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Fix legacy topology memory error
2018-04-17
Paul Baue
r
Fix legacy top
o
logy m
e
m
ory error
commit
|
commitdiff
|
tree
2018-04-17
Mark Abraham
Shif
t
pe
r
-step c
o
n
t
rol logic to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark A
b
raham
Break apart upda
t
e_constraints
commit
|
commitdiff
|
tree
2018-04-16
Szilá
r
d
Páll
Add post-
s
ubmi
t
test
w
ith hwloc of
f
commit
|
commitdiff
|
tree
2018-04-16
Berk
H
e
s
s
Move
n
atoms_mo
l
o
ut
o
f
gm
x
_m
o
lblock
_
t
commit
|
commitdiff
|
tree
2018-04-16
Mark Abraham
Updated md
r
u
n comparison i
n
fr
a
structure
commit
|
commitdiff
|
tree
2018-04-13
M
a
rk Ab
r
aham
Clean
u
p cons
t
raints code
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
R
e
m
ove use of where(), if DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abra
h
a
m
Reorganize energy evaluati
o
n for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleks
e
i Iupi
n
ov
Prevent
O
penCL t
i
min
g
memor
y
l
eak
commit
|
commitdiff
|
tree
2018-04-09
Berk Hes
s
Convert gmx_molblock_t to C++
commit
|
commitdiff
|
tree
2018-04-05
Mark
A
braha
m
Simplif
i
ed handlin
g
of sim
u
la
t
i
o
n
runners
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Create gro
m
acs/m
d
r
un module and move code t
h
e
r
e
commit
|
commitdiff
|
tree
2018-04-05
Szilár
d
Pá
l
l
Refa
c
tor
cj pre
l
o
a
d
in the non
b
onded
O
p
e
nC
L
k
ernel
s
commit
|
commitdiff
|
tree
2018-04-04
Mark Abr
a
ham
Quiet ch
e
ckpoint rea
d
ing
commit
|
commitdiff
|
tree
2018-04-04
Pasc
a
l Merz
Move che
c
kNumberOfBondedInteracti
o
ns
commit
|
commitdiff
|
tree
2018-04-03
Berk
H
ess
Convert gmx_m
t
op
_
t to C
+
+
commit
|
commitdiff
|
tree
2018-04-03
Mark Abr
a
ham
Remove le
f
tover mention
of twin-range scheme
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Merge "Mer
g
e
b
r
a
nch release-2018"
commit
|
commitdiff
|
tree
2018-03-29
Ber
k
Hess
Mo
v
e
f
i
l
e opening out of init_pull()
commit
|
commitdiff
|
tree
2018-03-29
Szilá
r
d
P
áll
Tweak/ena
b
le icc 18 post-submit tests
commit
|
commitdiff
|
tree
2018-03-29
M
a
gnus L
u
n
d
b
o
r
g
Improve
d
check of i
f
onl
y
forces are computed in d
o
_
pai
r
s()
commit
|
commitdiff
|
tree
2018-03-29
Paul Bauer
F
i
x cmake Sph
i
nx dete
c
tio
n
for ver
s
ions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szi
l
árd Páll
Switch CUD
A
9
.
0
/
gcc 5 test to
C
UDA 9
.
1/gc
c
6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modu
l
a
rize pull_coo
r
d_work_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abr
a
ham
Free more memory in grompp
a
nd mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk Hes
s
Remove mol
s
from
gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-28
Mark
A
braham
M
e
r
ge
b
r
a
n
c
h
r
e
leas
e
-201
8
commit
|
commitdiff
|
tree
2018-03-27
Mark
A
bra
h
am
C
l
arified md
p
options
rela
t
i
n
g
t
o bond
s
commit
|
commitdiff
|
tree
2018-03-27
M
ark Abra
h
am
More gcc-
8
fixes for POWER
commit
|
commitdiff
|
tree
2018-03-21
David van de
r
S
p
oe
l
R
ena
m
ed
entropy
.
