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Quotes from Gottingen workshop
2017-05-11
Teemu
M
u
rto
l
a
Generalize co
m
mand-line t
e
st
output file checking
commit
|
commitdiff
|
tree
2017-04-17
Teemu
Murtola
Consistent
approach for w
h
ole-progr
a
m tests
commit
|
commitdiff
|
tree
2017-04-11
Teemu
Murtola
I
mprov
e
k
e
y-
v
alue tree gm
x
dump support
commit
|
commitdiff
|
tree
2017-04-06
Tee
m
u
M
urto
l
a
Fix
memory acc
e
s
s
issues i
n
gmx solv
a
t
e
commit
|
commitdiff
|
tree
2017-04-06
Teemu M
u
rtola
Consisten
t
n
amin
g
for
g
mxana tests
commit
|
commitdiff
|
tree
2017-04-04
Teemu
Murtola
Utility
f
u
nctio
n
s fo
r
for
m
atting st
r
ing
v
al
u
es
commit
|
commitdiff
|
tree
2017-03-13
Tee
m
u
Murtola
Improve option
support &
t
e
s
ts for key-v
a
lue
t
rees
commit
|
commitdiff
|
tree
2017-03-13
Teemu Murto
l
a
Remove m
a
n
ual align
m
ent from In
M
e
mo
r
yS
e
r
iali
z
er
commit
|
commitdiff
|
tree
2017-03-12
Teemu
M
urtola
Consistent
T
extW
r
iter trailing white
s
pace handli
n
g
commit
|
commitdiff
|
tree
2017-03-11
T
e
emu Murtola
Upd
a
te copyright y
e
ar
for gmx -ve
r
s
ion
commit
|
commitdiff
|
tree
2017-03-04
Teemu Murtol
a
Remove
M
D
Modules
u
se
from mdlib
commit
|
commitdiff
|
tree
2017-03-04
Teemu Murt
o
la
Split md m
o
dule facets to dif
f
e
rent interfaces
commit
|
commitdiff
|
tree
2017-02-28
T
eemu
M
urtola
More documentati
o
n
for
key-value trees
commit
|
commitdiff
|
tree
2017-02-27
Teemu Murtola
De
c
o
u
ple
t
_input
r
ec fro
m
MDM
o
dules
commit
|
commitdiff
|
tree
2017-02-27
T
e
e
m
u Murtola
Remove
module
r
eferences from t_in
p
u
tre
c
commit
|
commitdiff
|
tree
2017-02-10
Teemu Murtola
Check log outp
u
t in
t
h
read a
f
fin
i
t
y
te
s
ts
commit
|
commitdiff
|
tree
2017-02-09
T
eemu Murtola
Mu
l
ti-r
a
nk thre
a
d a
f
finity tests
commit
|
commitdiff
|
tree
2017-02-09
Teemu
M
urtola
Document key-value tree transforms and im
p
rove checks
commit
|
commitdiff
|
tree
2017-02-09
T
eemu Murtola
Overview docum
e
ntation for new mdp input s
c
hem
e
commit
|
commitdiff
|
tree
2017-02-08
T
eemu Murtola
G
e
neric KeyValu
e
Tr
e
e br
o
a
dc
a
st
commit
|
commitdiff
|
tree
2017-02-08
T
e
emu M
u
rtola
G
eneric g
m
x check impleme
n
tation
w
ith
Ke
y
ValueTree
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
G
e
neric gmx dump
implementat
i
o
n
for KeyValueT
r
e
e
commit
|
commitdiff
|
tree
2017-02-08
Teemu
M
u
r
tola
Generic tpr
h
andling for electric
field
commit
|
commitdiff
|
tree
2016-12-12
Teemu Murt
o
la
Merge branch r
e
lea
s
e-2016
commit
|
commitdiff
|
tree
2016-12-10
T
e
emu Murtola
Mi
n
or CMake cleanup
&
m
oderniz
a
tion
commit
|
commitdiff
|
tree
2016-12-10
Teemu Murtola
Bui
l
d scripts for improve
d
release workfl
o
w
commit
|
commitdiff
|
tree
2016-12-08
Teemu Murtola
Fix
a
n
d cle
a
n up han
d
ling of s
o
me l
i
nking
commit
|
commitdiff
|
tree
2016-12-08
Te
e
mu
Murtola
F
ix pos
s
ible memory
er
r
or with lon
g
selections
commit
|
commitdiff
|
tree
2016-12-07
