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GROMACS 2018 first beta release
2017-11-28
Mark Abraham
GROMACS 201
8
first beta release
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
U
p
date d
e
veloper
g
uide
commit
|
commitdiff
|
tree
2017-11-24
Mar
k
Abra
h
am
Act
i
vat
e
PME on GPUs
commit
|
commitdiff
|
tree
2017-11-24
Mark
Abr
a
ham
Separ
a
te management of GPU context
s
from mo
d
ules
commit
|
commitdiff
|
tree
2017-11-24
Mark Abrah
a
m
Add PME integrat
i
on
test
commit
|
commitdiff
|
tree
2017-11-24
Mark A
b
rah
a
m
Extend task ass
i
gnment code
commit
|
commitdiff
|
tree
2017-11-21
Mark
A
braham
Use much less
P
added
R
VecVector
a
nd more Arra
y
Ref
o
f
.
.
.
commit
|
commitdiff
|
tree
2017-11-21
Mark Abraham
Suppor
t
pinnin
g
in HostAl
l
ocator
commit
|
commitdiff
|
tree
2017-11-20
Mark A
b
raham
Fix nightly matrix config
commit
|
commitdiff
|
tree
2017-11-19
Mark Abraham
Fix FindC
U
DA
.
cmake for -W
u
ndef
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
U
s
e HostAlloc
a
t
io
n
P
olicy for
c
har
g
e
A
commit
|
commitdiff
|
tree
2017-11-17
Mar
k
Abraham
A
d
d ch
e
ckin
g
fu
n
c
ti
o
n for whet
h
er a buffer is pinned
commit
|
commitdiff
|
tree
2017-11-17
Mark Abra
h
am
Impr
o
ve
h
andl
i
ng of PME GPU force buffer
commit
|
commitdiff
|
tree
2017-11-10
Mar
k
A
br
a
h
a
m
Import cmake Modul
e
s/F
i
n
d
CUDA
.
cma
k
e
commit
|
commitdiff
|
tree
2017-11-09
Mark Abra
h
am
Prepared t_
m
datoms for usin
g
v
e
ctor
commit
|
commitdiff
|
tree
2017-11-09
Mark
Abraham
Intro
d
uce HostAllocatio
n
Po
l
i
c
y
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Ref
o
r
m
g
m
x
_pme_
p
p allo
c
a
n
d use
vec
t
or
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
In
t
r
oduce
gmxopencl
.
h
commit
|
commitdiff
|
tree
2017-11-07
M
a
rk Abraham
Test c
l
ang
on ARM in n
i
ghtly mat
r
ix
commit
|
commitdiff
|
tree
2017-11-07
Mark A
b
raham
I
mp
r
ove
PME in
c
l
udes
commit
|
commitdiff
|
tree
2017-11-03
Mar
k
A
b
raham
Merge "Merge branc
h
release-2016"
commit
|
commitdiff
|
tree
2017-11-02
Mark Abraham
Merge bran
c
h
rele
a
se-2016
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Fix t
h
read-M
P
I rank
choice for orientation restraints
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
I
m
prove handling of GPU ID
s
commit
|
commitdiff
|
tree
2017-10-31
Mark Abraham
Update treatment
of GP
U
compat
i
b
i
lity d
a
ta struct
u
re
commit
|
commitdiff
|
tree
2017-10-30
Mark Ab
r
a
h
am
Fix a
n
d
u
pdate hw
_
info
commit
|
commitdiff
|
tree
2017-10-27
Mark
A
braham
Fix
hw
de
t
ecti
o
n more
commit
|
commitdiff
|
tree
2017-10-26
Ma
r
k
A
b
ra
h
am
Mak
e
release matrix
w
o
rk ag
a
in
commit
|
commitdiff
|
tree
2017-10-26
Mark Abra
h
am
New quote
commit
|
commitdiff
|
tree
2017-10-25
M
a
rk
A
br
a
ham
Teach the copyrigh
t
checker about templa
t
e
.
cpp
commit
|
commitdiff
|
tree
2017-10-20
M
ark Abraham
Clarify docs for Fmax in EM
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
Merge br
a
nch release
-
2
016
commit
|
commitdiff
|
tree
2017-10-16
Mark Abraham
Merge
b
ranch re
l
ease-2016
commit
|
commitdiff
|
tree
2017-10-13
Mark
A
braha
m
Update
tests for C++11 compiler and
s
ta
n
dard l
i
brary
commit
|
commitdiff
|
tree
2017-10-13
Mark Abraham
Fi
x
cpuinfo on clang
+ non-x86
commit
|
commitdiff
|
tree
2017-10-11
M
a
rk Abraha
m
Introduced
h
ead
e
r
f
or communicat
i
on to/from PME
r
ank
s
commit
|
commitdiff
|
tree
2017-10-11
Mark
A
b
r
ah
a
m
C
l
eaned up ewaldcoeff for PME-only ran
k
s
commit
|
commitdiff
|
tree
2017-10-11
Mar
k
Abraham
Use cl
a
ng-5 in J
e
nkins
commit
|
commitdiff
|
tree
2017-10-07
Mark Abra
h
am
Tel
l
cppchec
k
that
.
