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Improve mdrun performance user guide
2017-11-24
Ale
k
sei Iup
i
nov
Mak
e
FFT r
e
al-space grid use
C
U
D
A pin
n
ing for
m
ixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupin
o
v
Pin c
o
ordinates, forces a
n
d
c
h
a
rges for PME on GPU
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupinov
F
i
x CUDA release build warning
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupinov
Fix pi
n
n
ed me
m
ory status checker tests
commit
|
commitdiff
|
tree
2017-11-18
Aleksei Iupinov
As
y
nchronous
CUDA transfers are asserted to always
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
A
l
eksei Iupinov
Make gp
u
_utils-tes
t
b
u
ild with GMX_
C
LANG
_
CUDA
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iupinov
Rena
m
e
a
nd exp
o
se "generic"
GPU memory transfer functi
o
ns
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupinov
Rename
s
ynchronous
G
P
U transfer funct
i
ons to match
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Ale
k
s
e
i Iupin
o
v
Replace
math
.
h
by
c
m
a
th include
s
in cpp files
commit
|
commitdiff
|
tree
2017-11-01
A
l
e
ksei Iup
i
nov
Remov
e
unu
s
ed
PME
GPU
decl
a
ra
t
ions
commit
|
commitdiff
|
tree
2017-11-01
Al
e
k
sei Iupinov
Move pme_gpu_finis
h
_
c
omputation() doc
u
menta
t
io
n
to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Aleksei
I
upinov
Fix e
r
roneous PME GP
U
"step
"
namings
commit
|
commitdiff
|
tree
2017-11-01
A
leksei Iupi
n
ov
Simpl
i
fy PME GP
U
sy
n
chronization code
commit
|
commitdiff
|
tree
2017-10-31
Ale
k
s
ei Iupinov
Reus
e
epbcXY logic
commit
|
commitdiff
|
tree
2017-10-30
Al
e
ksei Iupinov
Fix reference
m
ode build unused
function warnin
g
s
commit
|
commitdiff
|
tree
2017-10-30
Alekse
i
Iu
p
inov
Bring P
M
E GPU/C
U
D
A
internal
structu
r
e nam
e
s to
C
amelCase
commit
|
commitdiff
|
tree
2017-10-30
Alek
s
ei Iup
i
nov
U
s
e
new/delete for gmx_pme_t
commit
|
commitdiff
|
tree
2017-10-30
Aleksei I
u
pinov
Simplify PME d
a
ta handling in runner
commit
|
commitdiff
|
tree
2017-10-29
Aleksei Iupinov
Make PME tuning logic
m
ore readable
commit
|
commitdiff
|
tree
2017-10-27
Aleksei Iupinov
Re
m
ove unused PME grid d
u
mp debug functio
n
s
commit
|
commitdiff
|
tree
2017-10-27
Al
e
ksei Iupinov
Replac
e
a
f
ew
a
s
s
erts w
i
th GMX
_
AS
S
ERT's
commit
|
commitdiff
|
tree
2017-10-27
Alek
s
ei
I
upinov
Remov
e
defunct PME initia
l
i
z
ation error
cod
e
return
commit
|
commitdiff
|
tree
2017-10-24
Al
e
ks
e
i
I
upinov
Remove duplicate
/
o
u
tdated fun
c
tion d
e
c
laration
commit
|
commitdiff
|
tree
2017-10-24
Aleksei
Iupinov
M
ove c
o
mmr
e
c duty ch
e
cking into sim
p
le getters
commit
|
commitdiff
|
tree
2017-10-23
A
l
eksei
I
upinov
Correct the page a
l
locator
d
escription
commit
|
commitdiff
|
tree
2017-10-22
Alek
s
ei Iupinov
Change
PME GPU gather
re
d
uction a
r
gu
m
ent from boo
l
ean
.
.
.
commit
|
commitdiff
|
tree
2017-10-21
Aleksei Iup
i
no
v
Add calls to
t
he PME GPU
s
tages
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iupinov
Relax PME spline com
p
uta
t
ion tolerance in double precision
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
A
leksei Iupino
v
Rem
o
ve useless extern C
U
DA text
u
re reference
declarations
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
Alek
s
ei
I
upinov
Revert "Drop NB_ fro
m
GMX_CUD
A
_N
B
_S
I
NGLE_COMPILATION_UNIT
.
.
.
