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Fix cmake Sphinx detection for versions >1.6.4
2018-03-29
Paul Bauer
Fix cmake Sphinx detectio
n
for versions
>
1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szil
á
rd P
á
ll
Switch CUDA 9
.
0/gcc 5 test to
CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Ber
k
Hess
Modula
r
ize pull_coord_wor
k
_t
commit
|
commitdiff
|
tree
2018-03-28
Mark A
b
raham
Free
m
ore memory in gr
o
mpp
a
nd mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
R
emove mols
f
r
o
m
g
mx_mtop_t
commit
|
commitdiff
|
tree
2018-03-21
David van der Sp
o
e
l
Rename
d
entropy
.
*
t
o
t
he
r
moche
m
istry
.
*
commit
|
commitdiff
|
tree
2018-03-20
Mark A
b
r
a
ha
m
U
pdate
u
se of gpu_id in Je
n
kins
commit
|
commitdiff
|
tree
2018-03-20
Mark Ab
r
a
ha
m
Add helper function
t
o ma
k
e a
vector from a
n
ArrayRef
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
On
l
y
free topology when allocat
e
d
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
Make a per
s
istent physical no
d
e com
m
u
nicator
commit
|
commitdiff
|
tree
2018-03-13
Szil
á
rd Páll
Requi
r
e OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Mark Abraham
Introduce constrain_shake
commit
|
commitdiff
|
tree
2018-03-13
Mar
k
Abrah
a
m
Merge "M
e
r
ge
b
ranch release
-
2018"
commit
|
commitdiff
|
tree
2018-03-06
B
e
rk Hess
Convert t_
f
ile
n
m t
o
C+
+
commit
|
commitdiff
|
tree
2018-03-06
Mark Ab
r
aha
m
Merge branc
h
release-
2
01
8
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
F
i
xed dvdlambda for SHAKE + FE
commit
|
commitdiff
|
tree
2018-03-05
Szilár
d
Páll
Add to the contrib
u
tor sect
i
on
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Detect AMD S
M
T topology
commit
|
commitdiff
|
tree
2018-02-28
Mark A
b
r
aham
M
o
ved
and removed constraint c
o
de
commit
|
commitdiff
|
tree
2018-02-28
M
a
rk Abrah
a
m
Reorgani
z
ed
c
onstraint c
o
de
commit
|
commitdiff
|
tree
2018-02-27
Mark Ab
r
aham
F
i
x GPU ut
i
l
s tes
t
commit
|
commitdiff
|
tree
2018-02-26
Pau
l
Bauer
C
hange
T
N
G
file
opening
commit
|
commitdiff
|
tree
2018-02-26
Mark Abraham
Permit de
f
ine
.
mdp field to a
s
sign val
u
es
commit
|
commitdiff
|
tree
2018-02-26
Aleksei Iupinov
Advice users
o
n infinit
e
output
o
f TPI
commit
|
commitdiff
|
tree
2018-02-26
Ma
r
k Abraham
Orga
n
i
ze for recording 2016
-
er
a
rele
a
s
e
notes and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
F
ix md integrator wit
h
Nose
-
Hoover c
o
u
p
ling
commit
|
commitdiff
|
tree
2018-02-21
Ma
r
k Abrah
a
m
Enhance
d
docs of pimpl pointer
h
elper
commit
|
commitdiff
|
tree
2018-02-16
M
a
r
k Abr
a
ha
m
Merge branch rel
e
ase-2
0
16
i
nto release-2018
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
Bu
m
ped pat
c
h vers
i
on for next
r
e
lease
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Correct
multisim
MP
I
barrier
commit
|
commitdiff
|
tree
2018-02-16
Mark
Abraham
Merge branc
h
r
elease
-
2018 int
o
master
commit
|
commitdiff
|
tree
2018-02-16
Mark Abr
a
ham
Ver
s
ion
20
1
6
.
