repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Use std::vector in nbnxn_search_t
2018-05-18
A
leksei
Iupinov
prepareGpuK
e
r
n
elArg
u
ments(
)
and lau
n
chGpuK
e
r
n
e
l
(
)
a
r
e
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei Iupinov
Import clFFT library in
t
o the Grom
a
cs sour
c
e
commit
|
commitdiff
|
tree
2018-05-04
Aleksei Iup
i
n
o
v
Add cl
e
arDeviceBufferAsync() for
C
UDA/Ope
n
C
L
commit
|
commitdiff
|
tree
2018-05-03
Ale
k
sei I
u
pinov
C
o
py missin
g
G
PU N
B
host deallo
c
atio
n
s fr
o
m OpenCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Ale
k
sei Iup
i
nov
replace cu_cop
y
_
* cal
l
s with DeviceBuffer fu
n
ction
s
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Al
e
k
s
ei
I
upinov
R
e
name OpenCL host memory r
o
u
t
ines to match t
h
e CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Alekse
i
I
u
pinov
M
a
ke asize()
a
proper templat
e
function i
n
s
t
ead of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei I
u
p
inov
Rename th
e
asize varia
b
l
e
to n
u
m
AlignmentAtoms
commit
|
commitdiff
|
tree
2018-04-26
Aleksei Iup
i
nov
Sepa
r
a
te PME GPU host-only
a
nd host/
d
evice d
a
ta st
r
uct
u
res
commit
|
commitdiff
|
tree
2018-04-26
Alekse
i
Iupi
n
ov
Add copyFromDeviceBuffe
r
() CUDA/OpenCL
i
mplementations
commit
|
commitdiff
|
tree
2018-04-23
A
leksei Iupinov
Remo
v
ed cu_re
a
lloc
_
buffered()
in
favor o
f
r
e
a
llocateDevic
e
Bu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei
Iup
i
nov
DeviceBuf
f
er headers are ad
d
ed
commit
|
commitdiff
|
tree
2018-04-12
Ale
k
sei Iupinov
Make in-sourc
e
O
p
enCL kernel
path a
p
er-module p
a
ra
m
eter
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Remove CUDA_FUNC macros fro
m
many functi
o
ns in PM
E
GPU
commit
|
commitdiff
|
tree
2018-04-12
Aleks
e
i
I
upino
v
Stop P
M
E GPU code
f
rom compiling
o
n non-CUDA b
u
ilds
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupin
o
v
Prevent Op
e
nC
L
timing memory leak
commit
|
commitdiff
|
tree
2018-03-20
Al
e
ksei Iupinov
Clar
i
fy the mdr
u
n
G
P
U o
p
tion
s
docs
commit
|
commitdiff
|
tree
2018-03-16
Al
e
ks
e
i Iupinov
Add
a bas
i
c TPI sanity
t
e
st
commit
|
commitdiff
|
tree
2018-03-16
A
l
eksei Iupinov
Sto
p
g
mx_feenableexcept() fro
m
returning previous
e
xception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Al
e
ksei Iup
i
n
o
v
R
estore the lost mc_temp
c
heck i
n
gr
o
mpp
commit
|
commitdiff
|
tree
2018-03-06
Aleksei Iupi
n
ov
Isolate PME GPU
spl
i
ne parameter indexing in
i
n
line
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupinov
Stop using
custom FindOp
e
nCL
.