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
F
ix clang warnings for PME CUDA kerne
l
s
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
R
e
lax
P
ME solving test comp
l
ex g
r
id tole
r
a
nce
commit
|
commitdiff
|
tree
2017-10-11
A
leksei Iupinov
CUDA
9
/
Volta
sup
p
ort for
PME
commit
|
commitdiff
|
tree
2017-10-11
A
l
e
k
s
ei Iu
p
inov
PME s
o
l
v
ing - CUDA kern
e
l + un
i
t tests
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iup
i
nov
P
M
E force ga
t
hering - CUDA kernel + u
n
it
t
ests
commit
|
commitdiff
|
tree
2017-10-11
Aleks
e
i I
u
pinov
Drop NB_ from
GMX_CUDA_N
B
_SINGL
E
_COM
P
I
LATION_UN
I
T
cmake
.
.
.
commit
|
commitdiff
|
tree
2017-10-11
Alekse
i
Iupinov
PME spli
n
e+
s
pread CUDA kern
e
l an
d
uni
t
t
e
sts
commit
|
commitdiff
|
tree
2017-10-09
Aleksei
I
u
p
inov
Remove s
o
m
e unnecessary inclu
d
es from PME
commit
|
commitdiff
|
tree
2017-10-09
Aleksei Iupinov
PM
E
GPU/CUDA data framework
.
commit
|
commitdiff
|
tree
2017-10-06
Aleksei Iupinov
Add
timing ac
c
umulati
o
n capa
b
ility into GpuRegionTimer
commit
|
commitdiff
|
tree
2017-10-04
Al
e
ksei Iupinov
Remove GPU
t
iming
functions
supers
e
ded
b
y
G
puRegio
n
Ti
m
er
commit
|
commitdiff
|
tree
2017-10-04
Ale
k
s
ei Iupino
v
Add Gp
u
Regio
n
Timer class
commit
|
commitdiff
|
tree
2017-10-03
Aleksei Iu
p
inov
B
r
ing
C
U
DA texture getters d
o
cume
n
tation up-to-dat
e
commit
|
commitdiff
|
tree
2017-10-03
Ale
k
sei Iupinov
T
emplate/move CUDA texture cleanup code
f
r
o
m NB CUDA
.
.
.
commit
|
commitdiff
|
tree
2017-10-03
Aleksei Iu
p
inov
Add Wi
n
A
P
I page
size
qu
e
ry for
allocator purposes
commit
|
commitdiff
|
tree
2017-09-26
Al
e
ksei Iupinov
M
ove C
U
DA te
x
ture set
u
p co
d
e fr
o
m NB CUDA mod
u
l
e to
.
.
.
commit
|
commitdiff
|
tree
2017-09-22
A
leksei Iupino
v
Tem
p
late
t
h
e CUDA te
x
ture setup code on raw value
type
T
commit
|
commitdiff
|
tree
2017-09-21
Aleksei Iupinov
Eliminate unused
Coulo
m
b corre
c
tion table size
c
oulomb
_
tab_
s
ize
commit
|
commitdiff
|
tree
2017-09-21
Aleksei Iupin
o
v
Eliminate duplic
a
te
C
U
D
A
texture setup
c
o
d
e
commit
|
commitdiff
|
tree
2017-09-18
Al
e
ksei Iupinov
Skip G
P
U
reallocation of an empty non-l
o
cal pairli
s
t
commit
|
commitdiff
|
tree
2017-09-14
Aleksei Iupinov
Fix non-SIMD build
f
a
i
ling
commit
|
commitdiff
|
tree
2017-09-12
A
leksei Iupinov
P
rev
e
nt refe
r
ence XML reader se
g
fault on nullptr err
o
r
.
.
.
commit
|
commitdiff
|
tree
2017-09-04
Alekse
i
Iup
i
nov
Merge
"
Merge br
a
nch release-
5
-
1
i
n
to
release-2016"
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
A
l
e
k
sei
Iupin
o
v
Bring back sp
a
ce lost i
n
commit e43e83b
f
commit
|
commitdiff
|
tree
2017-08-29
A
l
eksei Iupinov
Re
m
ove
l
eftover func
t
ion declaration
commit
|
commitdiff
|
tree
2017-08-29
A
leksei Iupinov
Fix typ
o
commit
|
commitdiff
|
tree
2017-08-29
Ale
k
sei I
u
pinov
A
l
low passing optional width
a
rgu
m
ent into CUDA
shuffl
e
.
.
