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Don't use fah_fsync
2020-09-29
A
r
tem Zhmu
r
ov
Don't use fah_fsync
commit
|
commitdiff
|
tree
2020-06-16
Artem Zhmuro
v
A
d
d missing end-of-line in the GPU update ass
i
gnment
.
.
.
commit
|
commitdiff
|
tree
2020-06-05
A
rtem
Z
hmurov
Make a e
r
ro
r
mess
a
g
e l
e
ss co
n
fusin
g
commit
|
commitdiff
|
tree
2020-06-04
Artem
Zhmurov
U
pdate the
r
elease notes
commit
|
commitdiff
|
tree
2020-04-29
Artem Zh
m
urov
Fi
x
the number of
steps check when c
h
eckpoint is loaded
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmurov
Fix th
e
removal of
COM vel
o
city in cas
e
of GPU up
d
ate
commit
|
commitdiff
|
tree
2020-03-02
Art
e
m Zhmurov
Upda
t
e
t
he message on whether update a
n
d constraints
.
.
.
commit
|
commitdiff
|
tree
2020-01-23
Art
e
m Zhmurov
F
ix a
c
ouple of commas in cool q
u
otes
commit
|
commitdiff
|
tree
2020-01-13
Ar
t
em Zhmurov
Report if update is run
n
ing
on th
e
GPU or on the
C
PU
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmuro
v
In
f
orm user
w
hy forc
i
ng GPU update is no
t
possible
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmu
r
o
v
A
d
d
desc
r
iption of GMX_FOR
C
E_UPDATE_
D
EFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Fix gpuupdate m
a
t
r
i
x
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmuro
v
Change t
h
e
be
h
avior of the GPU update
U
I
commit
|
commitdiff
|
tree
2019-12-27
Artem
Zhmurov
Add a not
e
to the log file w
h
en -update gpu
w
as set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Ar
t
e
m Z
h
mu
r
ov
Clean b
a
d aut
o
-format in decidegpuusag
e
doxygen
comment
s
commit
|
commitdiff
|
tree
2019-12-17
Artem
Z
hmurov
Clean-
u
p buff
e
r-ops
CU
D
A ker
n
els
commit
|
commitdiff
|
tree
2019-12-13
Artem Z
h
murov
C
l
e
an up outdated commen
t
s in md
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Art
e
m Zhmurov
Allow using
GP
U
upda
t
e with D
D
and update
g
roups
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmuro
v
Enab
l
e most of
the pulling fla
v
o
r
s wi
t
h GPU
u
pda
t
e
commit
|
commitdiff
|
tree
2019-12-11
A
r
tem
Zh
m
u
rov
Clarif
y
what setting zero
t
o
some output
m
dp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
A
r
tem Zhmurov
Set GPU update to false in
case
of a rerun
commit
|
commitdiff
|
tree
2019-12-06
A
rtem Zhm
u
rov
Pass array ref instead
o
f casting to basic array in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem
Zh
m
urov
Print
O
penCL error info in
c
a
s
e of f
a
iled asserti
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zh
m
u
ro
v
Ma
k
e
Leap-Frog CUDA ke
r
n
e
l sel
e
ction safer
commit
|
commitdiff
|
tree
2019-11-29
Art
e
m Zhmurov
Rename s
o
me var
i
ables in GPU Update
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Clear device
f
orce buffer
i
f it was
re
a
llocat
e
d
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Fix pr
e
ssure coupling wi
t
h G
P
U upd
a
te
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmuro
v
Combine
t
wo booleans
i
n md loop
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmur
o
v
Ad
d
method for coordinates sc
a
l
ing into G
P
U update
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Use
same matrix for
P
a
r
rinello
-
Rahman and Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmu
r
ov
Fix index mapping is
s
ue with LINC
S
on
G
PU
commit
|
commitdiff
|
tree
2019-11-23
A
rtem Z
h
murov
New cool quote
commit
|
commitdiff
|
tree
2019-11-20
Artem Zh
m
u
rov
Ad
d
D2H
copies
f
o
r the ch
e
ckpoi
n
t
i
ng
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
M
o
ve the c
o
py of the
v
elocitie
s
for the o
u
t
pu
t
clos
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
A
r
tem Z
h
murov
Fix icc-19 wa
r
ning in
n
ightly matrix
commit
|
commitdiff
|
tree
2019-10-31
Artem Zhmu
r
o
v
Remove excess
i
ve
H
2
D
an
d
D2H copies of forces when
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Ar
t
e
m
Zhmurov
Disable
G
PU update whe
n
coordinates swapping is enabl
e
d
commit
|
commitdiff
|
tree
2019-10-29
Ar
t
em Zhmurov
Switch
the GPU
b
uffe
r
ops on
when update is on GPU
commit
|
commitdiff
|
tree
2019-10-28
Artem Zh
m
urov
Fix miss
i
ng co
o
rdi
n
a
te D
2
H c
o
py
with G
P
U upda
t
e and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
A
r
tem
Z
hmurov
Add hav
e
C
p
uLo
c
alForces
f
lag to Domai
n
Lifeti
m
eWorkload
commit
|
commitdiff
|
tree
2019-10-28
Artem
Zhmurov
A
l
l
o
w
using update flag
commit
|
commitdiff
|
tree
2019-10-23
Ar
t
e
m
Zhmurov
Slight improvemen
t
s to decid
e
Wheth
e
rToUseGpuForUp
d
ate
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
A
rtem Zhmur
o
v
Remove unnecess
a
ry CUDA st
r
e
a
m
s
y
nchronization calls
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmuro
v
Ren
a
me h
a
vePosi
t
ionRestraints(
.