cmake, per
TODO
commit
|
commitdiff
|
tree
2018-03-05
Aleksei I
u
pinov
Correct the nbnxn_gpu
_
comp
i
l
e_kern
e
ls() docs
commit
|
commitdiff
|
tree
2018-03-02
Aleks
e
i
Iupinov
M
a
k
e TPI use doub
l
e prec
i
sion exp
commit
|
commitdiff
|
tree
2018-02-27
A
l
eksei Iupinov
Merge
b
r
anch 'rele
a
se-2018'
commit
|
commitdiff
|
tree
2018-02-26
A
l
eksei Iup
i
nov
Advice
u
sers on in
f
inite o
u
t
put o
f
TPI
commit
|
commitdiff
|
tree
2018-02-20
Aleks
e
i
Iup
i
n
o
v
Remove unuse
d
Open
C
L d
e
bug buffer
commit
|
commitdiff
|
tree
2018-02-18
A
l
eksei Iupinov
Re
p
lace *_fre
e
_b
u
ffered call
s
by freeDeviceBuffer
commit
|
commitdiff
|
tree
2018-02-16
Alek
s
ei I
u
pinov
F
ix
P
ME
f
or large
s
ystems with Fermi GP
U
s
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Update
F
FTW bui
l
d to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iu
p
inov
Add
freeDeviceBu
f
fer GPU utility function
commit
|
commitdiff
|
tree
2018-02-15
A
l
eksei
Iupinov
A
dd the mi
s
sing comma
in the quote
commit
|
commitdiff
|
tree
2018-02-14
Al
e
ksei Iupinov
R
e
place the rema
i
nin
g
EXPECT_DEA
T
H
with EXPECT_
D
EATH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
A
leksei Iupinov
Add Dev
i
ce
B
uffer
as a t
y
p
e
def for cl_mem
/
devic
e
pont
e
r
commit
|
commitdiff
|
tree
2018-02-13
Alek
s
e
i
Iupinov
Move GPU trait
s
into separate headers
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iupinov
Fix the i
n
clude
gua
r
d
commit
|
commitdiff
|
tree
2018-02-09
Ale
k
sei Iupino
v
R
e
vert "Enab
l
e deb
u
g FP e
x
ceptions w
i
thou
t
TPI,
not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Ale
k
s
ei Iupinov
Always
r
un the essential dynamics tests
commit
|
commitdiff
|
tree
2018-02-08
Al
e
ksei Iu
p
i
n
ov
E
nable deb
u
g
FP exce
p
tions without TPI, n
o
t with TPI
commit
|
commitdiff
|
tree
2018-02-08
Alekse
i
Iupinov
Me
r
ge bra
n
ch '
r
elease-2018' into master
commit
|
commitdiff
|
tree
2018-02-06
A
leksei I
u
pinov
Re
m
ove un
n
ecessary includes from domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
A
leksei Iupinov
Zero unused values
to silence the warnin
g
commit
|
commitdiff
|
tree
2018-02-06
Alek
s
ei Iupinov
Only setup Ewald in the generic grou
p
k
ernel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupin
o
v
M
ake ndx files optional in
S
imulationRunner
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupinov
Remove mdp
I
nputFileName_ from Si
m
ulat
i
onRunn
e
r, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
Don'
t
print impo
s
sible
CUDA version numb
e
rs
i
n absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleks
e
i Iupinov
Fix input MDP contents
for
s
w
ap a
n
d
IMD
t
ests
commit
|
commitdiff
|
tree
2018-02-01
Aleksei Iupi
n
ov
Check f
o
r G
T
E
S
T_IS
_
THREAD
S
A
FE being d
e
fi
n
e
d
commit
|
commitdiff
|
tree
2018-01-24
Aleks
e
i Iupinov
Remove unused fields per TO
D
O
commit
|
commitdiff
|
tree
2018-01-23
Aleks
e
i Iupinov
T
est the mixed mode P
M
E
with wa
l
ls and bo
x
sca
l
in
g
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iup
i
n
ov
Test PME
C
PU/
G
P
U
with w
a
lls and bo
x
scaling
commit
|
commitdiff
|
tree
2018-01-23
A
l
eksei Iu
p
inov
Wrap th
e
PME
t
es
t
ing
lo
o
p
in a
method
f
or exte
n
s
i
bi
l
ity
commit
|
commitdiff
|
tree
2018-01-19
A
leksei
Iupinov
Add a death test f
o
r the duplicate inputrec keys checking
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iup
i
nov
R
e
n
ame cl
a
ss BiasRe
a
de
r
to struct BiasOutputS
e
tup
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i Iupinov
Move the temporary file MPI
w
orkaround i
n
to the base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Aleksei
Iupinov
Make
t
h
e
r
eference d
a
ta
v
ariables lo
c
al in GetIrTest
commit
|
commitdiff
|
tree
2018-01-19
Alek
s
ei
Iupino
v
Merge
branch 'releas
e
-
2018' into
m
ast
e
r
commit
|
commitdiff
|
tree
2018-01-18
A
l
eksei
Iupinov
Got rid of manual memory management in the P
M
E overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iup
i
n
o
v
Re
-
e
n
a
ble multi
-
rank PME tests (wi
t
h the
f
ile race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Aleks
e
i Iupinov
Fix box scaling in PME
m
ixed mode
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iup
i
nov
Merge b
r
anch 'relea
s
e-2018' into mas
t
er
commit
|
commitdiff
|
tree
2018-01-16
Aleksei Iupinov
Always wri
t
e the input MDP fil
e
for tes
t
ing
just before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupinov
Move Octan
e
Sandwich
.
mdp
and spc2-IMD
.
mdp into st
r
ings
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupinov
Remove unus
e
d ala
n
ine_v
s
ite
.
