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Improve mdrun performance user guide
2018-12-22
Ale
k
s
e
i Iupinov
Add a san
i
ty
c
heck for OpenCL devi
c
es
commit
|
commitdiff
|
tree
2018-10-13
Aleksei Iupinov
A
d
d and enable PME Open
C
L
commit
|
commitdiff
|
tree
2018-08-27
Aleksei Iup
i
nov
Prepare pme-gpu-ty
p
es
.
h fo
r
OpenCL
commit
|
commitdiff
|
tree
2018-07-30
A
l
ek
s
ei Iupinov
Remo
v
e hardcoded
w
ar
p
_size == 32 assum
p
tion from
P
ME GPU
commit
|
commitdiff
|
tree
2018-06-25
Ale
k
s
e
i Iupi
n
ov
Mo
v
e v
e
ctype
_
ops
.
clh into
gpu_ut
i
ls
commit
|
commitdiff
|
tree
2018-06-25
Ale
k
se
i
Iupinov
Move t
h
e PME GPU
ker
n
e
l
la
u
nch
f
unc
t
ions into pme-gpu
.
.
.
commit
|
commitdiff
|
tree
2018-06-14
Ale
k
sei
I
u
pinov
Ens
u
re PME
with O
p
enCL does not attempt
t
o pin
commit
|
commitdiff
|
tree
2018-06-07
Aleksei Iupinov
Compile m
o
st of
P
M
E
G
PU
h
ost code w
i
th
OpenC
L
commit
|
commitdiff
|
tree
2018-05-31
Alekse
i
Iupinov
M
erge pme
.
c
u into pme-gp
u
-internal
.
c
pp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupino
v
PME OpenCL
3
D FFT
transform is impl
e
mented, using clFFT
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iup
i
no
v
Move pme-timi
n
g
s
.
cu t
o
p
m
e-gpu-timings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Prefer linking to sy
s
tem
c
lF
F
T r
a
ther
t
han
b
undled
o
ne
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Move the PmeGpuS
p
ecific structure into pme-gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei Iupinov
A
d
d
ed t
h
e bundled c
l
FFT into O
p
enCL builds
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iu
p
in
o
v
Add GpuEven
t
S
y
nch
r
onizer c
l
ass
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iu
p
in
o
v
Gather
t
he P
M
E GP
U
constants/macros i
n
a single header
commit
|
commitdiff
|
tree
2018-05-30
Ale
k
sei Iupi
n
ov
Make P
M
E
GPU structures us
e
D
evi
c
eBu
f
fe
r
commit
|
commitdiff
|
tree
2018-05-28
Al
e
ksei
Iupino
v
Support
p
ersistent device context-derived data in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-22
Alek
s
ei Iu
p
inov
Remove unus
e
d re
s
ults of cudaStreamQuery()
commit
|
commitdiff
|
tree
2018-05-18
Al
e
ksei I
u
pinov
prepare
G
puKern
e
lA
r
g
uments() and laun
c
h
G
puKe
r
nel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Aleksei Iupinov
Import clFFT librar
y
into th
e
G
ro
m
acs
s
ource
commit
|
commitdiff
|
tree
2018-05-04
Aleksei Iupinov
A
d
d
cl
e
arDe
v
iceBuffer
A
s
y
nc()
f
o
r
C
U
DA/
O
penCL
commit
|
commitdiff
|
tree
2018-05-03
Aleksei Iupin
o
v
Copy m
i
ssing GPU NB host dea
l
locations
f
rom Op
e
nCL
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Alekse
i
I
u
pinov
replace cu_copy_* cal
l
s w
i
th DeviceBuffer functions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Alek
s
ei
I
upi
n
ov
Renam
e
OpenCL host
mem
o
ry routines
to match
t
h
e
C
U
D
A
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleks
e
i Iupinov
M
a
ke
a
s
ize() a proper template function ins
t
ead of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupinov
Rename t
h
e as
i
z
e
var
i
a
ble to numAlign
m
en
t
Atoms
commit
|
commitdiff
|
tree
2018-04-26
Aleksei Iupinov
S
ep
a
rate P
M
E GPU host-only and host/device
d
ata structu
r
es
commit
|
commitdiff
|
tree
2018-04-26
A
l
e
k
sei I
u
pinov
Add
copyFromDeviceBuffer() CUDA/Ope
