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Update developer guide
2017-11-24
Ma
r
k Abraha
m
Update develop
e
r
g
uide
commit
|
commitdiff
|
tree
2017-11-24
Mark Abr
a
h
am
Act
i
vate PME on GPUs
commit
|
commitdiff
|
tree
2017-11-24
Mark
A
bra
h
am
Se
p
arat
e
managem
e
nt of GPU contexts fr
o
m modules
commit
|
commitdiff
|
tree
2017-11-24
Mark Abrah
a
m
A
d
d
PME i
n
tegration test
commit
|
commitdiff
|
tree
2017-11-24
Mark Ab
r
aham
Exten
d
task assignm
e
nt code
commit
|
commitdiff
|
tree
2017-11-21
Ma
r
k Ab
r
a
h
am
Us
e
m
uc
h
less PaddedRVecVector and
m
ore ArrayRef of
.
.
.
commit
|
commitdiff
|
tree
2017-11-21
M
ark Abraham
Suppo
r
t pinning in HostAlloca
t
or
commit
|
commitdiff
|
tree
2017-11-20
Mark Abraham
Fix nightly ma
t
r
i
x co
n
fig
commit
|
commitdiff
|
tree
2017-11-19
Mark Abraham
Fix FindCUDA
.
cmake
fo
r
-Wunde
f
commit
|
commitdiff
|
tree
2017-11-17
M
ark Ab
r
aham
Use
HostAllocatio
n
Policy for chargeA
commit
|
commitdiff
|
tree
2017-11-17
M
a
rk Abraham
A
d
d
checking
f
unction for whether a buf
f
er is p
i
n
n
ed
commit
|
commitdiff
|
tree
2017-11-17
Mark Abrah
a
m
Improve ha
n
d
ling
of PME
G
P
U force
buff
e
r
commit
|
commitdiff
|
tree
2017-11-10
Mark Abra
h
a
m
Im
p
o
r
t c
m
ake Modules/FindCUDA
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
M
a
rk Abraham
Prepared t_m
d
a
t
oms for
using vector
commit
|
commitdiff
|
tree
2017-11-09
M
ark Abr
a
ham
Introduce Ho
s
tAlloca
t
ionPoli
c
y
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Refo
r
m
gmx_
p
me_pp all
o
c and
us
e
v
ector
commit
|
commitdiff
|
tree
2017-11-07
Mark
A
braham
I
n
troduce gmxopencl
.
h
commit
|
commitdiff
|
tree
2017-11-07
M
a
rk
A
braham
Tes
t
clang on A
R
M in nightly
matrix
commit
|
commitdiff
|
tree
2017-11-07
Ma
r
k Ab
r
ah
a
m
Improve PME
i
ncl
u
de
s
commit
|
commitdiff
|
tree
2017-11-03
Mark
A
b
r
aham
Merge "Me
r
ge b
r
anch release-2
0
16"
commit
|
commitdiff
|
tree
2017-11-02
M
a
rk Abraham
Merge
b
r
a
nch rele
a
s
e
-2016
commit
|
commitdiff
|
tree
2017-11-01
M
a
rk Abraham
Fix thread-MPI rank
choi
c
e for orien
t
ation restraint
s
commit
|
commitdiff
|
tree
2017-11-01
Ma
r
k A
b
raham
I
mpr
o
ve h
a
ndling of GPU IDs
commit
|
commitdiff
|
tree
2017-10-31
Mark Abraham
Update treatment of
G
PU
c
o
m
patibility data structure
commit
|
commitdiff
|
tree
2017-10-30
Mar
k
Abraham
Fix and update hw
_
info
commit
|
commitdiff
|
tree
2017-10-27
M
ark
A
braham
Fix hw detection more
commit
|
commitdiff
|
tree
2017-10-26
M
ark
A
braham
Make relea
s
e
matrix work ag
a
in
commit
|
commitdiff
|
tree
2017-10-26
Mark Abra
h
am
New
q
uote
commit
|
commitdiff
|
tree
2017-10-25
Mark Abrah
a
m
Teach t
h
e
copyright chec
k
er
a
bou
t
t
e
mplat
e
.
cpp
commit
|
commitdiff
|
tree
2017-10-20
Ma
r
k
Abraham
Clarify do
c
s for Fmax
in EM
commit
|
commitdiff
|
tree
2017-10-20
M
a
rk
A
braha
m
Merge branch release-2016
commit
|
commitdiff
|
tree
2017-10-16
Mar
k
Abraham
Mer
g
e branch release-2016
commit
|
commitdiff
|
tree
2017-10-13
Mark Abrah
a
m
U
p
date t
e
sts for
C++11 compiler
a
nd standa
r
d library
commit
|
commitdiff
|
tree
2017-10-13
Mark
Abraham
Fix cpuinf
o
on clan
g
+
non-x
8
6
commit
|
commitdiff
|
tree
2017-10-11
Mark Abr
a
ham
Introduced header fo
r
commun
i
cation to/from PME
r
a
n
ks
commit
|
commitdiff
|
tree
2017-10-11
M
ar
k
Abraham
C
leaned
up ewaldcoeff
f
or PME-only ranks
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraha
m
Use clang-5 in Jenkin
s
commit
|
commitdiff
|
tree
2017-10-07
Mar
k
A
braham
Tel
l
c
ppch
e
ck that
.