5
commit
|
commitdiff
|
tree
2018-02-15
Mark Abraham
Use struc
t
for checkpo
i
nt
header cont
e
nts
commit
|
commitdiff
|
tree
2018-02-15
Al
e
ksei
I
upinov
Update FFTW
bu
i
ld
to
3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-14
Mark Abrah
a
m
R
emove re
a
d_checkp
o
int
_
state
commit
|
commitdiff
|
tree
2018-02-14
Berk H
e
ss
Re
m
o
v
e sup
p
o
r
t for tpx
versi
o
n
befor
e
58/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
M
a
rk Abr
a
ham
Use
std::vect
o
r f
o
r
checkpoint outputfiles
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Me
r
ge b
r
anch release-2016 into release
-
2018
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix range b
u
g in add_selec
t
ion_groups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupinov
Rep
l
ace the rema
i
n
i
ng E
X
PEC
T
_
DEATH with EXP
E
CT_DEA
T
H_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
A
lekse
i
I
upi
n
o
v
Add DeviceBu
f
fer as
a
typ
e
def for cl_mem/devi
c
e ponter
commit
|
commitdiff
|
tree
2018-02-14
S
zi
l
árd Páll
R
emove barriers
p
reve
n
ting t
e
x
ture
reference
races
commit
|
commitdiff
|
tree
2018-02-14
Berk
H
ess
Fix
gr
o
mpp
net
charge ch
e
ck
commit
|
commitdiff
|
tree
2018-02-14
Berk
H
ess
Fix grompp net charge check
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Prepar
e
r
e
lease notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-02-13
Ma
r
k Abraham
Use death test only when suppor
t
ed
commit
|
commitdiff
|
tree
2018-02-13
Mark Ab
r
aham
Separate multisim from com
m
r
ec
commit
|
commitdiff
|
tree
2018-02-12
M
a
rk Abr
a
ham
Analyse t
h
r
ea
d
s on nod
e
b
e
fore setting affinities
commit
|
commitdiff
|
tree
2018-02-12
M
a
r
k
A
braham
Fix reading
o
l
d
force field files
commit
|
commitdiff
|
tree
2018-02-09
Mark Abraham
Merge bra
n
ch re
l
e
ase-2018
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Merge "Merge branch release-2016 into relea
s
e-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Ma
r
k
A
b
raham
Me
r
g
e
branch r
e
lease-2016 into release-2018
commit
|
commitdiff
|
tree
2018-02-08
Aleksei
Iupinov
E
n
ab
l
e debug FP e
x
ceptions
without TPI, not
w
ith
T
PI
commit
|
commitdiff
|
tree
2018-02-08
Mark Abr
a
ham
Merge "M
e
rge
bran
c
h 'release-2018' into
ma
s
t
er"
commit
|
commitdiff
|
tree
2018-02-06
M
ark Abraha
m
Prevent log fil
e
energy
a
verage
printing divid
i
ng by
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
Do
n
't
p
rint impossible CUDA version numbers in absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-01
Paul Bauer
Add i
n
formation for n2t file format
commit
|
commitdiff
|
tree
2018-01-27
M
a
rk Abra
h
a
m
Remove unused declaration
commit
|
commitdiff
|
tree
2018-01-25
Mark Abr
a
ham
Remove unused fields o
f
t_c
o
mmrec
commit
|
commitdiff
|
tree
2018-01-25
Ma
r
k Abraham
Red
u
c
e
d
i
nclu
d
es
o
f common headers in headers
commit
|
commitdiff
|
tree
2018-01-25
Mark Ab
r
a
h
am
Remo
v
e
d
m
drun -mult
i
commit
|
commitdiff
|
tree
2018-01-24
Mark Abra
h
am
C
hange multi-sim t
e
sts
to use
-
m
ultidir
commit
|
commitdiff
|
tree
2018-01-24
Mark Abraham
R
e
m
o
ve gmx_
i
nli
n
e
commit
|
commitdiff
|
tree
2018-01-24
M
a
rk Abraham
Teach inclu
d
e
sorte
r
to ignore cm
a
ke-te
s
t files
commit
|
commitdiff
|
tree
2018-01-24
Mark Abrah
a
m
Mo
v
e Window
s
i
cc conf
i
g to p
o
st-
s
ubmit
te
s
t
i
ng
commit
|
commitdiff
|
tree
2018-01-24
Mark Ab
r
aham
Replace
gmx_bool
w
ith bool i
n
