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Fix CG with multiple domains
2018-07-30
Mark
Abraham
Fix CG wit
h
multiple doma
i
ns
commit
|
commitdiff
|
tree
2018-07-30
P
aul Bauer
Fix
bf
a
c
tor out
p
ut
commit
|
commitdiff
|
tree
2018-07-29
Szilárd Páll
Correc
t
ions to
t
he user guide mdr
u
n p
e
rf
s
ec
t
ion
commit
|
commitdiff
|
tree
2018-07-18
M
ark
A
braham
Fix pr
e
-s
u
b
m
it
matrix
commit
|
commitdiff
|
tree
2018-06-14
Mark Ab
r
aham
U
p
dated to prepar
e
for
2
018
.
3 rel
e
ase
commit
|
commitdiff
|
tree
2018-06-14
Mark Abraham
Version 2018
.
2
commit
|
commitdiff
|
tree
2018-06-13
Mark Ab
r
aham
Fix p
r
emature
r
eporting of act
i
on when GPUs are not
.
.
.
commit
|
commitdiff
|
tree
2018-06-13
Mark A
b
rah
a
m
U
p
d
a
t
e
top-le
v
e
l README
commit
|
commitdiff
|
tree
2018-06-13
Mar
k
Abraham
Fixed documentation typo
commit
|
commitdiff
|
tree
2018-06-12
Ber
k
Hess
A
dd
A
WH con
t
inuation
c
onsistency
checking
commit
|
commitdiff
|
tree
2018-06-12
Mark Ab
r
aham
More
fixe
s
to
s
uit gcc 8 for double b
u
ild
commit
|
commitdiff
|
tree
2018-06-12
Szil
á
rd Páll
Also issue
O
MP_NUM_THREAD
S
reading note
t
o the lo
g
commit
|
commitdiff
|
tree
2018-06-12
Viveca
L
ind
a
hl
C
h
a
ng
e
d histogram check interva
l
for multidimension
a
l
.
.
.
commit
|
commitdiff
|
tree
2018-06-12
Ber
k
Hess
Add fatal e
r
ror fo
r
i
nconsistent g
r
aph
commit
|
commitdiff
|
tree
2018-06-12
Berk
H
ess
A
v
oid COM remo
v
al m
o
ving fro
z
en atoms
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
Remov
e
co
n
straint v correction for
f
roz
e
n atoms
commit
|
commitdiff
|
tree
2018-06-06
Berk Hess
Fix MPI inconsis
t
enc
y
in EM a
f
ter c
o
ns
t
raint failure
commit
|
commitdiff
|
tree
2018-05-22
Aleksei Iupinov
Remove unused results of cudaStre
a
mQuery(
)
commit
|
commitdiff
|
tree
2018-04-10
Alekse
i
Iu
p
inov
Prevent OpenCL tim
i
ng memory leak
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Remove leftover mention of twin-ran
g
e
scheme
commit
|
commitdiff
|
tree
2018-03-27
Mark
A
b
r
aham
Cl
a
ri
f
i
e
d mdp
op
t
ions r
e
lating to bonds
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
More
g
c
c
-8
f
ixes for POWER
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
V
er
s
ion
2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
M
ark Abraha
m
Merge "Merge bra
n
ch
r
elease-201
6
int
o
rel
e
ase-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
M
a
rk Abraha
m
Update release notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark A
b
raham
Merge branch release-
2
016 into release-2018
commit
|
commitdiff
|
tree
2018-03-20
M
a
rk Abraham
Update use
of gpu_id
in Je
n
kins
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disal
l
ow
sin
g
le simu
l
ation with mu
l
tis
i
m
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Upd
a
te use
of gpu_id in J
e
nkins
commit
|
commitdiff
|
tree
2018-03-19
Mark Abraham
Fix V
S
X S
I
MD
w
ith gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Ber
k
He
s
s
Cor
r
ect PMF sign error in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve inte
r
-
s
imula
t
ion signaling
commit
|
commitdiff
|
tree
2018-03-14
Berk He
s
s
Fix mdrun signalling with AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-13
Ber
k
Hess
Add A
W
H fixes to release note
s
commit
|
commitdiff
|
tree
2018-03-13
Berk He
s
s
Fix AWH ensemble c
h
eckpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk H
e
ss
Fi
x
AWH deconvolution when sharing a bias
commit
|
commitdiff
|
tree
2018-03-13
Szilárd Páll
Fix clang 6
.
0 with CU
D
A 9
.