n
CL i
m
plementatio
n
s
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
Remov
e
d cu_real
l
oc_buffered() in favor of
re
a
llocateDeviceBu
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Aleks
e
i
Iup
i
n
o
v
Device
B
uffer he
a
ders ar
e
added
commit
|
commitdiff
|
tree
2018-04-12
Aleksei Iupinov
Make
i
n-source
O
penC
L
kernel path a per-module pa
r
ameter
commit
|
commitdiff
|
tree
2018-04-12
Aleksei I
u
pinov
Rem
o
ve
C
UDA
_
FUNC
m
acros fr
o
m many
f
unc
t
i
ons in
P
ME GPU
commit
|
commitdiff
|
tree
2018-04-12
Alek
s
ei Iupinov
Stop PME GPU code from compiling on
non-CUDA buil
d
s
commit
|
commitdiff
|
tree
2018-04-10
A
le
k
sei Iupinov
Prevent OpenCL
t
iming memor
y
leak
commit
|
commitdiff
|
tree
2018-03-20
Aleksei Iupinov
Clarify the mdrun GPU
options docs
commit
|
commitdiff
|
tree
2018-03-16
Alek
s
ei Iup
i
no
v
A
d
d
a bas
i
c TP
I
sanity
t
e
s
t
commit
|
commitdiff
|
tree
2018-03-16
Alekse
i
Iupi
n
ov
Stop gmx_feena
b
leexcept() from return
i
ng previous e
x
ception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iu
p
inov
Resto
r
e the
l
ost mc_temp check in
g
rompp
commit
|
commitdiff
|
tree
2018-03-06
Aleksei Iup
i
nov
I
solate
P
ME GPU
spline
p
a
rameter indexing in
i
n
line
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Aleks
e
i
Iupin
o
v
Stop usin
g
custom
FindOpenC
L
.
cm
a
ke, per TODO
commit
|
commitdiff
|
tree
2018-03-05
Al
e
ksei
I
up
i
nov
Correct the nbnxn_gpu_compile_kernels() docs
commit
|
commitdiff
|
tree
2018-03-02
Alek
s
ei Iupi
n
ov
M
a
ke
T
PI use d
o
ubl
e
p
r
ecision exp
commit
|
commitdiff
|
tree
2018-02-27
Aleksei
Iupinov
Mer
g
e branc
h
'
release
-
2018'
commit
|
commitdiff
|
tree
2018-02-26
Aleksei Iupinov
Advice use
r
s o
n
infinite output
of TPI
commit
|
commitdiff
|
tree
2018-02-20
Aleksei Iupin
o
v
Remove unused OpenCL
d
ebug
buffer
commit
|
commitdiff
|
tree
2018-02-18
Aleksei Iupinov
Replace *_free_bu
f
fered calls by freeDeviceBuff
e
r
commit
|
commitdiff
|
tree
2018-02-16
Ale
k
s
e
i Iup
i
nov
Fix PME for large systems with Fe
r
m
i GP
U
s
commit
|
commitdiff
|
tree
2018-02-15
Alekse
i
I
u
pinov
Update FFTW bui
l
d to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
A
l
eksei I
u
pinov
Add
f
reeDe
v
iceBuffe
r
GPU utilit
y
function
commit
|
commitdiff
|
tree
2018-02-15
A
l
eksei Iupinov
Add th
e
miss
i
ng c
o
mma
in the
q
uote
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupi
n
o
v
R
epla
c
e the remaining EXPECT_
D
EATH
with
EXPECT_D
E
ATH_IF_
S
U
PP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Add DeviceBuf
f
e
r
as
a typedef for cl
_
mem/device ponter
commit
|
commitdiff
|
tree
2018-02-13
A
l
e
ksei Iupinov
Mov
e
GPU traits into
s
epar
a
t
e
header
s
commit
|
commitdiff
|
tree
2018-02-12
Aleksei Iupin
o
v
Fix the include guard
commit
|
commitdiff
|
tree
2018-02-09
Aleksei Iupinov
Revert "Enable debug
F
P excepti
o
ns without
T
P
I, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Al
e
k
s
ei Iupi
n
ov
A
l
w
ays
run the es
s
ential
d
yn
a
m
ics
t
e
sts
commit
|
commitdiff
|
tree
2018-02-08
A
leks
e
i
I
upinov
Ena
b
l
e
debug FP e
x
c
eption
s
w
ithout TP
I
, no
t
with TPI
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
Merge br
a
nch 'releas
e
-2018' into m
a
ste
r
commit
|
commitdiff
|
tree
2018-02-06
A
leks
e
i
I
upinov
R
emov
e
unnecessary includes from d
o
md
e
c
.
