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GROMACS 2018 first beta release
2017-11-28
Mark Abraham
GROMACS 2018
f
irst beta release
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
Update d
e
veloper guide
commit
|
commitdiff
|
tree
2017-11-24
M
ark A
b
ra
h
am
Activ
a
te PM
E
o
n GPU
s
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
Separate manageme
n
t of
GP
U
contexts
f
rom modul
e
s
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
Add P
M
E integration test
commit
|
commitdiff
|
tree
2017-11-24
M
ark Abraham
Ex
t
end task as
s
ig
n
ment co
d
e
commit
|
commitdiff
|
tree
2017-11-21
Mark
Abra
h
am
Use much less Padde
d
RVecVector and more ArrayRef of
.
.
.
commit
|
commitdiff
|
tree
2017-11-21
Mark
Abraham
Support pinning in Ho
s
tAllocator
commit
|
commitdiff
|
tree
2017-11-20
M
ark
A
brah
a
m
Fix nightly matrix co
n
fig
commit
|
commitdiff
|
tree
2017-11-19
M
a
rk
A
braham
Fix
F
indC
U
DA
.
cmake for
-
Wund
e
f
commit
|
commitdiff
|
tree
2017-11-17
Mark
Abr
a
ha
m
U
se HostAllocationPo
l
icy
f
or chargeA
commit
|
commitdiff
|
tree
2017-11-17
Ma
r
k Abra
h
am
Add che
c
k
i
n
g
function
f
o
r
whether a buffer is pinn
e
d
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
I
mprove hand
l
ing
o
f
P
M
E GPU
force
b
uf
f
er
commit
|
commitdiff
|
tree
2017-11-10
M
a
r
k
Abraham
Import
cmake Module
s
/
FindCUDA
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
Ma
r
k Ab
r
aham
P
r
e
pa
r
ed t_mdatoms
f
or using vector
commit
|
commitdiff
|
tree
2017-11-09
Ma
r
k
Ab
r
ah
a
m
Introduce Ho
s
tAllocationPolicy
commit
|
commitdiff
|
tree
2017-11-07
M
a
rk Abraham
Reform gmx_
p
me_pp al
l
oc and use vec
t
or
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Introduce gm
x
opencl
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abr
a
ham
Test clan
g
on ARM
in nigh
t
ly
m
atr
i
x
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
I
m
pr
o
ve PME includes
commit
|
commitdiff
|
tree
2017-11-03
Mark Abraham
Mer
g
e
"
M
er
g
e branch
r
eleas
e
-201
6
"
commit
|
commitdiff
|
tree
2017-11-02
Mar
k
Abraham
Me
r
ge branch relea
s
e
-20
1
6
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Fi
x
thread-
M
PI rank
ch
o
ice for or
i
entation res
t
raints
commit
|
commitdiff
|
tree
2017-11-01
Mark
Abrah
a
m
Impr
o
ve handlin
g
of GPU IDs
commit
|
commitdiff
|
tree
2017-10-31
Mar
k
Abrah
a
m
Updat
e
treatment of GPU compatibility data struc
t
ur
e
commit
|
commitdiff
|
tree
2017-10-30
Mark Abraham
Fix and
up
d
a
t
e hw_
i
nf
o
commit
|
commitdiff
|
tree
2017-10-27
Mark Abraham
Fix hw d
e
tection more
commit
|
commitdiff
|
tree
2017-10-26
Mark Abra
h
a
m
Make rele
a
se
matrix
wor
k
ag
a
in
commit
|
commitdiff
|
tree
2017-10-26
Mark Abra
h
am
New quote
commit
|
commitdiff
|
tree
2017-10-25
Mark Abr
a
h
a
m
Tea
c
h the c
o
p
yright checker about temp
l
a
te
.
cpp
commit
|
commitdiff
|
tree
2017-10-20
M
a
r
k
A
b
raham
Clarify docs for Fmax in EM
commit
|
commitdiff
|
tree
2017-10-20
M
a
rk Abraham
Mer
g
e branch release-20
1
6
commit
|
commitdiff
|
tree
2017-10-16
Mark Abraham
Merge branch release-2016
commit
|
commitdiff
|
tree
2017-10-13
Mark Abr
a
ham
Update t
e
s
t
s for
C
++11 com
p
iler and stan
d
ard library
commit
|
commitdiff
|
tree
2017-10-13
Ma
r
k Abraham
F
ix cpuinfo on clang
+
non-x
8
6
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
I
ntroduced header for c
o
mm
u
n
i
c
ation
t
o
/from
PME ranks
commit
|
commitdiff
|
tree
2017-10-11
Mark Abrah
a
m
Cleaned
u
p ewaldcoeff
f
or P
M
E-only ranks
commit
|
commitdiff
|
tree
2017-10-11
M
a
rk Abraham
Use clang-5 in Jenk
i
n
s
commit
|
commitdiff
|
tree
2017-10-07
Mar
k
A
b
rah
a
m
Tell cppche
c
k that
.
