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Allow empty lines in hdb files
2017-12-20
Ale
k
s
ei Iupinov
Set GMX_
G
PU_AUTO to FALSE
w
ith
G
MX_G
P
U
def
i
n
e
d
commit
|
commitdiff
|
tree
2017-12-20
A
leksei Iupinov
Rem
o
ve pote
n
tially
wrong "per
u
se
r
request" note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Ale
k
sei Iupinov
Relaxe
d
prec
i
sion in spline interpolation t
e
sts
commit
|
commitdiff
|
tree
2017-12-06
Alekse
i
Iupin
o
v
Provide du
m
my
i
nitializ
a
t
i
on to sil
e
nc
e
a warning
commit
|
commitdiff
|
tree
2017-12-05
Al
e
ksei Iu
p
inov
Do not acce
p
t
unsuppor
t
e
d c
o
m
b
inat
i
on "-pme cpu
-
pme
f
ft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei Iupi
n
o
v
Reformula
t
e PME
s
o
l
vin
g
tests
tolerances
commit
|
commitdiff
|
tree
2017-11-28
Aleksei Iupinov
Repla
c
e
of
p
m
eGPU variable
name with pmeG
p
u
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Do not force s
e
p
arate
P
ME rank to
r
ecompute rec
i
proc
a
l
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Disable fa
i
ling separate PME rank
t
e
st
s
commit
|
commitdiff
|
tree
2017-11-27
Ale
k
sei
I
u
pino
v
Add
t
ests for PME tuni
n
g and fix m
i
xed PME mode with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Destroy PME GPU contex
t
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iupi
n
o
v
En
a
ble
separate PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
A
l
ekse
i
Iupin
o
v
Do not call mixe
d
C
P
U
+GPU
P
ME mode "H
y
br
i
d"
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupinov
Activa
t
e mixed
mode of PME on
G
PU
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iup
i
no
v
R
e
move outdated (alr
e
ady imp
l
emented
)
pinning TODO
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i
I
upinov
M
en
t
ion gmx_install_headers(
)
in
t
he developer manual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Mak
e
F
FT real
-
space grid
use
CUDA p
i
nning for
m
i
x
ed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupin
o
v
P
i
n coo
r
dinates, forces a
n
d charges for PME on GPU
commit
|
commitdiff
|
tree
2017-11-21
Ale
k
sei
I
up
i
nov
Fix C
U
DA
r
e
l
ease build
w
arn
i
n
g
commit
|
commitdiff
|
tree
2017-11-21
Ale
k
s
ei Iupin
o
v
Fix pinned m
e
mory sta
t
us c
h
ecker t
e
sts
commit
|
commitdiff
|
tree
2017-11-18
Aleks
e
i Iup
i
n
o
v
Async
h
ron
o
us CUDA
trans
f
e
rs are asserted to
always
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
A
l
eksei
Iupinov
Make gp
u
_uti
l
s
-test bui
l
d with GMX_CLA
N
G
_
CUDA
commit
|
commitdiff
|
tree
2017-11-15
Aleksei I
u
pinov
Rename and expo
s
e "
g
eneric" GPU
mem
o
ry tr
a
nsf
e
r
functions
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupinov
Rena
m
e synchronous GP
U
tran
s
f
e
r fun
c
tions to matc
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei Iupinov
Replace math
.