c
p
p and
.
cu fi
l
es
a
r
e c++
commit
|
commitdiff
|
tree
2017-10-05
Mark Abraham
Conti
n
ue rem
o
ving -nb gpu_c
p
u
commit
|
commitdiff
|
tree
2017-10-04
Mark
A
braham
Enable group-sch
e
me
S
I
M
D
with GMX_SIMD=AVX2_128
commit
|
commitdiff
|
tree
2017-10-03
Mark Abrah
a
m
Introduce and
use Align
e
dAlloca
t
ionPolicy
commit
|
commitdiff
|
tree
2017-09-19
Mark Abraham
U
pdate testing matrices to test with (latest
)
icc-1
8
commit
|
commitdiff
|
tree
2017-09-17
Mark Abraham
Merg
e
branch r
e
lease-2016
commit
|
commitdiff
|
tree
2017-09-15
Mark
A
br
a
h
a
m
Express intent of
m
atri
x
r
e
lease
b
uild types explicitly
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
Bu
m
ped patch version for next release
commit
|
commitdiff
|
tree
2017-09-15
Mark Abra
h
am
Vers
i
on 2016
.
4
commit
|
commitdiff
|
tree
2017-09-14
Mark Abra
h
am
Form
t
askassignment modul
e
commit
|
commitdiff
|
tree
2017-09-14
Mark
A
b
r
aham
Fix
c
o
m
p
at
module definitio
n
commit
|
commitdiff
|
tree
2017-09-12
Mark
A
b
r
aha
m
Merge branch r
e
l
ease
-
2016
commit
|
commitdiff
|
tree
2017-09-07
Mark Abraham
Introduce type
-
safe G
P
U emu
l
a
t
ion variable
s
commit
|
commitdiff
|
tree
2017-09-07
Ma
r
k
Abraham
Enable grou
p
-
schem
e
SI
M
D
k
ernels on recent
AVX e
x
tens
i
ons
commit
|
commitdiff
|
tree
2017-09-06
Ma
r
k
A
braham
Pr
e
pare Verl
e
t scheme later in
runner
commit
|
commitdiff
|
tree
2017-09-05
Mark A
b
raham
Fixes for Sol
a
r
i
s
commit
|
commitdiff
|
tree
2017-09-05
M
ark A
b
raham
Fix use of
G
PU inf
o
rmation
fo
r
threa
d
-MPI setup
commit
|
commitdiff
|
tree
2017-09-03
Mark Abraham
Fix compiler flags for usin
g
M
KL
commit
|
commitdiff
|
tree
2017-09-03
Ma
r
k
A
braha
m
Merge bran
c
h release-5-1 int
o
release-2016
commit
|
commitdiff
|
tree
2017-08-25
Mark Abraham
Fi
x
flat-bottomed position r
e
straints with multipl
e
.
.
.
commit
|
commitdiff
|
tree
2017-08-23
M
a
r
k
Abraham
Stopped checkpoint
i
nf
l
uen
c
ing par
a
l
l
elism setup
commit
|
commitdiff
|
tree
2017-08-22
M
ark Abr
a
ha
m
Run GPU d
e
tect
i
on e
v
en
f
or
mdrun -nb cpu
commit
|
commitdiff
|
tree
2017-08-22
Ma
r
k A
b
r
a
h
a
m
Fix
e
d thread-MPI with n
o
n-default -np
m
e
commit
|
commitdiff
|
tree
2017-08-22
Mark
A
braha
m
Fix missi
n
g
d
e
clara
t
ion of G
M
X_UNUSED_VALUE
commit
|
commitdiff
|
tree
2017-08-22
M
a
rk
Abraham
Merge branch release-2016
commit
|
commitdiff
|
tree
2017-08-21
Mark
A
b
raha
m
Moved
i
ncrea
s
e_nstlist() to nbnxn_tunin
g
.