cpp a
n
d
.
cu file
s
are
c++
commit
|
commitdiff
|
tree
2017-10-05
M
ark A
b
raham
Continue removing -n
b
gpu_cpu
commit
|
commitdiff
|
tree
2017-10-04
Ma
r
k Abraha
m
E
n
able gr
o
up-scheme SIM
D
with
GMX_SIMD=AVX2_128
commit
|
commitdiff
|
tree
2017-10-03
Mark Abraham
Introdu
c
e
a
nd use AlignedAl
l
o
c
ationPolicy
commit
|
commitdiff
|
tree
2017-09-19
M
a
rk A
b
raham
Update test
i
n
g
matrices
to test
w
i
t
h (lates
t
) icc-18
commit
|
commitdiff
|
tree
2017-09-17
Mark Abr
a
ham
M
erge branc
h
rel
e
as
e
-2
0
16
commit
|
commitdiff
|
tree
2017-09-15
Mark
Abraha
m
Exp
r
ess int
e
nt of matrix releas
e
build t
y
p
e
s
expl
i
citly
commit
|
commitdiff
|
tree
2017-09-15
Mark Ab
r
aham
Bumped patch versi
o
n
f
or n
e
xt rele
a
s
e
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
V
e
rsion 201
6
.
4
commit
|
commitdiff
|
tree
2017-09-14
M
ark Abraha
m
For
m
taskassig
n
ment mod
u
le
commit
|
commitdiff
|
tree
2017-09-14
Mark
A
brah
a
m
Fix
c
ompat module
d
e
finition
commit
|
commitdiff
|
tree
2017-09-12
Mark Abraham
M
e
rge br
a
nch release-2016
commit
|
commitdiff
|
tree
2017-09-07
Mark A
b
raham
In
t
roduce type-safe
G
PU emulation variables
commit
|
commitdiff
|
tree
2017-09-07
Mark
A
braham
Enable
group-scheme SIMD ker
n
els on recent AVX ex
t
ensions
commit
|
commitdiff
|
tree
2017-09-06
Mark Abraha
m
Pre
p
are Verlet scheme lat
e
r i
n
runner
commit
|
commitdiff
|
tree
2017-09-05
Ma
r
k Abraham
Fixes for Solaris
commit
|
commitdiff
|
tree
2017-09-05
Mark Abraham
Fix use of GPU
i
n
formation for thread-MPI s
e
t
u
p
commit
|
commitdiff
|
tree
2017-09-03
M
a
r
k
Abraham
F
i
x compiler flags for usi
n
g MKL
commit
|
commitdiff
|
tree
2017-09-03
Mark Abra
h
am
Merge bran
c
h
release-5-1 in
t
o rel
e
ase-20
1
6
commit
|
commitdiff
|
tree
2017-08-25
Mark Abraha
m
Fix
flat-bottomed position r
e
straints with multiple
.
.
.
commit
|
commitdiff
|
tree
2017-08-23
Mar
k
Abraham
St
o
pped checkpoin
t
influencing parallelism
setup
commit
|
commitdiff
|
tree
2017-08-22
Mark Abraham
Run GPU detection
e
v
e
n for mdr
u
n -nb
c
pu
commit
|
commitdiff
|
tree
2017-08-22
M
ark Abraha
m
Fixed
t
hread-MPI wi
t
h non-default -np
m
e
commit
|
commitdiff
|
tree
2017-08-22
Mark Abraham
Fix miss
i
ng declaration of GMX_UNUSED_VALUE
commit
|
commitdiff
|
tree
2017-08-22
Mark Abraham
Merge branch release-2016
commit
|
commitdiff
|
tree
2017-08-21
M
ar
k
Abraham
Moved increase_nst
l
ist(
)
to nbnxn_tu
n
i
n
g
.
