
commit
|
commitdiff
|
tree
2017-08-29
Aleksei Iupinov
Adjust PM
E
LJ solver tes
t
input coeff
i
cient
commit
|
commitdiff
|
tree
2017-08-22
Alekse
i
Iupin
o
v
Separate P
M
E spread a
n
d gath
e
r wallcycle co
u
nters
commit
|
commitdiff
|
tree
2017-08-21
Alekse
i
I
upinov
PME solving
tes
t
s
commit
|
commitdiff
|
tree
2017-08-17
Aleksei Iupin
o
v
Merge "Merge
b
r
a
nch r
e
lease-5-
1
into release-201
6
"
.
.
.
commit
|
commitdiff
|
tree
2017-06-30
Aleksei I
u
pino
v
Remove ou
t
dated c
m
a
ke nvcc log
i
c
commit
|
commitdiff
|
tree
2017-06-12
A
leks
e
i Iupino
v
Sto
r
e a physical node
c
o
m
municator in t_commrec
commit
|
commitdiff
|
tree
2017-03-17
Aleksei Iupi
n
ov
Fi
x
der
e
ferencin
g
nullptr in PME solve
w
ork de
s
tructor
commit
|
commitdiff
|
tree
2017-03-03
Aleksei Iupinov
Remove outdated CUDA
v
ersion ch
e
ck
commit
|
commitdiff
|
tree
2017-02-21
Aleksei Iupinov
Remove un
u
sed
f
un
c
tio
n
cu_synchstream_atdat
(
)
commit
|
commitdiff
|
tree
2017-02-09
Ale
k
sei
I
u
pi
n
ov
Add initia
l
i
zati
o
n t
o
dv
d
la
m
bda in b
o
nded
f
o
r
c
es
tests
commit
|
commitdiff
|
tree
2017-02-09
Aleksei Iu
p
inov
Fix typo (Dihedarl -> Dihedra
l
)
commit
|
commitdiff
|
tree
2017-02-08
Alekse
i
I
u
pi
n
ov
PME for
c
e
gathering tests
commit
|
commitdiff
|
tree
2017-02-08
A
l
eksei Iup
i
nov
F
ix i
n
v
a
lid triclinic box in t
h
e
P
ME t
e
st data
commit
|
commitdiff
|
tree
2017-01-24
Aleksei Iupinov
PME spline comp
u
t
a
tion and char
g
e
spreadi
n
g
tests
commit
|
commitdiff
|
tree
2017-01-24
Alek
s
ei Iup
i
no
v
Add c
o
nst qua
l
if
i
er to so
m
e PME spread arguments
commit
|
commitdiff
|
tree
2017-01-19
Aleksei I
u
pin
o
v
Simplify gm
x
_co
u
n
t
_gpu
_
dev_uni
q
ue
(
)
commit
|
commitdiff
|
tree
2017-01-19
Aleks
e
i Iu
p
inov
P
M
E
B-Spli
n
e
moduli comput
a
tio
n
u
nit
test
commit
|
commitdiff
|
tree
2017-01-05
Ale
k
sei Iup
i
no
v
F
ix
c
ompilatio
n
with CMAKE_C
X
X_FLAGS="-Wa
l
l
-
W
err
o
r"
commit
|
commitdiff
|
tree
2016-12-22
Aleksei Iupino
v
Remove unused member thr
e
ad_o
n
e from
the PME spline
.
.
.
commit
|
commitdiff
|
tree
next