h
b
y
cmat
h
incl
u
des in cpp
f
ile
s
commit
|
commitdiff
|
tree
2017-11-01
Alekse
i
Iupino
v
Remov
e
unused
PME GP
U
decl
a
rati
o
ns
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Move pme_gpu_finish_computatio
n
() doc
u
mentation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
Fi
x
erroneous
P
ME G
P
U
"
step" namin
g
s
commit
|
commitdiff
|
tree
2017-11-01
Al
e
ksei
I
u
p
inov
Simplify PME GPU s
y
nchronization co
d
e
commit
|
commitdiff
|
tree
2017-10-31
Aleksei
I
up
i
nov
Reuse
e
p
bcXY lo
g
i
c
commit
|
commitdiff
|
tree
2017-10-30
Alek
s
ei I
u
pinov
Fix reference mode bu
i
ld unused functi
o
n wa
r
nings
commit
|
commitdiff
|
tree
2017-10-30
A
l
eksei
Iupinov
Bri
n
g PME GPU/CUDA internal structure names to
CamelCase
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iup
i
nov
Use new/
d
elete for
gmx
_
p
me_t
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iupinov
Simp
l
i
fy PME d
a
ta ha
n
dl
i
n
g in runner
commit
|
commitdiff
|
tree
2017-10-29
Aleksei Iupinov
Ma
k
e PME tuning
logic mo
r
e readable
commit
|
commitdiff
|
tree
2017-10-27
A
l
eksei
I
u
pi
n
ov
R
e
mo
v
e unused PME gri
d
dump deb
u
g fun
c
tions
commit
|
commitdiff
|
tree
2017-10-27
Aleks
e
i
Iupinov
R
eplace a few asserts with
GMX_ASSERT's
commit
|
commitdiff
|
tree
2017-10-27
Aleksei I
u
pinov
Remove
d
efunct PME initialization error code ret
u
rn
commit
|
commitdiff
|
tree
2017-10-24
Aleksei
Iupin
o
v
Remove
dup
l
icate/outdated function declaration
commit
|
commitdiff
|
tree
2017-10-24
A
leksei
Iup
i
n
ov
Move commr
e
c duty checking i
n
to simple get
t
ers
commit
|
commitdiff
|
tree
2017-10-23
Aleksei Iupin
o
v
Correct th
e
page a
l
locator description
commit
|
commitdiff
|
tree
2017-10-22
Ale
k
sei Iupi
n
ov
Change PME GP
U
gather re
d
uction ar
g
ument fro
m
b
o
olean
.
.
.
commit
|
commitdiff
|
tree
2017-10-21
A
l
eksei Iupino
v
Ad
d
c
all
s
to
th
e
PME GPU st
a
ges
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iup
i
n
o
v
Rel
a
x PME spline c
o
m
putation
t
oleranc
e
in dou
b
le p
r
ec
i
s
ion
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
Aleksei Iupino
v
R
e
mo
v
e u
s
eless
extern
CUDA texture
r
eference decl
a
r
ations
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
Aleksei Iupi
n
ov
Revert "
D
r
op
NB_ from
GMX_C
U
DA_NB_SINGLE_COMPILAT
I
ON_UNI
T
.
.
.
commit
|
commitdiff
|
tree
2017-10-11
Aleksei I
u
pinov
Fix cla
n
g w
a
rnings
for PME CUD
A
kern
e
ls
commit
|
commitdiff
|
tree
2017-10-11
Al
e
ksei Iup
i
nov
Relax P
M
E
s
olv
i
ng test co
m
plex
g
r
i
d
t
ol
e
ranc
e
commit
|
commitdiff
|
tree
2017-10-11
A
leksei
I
upin
o
v
CUDA 9/Volta support for PME
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupin
o
v
PME solving - CUD
A
kern
e
l + unit test
s
commit
|
commitdiff
|
tree
2017-10-11
Alek
s
ei Iupinov
PME force
gat
h
e
r
in
g
- CUDA k
e
rnel + unit tests
commit
|
commitdiff
|
tree
2017-10-11
Aleksei
I
upinov
Drop NB_ from GMX_CUDA
_
NB_SINGLE_COMPI
L
ATION_UNIT cmake
.
.
