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Leave NVML use off by default
2017-09-04
Te
e
mu Murto
l
a
Introduce self-pairs
search in
nbsea
r
ch
commit
|
commitdiff
|
tree
2017-09-04
Teemu Murtola
R
e
factor ana
l
ysis nbsearch test
s
commit
|
commitdiff
|
tree
2017-08-21
Tee
m
u
Murtola
Simple
union-
f
in
d
st
r
ucture
commit
|
commitdiff
|
tree
2017-07-19
T
e
emu Murtola
Pr
u
ne
unnecessa
r
y
c
ells i
n
analysis nbsearch
commit
|
commitdiff
|
tree
2017-07-17
Teemu
M
urtola
F
ix hwloc d
e
tection
commit
|
commitdiff
|
tree
2017-07-11
Teemu
M
urtola
Support scoped k
e
y-valu
e
tree
transform rule
s
commit
|
commitdiff
|
tree
2017-07-06
Teemu Mur
t
ola
D
etect unknown mdp
o
pti
o
n
s
i
n gmx dump/chec
k
commit
|
commitdiff
|
tree
2017-06-30
T
eemu Murtola
Fix boole
a
n serialization
commit
|
commitdiff
|
tree
2017-06-30
Teemu M
u
rtola
Ext
e
nd key-val
u
e
t
ree com
p
ar
i
son and test
s
commit
|
commitdiff
|
tree
2017-06-29
Teemu Murtola
Generalize
I
ForceProv
i
der
commit
|
commitdiff
|
tree
2017-06-28
Teemu Murtola
Extend k
e
y-v
a
lue
t
ree s
e
r
i
alization an
d
tests
commit
|
commitdiff
|
tree
2017-06-27
T
ee
m
u M
u
r
tola
Do not
use conf-man
.
p
y
for non-manp
a
g
e
doc build
s
commit
|
commitdiff
|
tree
2017-05-29
Teemu M
u
rtola
Avoid so
m
e i
n
correct
b
ehavior
with gmx solvate
commit
|
commitdiff
|
tree
2017-05-29
T
e
emu Murtola
Remov
e
pbcutil <-> mdtype
s
c
y
clic dependency
commit
|
commitdiff
|
tree
2017-05-11
Teem
u
Murto
l
a
Gene
r
a
l
ize command-
l
ine test out
p
ut file checking
commit
|
commitdiff
|
tree
2017-04-17
Teem
u
Murtola
C
o
nsistent approa
c
h for
whole-program te
s
ts
commit
|
commitdiff
|
tree
2017-04-11
Teemu M
u
rtola
Impr
o
ve k
e
y-
v
al
u
e tree gmx dump su
p
port
commit
|
commitdiff
|
tree
2017-04-06
Teemu
Murtola
Fix memory ac
c
es
s
issues in
gmx solvate
commit
|
commitdiff
|
tree
2017-04-06
T
eemu Murtola
Con
s
istent nami
n
g for
g
mxana
t
ests
commit
|
commitdiff
|
tree
2017-04-04
Teemu Murtola
U
t
il
i
ty f
u
ncti
o
ns for fo
r
mattin
g
st
r
ing values
commit
|
commitdiff
|
tree
2017-03-13
Teemu Murtol
a
Improve option support & tests for k
e
y-value trees
commit
|
commitdiff
|
tree
2017-03-13
Tee
m
u Murt
o
la
Remove manual a
l
ignm
e
nt f
r
om
InMemorySer
i
alizer
commit
|
commitdiff
|
tree
2017-03-12
T
e
e
mu Murtola
Con
s
istent Text
W
riter trailing whitespace ha
n
d
l
i
n
g
commit
|
commitdiff
|
tree
2017-03-11
Teemu
Murtola
Update copyright year fo
r
gmx -vers
i
o
n
commit
|
commitdiff
|
tree
2017-03-04
T
e
emu M
u
rt
o
la
Remove
MDModules use
f
rom mdlib
commit
|
commitdiff
|
tree
2017-03-04
T
e
emu Murtola
Split md module fa
c
ets to diff
e
r
e
nt interf
a
ces
commit
|
commitdiff
|
tree
2017-02-28
Teem
u
M
u
rt
o
la
More do
c
umen
t
ation f
o
r
k
e
y
-value tre
e
s
commit
|
commitdiff
|
tree
2017-02-27
Teemu Mu
r
tola
Dec
o
uple t_inputrec from MDModul
e
s
commit
|
commitdiff
|
tree
2017-02-27
Teemu Mu
r
to
l
a
R
e
m
ove mo
d
ule references from t_inputrec
commit
|
commitdiff
|
tree
2017-02-10
T
eemu Mur
t
ola
Check log outp
u
t i
n
t
hread affinity tests
commit
|
commitdiff
|
tree
2017-02-09
Teem
u
Murtola
Mu
l
ti-rank thread affinity tests
commit
|
commitdiff
|
tree
2017-02-09
Teemu
Mur
t
ola
Document key-value tree tra