.
.
) to
h
aveRes
t
raints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Ar
t
em Z
h
m
u
rov
Update the copyright message
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
A
r
t
e
m Zhmurov
Add envi
r
o
nment
v
ariable
that changes
th
e
meaning o
f
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Art
e
m
Zhmuro
v
Remove e
x
cessive
H
2D
an
d
D2H coordinates copi
e
s
w
h
en
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Ar
t
em Zhmuro
v
Re
m
ove
e
xcess
i
ve H2D and D2H copies of velo
c
it
i
es when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem Zhmuro
v
L
i
nk GPU f
o
rc
e
producer and con
s
umer
tasks
commit
|
commitdiff
|
tree
2019-10-15
A
rtem
Zhmur
o
v
Fix the
s
ing
l
e-
G
PU
u
pdate
-
constraints
commit
|
commitdiff
|
tree
2019-10-14
Artem Zhmu
r
ov
Add sep
a
r
ate
const
r
uctor to
S
tatePropagatorD
a
taGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhm
u
rov
Centralize manageme
n
t
o
f fo
r
ces ready on
G
PU event
commit
|
commitdiff
|
tree
2019-10-12
Ar
t
e
m
Zhmurov
Change copy mode to Asyn
c
in
P
ME
o
nl
y
rank
commit
|
commitdiff
|
tree
2019-10-12
A
r
tem Zhmurov
Centralize management of co
o
r
d
ina
t
e
s ready on GPU e
v
ent
commit
|
commitdiff
|
tree
2019-10-11
Art
e
m Zhmurov
Wrong locali
t
y was u
s
ed when ign
o
ring the PME force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Art
e
m Zhmurov
A
d
d manag
e
ment
for velocities a
n
d fo
r
ces copy eve
n
ts
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Arte
m
Zhmurov
Fix for t
h
e
r
ecent
nightly fa
i
lu
r
e
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhm
u
rov
Pass th
e
GPU streams to StatePropagatorDataGpu constructo
r
commit
|
commitdiff
|
tree
2019-10-07
Ar
t
em Zhmurov
Clean up the comm
e
nt
s
sections in Update
-
Constrain
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Fix a bug in GPU
halo
exchange initializa
t
ion
commit
|
commitdiff
|
tree
2019-10-03
Artem
Z
hmurov
F
ix the b
u
g with
offl
o
adin
g
the
P
ME-only ranks t
o
GPU
commit
|
commitdiff
|
tree
2019-10-02
A
r
tem Zhmu
r
ov
Eliminate D
2
D
c
o
py in upd
a
te constraints
commit
|
commitdiff
|
tree
2019-10-01
Artem Zhmurov
S
t
atePropagatorDataGpu obj
e
ct to manag
e
GPU forces
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
A
r
t
e
m Zhmurov
S
light imp
r
ovemen
t
s to
G
PU update
/
c
onstraints initiali
z
ation
commit
|
commitdiff
|
tree
2019-09-27
A
rtem Zhmurov
Int
r
o
d
u
ce stream management to GPU Update-Constraints
commit
|
commitdiff
|
tree
2019-09-22
Artem Zhmur
o
v
Di
s
able GPU u
p
date/constr
a
in
t
s
when
n
either PME no
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Artem Zhmu
r
o
v
Ch
a
nge PaddedVector to PaddedHostVector for force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmur
o
v
Fix
for the post-s
u
bmit failure
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmuro
v
De
c
ouple GP
U
force buff
e
r manag
e
ment f
r
o
m
buf
f
er ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
A
r
tem Zhmurov
Deco
u
ple coordinates buff
e
r man
a
gement fr
o
m b
u
f
fe
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Arte
m
Zhmuro
v
Reorgani
z
e PME cod
e
:
commit
|
commitdiff
|
tree
2019-09-10
Artem Z
h
murov
Making
DeviceBuffer availible in non-GPU builds
commit
|
commitdiff
|
tree
2019-09-03
Artem Zhmurov
Ad
d
P
arrinello-Rah
m
a
n pressure coupling to CUDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Art
e
m Zhmurov
Add temperature coupling to CUDA Leap-Frog integrator
commit
|
commitdiff
|
tree
2019-08-25
A
rte
m
Zhmurov
Make use of recent changes
t
o prepareKernelAr
g
uments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
M
isceleneous
improv
e
ments to the Leap
F
rog
tests
commit
|
commitdiff
|
tree
2019-08-14
Artem Zhmurov
B
u
g
Fix
:
Zeroi
n
g the padded a
r
ea of coor
d
i
n
ates vectors
.
