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Update instructions in containers.rst
2018-12-22
Aleksei Iupin
o
v
Add
a sa
n
ity che
c
k for
O
penCL devices
commit
|
commitdiff
|
tree
2018-10-13
Al
e
k
s
ei Iupinov
Add and
enab
l
e PME Ope
n
CL
commit
|
commitdiff
|
tree
2018-08-27
Alek
s
ei Iupinov
Prepare pme-gp
u
-types
.
h
f
or
O
p
e
nCL
commit
|
commitdiff
|
tree
2018-07-30
Aleksei Iup
i
nov
Remove
hard
c
oded warp_size == 32 assumpt
i
on from PME
GPU
commit
|
commitdiff
|
tree
2018-06-25
A
lek
s
ei Iupinov
Mo
v
e vecty
p
e_ops
.
c
lh into gpu_utils
commit
|
commitdiff
|
tree
2018-06-25
Aleksei Iupinov
M
ove t
h
e
P
ME GPU
k
e
rnel launch functions into pme-gpu
.
.
.
commit
|
commitdiff
|
tree
2018-06-14
Aleks
e
i Iupinov
Ensur
e
PME w
i
th Ope
n
CL
does
n
ot attempt to pin
commit
|
commitdiff
|
tree
2018-06-07
Aleksei Iupinov
Compile most of
P
ME GP
U
host
c
od
e
with
O
p
enCL
commit
|
commitdiff
|
tree
2018-05-31
Alek
s
ei Iupinov
Merge
p
me
.
c
u into pme-gpu
-
internal
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
PM
E
OpenCL
3D
FFT trans
f
orm
i
s i
m
p
l
e
mented,
us
i
n
g
clFFT
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iup
i
nov
Move pme
-
timings
.
cu
to pme-g
p
u
-
timings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Alekse
i
Iupi
n
ov
Pr
e
fer linking
to syste
m
clFFT ra
t
h
er
t
han bund
l
ed one
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Move
the PmeGpuSpecific structur
e
into pme-gpu-typ
e
s
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
sei I
u
pino
v
Added the bundle
d
c
l
FFT into
OpenCL builds
commit
|
commitdiff
|
tree
2018-05-31
Al
e
ksei I
u
pinov
Add
G
p
u
E
v
entSynchroni
z
er
c
la
s
s
commit
|
commitdiff
|
tree
2018-05-31
Aleksei I
u
pinov
Gather the
PME GPU
c
onsta
n
ts/macros in a singl
e
header
commit
|
commitdiff
|
tree
2018-05-30
Aleksei Iupinov
Make
P
ME GPU structures use Devic
e
Buffer
commit
|
commitdiff
|
tree
2018-05-28
Alek
s
ei Iupin
o
v
S
uppo
r
t persistent device co
n
text-de
r
i
v
ed data
in P
M
E
.
.
.
commit
|
commitdiff
|
tree
2018-05-22
Aleksei
I
upinov
R
e
move unused results of cudaS
t
reamQue
r
y
()
commit
|
commitdiff
|
tree
2018-05-18
Ale
k
sei Iup
i
n
ov
p
r
epareGpuKernelArguments() a
n
d launchGpuKernel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei Iupinov
I
mport clFFT librar
y
into the
Gromacs
s
ource
commit
|
commitdiff
|
tree
2018-05-04
A
l
eksei Iupinov
Add clear
D
ev
i
ceBufferAsync() for CU
D
A
/
Op
e
n
CL
commit
|
commitdiff
|
tree
2018-05-03
A
l
eksei Iupinov
Copy missing GPU
N
B host dealloca
t
ions
f
rom OpenCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
A
lek
s
ei Iup
i
nov
replace cu_c
o
py_* calls with Device
B
uffer
f
unctions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Aleksei Iupino
v
Rename O
p
enCL
h
o
st me
m
ory r
o
utines to
m
atch the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Ale
k
sei Iupinov
M
ake asize() a proper template functio
n
inst
e
ad of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei
Iupi
n
ov
Re
n
a
m
e
t
h
e
asize variable
to
numAlign
m
e
ntAto
m
s
commit
|
commitdiff
|
tree
2018-04-26
A
l
eksei Iupinov
Sepa
r
ate
PME
G
P
U host-only and host
/
dev
i
ce data structures
commit
|
commitdiff
|
tree
2018-04-26
A
leksei Iup
i
nov
A
dd copyFromDeviceBuffer() CUDA
/
O
p
e
nCL implementati
o
ns
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
Re
m
oved cu_realloc_buffer
e
d()
i
n favor o
f
real
l
ocateDev
i
ceBu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupin
o
v
Devi
c
eBuffer hea
d
ers
a
r
e
add
e
d
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Make in-source Ope
n
CL kernel p
a
th a pe
r
-
m
odule parameter
commit
|
commitdiff
|
tree
2018-04-12
A
leksei Iupino
v
Rem
o
ve CUDA
_
FUNC macros
f
rom many functions in P
M
E GP
U
commit
|
commitdiff
|
tree
2018-04-12
Ale
k
sei Iupinov
S
t
op P
M
E GP
U
c
o
de f
r
om compili
n
g on no
n
-CUDA
b
uilds
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
Prevent OpenCL
timing memory leak
commit
|
commitdiff
|
tree
2018-03-20
Aleksei
I
upinov
Clarify the mdrun GPU options docs
commit
|
commitdiff
|
tree
2018-03-16
A
l
ekse
i
Iupinov
A
d
d a basic TPI sanity test
commit
|
commitdiff
|
tree
2018-03-16
Aleksei
I
u
pinov
Sto
p
gmx_feenableexce
p
t(
)
f
r
om
returning previous
exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
A
leksei Iupinov
Restore
t
he lost mc_temp check in
g
rompp
commit
|
commitdiff
|
tree
2018-03-06
A
l
e
ksei Iupinov
I
solate
P
ME GPU sp
l
i
ne parame
t
er
i
ndexing in inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupino
v
St
o
p using
c
ustom
Fi
n
dOpenCL
.