n
sfor
m
s and impro
v
e checks
commit
|
commitdiff
|
tree
2017-02-09
Teemu M
u
r
to
l
a
Overview do
c
u
m
entat
i
o
n f
o
r ne
w
m
d
p inp
u
t sch
e
me
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtol
a
Gener
i
c Ke
y
Value
T
ree broadc
a
st
commit
|
commitdiff
|
tree
2017-02-08
Tee
m
u
Murtol
a
G
eneric gmx check impl
e
m
e
ntation with KeyV
a
lueTree
commit
|
commitdiff
|
tree
2017-02-08
Teem
u
Murtola
Generic gmx
d
um
p
i
mplem
e
ntation fo
r
Ke
y
Value
T
r
e
e
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
Generic
tpr h
a
ndling for electric field
commit
|
commitdiff
|
tree
2016-12-12
Teemu Mur
t
ola
Merge branch release-
2
016
commit
|
commitdiff
|
tree
2016-12-10
Teemu M
u
rtola
Minor CMak
e
cleanup &
moderni
z
ation
commit
|
commitdiff
|
tree
2016-12-10
Teemu
Murto
l
a
Buil
d
s
cripts f
o
r improve
d
release workfl
o
w
commit
|
commitdiff
|
tree
2016-12-08
Tee
m
u Mur
t
ola
Fix a
n
d clean up ha
n
dli
n
g o
f
some li
n
king
commit
|
commitdiff
|
tree
2016-12-08
Teemu Murtola
Fix p
o
ssible memory error with long selections
commit
|
commitdiff
|
tree
2016-12-07
Teemu Murtola
F
i
x use of positi
o
n variables with pl
u
s/merge
commit
|
commitdiff
|
tree
2016-11-29
Teemu Mu
r
tola
Addit
i
onal sel
e
ction h
e
lp
commit
|
commitdiff
|
tree
2016-11-06
Te
e
mu Murtola
Add selection-ena
b
led
gmx traj
commit
|
commitdiff
|
tree
2016-10-30
Teemu
M
urtola
Support
normalizing
values i
n
KeyValueTree
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murtola
E
l
ectric field
mdp parsing usi
n
g option
s
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murtola
Support for
default values from Options to KeyValueTr
e
e
commit
|
commitdiff
|
tree
2016-10-21
Teemu Murtola
Clea
n
up
option (d
e
fault) v
a
lue access
commit
|
commitdiff
|
tree
2016-10-19
Teemu Murtola
S
e
r
ializati
o
n suppo
r
t for Key
V
a
l
ueTree
commit
|
commitdiff
|
tree
2016-10-17
Teemu
Murtol
a
S
u
ppo
r
t option assignment from d
i
fferent precisi
o
n
commit
|
commitdiff
|
tree
2016-10-17
Te
e
m
u
Murtola
Add support for r
e
a
ding va
l
u
e
s from refdata
commit
|
commitdiff
|
tree
2016-10-16
Teemu
Murtola
I
m
p
r
oved error handling f
o
r
K
eyV
a
l
u
eTree operations
commit
|
commitdiff
|
tree
2016-10-15
Teemu M
u
rtola
Impro
v
ed address sanitizer suppo
r
t
commit
|
commitdiff
|
tree
2016-10-15
Teem
u
M
u
rtola
W
o
rk
around memor
y
leak
in t_st
a
te
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtola
Fix most me
m
o
r
y leaks
r
ecently intro
d
uced
commit
|
commitdiff
|
tree
2016-10-14
Teem
u
M
u
r
t
ol
a
Use gmx_
m
top
_
t in selections,
pa
r
t
3
commit
|
commitdiff
|
tree
2016-10-14
Teemu Murt
o
la
Use
gmx_mto
p
_t in selection
s
, part
2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Mur
t
ol
a
Use gmx_mtop_t in selections, part 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murto
l
a
Add b
a
ck-mapping to
KeyValue
T
reeTransform
commit
|
commitdiff
|
tree
2016-10-13
Te
e
mu
M
u
rtola
Upd
a
te bundled TNG
commit
|
commitdiff
|
tree
2016-10-13
Teem
u
Murtola
G
e
t
t
er
for
mapped
p
aths from
K
e
yValu
e
T
r
ee
T
ra
n
sform
commit
|
commitdiff
|
tree
2016-10-12
Teemu Murtola
Use
gmx_mtop_t in
selec
t
ions, part 1
commit
|
commitdiff
|
tree
2016-10-12
Teemu Murtola
Wrap sel
.