bitmask funct
i
o
n
s
commit
|
commitdiff
|
tree
2018-01-23
Mark Ab
r
aham
Remo
v
e
s
u
p
p
o
rt for
implicit solvation
commit
|
commitdiff
|
tree
2018-01-23
Mark Abraha
m
R
emove topology support for impl
i
cit solv
a
tion
commit
|
commitdiff
|
tree
2018-01-23
Aleksei
I
upi
n
o
v
Test
P
ME C
P
U
/
G
PU with walls and box scaling
commit
|
commitdiff
|
tree
2018-01-23
Aleksei Iupinov
Wrap the PME testing loop in
a
me
t
hod for
exten
s
ibi
l
ity
commit
|
commitdiff
|
tree
2018-01-23
Mark Abrah
a
m
Preliminary cl
e
anup bef
o
re re
m
oving ifdef
c
plusplus
commit
|
commitdiff
|
tree
2018-01-19
Aleksei
Iu
p
inov
A
d
d a death tes
t
for the duplicate i
n
p
utrec keys checking
commit
|
commitdiff
|
tree
2018-01-19
Mark Abraham
Merge "Merge branch 're
l
ease-2018
'
into master"
commit
|
commitdiff
|
tree
2018-01-19
Aleks
e
i Iupi
n
ov
Rename class BiasReader t
o
struct BiasOut
p
u
t
S
e
t
up
commit
|
commitdiff
|
tree
2018-01-19
Mark Abraham
Add de
v
-g
u
ide
d
ocs for automati
c
up
d
ate of regres
s
io
n
t
e
sts
commit
|
commitdiff
|
tree
2018-01-19
Aleksei Iupi
n
ov
Make the refe
r
ence data varia
b
les l
o
cal in
G
e
tIr
T
e
st
commit
|
commitdiff
|
tree
2018-01-19
Mark Abraham
Fi
x
e
s
for issues
f
ound by c
l
ang 6
commit
|
commitdiff
|
tree
2018-01-18
Mark
Ab
r
aha
m
Rem
o
ve support for BlueGen
e
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix COMM re
m
oval
on part of the system
commit
|
commitdiff
|
tree
2018-01-18
Paul Bauer
Add contribu
t
i
on info
r
mation to webpa
g
e
commit
|
commitdiff
|
tree
2018-01-17
A
leksei
Iupinov
Fix bo
x
s
c
aling i
n
PME
m
ixed mo
d
e
commit
|
commitdiff
|
tree
2018-01-17
Be
r
k
Hess
Re-enable GP
U
with walls a
n
d 1
e
nergy group
commit
|
commitdiff
|
tree
2018-01-16
Mark Abraham
Merge "M
e
rge release-2018 into m
a
ster"
commit
|
commitdiff
|
tree
2018-01-16
Roland Sch
u
lz
Merg
e
releas
e
-2018 i
n
to
master
commit
|
commitdiff
|
tree
2018-01-16
B
e
rk Hes
s
Avoi
d
m
d
run echoing
"
No option -mu
l
ti"
commit
|
commitdiff
|
tree
2018-01-11
Mark Abrah
a
m
Bumped versio
n
for next patch releas
e
commit
|
commitdiff
|
tree
2018-01-11
Mark A
b
raham
Version 2018
commit
|
commitdiff
|
tree
2018-01-11
Mark Abraham
Announce
in user log fil
e
s tha
t
feat
u
res are depreca
t
ed
.
commit
|
commitdiff
|
tree
2018-01-11
R
oland Schulz
Fix G
M
X_
E
NABLE_AV
X
512_TESTS b
e
ing int
e
rnal
commit
|
commitdiff
|
tree
2018-01-10
Mark Abraham
Fix
a
u
tomated GPU
I
D assignmen
t
commit
|
commitdiff
|
tree
2018-01-10
Szi
l
á
r
d P
á
ll
User gu
i
de updates to GPU section
commit
|
commitdiff
|
tree
2018-01-10
Szi
l
árd Páll
Rele
a
se notes
t
weaks
commit
|
commitdiff
|
tree
2018-01-10
Mar
k
Abr
a
ham
Add release notes t
o
s
o
urc
e
repo
commit
|
commitdiff
|
tree
2018-01-10
Erik Lin
d
ahl
Impr
o
ve pdb2gmx for nonsta
n
dard residu
e
t
ypes
commit
|
commitdiff
|
tree
2018-01-10
Sz
i
lárd Páll
In
s
t
a
ll
g
u
ide updates
commit
|
commitdiff
|
tree
2018-01-10
Szilárd Páll
E
n
v
ironmen
t
v
ariable
d
ocs maint
e
n
anc
e
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iu
p
i
n
o
v
Do not print PME counter brea
k
d
own if it
'
s empty
commit
|
commitdiff
|
tree
2018-01-10
M
ark Abraham
Han
d
l
e
erroneous command line args better
commit
|
commitdiff
|
tree
2018-01-10
E
rik Linda
h
l
Clarified
gmx rmsf
d
ocumentati
o
n
commit
|
commitdiff
|
tree
2018-01-09
Mark Abraham
C
lean u
p
user guide for release
commit
|
commitdiff
|
tree
next