.
commit
|
commitdiff
|
tree
2017-10-11
Ale
k
sei Iupinov
PME spline+s
p
read CUDA kernel and unit
t
e
sts
commit
|
commitdiff
|
tree
2017-10-09
Ale
k
sei Iupinov
Remove some
un
n
ecessary incl
u
d
es from PM
E
commit
|
commitdiff
|
tree
2017-10-09
Ale
k
se
i
Iupinov
PME GP
U
/CUDA data fr
a
m
ework
.
commit
|
commitdiff
|
tree
2017-10-06
Al
e
ksei Iu
p
inov
Add timing accumulation capability into Gpu
R
egionTim
e
r
commit
|
commitdiff
|
tree
2017-10-04
Alek
s
ei
I
u
pinov
R
emove
GPU timing functions superseded by GpuReg
i
onTimer
commit
|
commitdiff
|
tree
2017-10-04
Aleksei Iupin
o
v
Add GpuRegion
T
i
m
e
r
clas
s
commit
|
commitdiff
|
tree
2017-10-03
A
l
eksei
I
upinov
Bring C
U
D
A
tex
t
u
r
e getters documentation
u
p-
t
o
-date
commit
|
commitdiff
|
tree
2017-10-03
A
leksei Iup
i
nov
Template/move CUDA texture cl
e
an
u
p code from NB CU
D
A
.
.
.
commit
|
commitdiff
|
tree
2017-10-03
A
l
eks
e
i Iupinov
Add WinAPI page s
i
ze query fo
r
allocator purpose
s
commit
|
commitdiff
|
tree
2017-09-26
Aleksei Iupin
o
v
Move CUD
A
te
x
tu
r
e s
e
tup c
o
de fro
m
NB CUDA module to
.
.
.
commit
|
commitdiff
|
tree
2017-09-22
Aleksei Iupin
o
v
Template
t
he
C
UDA texture s
e
tup code o
n
raw
valu
e
type T
commit
|
commitdiff
|
tree
2017-09-21
Al
e
k
s
ei Iupin
o
v
El
i
minate unused Cou
l
omb correction tab
l
e
s
ize c
o
ulo
m
b_tab_
s
ize
commit
|
commitdiff
|
tree
2017-09-21
Aleksei Iupinov
Eliminate d
u
plicate CUDA texture
s
etup cod
e
commit
|
commitdiff
|
tree
2017-09-18
Aleksei Iupi
n
ov
Skip GPU reall
o
cation of an empty non
-
local pairlist
commit
|
commitdiff
|
tree
2017-09-14
Aleksei Iupinov
Fix non-SIMD build f
a
iling
commit
|
commitdiff
|
tree
2017-09-12
Alekse
i
Iupi
n
ov
Prevent reference XML reader seg
f
ault
o
n nullptr error
.
.
.
commit
|
commitdiff
|
tree
2017-09-04
Al
e
ksei Iu
p
inov
Merge "Merge br
a
nc
h
release-5-1 into
release
-
2
016"
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Aleksei Iupinov
B
ring back space lo
s
t in commit e43e
8
3
b
f
commit
|
commitdiff
|
tree
2017-08-29
Al
e
ks
e
i Iupinov
Remove leftover funct
i
on declara
t
ion
commit
|
commitdiff
|
tree
2017-08-29
Aleksei Iupi
n
ov
Fi
x
typ
o
commit
|
commitdiff
|
tree
2017-08-29
Alekse
i
Iupinov
Allow pas
s
ing optio
n
al width argument i
n
t
o C
U
DA shuffle
.
.
.
commit
|
commitdiff
|
tree
2017-08-29
Aleksei Iupinov
Adjust PME LJ solver t
e
st input coefficient
commit
|
commitdiff
|
tree
2017-08-22
Alekse
i
Iupinov
Separate
P
ME spread and gather wa
l
lcycle counters
commit
|
commitdiff
|
tree
2017-08-21
Aleksei Iupino
v
P
M
E
solving tests
commit
|
commitdiff
|
tree
2017-08-17
A
l
eksei Iupino
v
Merge "Merge br
a
n
c
h release-5-1 into
release-2
0
16"
.
.