cmake, per TODO
commit
|
commitdiff
|
tree
2018-03-05
Aleksei I
u
pinov
Correct the nbnxn_gpu
_
compil
e
_
k
ernels() do
c
s
commit
|
commitdiff
|
tree
2018-03-02
Aleks
e
i Iup
i
nov
Make T
P
I use
doub
l
e prec
i
s
i
on exp
commit
|
commitdiff
|
tree
2018-02-27
Alek
s
ei
Iupinov
Merge branch 'release-2018'
commit
|
commitdiff
|
tree
2018-02-26
Aleksei Iupi
n
ov
Advice us
e
rs on infini
t
e ou
t
pu
t
of TPI
commit
|
commitdiff
|
tree
2018-02-20
Aleksei Iupino
v
Remove unused O
p
enCL debug bu
f
fer
commit
|
commitdiff
|
tree
2018-02-18
Aleksei Iupino
v
Rep
l
a
ce
*
_free_bu
f
fe
r
ed calls by
f
ree
D
evice
B
uffer
commit
|
commitdiff
|
tree
2018-02-16
Aleksei Iupin
o
v
Fix PME for large sy
s
tems with Fermi GPUs
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iupinov
Update FFTW b
u
i
l
d to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
A
leksei Iupinov
Add freeDevi
c
eBuffer GPU utility function
commit
|
commitdiff
|
tree
2018-02-15
Aleksei Iu
p
i
n
o
v
Add
the mis
s
ing com
m
a in th
e
q
u
ote
commit
|
commitdiff
|
tree
2018-02-14
Alekse
i
Iupinov
Replace
the r
e
m
a
i
ning EXPECT_DEATH with EX
P
E
CT_DEATH_
I
F_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Alek
s
ei Iupi
n
ov
Add Dev
i
ceBuffer a
s
a
typedef for cl_me
m
/device pont
e
r
commit
|
commitdiff
|
tree
2018-02-13
Aleks
e
i
Iupin
o
v
Move GPU
trait
s
i
nto
s
ep
a
r
a
te
h
eaders
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iupinov
Fix the includ
e
guard
commit
|
commitdiff
|
tree
2018-02-09
Aleksei Iupin
o
v
R
e
ve
r
t "Enable debug F
P
exceptions wit
h
out TPI
,
no
t
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Al
e
ks
e
i Iupinov
Always run the essential dy
n
amic
s
tests
commit
|
commitdiff
|
tree
2018-02-08
A
lek
s
ei Iupinov
E
nable debug FP exceptions witho
u
t TPI, not with
T
PI
commit
|
commitdiff
|
tree
2018-02-08
Aleks
e
i I
u
pinov
Mer
g
e br
a
nch
'release
-
2018'
i
nto mast
e
r
commit
|
commitdiff
|
tree
2018-02-06
Alek
s
ei Iupinov
Re
m
ove un
n
ecessary includes from domdec
.