0
commit
|
commitdiff
|
tree
2018-03-09
B
e
rk
H
ess
Correct
pd
b
2gmx -missing
o
p
t
i
on
commit
|
commitdiff
|
tree
2018-03-06
Mark Abr
a
h
a
m
Fixe
d
d
v
dl
a
mbd
a
for SHAKE + FE
commit
|
commitdiff
|
tree
2018-03-05
Szilárd
P
áll
A
d
d
to the contributor sectio
n
commit
|
commitdiff
|
tree
2018-03-01
Be
r
k Hess
Detect
AMD SMT topology
commit
|
commitdiff
|
tree
2018-02-27
Mar
k
Abraham
Fix GPU utils tes
t
commit
|
commitdiff
|
tree
2018-02-26
Mark Abraham
Permit define
.
md
p
f
ield to assign
values
commit
|
commitdiff
|
tree
2018-02-26
M
ark Abra
h
a
m
Organize
for
r
e
cording 2016-era rele
a
se notes an
d
add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
B
e
rk Hess
Fix md integrator with
N
ose-Hoover
c
oup
l
i
ng
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
Merge branc
h
re
l
ease-
2
016 into rele
a
se
-
2018
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
Bump
e
d p
a
tch version fo
r
ne
x
t release
commit
|
commitdiff
|
tree
2018-02-16
Berk
H
ess
Correc
t
multisim
MPI barrier
commit
|
commitdiff
|
tree
2018-02-16
M
a
rk Abraha
m
Version
2016
.
5
commit
|
commitdiff
|
tree
2018-02-14
Mar
k
Abr
a
ham
Merge bra
n
ch re
l
ease-2016 into
r
elease-2018
commit
|
commitdiff
|
tree
2018-02-14
Berk
Hess
Fix ran
g
e
bug in
a
dd_sel
e
cti
o
n_groups in tngio
.
c
p
p
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix g
r
o
mpp net
ch
a
r
ge c
h
e
c
k
commit
|
commitdiff
|
tree
2018-02-14
Berk
Hess
Fix gr
o
m
p
p
net cha
r
g
e c
h
eck
commit
|
commitdiff
|
tree
2018-02-14
Ma
r
k Abr
a
ham
Prepare release notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-02-13
Mark Abra
h
am
Use
d
eath tes
t
only when
s
u
pport
e
d
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Merge "
M
erge branch release-2
0
16 into
rel
e
ase-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
M
a
rk Abraham
Merge bra
n
ch relea
s
e
-2
0
16 into r
e
lease-20
1
8
commit
|
commitdiff
|
tree
2018-02-06
Mark Abraham
Prevent log
f
i
l
e energy average printing dividin
g
b
y
.
.
.
commit
|
commitdiff
|
tree
2018-01-24
Mark Abraham
Move Windows icc config to po
s
t-subm
i
t testing
commit
|
commitdiff
|
tree
2018-01-18
Ber
k
He
s
s
Fix COMM rem
o
val on part
of the sy
s
tem
commit
|
commitdiff
|
tree
2018-01-17
Ale
k
sei Iupin
o
v
Fix box scaling in PME m
i
xed mode
commit
|
commitdiff
|
tree
2018-01-17
Ber
k
H
ess
Re-enab
l
e G
P
U with walls an
d
1 en
e
rgy group
commit
|
commitdiff
|
tree
2018-01-16
Berk Hes
s
Avoid
mdrun echoing "No option -multi"
commit
|
commitdiff
|
tree
2018-01-11
Mark
A
braham
B
u
mped version f
o
r next patc
h
r
elease
commit
|
commitdiff
|
tree
2018-01-11
Mark Abraham
Version 2018
commit
|
commitdiff
|
tree
2018-01-11
Ma
r
k Abr
a
ham
Announc
e
i
n user log
files th
a
t feat
u
res ar
e
deprecated
.
