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Change use of t_inpfile to std::vector
2018-06-07
Aleksei
I
upinov
Compile
m
ost
of P
M
E GPU ho
s
t c
o
de with
O
penCL
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
sei
Iupinov
Merge
p
me
.
cu i
n
to pme-gpu-internal
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei Iupinov
P
M
E OpenCL 3D
F
FT transform is
implemented, using
c
lFFT
commit
|
commitdiff
|
tree
2018-05-31
Aleks
e
i
I
upinov
Move p
m
e-ti
m
in
g
s
.
cu to p
m
e-gpu-tim
i
ngs
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei I
u
pinov
Pref
e
r linking to system clFFT
rather
t
han bundled
o
ne
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei Iupinov
Move the Pme
G
puSpecific structure
i
n
t
o pme-gpu-t
y
pes
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei Iupin
o
v
Adde
d
t
h
e
bundled cl
F
FT into OpenCL
builds
commit
|
commitdiff
|
tree
2018-05-31
A
leksei Iupinov
Add GpuEventS
y
nchron
i
z
er class
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
Iupinov
Gat
h
er the PM
E
GP
U
constants/mac
r
os in a
si
n
g
l
e
he
a
der
commit
|
commitdiff
|
tree
2018-05-30
Aleksei I
u
p
in
o
v
Make PME GPU st
r
uctures use Device
B
uffer
commit
|
commitdiff
|
tree
2018-05-28
Aleksei Iup
i
no
v
S
upport persist
e
nt
device cont
e
xt-derived data in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-18
A
leksei Iupinov
prepareGpuKernelArgum
e
nts() and
l
aunchGpuKernel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Ale
k
se
i
Iupinov
Impor
t
clFFT
l
ibrary
int
o
the Gro
m
acs source
commit
|
commitdiff
|
tree
2018-05-04
Aleksei Iupinov
Add clearDeviceBufferAsyn
c
()
for C
U
D
A/Open
C
L
commit
|
commitdiff
|
tree
2018-05-03
Alekse
i
Iupino
v
Copy missing
G
PU
NB host
deallocations from OpenCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Aleksei I
u
p
i
no
v
rep
l
a
c
e
cu_copy_* calls with DeviceBuffer functions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Aleksei Iupinov
Re
n
ame OpenCL
h
os
t
memor
y
routines
t
o
match the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei
Iupin
o
v
Ma
k
e asiz
e
() a proper template function i
n
stead of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupinov
R
e
na
m
e the
asize variable
t
o nu
m
A
lignmentAtoms
commit
|
commitdiff
|
tree
2018-04-26
Alek
s
ei Iup
i
nov
Separate
PME GPU h
o
st
-
only and host/devic
e
data structu
r
es
commit
|
commitdiff
|
tree
2018-04-26
Aleksei Iupin
o
v
Add co
p
y
FromDeviceBu
f
fer()
C
UDA/OpenCL implementations
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iu
p
inov
Removed cu_realloc_buffered() in fa
v
or of reallocateDevic
e
Bu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Alek
s
ei Iupinov
Dev
i
ceBuffer hea
d
ers a
r
e adde
d
commit
|
commitdiff
|
tree
2018-04-12
Al
e
ksei Iupinov
Make in-source Op
e
nCL kernel pat
h
a per-modul
e
para
m
eter
commit
|
commitdiff
|
tree
2018-04-12
Aleksei
I
upinov
Rem
o
ve CU
D
A
_
F
UNC
macros f
r
om many functions in PME G
P
U
commit
|
commitdiff
|
tree
2018-04-12
Aleksei I
u
pino
v
Stop PME
G
PU code from co
m
piling on non-CUDA builds
commit
|
commitdiff
|
tree
2018-04-10
Alek
s
ei Iupinov
P
revent
O
penCL timing m
e
m
o
r
y
leak
commit
|
commitdiff
|
tree
2018-03-20
Al
e
k
s
ei Iupinov
Clarify
the mdr
u
n GPU options docs
commit
|
commitdiff
|
tree
2018-03-16
Aleksei
Iu
p
inov
Add
a
basic
T
P
I
sanity test
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
Stop gm
x
_fe
e
nableexc
e
pt() from r
e
turn
i
n
g previous
exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupi
n
ov
Res
t
ore the lost mc_temp check
in gr
o
mpp
commit
|
commitdiff
|
tree
2018-03-06
Alek
s
e
i
I
u
pinov
Is
o
l
a
te
PME GPU spli
n
e parameter indexing in i
n
l
i
ne
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupi
n
ov
St
o
p using cus
t
o
m
F
indOpenCL
.