h
commit
|
commitdiff
|
tree
2018-02-06
Aleksei I
u
pinov
Zero
unused values to
s
ilenc
e
th
e
warni
n
g
commit
|
commitdiff
|
tree
2018-02-06
Aleksei
I
upinov
O
n
l
y setu
p
Ewa
l
d in
the generic group k
e
r
n
e
l if
it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Aleks
e
i Iupin
o
v
Make ndx files opt
i
onal in Simula
t
ionRu
n
ner
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupinov
R
e
move
mdpIn
p
utFile
N
ame_ from Simula
t
ionRunner,
p
er
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Alek
s
ei Iupino
v
Don't print impossible CUDA versio
n
numb
e
rs in
abse
n
c
e
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
F
ix input MDP conten
t
s
f
or
swap an
d
IMD tests
commit
|
commitdiff
|
tree
2018-02-01
Ale
k
se
i
Iupinov
C
h
e
ck
for
G
TEST_IS_THREADSAFE b
e
ing defined
commit
|
commitdiff
|
tree
2018-01-24
Al
e
ks
e
i Iupinov
R
emov
e
un
u
sed fields
per TOD
O
commit
|
commitdiff
|
tree
2018-01-23
A
leksei Iupi
n
ov
Test
the mix
e
d mode PME with walls and box scali
n
g
commit
|
commitdiff
|
tree
2018-01-23
Aleks
e
i Iupinov
T
es
t
PME CPU/
G
PU
w
i
th w
a
l
ls and box
scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Wrap the
P
ME t
e
sting
loop
i
n a me
t
ho
d
for ex
t
e
n
sibility
commit
|
commitdiff
|
tree
2018-01-19
A
leksei Iupinov
Add a death test for the duplicate inputrec k
e
ys checking
commit
|
commitdiff
|
tree
2018-01-19
A
leksei
Iupinov
Rename
c
lass BiasReader to s
t
ruct B
i
asO
u
tputSetup
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupino
v
Mo
v
e
t
he temporary file MPI workarou
n
d into the base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
sei Iupinov
Make the reference
d
ata var
i
ables
l
o
c
a
l
in Get
I
rTest
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
s
e
i
Iupinov
Me
r
ge branch 'release-2018' in
t
o
m
aster
commit
|
commitdiff
|
tree
2018-01-18
Aleks
e
i Iupinov
G
o
t rid of manual memory man
a
gement in the PME ove
r
lap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupi
n
o
v
Re-enable multi-ra
n
k PME tests (with th
e
f
ile
race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Fix box scaling in PME
m
ixed mo
d
e
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
M
e
rge branch 'release-
2
018' in
t
o
m
aster
commit
|
commitdiff
|
tree
2018-01-16
Aleksei Iupinov
Always writ
e
the input MDP
file for testing just before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Alek
s
ei Iupi
n
ov
Move
Oc
t
aneS
a
ndwic
h
.
mdp and spc2-
I
MD
.
m
d
p into str
i
ngs
commit
|
commitdiff
|
tree
2018-01-11
Aleksei
I
upin
o
v
Remove unu
s
ed alanin
e
_vsi
t
e
.
m
d
p
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupinov
D
o
n
o
t prin
t
PME cou
n
te
r
breakdown if
it's emp
t
y
commit
|
commitdiff
|
tree
2017-12-20
Aleksei
I
u
p
inov
Set GMX_GPU_AUT
O
to FALSE with
G
M
X_G
P
U defi
n
ed
commit
|
commitdiff
|
tree
2017-12-20
Ale
k
sei Iupinov
R
emove p
o
tent
i
al
l
y
wrong "per us
e
r reques
t
" note
f
rom
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Aleksei Iupinov
Relaxed precis
i
on in
spline i
n
terp
o
lation tests
commit
|
commitdiff
|
tree
2017-12-06
Aleks
e
i Iupinov
Prov
i
de dummy
initi
a
l
i
zati
o
n to silence a
w
ar
n
ing
commit
|
commitdiff
|
tree
2017-12-05
Aleksei I
u
p
ino
v
Do
not a
c
cept un
s
upported comb
i
n
ation "-pm
e
cpu -pmeff
t
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei Iu
p
inov
Reformulate PME solvin
g
tests
toleran
c
es
commit
|
commitdiff
|
tree
2017-11-28
Aleks
e
i I
u
pinov
Re
p
lace
of
p
m
eGPU variab
l
e name with
p
meGpu
commit
|
commitdiff
|
tree
2017-11-27
Alekse
i
Iupi
n
ov
Do not force sep
a
rate
PME rank to
recompute recip
r
o
c
al
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Alek
s
ei Iup
i
nov
Disable fail
i
ng
s
eparate PM
E
rank tests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupinov
Add tests for PME tuni
n
g
a
n
d
fix mixe
d
P
ME mode with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
A
le
k
sei Iupinov
D
estroy
P
ME GPU
c
o
n
t
ext
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei
Iupinov
Enable sepa
r
ate PME
G
P
U rank
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupinov
Do not call
m
ixed CPU+GPU
PME mod
e
"Hybrid"
commit
|
commitdiff
|
tree
2017-11-24
A
l
eksei Iupi
n
ov
Activate m
i
xed
m
ode of PME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-24
A
leksei
I
upinov
Remove outdated (already i
m
plemented) pi
n
n
i
n
g
TODO
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
upi
n
ov
M
e
ntion
g
mx
_
inst
a
ll_heade
r
s() i
n
the developer manual
commit
|
commitdiff
|
tree
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