*
to t
h
ermoc
h
emistry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Vers
i
on 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abr
a
h
am
Merge "Merge branch
r
elease-2
0
16 into release
-
2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark
A
b
r
a
h
am
Update re
l
ease notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Ab
r
aham
Merge br
a
nc
h
rele
a
se-2
0
16 into release-2018
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
Abraham
Update use of
g
p
u
_id in Jen
k
i
n
s
commit
|
commitdiff
|
tree
2018-03-20
B
erk Hess
Disal
l
ow single simulation with m
u
ltis
i
m
commit
|
commitdiff
|
tree
2018-03-20
M
ark
Abr
a
ham
Update use of gpu_id
in
J
enk
i
ns
commit
|
commitdiff
|
tree
2018-03-20
Mark Abra
h
am
Updat
e
use of gpu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
Ab
r
aham
Add
h
elper
f
u
nction to make a vect
o
r from an Array
R
ef
commit
|
commitdiff
|
tree
2018-03-19
M
ark
Abraha
m
Fi
x
VS
X
SIMD w
i
th
g
cc
8
commit
|
commitdiff
|
tree
2018-03-16
P
a
ul
B
auer
Only free topolo
g
y when allocated
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
C
o
r
rect PM
F
sign error in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve i
n
te
r
-simulation signaling
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
Ma
k
e a persistent physical node commu
n
i
c
ator
commit
|
commitdiff
|
tree
2018-03-14
Berk Hes
s
Fix mdrun signalling
w
i
th
A
W
H bia
s
sharing
commit
|
commitdiff
|
tree
2018-03-13
Berk He
s
s
Add AW
H
fixes to release notes
commit
|
commitdiff
|
tree
2018-03-13
Szilárd Páll
Require OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hes
s
F
ix AWH ensem
b
le checkpoi
n
ting
commit
|
commitdiff
|
tree
2018-03-13
Berk He
s
s
F
i
x AWH decon
v
o
l
ution when sharing a bias
commit
|
commitdiff
|
tree
2018-03-13
Mark A
b
rah
a
m
Introd
u
c
e
c
o
nstrain_s
h
ak
e
commit
|
commitdiff
|
tree
2018-03-13
Szil
á
r
d
Páll
F
i
x clang 6
.
0 with CUD
A
9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Mark Abraham
Merge
"Merge branch release-2018
"
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Correct pdb2gmx -missing
o
p
t
i
on
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Co
n
v
e
rt t_f
i
lenm to C++
commit
|
commitdiff
|
tree
2018-03-06
Mark A
b
raham
Merge
b
r
a
n
c
h
r
ele
a
se-2018
commit
|
commitdiff
|
tree
2018-03-06
M
a
rk Abraham
Fixed dvdlambda for
SHAKE +
FE
commit
|
commitdiff
|
tree
2018-03-05
Szilárd Pál
l
Add to
the contrib
u
tor section
commit
|
commitdiff
|
tree
2018-03-01
B
e
r
k
H
ess
Dete
c
t AM
D
SMT topology
commit
|
commitdiff
|
tree
2018-02-28
Mark Ab
r
aham
Move
d
and removed c
o
n
straint code
commit
|
commitdiff
|
tree
2018-02-28
Mark Ab
r
aham
Re
o
r
g
anized c
o
nstra
i
nt code
commit
|
commitdiff
|
tree
2018-02-27
Mark
A
bra
h
a
m
Fix GPU util
s
tes
t
commit
|
commitdiff
|
tree
2018-02-26
Paul B
a
uer
C
han
g
e
T
N
G
file
o
pen
i
ng
commit
|
commitdiff
|
tree
2018-02-26
M
ark Abr
a
ham
Pe
r
mit defi
n
e
.
m
dp fi
e
ld to assig
n
values
commit
|
commitdiff
|
tree
2018-02-26
A
l
eksei Iupinov
Advice users on infinite output of TPI
commit
|
commitdiff
|
tree
2018-02-26
Ma
r
k Abraha
m
Org
a
nize for recording 2016-era relea
s
e
notes
and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix m
d
integrator with
No
s
e-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-21
M
a
rk Abraham
Enhanced d
o
cs of
p
impl pointer helper
commit
|
commitdiff
|
tree
2018-02-16
M
a
rk Abraham
M
e
rge branch r
e
lease-2016 in
t
o relea
s
e-2018
commit
|
commitdiff
|
tree
2018-02-16
M
a
rk Abraham
B
u
mpe
d
patch
v
ersio
n
f
or next release
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
C
o
rrect
m
ulti
s
im
M
PI barrie
r
commit
|
commitdiff
|
tree
2018-02-16
Ma
r
k Abraham
Mer
g
e
b
ranch rele
a
se-2018 i
n
to master
commit
|
commitdiff
|
tree
2018-02-16
Mark Abra
h
am
Vers
i
on 2016
.