.
commit
|
commitdiff
|
tree
2017-06-30
A
lek
s
ei Iu
p
i
n
o
v
R
e
move outdated cmak
e
n
vcc logic
commit
|
commitdiff
|
tree
2017-06-12
Aleksei
I
upi
n
o
v
Store a physical node communicator
i
n t_com
m
re
c
commit
|
commitdiff
|
tree
2017-03-17
Aleksei Iupinov
Fix derefe
r
encing nullpt
r
in PME
s
olve work destruc
t
or
commit
|
commitdiff
|
tree
2017-03-03
Al
e
ksei Iupinov
Remov
e
outdate
d
CUDA versio
n
check
commit
|
commitdiff
|
tree
2017-02-21
Aleksei Iupin
o
v
Remov
e
unus
e
d
fun
c
t
i
o
n
c
u
_syn
c
hstream_
a
tdat()
commit
|
commitdiff
|
tree
2017-02-09
Alek
s
ei Iupinov
Add initializat
i
on to dvdlam
b
d
a
i
n bonded forces tests
commit
|
commitdiff
|
tree
2017-02-09
Aleksei Iu
p
inov
Fix t
y
po
(D
i
h
edarl -
>
Dihedral)
commit
|
commitdiff
|
tree
2017-02-08
Aleksei Iu
p
i
nov
P
M
E
force gat
h
eri
n
g
tests
commit
|
commitdiff
|
tree
2017-02-08
Aleksei
I
upinov
F
ix inva
l
id
t
r
i
clin
i
c box in the PME
t
est data
commit
|
commitdiff
|
tree
2017-01-24
Aleksei Iupinov
PME spline computation
a
nd
charge sp
r
eading tes
t
s
commit
|
commitdiff
|
tree
2017-01-24
A
l
eksei Iupinov
Add cons
t
qualifier to some P
M
E s
p
read arg
u
m
e
nts
commit
|
commitdiff
|
tree
2017-01-19
Aleksei Iupinov
S
implify gmx_
c
ount_gp
u
_dev
_
unique()
commit
|
commitdiff
|
tree
2017-01-19
Al
e
ksei
I
u
pinov
PME B-Spli
n
e
moduli computation uni
t
tes
t
commit
|
commitdiff
|
tree
2017-01-05
Alekse
i
Iupinov
Fi
x
compilation wi
t
h
C
M
A
KE
_
CXX_FLAG
S
="-W
a
ll
-
Werror"
commit
|
commitdiff
|
tree
2016-12-22
Aleksei Iupinov
Re
m
ove
u
nused member thread_o
n
e from the PM
E
sp
l
ine
.
.
.
commit
|
commitdiff
|
tree
2016-12-05
Ale
k
sei
Iupinov
Stop
in
c
luding pa
r
allel_3dfft
.
h
in hea
d
ers
commit
|
commitdiff
|
tree
2016-12-01
Aleksei Iupinov
Move GPU assi
g
n
men
t
fu
n
ctions into a separate file
commit
|
commitdiff
|
tree
2016-11-21
Al
e
ksei Iupinov
Mov
e
hardco
d
ed PME grid indexi
n
g con
s
tants into header
commit
|
commitdiff
|
tree
2016-11-01
Aleksei Iupinov
R
emo
v
e
ima
t
r
i
x type and
r
el
a
t
e
d unused/erroneous
c
ode
commit
|
commitdiff
|
tree
2016-10-24
Alekse
i
Iupinov
T
r
e
a
t
CUDA files a
s
C++
during cppche
c
k
commit
|
commitdiff
|
tree
2016-10-10
A
leksei Iupinov
F
ix trivial
P
M
E
memory leaks
commit
|
commitdiff
|
tree
2016-09-15
Alekse
i
Iupinov
Move the PME
E
wald c
o
efficients to the P
M
E structure
commit
|
commitdiff
|
tree
2016-09-10
Aleksei
I
u
p
inov
Fi
x
P
M
E d
a
ta
d
estruc
t
or not being cal
l
ed
commit
|
commitdiff
|
tree