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Fix small leak in forcerec
2018-10-13
Aleksei Iupinov
Add and enable P
M
E OpenCL
commit
|
commitdiff
|
tree
2018-08-27
A
leksei Iupino
v
P
r
epare pme-gpu
-
types
.
h for OpenCL
commit
|
commitdiff
|
tree
2018-07-30
Ale
k
sei Iupinov
Re
m
ove h
a
r
d
cod
e
d wa
r
p_size == 32 ass
u
mption from P
M
E GPU
commit
|
commitdiff
|
tree
2018-06-25
A
l
eksei Iupinov
Mo
v
e vectype_ops
.
clh in
t
o
gpu_utils
commit
|
commitdiff
|
tree
2018-06-25
Aleksei I
u
pinov
M
o
ve
t
he PME GPU
k
ern
e
l launch functions into
p
m
e-
g
pu
.
.
.
commit
|
commitdiff
|
tree
2018-06-14
Aleks
e
i Iupinov
E
nsure PME with Ope
n
C
L
does not attempt to pin
commit
|
commitdiff
|
tree
2018-06-07
Al
e
ksei Iupinov
C
o
mpile mo
s
t of PME GP
U
host
c
o
de wit
h
OpenC
L
commit
|
commitdiff
|
tree
2018-05-31
A
l
e
k
sei I
u
pinov
Merge pme
.
cu i
n
to p
m
e-gpu-internal
.
c
pp
commit
|
commitdiff
|
tree
2018-05-31
Alek
s
ei Iupinov
PME OpenCL 3D FFT tra
n
s
form i
s
imp
l
e
m
e
n
ted
,
usin
g
clFFT
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei
I
u
p
ino
v
M
ove
p
me-timings
.
cu to pme-gpu-ti
m
i
ngs
.
c
pp
commit
|
commitdiff
|
tree
2018-05-31
Al
e
k
sei Iupinov
Prefer linki
n
g to system c
l
FFT rather t
h
an bundled one
commit
|
commitdiff
|
tree
2018-05-31
A
l
ek
s
e
i
Iupi
n
ov
Mov
e
the P
m
eGpuS
p
ec
i
f
ic structure i
n
to
p
me
-
gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Alek
s
ei Iupi
n
ov
Added
the bund
l
e
d
clF
F
T into Open
C
L bui
l
ds
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
upin
o
v
A
d
d GpuEven
t
Synchro
n
izer c
l
ass
commit
|
commitdiff
|
tree
2018-05-31
Al
e
ksei Iupin
o
v
Gather
t
h
e
PME
GPU
constant
s
/macros in a single
header
commit
|
commitdiff
|
tree
2018-05-30
Al
e
ksei
I
up
i
nov
Make PME GPU structures use Devi
c
eBuffer
commit
|
commitdiff
|
tree
2018-05-28
Aleks
e
i I
u
pinov
S
u
p
p
o
r
t
p
ersistent d
e
vice con
t
ext-derived data
i
n PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-22
Aleksei Iupinov
Remove unuse
d
r
e
sults
of cudaStreamQuery()
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iupi
n
ov
prepa
r
eGpuKernelA
r
gument
s
()
and launch
G
puKer
n
el() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-08
Alek
s
e
i
Iupinov
Import clFFT li
b
rary int
o
the
Gromacs so
u
r
ce
commit
|
commitdiff
|
tree
2018-05-04
Al
e
ksei
I
upinov
Add clearDeviceB
u
ff
e
r
A
sync() for CUD
A
/OpenCL
commit
|
commitdiff
|
tree
2018-05-03
Aleksei Iupinov
C
o
p
y
missing GPU NB
host deallocations from Op
e
n
C
L
.
.
.
commit
|
commitdiff
|
tree
2018-05-03
Alekse
i
Iupino
v
replace cu_
c
op
y
_* calls with
D
e
viceBuffe
r
f
u
nctions
.
.
.
commit
|
commitdiff
|
tree
2018-05-02
Al
e
ksei
I
up
i
nov
Rename
O
penC
L
host mem
o
ry routines to
m
atch the CUDA
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Ale
k
sei Iupi
n
ov
Mak
e
asize() a proper templ
a
te function
instead of
.
.
.
commit
|
commitdiff
|
tree
2018-04-27
Aleksei Iupi
n
ov
Rename the asi
z
e v
a
riable
to numAlignmentAtoms
commit
|
commitdiff
|
tree
2018-04-26
Aleksei Iupino
v
S
e
parate
P
M
E GPU host-only and
host/device data struct
u
res
commit
|
commitdiff
|
tree
2018-04-26
Aleksei Iup
i
nov
Add copyFromDevice
B
uffer() CUDA/OpenCL implementations
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
Rem
o
ve
d
cu_realloc_buffere
d
() in favor of rea
l
locateDevice
B
u
.
.