.
.
commit
|
commitdiff
|
tree
2019-08-13
Arte
m
Zhmuro
v
Ma
k
e use of reference data
i
n integrator tes
t
s
commit
|
commitdiff
|
tree
2019-08-13
Artem
Zhmurov
M
ake use of refer
e
n
c
e
d
ata in SETTLE tests
commit
|
commitdiff
|
tree
2019-08-09
Artem
Z
h
murov
Prepare U
p
date and Constr
a
ints for Domain Decompo
s
i
tion
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmurov
Refactoring o
f
t
h
e SETTLE
t
est
s
commit
|
commitdiff
|
tree
2019-08-08
Artem Z
h
muro
v
R
e
factor Leap-Frog tests and
c
onnect them to C
P
U version
commit
|
commitdiff
|
tree
2019-08-06
Artem Zhmurov
Fix f
o
r cmake lists in m
d
lib
t
ests
commit
|
commitdiff
|
tree
2019-08-06
Artem
Z
hm
u
rov
Remove PImpl scaffolding from CUDA version of L
e
ap
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmu
r
ov
Change the file stru
c
t
ure in constrain
t
s
tests
commit
|
commitdiff
|
tree
2019-07-31
A
r
te
m
Zhmu
r
ov
I
n
tr
o
duce funct
i
on that che
c
ks if
t
h
e
com
p
utations
.
.
.
commit
|
commitdiff
|
tree
2019-07-26
Artem Zhmurov
R
e
m
o
ve PImpl s
c
affo
l
ding from CUDA version of SETTLE
commit
|
commitdiff
|
tree
2019-07-05
Artem Zhmurov
Remove
P
I
mpl scaffolding f
r
om C
U
D
A vers
i
on of LI
N
CS
commit
|
commitdiff
|
tree
2019-07-04
A
rtem
Zhmu
r
ov
Use reallocate
D
ev
i
c
e
Buffer(
.
.
.
) in CUDA
v
ersio
n
of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Artem
Z
hmuro
v
Early exit for CUDA versions
o
f SETTLE and LINCS
commit
|
commitdiff
|
tree
2019-07-03
Artem Zh
m
u
r
ov
M
emory managem
e
nt fi
x
e
s i
n
CUDA
v
e
r
s
ion of
LINCS
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Com
b
ine CUDA
L
e
ap-Frog, LI
N
CS
and SETTLE
.
II
.
commit
|
commitdiff
|
tree
2019-06-18
Artem Zhmurov
C
ombine
CUDA Leap-Frog, LINCS and SETT
L
E
.
I
.
commit
|
commitdiff
|
tree
2019-06-18
Artem
Z
hmurov
B
ug
fix: Const
r
aints
t
ests ar
e
not instantia
t
ed with
.
.
.
commit
|
commitdiff
|
tree
2019-05-24
A
r
t
em Zh
m
urov
Clar
i
f
y which
of the main
e
nergy ter
m
s a
r
e print
e
d
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Zh
m
urov
Clar
i
fy the Energy
O
utput III
commit
|
commitdiff
|
tree
2019-05-24
Artem Z
h
muro
v
Clarif
y
t
he En
e
rgyOutput II
commit
|
commitdiff
|
tree
2019-05-13
Art
e
m Zhmuro
v
Clarify
the EnergyOutput I
commit
|
commitdiff
|
tree
2019-05-12
Artem Zhmurov
CUDA
v
ersion
o
f Leap-Frog
i
ntegrator wit
h
basic t
e
sts
commit
|
commitdiff
|
tree
2019-05-06
Artem Zhmurov
Fix
i
ng minor mem
o
ry
issues
in MDLib
commit
|
commitdiff
|
tree
next