meth
o
d
evaluation parame
t
ers to stru
c
t
commit
|
commitdiff
|
tree
2016-10-11
T
eemu
Murtola
Suppor
t
conc
u
rrent t_top
o
logy and gmx_mt
o
p_t
u
se
commit
|
commitdiff
|
tree
2016-10-11
T
eemu
Murtola
C
heck atom ma
s
s avai
l
ability in sele
c
tions
commit
|
commitdiff
|
tree
2016-10-05
Teemu Murtola
S
u
ppo
r
t different key matching in KeyValue
T
reeTransform
commit
|
commitdiff
|
tree
2016-10-05
T
e
emu Murt
o
la
Merge "Merge branch re
l
ease-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
T
eemu Murtola
Fix default n
i
ce level
i
n
mdrun-only build
commit
|
commitdiff
|
tree
2016-09-12
Teem
u
Murtola
F
i
x various memory leaks
commit
|
commitdiff
|
tree
2016-09-07
Teemu Murtola
Clean u
p
CTest test managemen
t
commit
|
commitdiff
|
tree
2016-08-30
Te
e
mu Murto
l
a
Basic
support for tran
s
forming KeyValueTrees
commit
|
commitdiff
|
tree
2016-08-27
Teemu Murtola
S
u
pport KeyValueT
r
ee obje
c
ts in ref
d
a
t
a
commit
|
commitdiff
|
tree
2016-08-18
T
eemu Murtola
C
h
e
c
k
f
o
r u
n
used ref
d
ata val
u
es
commit
|
commitdiff
|
tree
2016-08-18
Teemu Mu
r
tola
Generic struct
u
red key-va
l
u
e
tr
e
e
for opt
i
ons
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murt
o
l
a
S
upport for
n
o
n-strin
g
option value as
s
ignment
commit
|
commitdiff
|
tree
2016-08-17
Teemu
Murtol
a
Basic support for array-of-s
t
ru
c
ts in options
commit
|
commitdiff
|
tree
2016-08-17
Te
e
mu Murt
o
la
Generalize and simplify option value storage
commit
|
commitdiff
|
tree
2016-08-17
Tee
m
u Mu
r
to
l
a
Generalize option section
in
t
ernals
commit
|
commitdiff
|
tree
2016-08-17
Teem
u
Murtola
Reimplement subsections in
O
ptions
commit
|
commitdiff
|
tree
2016-08-04
Tee
m
u Murtola
Fix/impro
v
e
doc links in template/RE
A
DME
commit
|
commitdiff
|
tree
2016-08-01
Teemu Murtola
Fu
n
ction to split
del
i
mited stri
n
gs
commit
|
commitdiff
|
tree
2016-07-14
Teemu Murto
l
a
Use newer gcc
f
or coverag
e
commit
|
commitdiff
|
tree
2016-07-07
T
eemu Murtola
Change handling f
o
r missing
rele
n
g docs
commit
|
commitdiff
|
tree
2016-06-30
Teemu Murtola
Extra
c
t str
i
ng parsing routin
e
s to
ut
i
lity
commit
|
commitdiff
|
tree
2016-06-28
T
e
emu Murtola
Split up compare
.
*
commit
|
commitdiff
|
tree
2016-06-27
T
eemu Murto
l
a
Facto
r
y
fo
r
creating t_inp
u
tr
e
c
commit
|
commitdiff
|
tree
2016-06-01
Teemu
M
urtola
Use C++ repla
c
emen
t
for md_logging
.
*
commit
|
commitdiff
|
tree
2016-06-01
T
e
emu Murtola
B
a
sic
C++ logg
i
ng in
t
erfac
e
commit
|
commitdiff
|
tree
2016-05-31
T
e
emu Mur
t
o
l
a
Improve make_ndx help text
commit
|
commitdiff
|
tree
2016-05-25
T
eemu Murtola
Support for real MPI unit tests
commit
|
commitdiff
|
tree
2016-05-24
Teemu Murtola
T
e
sts for
s
i
ngle-rank
thread affinity s
e
tting
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
Pass number of loca
l
threa
d
s to
threa
d
a
ff
i
nity
commit
|
commitdiff
|
tree
2016-05-21
Tee
m
u Murtol
a
Allow c
r
eating mo
c
k
HardwareTopolo
g
y obj
e
cts
commit
|
commitdiff
|
tree
2016-05-21
Teemu M
u
rtola
U
s
e only HardwareTopology for thread affinity
commit
|
commitdiff
|
tree
2016-05-21
Te
e
m
u Murto
l
a
M
e
rge
b
ranch release-2016
commit
|
commitdiff
|
tree
2016-05-21
T
ee
m
u Murt
o
la
Bump version numbers for 2
0
17 de
v
elopment
commit
|
commitdiff
|
tree
2016-05-17
Te
e
mu Murtola
Fi
x
some
t
hread aff
i
nity cases
commit
|
commitdiff
|
tree
2016-05-10
Teemu
M
u
rt
o
la
Additi
o
nal
Jenkins d
o
cumentation
commit
|
commitdiff
|
tree
2016-05-10
Teemu Mu
r
tola
In
c
lude releng d
o
cumen
t
ati
o
n to devel
o
p
er
g
uid
e
commit
|
commitdiff
|
tree
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