h
commit
|
commitdiff
|
tree
2017-08-21
Mark Abraham
Fix compila
t
ion
issues
with A
R
M S
I
MD
commit
|
commitdiff
|
tree
2017-08-17
Mark Abraham
Replac
e
consisten
c
y checking wit
h
assertion
commit
|
commitdiff
|
tree
2017-08-16
Mark Abraham
P
a
rse us
e
r-s
u
pplied GPU
task
a
ss
i
gnm
e
nt only when
n
eeded
commit
|
commitdiff
|
tree
2017-08-16
M
ar
k
Abraham
R
e
move dup
l
icate GPU non-usage h
i
n
t
commit
|
commitdiff
|
tree
2017-08-16
Mark Abrah
a
m
Mo
v
e
d
l
o
gging functiona
l
ity
into GPU usage report
commit
|
commitdiff
|
tree
2017-08-15
M
a
rk Ab
r
aham
Merge b
r
anch release-5-1 into re
l
ease-
2
016
commit
|
commitdiff
|
tree
2017-08-15
M
ark
Abraham
Fix value
o
f
Ewald shi
f
t
commit
|
commitdiff
|
tree
2017-08-10
Mark Abraham
Clarify
data flow in
GPU
t
ask assignmen
t
commit
|
commitdiff
|
tree
2017-08-07
Mar
k
Abraham
Fix
includ
e
depende
n
cy for geten
v
commit
|
commitdiff
|
tree
2017-08-07
Mark
Abraha
m
S
i
m
plif
i
ed handling of GPU device IDs
commit
|
commitdiff
|
tree
2017-08-06
Mark Abraham
Simplify resource-division effici
e
ncy check
commit
|
commitdiff
|
tree
2017-08-06
Mark Abrah
a
m
Split prin
t
har
d
ware from detecthar
d
ware
commit
|
commitdiff
|
tree
2017-08-06
Mar
k
Abra
h
am
Decouple t
a
sk assignme
n
t from task execution
commit
|
commitdiff
|
tree
2017-08-06
Mark A
b
r
a
ha
m
Removed
u
nused host-side a
l
location code
commit
|
commitdiff
|
tree
2017-08-04
Mar
k
Abraham
S
to
p
using hwinfo_g for repor
t
in
g
code
commit
|
commitdiff
|
tree
2017-08-03
Mark Abraham
R
em
o
v
e
d
unused
i
n
c
l
u
de statements
commit
|
commitdiff
|
tree
2017-08-01
Mark Ab
r
aham
Int
r
oduced M
d
ru
n
ner high-lev
e
l
c
lass
commit
|
commitdiff
|
tree
2017-07-27
Mark Abra
h
am
Enhance cm
a
ke a
n
d releng handling o
f
GMX_USE_R
D
TSCP
commit
|
commitdiff
|
tree
2017-07-24
Ma
r
k Abra
h
am
Separate
d
respon
s
ibili
t
y
f
o
r
consistenc
y
ch
e
ck
i
ng
commit
|
commitdiff
|
tree
2017-07-24
Mark Abraham
Remove unnecessary GPU ch
e
c
k
ing code
commit
|
commitdiff
|
tree
2017-07-20
Mark Ab
r
aham
C
l
eane
d
up bUseGpu in runner
commit
|
commitdiff
|
tree
2017-07-20
Mark Abraham
Stop duplic
a
te printing of detected GPUs
commit
|
commitdiff
|
tree
2017-07-20
M
a
r
k Abraham
Fix use of GMX_SIMD
i
n own-fftw bui
l
d
commit
|
commitdiff
|
tree
2017-07-19
Mark A
b
raham
Made post-submit confi
g
t
o
t
e
st clang+o
p
enmp
.
commit
|
commitdiff
|
tree
2017-07-19
Mark Abraham
Improve CMa
k
e implementation for GMX_SIMD
commit
|
commitdiff
|
tree
2017-07-18
Mar
k
Abraham
Converted some const pointers into const refer
e
nces
.
.
.
commit
|
commitdiff
|
tree
2017-07-18
Mark Abraham
Eliminated pick_nbnxn_resources
commit
|
commitdiff
|
tree
2017-07-14
Mark Abraham
Imp
l
emen
t
ed g
r
ompp -po
fo
r
op
t
ions
-
style mdp
h
andling
commit
|
commitdiff
|
tree
2017-07-14
Mark Abr
a
ham
Clean up c
m
ake bui
l
d
host
d
etection
commit
|
commitdiff
|
tree
2017-07-13
Mark Ab
r
aham
Clean up gmx
_
mdrun()
commit
|
commitdiff
|
tree
2017-07-13
Mark Abra
h
a
m
Cleaned u
p
m
d
r
unne
r
_start_threads
commit
|
commitdiff
|
tree
2017-07-13
M
a
rk Abraham
Mor
e
upd
a
tes to tes
t
i
n
g matrix
commit
|
commitdiff
|
tree
2017-07-07
Mark Abraham
R
efacto
r
error
handl
i
ng in
i
nit_gpu
commit
|
commitdiff
|
tree
2017-07-06
Mark Abraham
Simplify gm
x
_gpu_o
p
t_t
commit
|
commitdiff
|
tree
2017-07-04
M
a
rk Abraham
Clean up pick_nbnxn_re
s
our
c
es
commit
|
commitdiff
|
tree
2017-07-01
Mar
k
A
b
raham
Cleaned up GPU emul
a
t
ion l
o
gic
commit
|
commitdiff
|
tree
2017-06-28
Mark
A
braham
Cleaned up high-level boole
a
n variable naming
commit
|
commitdiff
|
tree
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