cmake, per TO
D
O
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iu
p
inov
Correct
the
n
bnx
n
_gpu_co
m
pile_kern
e
ls() docs
commit
|
commitdiff
|
tree
2018-03-02
Aleksei Iupinov
Make TPI use doub
l
e precision exp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei
I
upinov
Merge
branch 'relea
s
e-2018
'
commit
|
commitdiff
|
tree
2018-02-26
A
leksei Iupinov
Advice u
s
ers o
n
i
nfinite output of TPI
commit
|
commitdiff
|
tree
2018-02-20
Ale
k
s
e
i Iupinov
R
emove
unuse
d
OpenCL debug
b
uf
f
er
commit
|
commitdiff
|
tree
2018-02-18
Aleksei
I
upino
v
Replace
*
_fre
e
_buffer
e
d
calls by free
D
eviceBuffer
commit
|
commitdiff
|
tree
2018-02-16
Aleks
e
i Iupinov
Fix PME for large systems w
i
th Fermi G
P
Us
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Update FF
T
W build to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupino
v
Ad
d
freeDeviceBuffer GPU utility functio
n
commit
|
commitdiff
|
tree
2018-02-15
Al
e
ksei
I
upinov
A
d
d the
missing
c
o
m
ma in the quot
e
commit
|
commitdiff
|
tree
2018-02-14
A
le
k
sei Iupinov
Replace the
remai
n
ing EXP
E
CT_DE
A
TH
w
i
t
h EXPECT
_
DEATH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Alekse
i
Iupi
n
ov
Add Device
B
uffer
a
s a
typedef for cl_mem/device ponter
commit
|
commitdiff
|
tree
2018-02-13
A
l
eksei
I
upinov
Move GPU tra
i
ts into
s
eparat
e
headers
commit
|
commitdiff
|
tree
2018-02-12
A
leksei I
u
pinov
Fix the include guard
commit
|
commitdiff
|
tree
2018-02-09
Aleks
e
i I
u
pinov
Revert
"Enable
d
ebug
FP exceptions
without TPI, no
t
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
A
lways run t
h
e es
s
ential dyn
a
m
i
c
s tests
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
Enable
d
e
bug FP exceptio
n
s withou
t
T
P
I, not with TPI
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
M
erge branch 'release
-
2018' into master
commit
|
commitdiff
|
tree
2018-02-06
Al
e
ks
e
i
Iupin
o
v
Remove unnecessary inclu
d
es from domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Zero unu
s
ed value
s
to silence t
h
e warning
commit
|
commitdiff
|
tree
2018-02-06
Aleks
e
i
I
upinov
Only setup Ew
a
ld in
t
he generic group k
e
rnel
i
f
it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Aleksei I
u
pinov
M
a
k
e ndx files opti
o
nal in SimulationRun
n
er
commit
|
commitdiff
|
tree
2018-02-05
A
l
ek
s
ei Iupino
v
Remove mdpInp
u
tFile
N
ame_ from Sim
u
l
ationRunner, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
l
ekse
i
Iup
i
no
v
Don't
print impossible CUDA v
e
r
sion nu
m
b
e
rs in
a
bsen
c
e
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Ale
k
s
ei Iupinov
Fi
x
i
n
p
ut MDP conten
t
s for swap an
d
IMD tests
commit
|
commitdiff
|
tree
2018-02-01
Aleksei Iupinov
Check for GTEST_IS_T
H
READSA
F
E being de
f
ined
commit
|
commitdiff
|
tree
2018-01-24
Aleksei Iupinov
Re
m
ove unu
s
ed fiel
d
s per TODO
commit
|
commitdiff
|
tree
2018-01-23
Alek
s
ei I
u
pinov
T
e
st the m
i
xed mode PME wi
t
h walls and box s
c
aling
commit
|
commitdiff
|
tree
2018-01-23
Alekse
i
Iupinov
T
est PME CPU/G
P
U with walls
a
nd bo
x
scaling
commit
|
commitdiff
|
tree
2018-01-23
A
l
e
k
s
e
i Iupino
v
Wrap the PME testing loop in a method for exten
s
ibil
i
ty
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i Iupinov
Add a d
e
ath test
f
or t
h
e dup
l
icate
i
nputrec
keys check
i
ng
commit
|
commitdiff
|
tree
2018-01-19
Aleksei
I
u
pinov
Ren
a
me clas
s
BiasRea
d
er to st
r
uct
B
i
asOutputS
e
tup
commit
|
commitdiff
|
tree
2018-01-19
A
l
eksei Iupinov
Move the temporary file MPI workaround int
o
the
bas
e
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
sei Iupinov
Make the refe
r
en
c
e data vari
a
ble
s
local in GetIrTe
s
t
commit
|
commitdiff
|
tree
2018-01-19
Aleksei
I
upinov
Merge branch 'release-2018' into mast
e
r
commit
|
commitdiff
|
tree
2018-01-18
A
leks
e
i Iupinov
G
o
t rid of man
u
al memory m
a
nagement
i
n the
P
M
E overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Re
-
e
n
ab
l
e multi-rank
P
ME t
e
st
s
(wit
h
the file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Alekse
i
Iupi
n
ov
Fix box
sca
l
ing i
n
P
M
E mixe
d
mode
commit
|
commitdiff
|
tree
2018-01-17
Al
e
ksei Iupinov
Merge branch
'relea
s
e-2018' into
m
a
ster
commit
|
commitdiff
|
tree
2018-01-16
Aleksei Iupinov
Always write the inpu
t
MDP file
for testi
n
g
ju
s
t before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iupin
o
v
Move
O
ctaneSandwich
.