h
commit
|
commitdiff
|
tree
2017-08-21
Mark Abraham
Fix compi
l
ation i
s
sues w
i
th ARM SIMD
commit
|
commitdiff
|
tree
2017-08-17
M
ark Abrah
a
m
R
e
place consist
e
ncy checking wi
t
h asser
t
ion
commit
|
commitdiff
|
tree
2017-08-16
M
a
r
k
Abraham
Pars
e
us
e
r-supp
l
ied GPU task assignment only wh
e
n needed
commit
|
commitdiff
|
tree
2017-08-16
Mark Abrah
a
m
Remove dupli
c
ate GPU non-u
s
age
hint
commit
|
commitdiff
|
tree
2017-08-16
Mar
k
Abr
a
ha
m
Moved logging f
u
nctionalit
y
into GPU usage r
e
port
commit
|
commitdiff
|
tree
2017-08-15
Mark Abraham
Merge bran
c
h release
-
5-1
into
r
eleas
e
-2016
commit
|
commitdiff
|
tree
2017-08-15
Mark Abraham
F
ix
valu
e
of Ewald
shi
f
t
commit
|
commitdiff
|
tree
2017-08-10
M
a
rk Abra
h
am
Clarify data fl
o
w in
G
P
U
task
a
s
sign
m
ent
commit
|
commitdiff
|
tree
2017-08-07
Ma
r
k Abr
a
h
am
Fi
x
include dependency for getenv
commit
|
commitdiff
|
tree
2017-08-07
Mark Abraham
Simpl
i
f
i
ed ha
n
dling of GPU device IDs
commit
|
commitdiff
|
tree
2017-08-06
Mark Ab
r
aham
Si
m
plify resource
-
divisio
n
e
ffi
c
ienc
y
check
commit
|
commitdiff
|
tree
2017-08-06
Ma
r
k
Abraham
Spl
i
t printhardware
from detecth
a
rdwar
e
commit
|
commitdiff
|
tree
2017-08-06
M
ark Abra
h
a
m
D
e
couple task assignment
from task execu
t
ion
commit
|
commitdiff
|
tree
2017-08-06
M
ark Abr
a
h
a
m
Removed
u
nused host-side allocation
c
ode
commit
|
commitdiff
|
tree
2017-08-04
Mark
Abraham
Stop
using
h
winfo_g for rep
o
rting
c
ode
commit
|
commitdiff
|
tree
2017-08-03
Mark Abraham
Removed unused inc
l
ude statements
commit
|
commitdiff
|
tree
2017-08-01
Mark A
b
ra
h
am
Introduced Mdrunner hi
g
h-level class
commit
|
commitdiff
|
tree
2017-07-27
Mark Abraham
Enhan
c
e cmake a
n
d releng handlin
g
o
f
GMX_USE_RDTSCP
commit
|
commitdiff
|
tree
2017-07-24
Mark Abraham
S
e
pa
r
a
t
ed re
s
ponsibility for consistency checkin
g
commit
|
commitdiff
|
tree
2017-07-24
M
a
rk Abraham
R
e
move unnecessary GP
U
c
h
e
ckin
g
code
commit
|
commitdiff
|
tree
2017-07-20
Mark Abraha
m
Clea
n
ed up bUseGpu in runner
commit
|
commitdiff
|
tree
2017-07-20
M
a
rk Abr
a
h
a
m
Stop duplicate printing
of
detected GPUs
commit
|
commitdiff
|
tree
2017-07-20
Mark Abraha
m
Fix
us
e
of GMX_SIMD in own-fftw
b
u
i
ld
commit
|
commitdiff
|
tree
2017-07-19
Mark Abraham
Made
post-su
b
mit c
o
n
f
i
g
to test clang+openmp
.
commit
|
commitdiff
|
tree
2017-07-19
Mark Abr
a
ham
Improve CMake implementat
i
on for
G
MX_SIMD
commit
|
commitdiff
|
tree
2017-07-18
Mark Ab
r
aham
Conv
e
r
ted
s
o
m
e cons
t
poin
t
ers in
t
o c
o
nst
r
efe
r
ences
.
.
.
commit
|
commitdiff
|
tree
2017-07-18
Mark Abrah
a
m
E
limi
n
ated pick_nbnxn_res
o
u
rces
commit
|
commitdiff
|
tree
2017-07-14
Ma
r
k
Abraha
m
Implemented grompp
-
po for opti
o
n
s-s
t
yle mdp handling
commit
|
commitdiff
|
tree
2017-07-14
Mark
Abraham
Cl
e
an up
cm
a
ke build h
o
st detection
commit
|
commitdiff
|
tree
2017-07-13
Ma
r
k A
b
raham
Clean up gmx_mdrun()
commit
|
commitdiff
|
tree
2017-07-13
M
a
rk
A
brah
a
m
Cleaned up md
r
unner
_
start_threads
commit
|
commitdiff
|
tree
2017-07-13
Mark Abraha
m
More u
p
dates to te
s
tin
g
matrix
commit
|
commitdiff
|
tree
2017-07-07
Mark Abraham
R
efactor e
r
ror handlin
g
i
n
init_gpu
commit
|
commitdiff
|
tree
2017-07-06
Mark Abraham
Simplify gm
x
_gpu_op
t
_t
commit
|
commitdiff
|
tree
2017-07-04
M
a
rk
A
braham
Clean up pick_nbnxn_re
s
ources
commit
|
commitdiff
|
tree
2017-07-01
Mar
k
A
b
ra
h
am
Cleaned up G
P
U emulation logic
commit
|
commitdiff
|
tree
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