5
commit
|
commitdiff
|
tree
2018-02-15
Mark Abr
a
ham
U
s
e struct for
c
heckpo
i
nt hea
d
er
conte
n
ts
commit
|
commitdiff
|
tree
2018-02-15
Alek
s
ei Iupinov
Update FFTW build
to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-14
M
a
rk
A
braham
Remov
e
read_ch
e
ckpoint_state
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Remove
s
upp
o
rt
f
o
r tpx ver
s
ion before 58/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Use std::ve
c
tor for
c
h
eckpoint outputf
i
les
commit
|
commitdiff
|
tree
2018-02-14
Mark A
b
ra
h
am
M
e
r
ge b
r
anch
r
elease-2016 into release-2018
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix range
bug i
n
add_selection
_
groups i
n
tng
i
o
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Replac
e
the remai
n
ing EXPECT_DEAT
H
with EXPEC
T
_
D
E
A
TH_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Al
e
ks
e
i I
u
pinov
Add DeviceBuffer
a
s a t
y
pede
f
for cl
_
mem/
d
evice pon
t
er
commit
|
commitdiff
|
tree
2018-02-14
Szilárd Pál
l
R
e
move b
a
rriers preventing
t
e
xt
u
re reference races
commit
|
commitdiff
|
tree
2018-02-14
Be
r
k
Hess
Fix gro
m
pp
net
c
harge check
commit
|
commitdiff
|
tree
2018-02-14
Ber
k
Hess
F
ix grompp net charge check
commit
|
commitdiff
|
tree
2018-02-14
Mark
Abrah
a
m
Prepare relea
s
e
note
s
for 2018
.
1
commit
|
commitdiff
|
tree
2018-02-13
M
ark Abr
a
ham
Use deat
h
test only when
s
upp
o
rted
commit
|
commitdiff
|
tree
2018-02-13
M
ark Abraham
Se
p
arat
e
multi
s
im from comm
r
ec
commit
|
commitdiff
|
tree
2018-02-12
Mark
Abraham
Analyse threads on node be
f
o
r
e
setting affinities
commit
|
commitdiff
|
tree
2018-02-12
Mark Abraham
F
i
x re
a
ding old fo
r
ce field
f
i
les
commit
|
commitdiff
|
tree
2018-02-09
Mark Abrah
a
m
Merge bran
c
h re
l
ease-2018
commit
|
commitdiff
|
tree
2018-02-08
M
a
rk Abraham
M
er
g
e "Merge branc
h
release-2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Merge branc
h
re
l
e
a
s
e
-2016 into release-2018
commit
|
commitdiff
|
tree
2018-02-08
Aleksei I
u
pinov
Enable
d
e
b
ug FP exceptions
w
ithout TPI, no
t
with TP
I
commit
|
commitdiff
|
tree
2018-02-08
Mark Abr
a
ham
M
erge "Merge branch
'
release-2018' into master"
commit
|
commitdiff
|
tree
2018-02-06
Mark
A
b
r
aham
Prevent l
o
g f
i
le energy average p
r
inti
n
g dividing by
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
Don
'
t pr
i
n
t
impossible CUDA version numbers i
n
abse
n
ce
.
.
.
commit
|
commitdiff
|
tree
2018-02-01
P
au
l
Bauer
Add info
r
m
a
tion for n
2
t file format
commit
|
commitdiff
|
tree
2018-01-27
Ma
r
k Abraham
Re
m
ove unused
declaration
commit
|
commitdiff
|
tree
2018-01-25
Mark
Abraham
Re
m
ov
e
unused fields of t_commrec
commit
|
commitdiff
|
tree
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