c
pp
and
.
cu
files ar
e
c++
commit
|
commitdiff
|
tree
2017-10-05
M
ark Abraham
Continue
r
emov
i
ng -nb gpu_
c
pu
commit
|
commitdiff
|
tree
2017-10-04
Mark Abrah
a
m
Enable grou
p
-scheme
S
IMD w
i
th GMX_S
I
MD=AVX2_128
commit
|
commitdiff
|
tree
2017-10-03
Mark Abraham
Introduce and
u
se Aligne
d
AllocationPolicy
commit
|
commitdiff
|
tree
2017-09-19
Mark
Ab
r
a
ham
Update t
e
sting matrices to t
e
st with
(
latest) icc-18
commit
|
commitdiff
|
tree
2017-09-17
Mark Abraha
m
Merge branch release-2
0
16
commit
|
commitdiff
|
tree
2017-09-15
M
ark Abraham
Express intent of matr
i
x
r
elease build types explicitly
commit
|
commitdiff
|
tree
2017-09-15
Mar
k
Abraham
Bump
e
d patch version f
o
r next release
commit
|
commitdiff
|
tree
2017-09-15
Mark
A
b
r
ah
a
m
Version 2
0
1
6
.
4
commit
|
commitdiff
|
tree
2017-09-14
Mark Abraha
m
Form taskassi
g
nm
e
nt module
commit
|
commitdiff
|
tree
2017-09-14
M
a
rk Abraham
F
i
x
compa
t
module d
e
finit
i
on
commit
|
commitdiff
|
tree
2017-09-12
Mark Abra
h
a
m
Merge branch release-2016
commit
|
commitdiff
|
tree
2017-09-07
Mark Abraham
Introduce
type-saf
e
GPU emu
l
ation variables
commit
|
commitdiff
|
tree
2017-09-07
Mark Abraha
m
Enab
l
e
g
r
oup-scheme SIMD ke
r
n
els on re
c
e
n
t AVX extensions
commit
|
commitdiff
|
tree
2017-09-06
M
ark Abraham
Prepare V
e
r
l
e
t scheme later in runner
commit
|
commitdiff
|
tree
2017-09-05
Mark
Abraham
Fixes for Solaris
commit
|
commitdiff
|
tree
2017-09-05
Mar
k
Abraham
Fix
use of
GPU information for thread-MP
I
setu
p
commit
|
commitdiff
|
tree
2017-09-03
Mark Ab
r
a
h
am
Fi
x
c
o
m
pil
e
r fla
g
s
f
or usin
g
MKL
commit
|
commitdiff
|
tree
2017-09-03
Ma
r
k Abrah
a
m
Mer
g
e branch rel
e
a
se-5-1
i
nto
r
elea
s
e-2016
commit
|
commitdiff
|
tree
2017-08-25
M
ark
A
braha
m
Fi
x
flat
-
bottomed p
o
sition
r
estraints with mu
l
tiple
.
.
.
commit
|
commitdiff
|
tree
2017-08-23
Mark Ab
r
aha
m
Stoppe
d
checkpo
i
n
t
influe
n
cing para
l
le
l
ism se
t
up
commit
|
commitdiff
|
tree
2017-08-22
Mark Abraha
m
Run GP
U
detection even f
o
r md
r
u
n
-nb cpu
commit
|
commitdiff
|
tree
2017-08-22
Mark Abraham
Fixed th
r
e
a
d
-MPI
w
ith non-default
-
npme
commit
|
commitdiff
|
tree
2017-08-22
M
ark
A
braham
Fix mis
s
ing decl
a
ration of G
M
X_UNUSED_VALUE
commit
|
commitdiff
|
tree
2017-08-22
Mark
A
braham
Merge bran
c
h
re
l
ease-2016
commit
|
commitdiff
|
tree
2017-08-21
Mark
A
braham
Moved increase_nstlis
t
() to nbn
x
n_tuning
.