md
p
and spc2-IMD
.
mdp into strings
commit
|
commitdiff
|
tree
2018-01-11
Al
e
ksei I
u
p
i
nov
Remove unused
a
lanine_vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Al
e
ksei Iu
p
in
o
v
Do
no
t
print P
M
E counter
b
reakdown if it's empty
commit
|
commitdiff
|
tree
2017-12-20
A
l
eksei Iupin
o
v
Set GMX
_
GPU_A
U
TO to FALSE with GMX_GPU defined
commit
|
commitdiff
|
tree
2017-12-20
Aleksei
I
upinov
Remove po
t
entially wrong "per user reque
s
t
"
note f
r
om
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Alekse
i
I
u
p
i
nov
Relaxed precisi
o
n in spline interpolatio
n
tests
commit
|
commitdiff
|
tree
2017-12-06
Alek
s
ei Iupino
v
Provi
d
e
d
u
mmy i
n
itialization to silen
c
e
a w
a
r
n
ing
commit
|
commitdiff
|
tree
2017-12-05
A
l
e
ksei Iupinov
Do
n
ot accept uns
u
pported
c
o
m
b
i
nati
o
n "
-
pme c
p
u -pmefft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei I
u
pinov
R
e
formul
a
te
PME so
l
ving tes
t
s tol
e
rance
s
commit
|
commitdiff
|
tree
2017-11-28
Alekse
i
Iup
i
nov
Replace of pmeGP
U
v
aria
b
le name with
pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
Aleks
e
i Iupinov
Do not force
s
ep
a
ra
t
e PM
E
r
ank to recompute reciprocal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
I
upi
n
ov
Disable
f
ai
l
ing separat
e
PM
E
r
ank
t
est
s
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Add
tes
t
s for P
M
E
t
u
n
i
ng an
d
fix mixed PME mod
e
with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i Iupinov
Destroy
P
ME GPU
c
ontext
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
upinov
Enable
s
eparate
P
ME GPU ran
k
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iupinov
Do not call mix
e
d CPU+GPU P
M
E mode "Hybrid
"
commit
|
commitdiff
|
tree
2017-11-24
A
le
k
sei Iu
p
in
o
v
Activate mixed m
o
de of PME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
u
p
inov
Re
m
ove outdated (already imple
m
ented) pinning TODO
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i Iupinov
Mention g
m
x_i
n
stall_headers() in the develo
p
e
r man
u
al
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei Iu
p
inov
Make FFT
real-spa
c
e grid
use C
U
D
A
pinni
n
g for m
i
xed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
P
in coordinates, forces and cha
r
g
e
s for PME on
GPU
commit
|
commitdiff
|
tree
2017-11-21
Aleks
e
i
I
upinov
Fix
C
UDA
r
elease build warning
commit
|
commitdiff
|
tree
2017-11-21
Aleksei Iupinov
Fix pi
n
ned memory status ch
e
ck
e
r t
e
st
s
commit
|
commitdiff
|
tree
2017-11-18
A
l
ekse
i
Iupinov
Asynchronou
s
CUDA tra
n
sfe
r
s are as
s
erted to al
w
a
ys
.
.
.
commit
|
commitdiff
|
tree
2017-11-17
Alek
s
ei Iupi
n
ov
M
a
k
e
gpu_util
s
-test
b
uil
d
with GMX_CLANG_
C
UD
A
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iupinov
Rename and exp
o
se "generic" GPU
me
m
o
ry
tr
a
nsfer function
s
commit
|
commitdiff
|
tree
2017-11-09
A
leksei
I
upinov
Rename synchronous GPU transfer functions to ma
t
ch
.
.
.
commit
|
commitdiff
|
tree
next