m
d
p
commit
|
commitdiff
|
tree
2018-01-10
A
l
eksei Iup
i
nov
Do not print PME counter br
e
a
k
down if it's empty
commit
|
commitdiff
|
tree
2017-12-20
Aleksei I
u
pinov
Se
t
G
M
X_GPU
_
AUTO to FALS
E
with GMX_GPU
d
efine
d
commit
|
commitdiff
|
tree
2017-12-20
Aleksei
Iupinov
R
e
move pot
e
nt
i
ally wrong "per use
r
r
e
q
ue
s
t" not
e
from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Al
e
ksei Iu
p
inov
Rel
a
x
ed
p
rec
i
sion in
s
pline int
e
rpolati
o
n
t
ests
commit
|
commitdiff
|
tree
2017-12-06
Aleksei Iupinov
Provide dummy
i
nitialization to s
i
lence
a
warning
commit
|
commitdiff
|
tree
2017-12-05
Aleksei Iupinov
Do not accept un
s
uppo
r
ted c
o
mbination
"-
p
me cpu -pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei Iupin
o
v
Refo
r
m
u
l
ate
P
ME solvin
g
t
e
s
ts tolerance
s
commit
|
commitdiff
|
tree
2017-11-28
Al
e
ksei Iupinov
Replac
e
of pmeGPU var
i
able
n
ame with pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iu
p
inov
Do
n
o
t force sep
a
rate PM
E
rank to
r
ecompute reciprocal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
D
i
sable fai
l
i
ng separate PME r
a
nk te
s
ts
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
Iupinov
Add tests for PME tuning and fix mixed PME mode wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iupinov
Destroy PME GPU c
o
ntext
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Enable separate PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei Iupi
n
ov
D
o
not call mixed
C
PU+GPU PME mod
e
"Hybri
d
"
commit
|
commitdiff
|
tree
2017-11-24
A
leksei Iupin
o
v
Activat
e
mixed mo
d
e
o
f PM
E
on GPU
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
upinov
Remove ou
t
dated (alr
e
a
dy
i
mplemented
)
p
i
nning TODO
commit
|
commitdiff
|
tree
2017-11-24
Aleksei I
u
pinov
Mention gm
x
_i
n
stall_headers() in the
developer
m
anual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupi
n
ov
M
a
ke F
F
T real-space grid use CUDA pinnin
g
for mixed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei Iup
i
nov
P
in coordinat
e
s, force
s
a
nd charges for PME on GP
U
commit
|
commitdiff
|
tree
2017-11-21
A
l
e
k
sei I
u
p
i
no
v
Fix
CUDA
r
e
lease build warning
commit
|
commitdiff
|
tree
2017-11-21
Ale
k
sei Iupinov
Fix pinned memor
y
status c
h
eck
e
r te
s
ts
commit
|
commitdiff
|
tree
2017-11-18
A
leksei Iupinov
Asynchr
o
nous CUDA transfe
r
s are
ass
e
rted to
a
lways
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Aleksei Iupino
v
Make gp
u
_utils-
t
e
st bu
i
ld
w
i
th GMX_CLANG_CUDA
commit
|
commitdiff
|
tree
2017-11-15
Alek
s
ei
Iup
i
no
v
Rename
a
nd expose "gene
r
i
c
" G
P
U
m
e
m
ory trans
f
er func
t
ions
commit
|
commitdiff
|
tree
2017-11-09
Al
e
ksei
Iupi
n
ov
R
ename syn
c
hronous GP
U
trans
f
er function
s
to matc
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei
I
u
pinov
Replace
m
ath
.
h by cmath
i
n
clud
e
s
i
n
cpp files
commit
|
commitdiff
|
tree
2017-11-01
Alekse
i
Iupinov
Remove unused PME GPU declarations
commit
|
commitdiff
|
tree
2017-11-01
A
l
eksei I
u
pi
n
ov
Move pme_gpu_finish_computation() docum
e
ntatio
n
to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupi
n
ov
F
i
x erroneous PME GPU "step
"
n
a
mings
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iupinov
S
implify PME GPU syn
c
hr
o
ni
z
a
t
i
on code
commit
|
commitdiff
|
tree
2017-10-31
A
l
eksei I
u
pinov
R
euse epbcXY logi
c
commit
|
commitdiff
|
tree
2017-10-30
Alek
s
e
i Iupinov
F
ix referen
c
e mod
e
bu
i
l
d unused function warnings
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iu
p
i
n
ov
Bring PM
E
GPU/CUDA in
t
ernal st
r
ucture names to CamelCa
s
e
commit
|
commitdiff
|
tree
2017-10-30
Aleksei Iup
i
no
v
Use new/
d
elet
e
for gmx_pme_t
commit
|
commitdiff
|
tree
2017-10-30
A
l
eksei Iupinov
Simplify PME data
handling in runner
commit
|
commitdiff
|
tree
2017-10-29
Aleksei
Iupinov
Mak
e
PME
tun
i
ng
lo
g
ic m
o
r
e
r
e
ad
a
bl
e
commit
|
commitdiff
|
tree
next