h
commit
|
commitdiff
|
tree
2017-08-21
Mark Abraham
Fix compilation issues wi
t
h A
R
M
SIM
D
commit
|
commitdiff
|
tree
2017-08-17
Mark Abraham
Replace
c
onsisten
c
y chec
k
ing w
i
t
h as
s
e
rtion
commit
|
commitdiff
|
tree
2017-08-16
M
a
rk Abraham
Par
s
e user-su
p
plied GP
U
task assignment onl
y
when needed
commit
|
commitdiff
|
tree
2017-08-16
M
ark
Abr
a
ha
m
Remove duplicate GPU non-usage
h
int
commit
|
commitdiff
|
tree
2017-08-16
M
ark Abr
a
ham
Moved logging
f
unct
i
onality
i
nto
G
P
U usage re
p
or
t
commit
|
commitdiff
|
tree
2017-08-15
M
a
rk Abraham
Merge branch
r
elease-5-1 into rele
a
se-2016
commit
|
commitdiff
|
tree
2017-08-15
Mark A
b
raham
Fix va
l
ue of Ewa
l
d s
h
ift
commit
|
commitdiff
|
tree
2017-08-10
Mark Abr
a
ham
Cla
r
i
f
y d
a
ta flow
i
n
G
P
U ta
s
k
assignment
commit
|
commitdiff
|
tree
2017-08-07
Mark
A
b
raham
Fix include dependency for getenv
commit
|
commitdiff
|
tree
2017-08-07
Mark Abraham
Simplified handling of GPU device ID
s
commit
|
commitdiff
|
tree
2017-08-06
M
a
r
k
Abraham
Simplify resourc
e
-divisi
o
n ef
f
iciency check
commit
|
commitdiff
|
tree
2017-08-06
Mark Abraha
m
Split printhardware from
d
et
e
c
t
h
ardware
commit
|
commitdiff
|
tree
2017-08-06
Mark Abraham
Deco
u
p
l
e task assignment fro
m
t
ask execution
commit
|
commitdiff
|
tree
2017-08-06
M
ark Abraham
Remove
d
unused ho
s
t-
s
ide
a
llocation code
commit
|
commitdiff
|
tree
2017-08-04
M
ark Abra
h
am
Stop using hwinfo_g for
repor
t
ing code
commit
|
commitdiff
|
tree
2017-08-03
Mark Abraham
Removed un
u
se
d
in
c
lude
s
t
atemen
t
s
commit
|
commitdiff
|
tree
2017-08-01
Mark Abraham
Introd
u
c
e
d
M
drun
n
er high-leve
l
class
commit
|
commitdiff
|
tree
2017-07-27
M
ark Abraham
E
n
hance cmake and releng handling of
G
MX_
U
SE_RDTSCP
commit
|
commitdiff
|
tree
2017-07-24
M
a
rk A
b
raham
Separat
e
d responsibility for consisten
c
y
checkin
g
commit
|
commitdiff
|
tree
2017-07-24
Mark A
b
raham
Remove unne
c
essary GPU checking code
commit
|
commitdiff
|
tree
2017-07-20
M
ark Ab
r
aham
Cleaned up
b
Us
e
Gpu in runner
commit
|
commitdiff
|
tree
2017-07-20
Mar
k
Abra
h
a
m
Stop duplicat
e
printing of d
e
tecte
d
GPU
s
commit
|
commitdiff
|
tree
2017-07-20
Mark
A
br
a
ham
Fix
u
se of GMX_SIMD
i
n
own-
f
ftw b
u
il
d
commit
|
commitdiff
|
tree
2017-07-19
M
ark Abraha
m
Made post-su
b
mit
c
onfig
to test clang+openmp
.
commit
|
commitdiff
|
tree
2017-07-19
Mark Abraham
Improve C
M
ak
e
implementa
t
ion for GMX_SIMD
commit
|
commitdiff
|
tree
2017-07-18
Mark Abraham
Converted some
c
onst pointers
i
nto
c
onst referen
c
es
.
.
.
commit
|
commitdiff
|
tree
2017-07-18
Mark Abraha
m
E
liminated pi
c
k
_
nbnxn_resourc
e
s
commit
|
commitdiff
|
tree
2017-07-14
M
a
rk Abraham
Implemented gro
m
pp -po for opti
o
n
s-style mdp ha
n
dling
commit
|
commitdiff
|
tree
2017-07-14
M
a
r
k
Ab
r
aham
C
l
ean u
p
c
m
ake bui
l
d host detection
commit
|
commitdiff
|
tree
2017-07-13
Mark Abraham
Clea
n
up gmx_mdrun()
commit
|
commitdiff
|
tree
2017-07-13
Mark Abr
a
ham
Cleaned up
mdrunner_st
a
rt_threads
commit
|
commitdiff
|
tree
2017-07-13
Mark Ab
r
a
h
am
M
o
re updates t
o
testing matr
i
x
commit
|
commitdiff
|
tree
2017-07-07
M
a
rk Ab
r
aham
Refactor error handling in init_
g
pu
commit
|
commitdiff
|
tree
2017-07-06
Ma
r
k
Abrah
a
m
Simplify gmx_
g
pu_opt_t
commit
|
commitdiff
|
tree
2017-07-04
Mark
A
braham
Clean up
pick_n
b
nxn_
r
esour
c
e
s
commit
|
commitdiff
|
tree
2017-07-01
Mark Abraham
Cleaned up GPU emul
a
t
i
on l
o
g
ic
commit
|
commitdiff
|
tree
next