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Merge branch release-2018
2018-03-28
M
ark
A
b
r
aham
Merge
bran
c
h release-2018
commit
|
commitdiff
|
tree
2018-03-27
Mark
A
braham
More gcc-8 fixes for POW
E
R
commit
|
commitdiff
|
tree
2018-03-21
Davi
d
van
d
er S
p
oel
Renam
e
d
ent
r
opy
.
* t
o
th
e
rmochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Ma
r
k
A
b
ra
h
am
Ve
r
sion 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
M
ark Abraham
Me
r
ge "Merg
e
branch relea
s
e-2016 i
n
to
release
-
2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Update rele
a
se notes for 20
1
8
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark A
b
raham
Merge branch release-2016 into
releas
e
-
2018
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
braha
m
Upd
a
te us
e
of gpu_i
d
in
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
B
e
rk Hess
Disallow singl
e
s
i
m
ulation with
multisi
m
commit
|
commitdiff
|
tree
2018-03-20
M
ark
Abrah
a
m
Upda
t
e us
e
of
g
pu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update use
of
g
pu_id in
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abraham
A
d
d helper fu
n
ction to ma
k
e a vector from an ArrayRef
commit
|
commitdiff
|
tree
2018-03-19
M
a
rk Abrah
a
m
Fix VSX SIMD with gcc
8
commit
|
commitdiff
|
tree
2018-03-16
Pau
l
Ba
u
er
Only free topology w
h
en allocated
commit
|
commitdiff
|
tree
2018-03-16
Berk He
s
s
C
orrect PMF sign erro
r
i
n AWH bias sharin
g
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Impr
o
ve inte
r
-simulation
s
ignaling
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
Make a persist
e
nt physical no
d
e communicato
r
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix md
r
un
s
ignall
i
ng with A
W
H
bias sh
a
ring
commit
|
commitdiff
|
tree
2018-03-13
Berk
H
e
s
s
A
d
d AWH f
i
xes to release not
e
s
commit
|
commitdiff
|
tree
2018-03-13
Szilárd Páll
Require O
p
enCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
B
erk Hes
s
Fix
A
WH ensemble
check
p
ointing
commit
|
commitdiff
|
tree
2018-03-13
Berk H
e
ss
F
i
x AWH deconvolution when sharing a bias
commit
|
commitdiff
|
tree
2018-03-13
Mar
k
A
b
raham
I
n
troduce
c
onst
r
ain_shak
e
commit
|
commitdiff
|
tree
2018-03-13
Szilárd Páll
Fix clang
6
.
0 with CUDA 9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Mark Abra
h
am
Merge "Merge bra
n
ch rel
e
ase-
2
0
18"
commit
|
commitdiff
|
tree
2018-03-09
Berk H
e
ss
C
orrect pd
b
2gmx -missing option
commit
|
commitdiff
|
tree
2018-03-06
Berk He
s
s
C
o
nve
r
t t_file
n
m to
C++
commit
|
commitdiff
|
tree
2018-03-06
Mark A
b
raham
M
e
rge b
r
anch rel
e
ase-2018
commit
|
commitdiff
|
tree
2018-03-06
Mark
A
b
raha
m
Fixe
d
d
vdlamb
d
a for
SH
A
K
E + FE
commit
|
commitdiff
|
tree
2018-03-05
Szilárd
P
áll
Add
to the co
n
t
r
ibutor section
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Detect AMD SMT t
o
pology
commit
|
commitdiff
|
tree
2018-02-28
M
ark
A
braham
Mo
v
ed and r
e
moved constr
a
int c
o
de
commit
|
commitdiff
|
tree
2018-02-28
Mark Abraha
m
Reorganize
d
cons
t
raint co
d
e
commit
|
commitdiff
|
tree
2018-02-27
Mark
Abraham
Fix GPU u
t
i
ls test
commit
|
commitdiff
|
tree
2018-02-26
Paul Bauer
Change T
N
G file
opening
commit
|
commitdiff
|
tree
2018-02-26
Mark Abraham
Permit define
.