.
commit
|
commitdiff
|
tree
2018-04-23
Alekse
i
Iup
i
nov
Devi
c
eBuff
e
r
h
eaders are added
commit
|
commitdiff
|
tree
2018-04-12
Aleks
e
i Iupinov
Ma
k
e
i
n-source OpenCL kernel path
a per-m
o
d
ul
e
param
e
ter
commit
|
commitdiff
|
tree
2018-04-12
Aleksei
Iupinov
Remo
v
e
C
UDA_FUN
C
macr
o
s from m
a
ny functions in PM
E
GPU
commit
|
commitdiff
|
tree
2018-04-12
Ale
k
sei Iupi
n
ov
Stop PME GPU code
fro
m
compiling on non-CU
D
A buil
d
s
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iup
i
nov
Prev
e
n
t OpenCL timing memor
y
l
e
ak
commit
|
commitdiff
|
tree
2018-03-20
Aleksei I
u
pi
n
o
v
Clarify the m
d
run GPU options docs
commit
|
commitdiff
|
tree
2018-03-16
A
l
e
k
sei Iupinov
Add a bas
i
c TP
I
sanit
y
test
commit
|
commitdiff
|
tree
2018-03-16
Ale
k
sei I
u
pi
n
ov
Stop
gmx_feenableexcept() from returni
n
g
previous exception
.
.
.
commit
|
commitdiff
|
tree
2018-03-16
Aleksei
I
u
pin
o
v
Restore the
lost
mc_t
e
m
p
check in grompp
commit
|
commitdiff
|
tree
2018-03-06
A
l
eksei Iupin
o
v
Isolate PME GPU sp
l
ine parameter index
i
ng in i
n
line
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Ale
k
sei Iupinov
Stop using cus
t
om F
i
ndOpenCL
.
cmake, pe
r
T
O
D
O
commit
|
commitdiff
|
tree
2018-03-05
Aleksei Iupinov
Co
r
r
ect t
h
e
n
b
nxn_gpu_compile_kernels() docs
commit
|
commitdiff
|
tree
2018-03-02
Aleksei Iupinov
Make TPI
u
s
e double precision ex
p
commit
|
commitdiff
|
tree
2018-02-27
A
l
e
k
sei Iupinov
Merge branch 'release-2018'
commit
|
commitdiff
|
tree
2018-02-26
Alek
s
ei Iupinov
Adv
i
c
e
u
s
ers on
i
nf
i
nite
output of TPI
commit
|
commitdiff
|
tree
2018-02-20
A
l
eksei I
u
p
inov
Remove unused Open
C
L
debug buffer
commit
|
commitdiff
|
tree
2018-02-18
A
l
eksei Iupinov
R
eplace
*_free_buffered calls b
y
freeDeviceBuffer
commit
|
commitdiff
|
tree
2018-02-16
Aleksei Iupinov
Fix PME for large systems with Fermi GPU
s
commit
|
commitdiff
|
tree
2018-02-15
Al
e
ksei I
u
pino
v
Update FFTW build to
3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-15
A
leks
e
i
I
upinov
Add freeDevic
e
Bu
f
fer GPU utility functio
n
commit
|
commitdiff
|
tree
2018-02-15
Ale
k
s
ei Iupinov
Add the missing comma in the quot
e
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupino
v
Replace the
r
ema
i
ning EXPECT_
D
EATH with
EX
P
ECT
_
DE
A
T
H_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Add DeviceBuff
e
r
as a typedef fo
r
c
l
_mem/d
e
vi
c
e ponter
commit
|
commitdiff
|
tree
2018-02-13
Al
e
ksei Iupinov
Move GPU tra
i
ts into separa
t
e headers
commit
|
commitdiff
|
tree
2018-02-12
Ale
k
sei
Iupinov
Fi
x
the include gu
a
r
d
commit
|
commitdiff
|
tree
2018-02-09
Al
e
ksei I
u
pinov
Revert "Enable deb
u
g FP exceptions without TPI, not
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Ale
k
s
ei I
u
p
inov
Always run the essential dynamic
s
tests
commit
|
commitdiff
|
tree
2018-02-08
Ale
k
s
ei Iu
p
i
n
ov
Enable debug FP e
x
c
eptions witho
u
t T
P
I, not wi
t
h TPI
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
Merge branch 'release-20
1
8' into
m
ast
e
r
commit
|
commitdiff
|
tree
2018-02-06
Aleksei I
u
pinov
Remove
u
nnecessa
r
y inclu
d
es
f
rom do
m
dec
.