commit
|
commitdiff
|
tree
2018-01-11
R
o
la
n
d Schul
z
Fix GM
X
_ENABL
E
_AVX512_
T
ESTS being internal
commit
|
commitdiff
|
tree
2018-01-10
Mark Abrah
a
m
Fix
au
t
omated G
P
U I
D
assig
n
me
n
t
commit
|
commitdiff
|
tree
2018-01-10
Szilárd
Pál
l
User guide updates to GPU section
commit
|
commitdiff
|
tree
2018-01-10
Szilárd
Páll
Release not
e
s t
w
eaks
commit
|
commitdiff
|
tree
2018-01-10
M
a
r
k
Abraha
m
Add re
l
ease notes to source repo
commit
|
commitdiff
|
tree
2018-01-10
Erik Lindahl
Improve pdb2gmx f
o
r
n
o
nsta
n
dard residue types
commit
|
commitdiff
|
tree
2018-01-10
Szilárd Páll
Insta
l
l g
u
ide updates
commit
|
commitdiff
|
tree
2018-01-10
Szilárd Pá
l
l
E
nvi
r
on
m
ent va
r
iable
d
ocs ma
i
nt
e
nance
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupinov
Do no
t
p
r
int
P
ME coun
t
er
break
d
own
i
f it
'
s
e
mpty
commit
|
commitdiff
|
tree
2018-01-10
Mar
k
Abraham
Handle
e
rroneous
c
ommand l
i
ne args better
commit
|
commitdiff
|
tree
2018-01-10
Erik Lin
d
ahl
Clarified
gmx rmsf docume
n
tat
i
o
n
commit
|
commitdiff
|
tree
2018-01-09
Mark
Abr
a
ham
Clean up
u
ser guide for release
commit
|
commitdiff
|
tree
2018-01-09
Ma
r
k A
b
raham
Mer
g
e
branch
rele
a
se-2
0
1
6 int
o
release-2018
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do
not turn on DLB at r
e
p
l
i
ca exchange
commit
|
commitdiff
|
tree
2018-01-04
Erik Lindahl
Implement ch
a
n
ges for CMake policy 0068
commit
|
commitdiff
|
tree
2018-01-04
M
a
r
k Abraham
Add test confi
g
of GPU bu
i
l
d
on slav
e
w
ithout
GPU
commit
|
commitdiff
|
tree
2018-01-04
P
aul Bauer
Fix gmx
msd when using C
O
M removal and
molecules
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindahl
Fix index error in gmx chi
commit
|
commitdiff
|
tree
2018-01-03
Paul Bauer
Correct dih
e
dral
restr
a
int s
e
ction in
Manual
commit
|
commitdiff
|
tree
2018-01-03
E
r
ik Linda
h
l
Avoid FTZ triggering simd test failur
e
s
commit
|
commitdiff
|
tree
2018-01-02
E
r
ik Lindahl
F
i
x OpenCL compil
e
s
on Mac OS
commit
|
commitdiff
|
tree
2018-01-02
Erik Lindahl
I
m
prove ma
n
ua
l
from
c
om
m
ents b
y
G
an
g
Liu
commit
|
commitdiff
|
tree
2018-01-02
Erik Lind
a
hl
Mak
e
it ex
p
lici
t
t
h
at
t
ime units a
p
ply to
b
egin/end
.
.
.
commit
|
commitdiff
|
tree
2018-01-02
Erik Lindahl
D
o
n'
t
r
e
qui
r
e match
i
ng name
s
betwe
e
n rtp and t
d
b
f
i
les
commit
|
commitdiff
|
tree
2018-01-02
Er
i
k
Lindahl
Don't write reference
pull
group 0 to
log
commit
|
commitdiff
|
tree
2017-12-30
Mar
k
Abr
a
h
a
m
First release candidate
f
or
vers
i
on 2018
commit
|
commitdiff
|
tree
2017-12-26
E
ri
k
Lindah
l
Fix bui
l
ds o
n
ARM & clarify
(
ARM) GPU
s
up
p
ort
commit
|
commitdiff
|
tree
2017-12-22
Mark
Abraham
Merge branch release-2016
i
nto release-2018
commit
|
commitdiff
|
tree
2017-12-21
Mark Abraham
M
e
r
ge
b
ranch r
e
lease-5-1 into
r
e
lease-2016
commit
|
commitdiff
|
tree
2017-12-21
M
a
rk Ab
r
aham
Bu
m
p m
i
n
o
r version for theoretical new release
commit
|
commitdiff
|
tree
2017-12-21
Pascal M
e
rz
D
ocumentation and fixes
f
or physical validation
commit
|
commitdiff
|
tree
2017-12-21
Mark Abraham
U
pdate
double-
p
rec
i
s
i
on test configurations
commit
|
commitdiff
|
tree
2017-12-21
Ro
l
and
S
chulz
U
pd
a
te
c
hecks for BuildOwnFFT
commit
|
commitdiff
|
tree
2017-12-20
Mark Abraham
U
s
e n
e
w defaultRe
a
lTole
r
ance() to stabilise
some tests
commit
|
commitdiff
|
tree
next