mdp fiel
d
to
a
ssi
g
n
values
commit
|
commitdiff
|
tree
2018-02-26
Aleksei Iup
i
n
ov
Advic
e
u
s
ers o
n
infinite outp
u
t of
T
PI
commit
|
commitdiff
|
tree
2018-02-26
Mark Abrah
a
m
O
r
gan
i
ze for r
e
cor
d
ing 2016-er
a
release no
t
es
and ad
d
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Berk
Hess
Fix m
d
i
n
tegrator
w
ith Nose-
H
oover cou
p
ling
commit
|
commitdiff
|
tree
2018-02-21
Mark Abra
h
am
Enhanced docs of pi
m
pl pointer helper
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
Merge bra
n
ch rele
a
se
-
2
0
16 into release-
2
018
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
Bu
m
ped p
a
tch
v
ersi
o
n
for next
r
elease
commit
|
commitdiff
|
tree
2018-02-16
Berk
Hess
Correct mul
t
isim
MPI barrier
commit
|
commitdiff
|
tree
2018-02-16
Ma
r
k Abr
a
ham
Merge bra
n
ch relea
s
e-20
1
8
into master
commit
|
commitdiff
|
tree
2018-02-16
M
a
rk Abraham
Version
2
016
.
5
commit
|
commitdiff
|
tree
2018-02-15
Mark
Abraham
Use st
r
uct
for check
p
oi
n
t h
e
ader
c
ontents
commit
|
commitdiff
|
tree
2018-02-15
Aleksei
I
u
p
inov
Update
FFTW
b
uild to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-14
Mar
k
Abraham
Remove
r
e
a
d_checkpoint_s
t
a
t
e
commit
|
commitdiff
|
tree
2018-02-14
Berk
Hess
Remove support for tpx version before 58/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
M
a
rk Abraham
U
s
e std::vector f
o
r checkpoint outputfile
s
commit
|
commitdiff
|
tree
2018-02-14
M
a
rk Abra
h
am
M
e
rg
e
b
r
anc
h
re
l
e
ase-2016 into release-20
1
8
commit
|
commitdiff
|
tree
2018-02-14
B
e
rk Hess
F
i
x rang
e
bug in add_selec
t
ion_gro
u
ps in tn
g
io
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Repla
c
e the
remai
n
ing EXP
E
C
T_DEATH w
i
th EXPECT_DEATH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Add DeviceBuf
f
er as a
t
yped
e
f
f
or
c
l_mem/
d
evice pont
e
r
commit
|
commitdiff
|
tree
2018-02-14
Szilárd Pá
l
l
Remove
b
arriers pr
e
v
e
nt
i
ng texture
re
f
erence r
a
ces
commit
|
commitdiff
|
tree
2018-02-14
Be
r
k H
e
ss
F
i
x grompp net
c
h
arge che
c
k
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix gromp
p
net charg
e
check
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Prepa
r
e
releas
e
notes for 2
0
18
.
1
commit
|
commitdiff
|
tree
2018-02-13
Mark
A
b
raham
Use death test o
n
l
y
when su
p
ported
commit
|
commitdiff
|
tree
2018-02-13
Mark Abr
a
ham
Separate mul
t
isim from commrec
commit
|
commitdiff
|
tree
2018-02-12
Mark Abraham
Analyse th
r
ea
d
s on node before set
t
i
ng affinities
commit
|
commitdiff
|
tree
2018-02-12
Mark Abraham
Fix reading old
f
orce f
i
eld fil
e
s
commit
|
commitdiff
|
tree
2018-02-09
M
a
rk Abraham
Merge bra
n
ch release-2018
commit
|
commitdiff
|
tree
2018-02-08
M
a
r
k
Abrah
a
m
Mer
g
e "Merge
b
r
a
n
c
h rele
a
se-20
1
6 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Merge branch release-2
0
16 in
t
o re
l
ease
-
20
1
8
commit
|
commitdiff
|
tree
2018-02-08
Alekse
i
Iupinov
Enab
l
e
debug
F
P exc
e
p
tions withou
t
TPI
,
no
t
with TP
I
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
M
e
rge "Merge branch 'release
-
2
0
18'
i
nto master"
commit
|
commitdiff
|
tree
2018-02-06
Mark A
b
rah
a
m
P
r
e
v
e
nt log file
e
n
ergy a
v
erag
e
pr
i
nting
d
i
v
iding by
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Al
e
ksei Iupinov
Do
n
't print impossible CUDA version
num
b
e
rs in ab
s
ence
.
.