h
commit
|
commitdiff
|
tree
2018-02-06
A
l
eksei Iu
p
i
nov
Zero unus
e
d values to silence t
h
e warning
commit
|
commitdiff
|
tree
2018-02-06
Al
e
ksei
I
upinov
O
nly setup
Ewald i
n
th
e
g
eneric group k
e
r
ne
l
if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
A
leksei Iu
p
inov
Make
n
d
x files
optional in Simulation
R
unner
commit
|
commitdiff
|
tree
2018-02-05
Aleksei Iup
i
nov
Remove m
d
pInput
F
i
l
eNa
m
e_ fro
m
Simul
a
tionRu
n
n
er, per
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei
Iupino
v
Don't print impossible CUDA version n
u
mbers in abse
n
c
e
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
F
i
x
input MDP co
n
t
ents fo
r
swap
a
nd IMD test
s
commit
|
commitdiff
|
tree
2018-02-01
Aleksei Iupino
v
Check for
G
TEST_IS_
T
H
READSAFE
b
eing defined
commit
|
commitdiff
|
tree
2018-01-24
Aleksei Iupi
n
ov
Remov
e
unused fields per
T
OD
O
commit
|
commitdiff
|
tree
2018-01-23
A
leksei
Iupinov
Test the mixed mode
P
M
E wit
h
walls
an
d
b
o
x
scal
i
ng
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
T
e
s
t
P
M
E CPU/GPU with walls and
b
o
x scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iup
i
nov
Wr
a
p the
P
ME testing loop in a method for
e
xtensibilit
y
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i
Iup
i
no
v
Add a death test f
o
r
t
he duplicate inputrec keys
che
c
king
commit
|
commitdiff
|
tree
2018-01-19
Ale
k
sei Iu
p
inov
Rename c
l
ass B
i
asReader to struct BiasOutputSetup
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iu
p
inov
Move the t
e
mp
o
rary file MPI
w
orkaroun
d
into the base
.
.
.
commit
|
commitdiff
|
tree
2018-01-19
A
l
eksei Iupin
o
v
Make the reference data
v
ariables local in G
e
tIrTest
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i
Iupi
n
o
v
M
erge branch
'release-2018'
into
m
aster
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
Got rid of manual memor
y
management in the PME
ov
e
rlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Al
e
ksei Iup
i
nov
R
e-enable multi-rank PME te
s
ts (with th
e
file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-17
Alek
s
ei Iupino
v
Fix box
scaling in P
M
E
m
ixed mode
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
Mer
g
e branch 'release-2018
'
i
nto master
commit
|
commitdiff
|
tree
2018-01-16
Aleksei Iupinov
A
l
ways write th
e
input MDP
file
f
or testing just before
.
.
.
commit
|
commitdiff
|
tree
2018-01-11
A
lek
s
ei Iu
p
ino
v
Mo
v
e OctaneSandw
i
ch
.
mdp and sp
c
2-IMD
.
mdp i
n
to strings
commit
|
commitdiff
|
tree
2018-01-11
A
l
eksei I
u
p
in
o
v
Remove unuse
d
alan
i
ne_vsite
.
mdp
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupinov
Do not prin
t
P
ME counter breakd
o
w
n i
f
it's empty
commit
|
commitdiff
|
tree
2017-12-20
Alek
s
ei Iupinov
Set G
M
X
_
GPU_AUT
O
to FALSE with GMX_GPU defined
commit
|
commitdiff
|
tree
2017-12-20
Aleksei Iupinov
Remove p
o
te
n
tia
l
ly wrong "p
e
r
user request" note
from
.
.
.
commit
|
commitdiff
|
tree
2017-12-07
A
l
eksei
I
up
i
nov
Relaxed
p
recisi
o
n
i
n
spline in
t
erpola
t
ion
t
ests
commit
|
commitdiff
|
tree
2017-12-06
A
l
eksei
Iupinov
Provide
d
um
m
y ini
t
ializati
o
n to s
i
l
e
nce a warning
commit
|
commitdiff
|
tree
2017-12-05
Aleksei Iupin
o
v
Do not acc
e
pt unsu
p
port
e
d combination "-pme
c
p
u -pme
f
ft
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Aleksei Iupinov
Reformulate PME solving t
e
sts tol
e
r
ances
commit
|
commitdiff
|
tree
2017-11-28
Alekse
i
Iupin
o
v
Replace
o
f
p
meGPU
v
ariable name
w
ith pmeGpu
commit
|
commitdiff
|
tree
2017-11-27
A
l
eksei Iupinov
Do not force separate PME rank t
o
recompute reciprocal
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Aleksei
Iupin
o
v
Disable failing separate PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Alek
s
e
i Iupinov
Add tests
f
o
r PME t
u
ning an
d
fix mixed
PME mode wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Aleksei
I
upinov
D
e
stroy
P
ME GPU c
o
ntext
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupi
n
o
v
Enable
s
eparate PME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
A
l
eks
e
i Iupinov
Do
n
ot c
a
ll mixed CPU+GPU PME mode
"
Hybrid"
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupi
n
ov
Activate mixe
d
mode of PME
o
n GPU
commit
|
commitdiff
|
tree
2017-11-24
Alek
s
ei Iupi
n
ov
Remo
v
e outdated (already impl
e
ment
e
d
)
pinning TOD
O
commit
|
commitdiff
|
tree
2017-11-24
Al
e
kse
i
Iup
i
nov
M
ention
g
mx
_
install_headers() in the
developer manua
l
commit
|
commitdiff
|
tree
2017-11-24
Aleks
e
i Iupino
v
Make FFT r
e
al-space
g
r
i
d
use
C
UDA pinning for
mixed
.
.
.
commit
|
commitdiff
|
tree
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