.
commit
|
commitdiff
|
tree
2017-08-29
Al
e
kse
i
I
upinov
Adjus
t
PME
L
J solv
e
r test input c
o
e
f
f
i
cient
commit
|
commitdiff
|
tree
2017-08-22
Aleksei Iupinov
S
e
pa
r
ate PME spread and gathe
r
wallcycle counters
commit
|
commitdiff
|
tree
2017-08-21
Ale
k
sei I
u
pinov
P
ME solving
t
ests
commit
|
commitdiff
|
tree
2017-08-17
Aleksei Iupino
v
M
er
g
e "Me
r
g
e br
a
nch
releas
e
-
5-1 into
r
elease-2016"
.
.
.
commit
|
commitdiff
|
tree
2017-06-30
A
l
eksei Iupinov
Remove outd
a
ted cmake nv
c
c logi
c
commit
|
commitdiff
|
tree
2017-06-12
A
le
k
sei Iupinov
S
tore a p
h
ysical node
c
ommun
i
cator in t_
c
ommr
e
c
commit
|
commitdiff
|
tree
2017-03-17
Aleksei
Iupinov
Fix de
r
eferencing nullptr in
P
ME
solve work d
e
s
truct
o
r
commit
|
commitdiff
|
tree
2017-03-03
A
l
eksei Iupino
v
Remove
o
utda
t
ed CU
D
A ver
s
ion check
commit
|
commitdiff
|
tree
2017-02-21
Aleks
e
i Iup
i
nov
Remove unused
f
unction cu_synchs
t
rea
m
_
a
tdat()
commit
|
commitdiff
|
tree
2017-02-09
Aleksei Iup
i
nov
Add initializatio
n
to
d
vdlambda in bond
e
d
forces
t
ests
commit
|
commitdiff
|
tree
2017-02-09
A
l
e
ksei I
u
pi
n
o
v
Fi
x
typo (D
i
h
edarl -> Dih
e
dral)
commit
|
commitdiff
|
tree
2017-02-08
Alekse
i
Iupinov
P
ME
f
orce gatheri
n
g
t
e
sts
commit
|
commitdiff
|
tree
2017-02-08
A
leksei Iupinov
Fix in
v
a
l
id triclinic
b
ox in
the PME test
d
a
t
a
commit
|
commitdiff
|
tree
2017-01-24
Aleksei Iupinov
PME spline comput
a
tion and
c
harge spreading tests
commit
|
commitdiff
|
tree
2017-01-24
Alek
s
ei
Iupinov
Add
cons
t
qualifier to so
m
e
PME sprea
d
argume
n
ts
commit
|
commitdiff
|
tree
2017-01-19
Alek
s
ei Iu
p
inov
Simplif
y
gmx_
c
ount_gpu_
d
ev
_
unique(
)
commit
|
commitdiff
|
tree
2017-01-19
Aleksei
I
up
i
nov
PM
E
B-S
p
l
i
n
e
m
oduli computatio
n
unit test
commit
|
commitdiff
|
tree
2017-01-05
Al
e
ksei Iupinov
Fix compi
l
ation with CM
A
KE_CXX_FLAGS=
"
-
Wall -Werror"
commit
|
commitdiff
|
tree
2016-12-22
Ale
k
sei Iupinov
Remove
u
nused member
thr
e
ad_
o
ne f
r
om t
h
e PME s
p
line
.
.
.
commit
|
commitdiff
|
tree
2016-12-05
Aleks
e
i Iupinov
St
o
p
inclu
d
ing par
a
llel_3
d
ff
t
.
h in head
e
rs
commit
|
commitdiff
|
tree
2016-12-01
Alek
s
ei Iupinov
Move GPU assignmen
t
functions into
a separ
a
te fil
e
commit
|
commitdiff
|
tree
2016-11-21
Aleksei Iupinov
Move hardc
o
d
e
d PME g
r
id indexin
g
const
a
nts in
t
o hea
d
er
commit
|
commitdiff
|
tree
2016-11-01
Al
e
ksei Iupinov
Rem
o
ve imatrix type
a
n
d related unused/
e
rr
o
neous code
commit
|
commitdiff
|
tree
2016-10-24
Alek
s
e
i Iupi
n
ov
T
r
e
a
t CUDA files as C++ during cppcheck
commit
|
commitdiff
|
tree
2016-10-10
Ale
k
sei Iup
i
nov
Fix trivial PME me
m
o
r
y le
a
ks
commit
|
commitdiff
|
tree
2016-09-15
A
l
eks
e
i Iu
p
inov
Mo
v
e the PME
E
w
ald coeffi
c
ien
t
s to the PME structure
commit
|
commitdiff
|
tree
2016-09-10
Aleksei Iupinov
Fix PME data destr
u
ctor not b
e
i
ng calle
d
commit
|
commitdiff
|
tree