.
commit
|
commitdiff
|
tree
2018-02-01
Pau
l
Bauer
Ad
d
information for n2t fi
l
e form
a
t
commit
|
commitdiff
|
tree
2018-01-27
Mark Abrah
a
m
Remove unused
declaration
commit
|
commitdiff
|
tree
2018-01-25
M
ark Abraham
R
emove unused fie
l
d
s
o
f
t_commrec
commit
|
commitdiff
|
tree
2018-01-25
M
a
rk Abraham
R
e
duced
i
nclude
s
of com
m
on
h
eaders in headers
commit
|
commitdiff
|
tree
2018-01-25
Mark Abraham
R
emo
v
ed md
r
un -multi
commit
|
commitdiff
|
tree
2018-01-24
Mar
k
Abra
h
am
Change mu
l
ti-sim tests
t
o
use -multidir
commit
|
commitdiff
|
tree
2018-01-24
Mark Ab
r
ah
a
m
Remove gmx_i
n
line
commit
|
commitdiff
|
tree
2018-01-24
Mark Abraham
Teach incl
u
de sorter to
ignore c
m
a
k
e-te
s
t files
commit
|
commitdiff
|
tree
2018-01-24
M
a
rk
Abraham
M
ove Windows icc
c
onfig to post-sub
m
it
t
esting
commit
|
commitdiff
|
tree
2018-01-24
Mark
Abraham
Replace gmx_bool wi
t
h
boo
l
in bitma
s
k f
u
n
ctions
commit
|
commitdiff
|
tree
2018-01-23
M
ark
Ab
r
aham
R
emove support for
i
mplicit solvati
o
n
commit
|
commitdiff
|
tree
2018-01-23
Mark Ab
r
aham
R
e
move topology support
f
o
r
implici
t
solva
t
ion
commit
|
commitdiff
|
tree
2018-01-23
A
leksei Iupinov
Test
P
ME C
P
U/GPU
wi
t
h walls and box scaling
commit
|
commitdiff
|
tree
2018-01-23
Al
e
k
s
ei
I
upinov
W
r
ap the PME testing loop in a me
t
hod for extensibili
t
y
commit
|
commitdiff
|
tree
2018-01-23
Mark Abraham
Preliminary cleanup befo
r
e rem
o
ving ifd
e
f cplusplu
s
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
A
dd
a
death
test for
the
d
uplic
a
t
e
in
p
utrec ke
y
s checking
commit
|
commitdiff
|
tree
2018-01-19
Mark
A
braha
m
Merge "Mer
g
e br
a
n
ch
'
r
el
e
as
e
-2018
'
into
mas
t
er"
commit
|
commitdiff
|
tree
2018-01-19
A
l
eksei Iupinov
Rename
c
las
s
B
i
asR
e
ad
e
r to struct BiasOu
t
putSetup
commit
|
commitdiff
|
tree
2018-01-19
Ma
r
k
Abrah
a
m
Add dev-guide docs for au
t
omatic
u
pdate of regressiontests
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupinov
Make the reference d
a
ta
vari
a
bles local in GetIrTest
commit
|
commitdiff
|
tree
2018-01-19
Mark Ab
r
a
ham
F
i
x
es for issues found b
y
clang 6
commit
|
commitdiff
|
tree
2018-01-18
Mark Abraham
Rem
o
ve support for
BlueGe
n
e
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fi
x
COMM removal
o
n p
a
r
t of the system
commit
|
commitdiff
|
tree
2018-01-18
P
a
ul
B
auer
Add
c
ontribution information to
w
ebpage
commit
|
commitdiff
|
tree
2018-01-17
Aleksei
Iu
p
i
n
ov
Fix
b
o
x
scal
i
ng i
n
PME mixed
m
ode
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
Re-
e
nable GPU
w
it
h
walls
and 1
energ
y
g
r
o
up
commit
|
commitdiff
|
tree
2018-01-16
Mark Abr
a
ham
Merge "M
e
rge re
l
ease-2018 into master"
commit
|
commitdiff
|
tree
2018-01-16
Roland Schulz
Merge
release-2018 into ma
s
ter
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Avoid
m
drun echoi
n
g
"
No option -m
u
lti"
commit
|
commitdiff
|
tree
2018-01-11
Mark Abraham
Bu
m
ped version fo
r
n
e
xt p
a
tch
r
el
e
a
se
commit
|
commitdiff
|
tree
2018-01-11
Mark Abraham
V
e
rsion 20
1
8
commit
|
commitdiff
|
tree
next