h
commit
|
commitdiff
|
tree
2018-02-06
Al
e
ksei I
u
pino
v
Zero
u
n
u
sed va
l
ues
t
o silence the warning
commit
|
commitdiff
|
tree
2018-02-06
Aleksei Iupinov
Only se
t
up
E
w
ald
in the ge
n
eric gr
o
up
k
ernel i
f
i
t
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Ale
k
sei Iupinov
M
ake ndx
files optional
i
n
SimulationRunner
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iupi
n
ov
Remove mdp
I
nput
F
ileNa
m
e_ from SimulationRu
n
ner, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleks
e
i Iupi
n
ov
D
on't print imp
o
ssi
b
l
e CUD
A
version numbers i
n
a
bse
n
ce
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
Fix
i
nput
M
DP
con
t
ents for
s
wap and IMD tests
commit
|
commitdiff
|
tree
2018-02-01
Aleksei I
u
pinov
C
he
c
k fo
r
GTEST_IS_THREAD
S
AFE b
e
ing defin
e
d
commit
|
commitdiff
|
tree
2018-01-24
Al
e
ksei Iupinov
R
e
mo
v
e
u
n
u
sed fields per TODO
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Test the
m
i
x
e
d mode PME with
w
al
l
s and box
s
caling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
T
est P
M
E CPU/GPU with w
a
lls a
n
d box sca
l
ing
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupin
o
v
Wrap the PME testing loop in a
m
e
t
hod for ex
t
ensib
i
lity
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Add a
d
eath
test for the duplicate inputre
c
keys c
h
ecki
n
g
commit
|
commitdiff
|
tree
2018-01-19
Al
e
ksei
I
upi
n
ov
Rename cla
s
s
BiasRea
d
e
r to
s
t
ruct
BiasO
u
tput
S
e
t
up
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
se
i
I
upino
v
Move the temporary file
M
PI work
a
rou
n
d into
t
he
b
ase
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
Alek
s
ei Iupinov
M
a
ke the re
f
er
e
nce data variables loca
l
in Ge
t
IrTest
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i
I
u
pinov
M
e
r
ge bra
n
ch 'release-2018
'
i
nto master
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Got
rid of manual memory m
a
nagement in the PME ove
r
la
p
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei I
u
pin
o
v
Re-
e
nable
m
ulti-
r
ank PME tests (with the file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Fix
b
ox scaling in PME m
i
xed
m
ode
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Merge branch 'r
e
lease-2018' into master
commit
|
commitdiff
|
tree
2018-01-16
Aleksei
Iupi
n
o
v
Always write the inp
u
t MDP file f
o
r
t
esting jus
t
before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
Aleksei Iup
i
nov
M
ov
e
OctaneSandwich
.
mdp and spc
2
-
IMD
.
m
dp into strings
commit
|
commitdiff
|
tree
2018-01-11
Ale
k
sei
I
upinov
Re
m
ov
e
un
u
s
e
d
alanine_vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Al
e
ks
e
i Iupinov
Do
n
ot
p
rint
PME counter
b
rea
k
down if i
t
'
s emp
t
y
commit
|
commitdiff
|
tree
2017-12-20
A
l
eksei Iupinov
S
et
GM
X
_GPU_
A
UTO to
F
ALSE with GMX_GPU defined
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupino
v
Remove p
o
t
e
ntial
l
y wrong "per us
e
r request"
note from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
Aleksei Iu
p
inov
Relaxed pre
c
i
s
ion
i
n
spl
i
ne i
n
terpola
t
i
o
n tes
t
s
commit
|
commitdiff
|
tree
2017-12-06
Aleksei
Iupin
o
v
Provide
d
ummy initializatio
n
to
silence a
w
arning
commit
|
commitdiff
|
tree
2017-12-05
A
leksei I
u
pinov
Do
n
ot
a
ccept unsupported comb
i
natio
n
"
-
p
me cpu -pme
f
ft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Al
e
ksei Iupinov
Reform
u
late
P
M
E solving te
s
t
s
tolera
n
ces
commit
|
commitdiff
|
tree
2017-11-28
A
l
e
ksei I
u
pinov
Replace of pmeGPU v
a
ri
a
ble name with pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
Ale
k
s
e
i
I
u
pinov
Do not force se
p
arate P
M
E rank
t
o recomp
u
te
recipro
c
al
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
Iupinov
Disable failing separate
PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Aleksei Iupi
n
ov
Add tests for P
M
E tuning
and fix mixed PME mo
d
e with
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iupi
n
ov
Destroy PME GPU c
o
ntex
t
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
E
n
a
b
le separate PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
A
l
e
k
sei I
u
pinov
Do not call mixed C
P
U+GPU PME mode "Hybrid"
commit
|
commitdiff
|
tree
2017-11-24
Ale
k
sei I
u
pinov
Activate mixe
d
mod
e
of
P
ME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
e
i Iupinov
Rem
o
ve outdat
e
d
(already implemented)
pi
n
ning TODO
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
Iu
p
inov
Mention
g
mx_in
s
tall
_
headers() in t
h
e
deve
l
oper manual
commit
|
commitdiff
|
tree
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