Teemu Murtola
Fix u
s
e
of position v
a
riables with plus/merge
commit
|
commitdiff
|
tree
2016-11-29
Teemu Mu
r
tola
Additional
s
el
e
ction help
commit
|
commitdiff
|
tree
2016-11-06
T
e
e
m
u Murto
l
a
A
d
d selecti
o
n-enabled
g
mx tra
j
commit
|
commitdiff
|
tree
2016-10-30
Teemu Murtola
Support norm
a
lizing
v
al
u
es i
n
KeyV
a
lu
e
Tree
commit
|
commitdiff
|
tree
2016-10-24
Tee
m
u Murtola
E
l
e
c
tric field mdp p
a
rsing using options
commit
|
commitdiff
|
tree
2016-10-24
T
e
emu Murtola
Suppor
t
fo
r
default values from
O
ption
s
t
o KeyValueTree
commit
|
commitdiff
|
tree
2016-10-21
Teemu
Murtola
Clean
up option (defaul
t
) value a
c
cess
commit
|
commitdiff
|
tree
2016-10-19
Teemu Murtola
S
erialization suppo
r
t for KeyV
a
lueTree
commit
|
commitdiff
|
tree
2016-10-17
Tee
m
u Mu
r
tola
Su
p
port o
p
t
i
o
n
a
s
signment from different
pre
c
isio
n
commit
|
commitdiff
|
tree
2016-10-17
Te
e
mu Murtola
Add
s
u
p
port
f
or
r
ea
d
i
ng
value
s
fr
o
m
r
e
fdat
a
commit
|
commitdiff
|
tree
2016-10-16
T
e
emu Murtola
Im
p
rov
e
d
e
r
r
or handling for KeyValue
T
ree operation
s
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murtola
Improved address
sanitizer sup
p
o
rt
commit
|
commitdiff
|
tree
2016-10-15
Te
e
mu Murtola
Wo
r
k around
memory
lea
k
i
n
t_state
commit
|
commitdiff
|
tree
2016-10-15
Teemu
M
u
r
tola
Fix most memory leaks recently
i
ntroduced
commit
|
commitdiff
|
tree
2016-10-14
T
eemu M
u
rtola
Use gmx_mtop_t in s
e
l
e
cti
o
ns,
p
a
rt 3
commit
|
commitdiff
|
tree
2016-10-14
Teemu Mur
t
ola
Use gmx_mto
p
_t in selectio
n
s, part 2
commit
|
commitdiff
|
tree
2016-10-13
Teem
u
Murtola
Use gmx_mtop_t in select
i
ons, part 2
commit
|
commitdiff
|
tree
2016-10-13
Teemu
M
urtola
Add bac
k
-mapping to
K
e
yValueTreeTransform
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murto
l
a
Up
d
a
t
e bun
d
l
ed
T
NG
commit
|
commitdiff
|
tree
2016-10-13
Teemu Mu
r
tola
Getter for mapped p
a
ths
f
rom KeyValu
e
TreeTransform
commit
|
commitdiff
|
tree
2016-10-12
Teemu Murt
o
la
U
s
e gmx_mtop_t
in se
l
ections, part
1
commit
|
commitdiff
|
tree
2016-10-12
Te
e
mu Murtola
Wrap sel
.
method evaluat
i
on p
a
rameter
s
to struct
commit
|
commitdiff
|
tree
2016-10-11
T
e
emu Mur
t
ola
S
up
p
or
t
concurrent
t_top
o
lo
g
y and gmx_mtop_t
u
s
e
commit
|
commitdiff
|
tree
2016-10-11
T
e
e
m
u
Mur
t
o
l
a
Check atom mass
ava
i
l
a
bility
in se
l
e
ctions
commit
|
commitdiff
|
tree
2016-10-05
Teemu
M
urtola
Support diff
e
r
ent key matching in KeyValueT
r
eeTransform
commit
|
commitdiff
|
tree
2016-10-05
Teem
u
Murtola
Merg
e
"Merg
e
branch release-5-1 into release-201
6
"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
Te
e
mu M
u
r
t
ola
F
i
x
default nice
level
in mdrun-only build
commit
|
commitdiff
|
tree
2016-09-12
T
eemu Murtola
Fix var
i
ous memory lea
k
s
commit
|
commitdiff
|
tree
2016-09-07
Teemu M
u
r
tola
Clean
u
p CTes
t
test
m
anagement
commit
|
commitdiff
|
tree
2016-08-30
Tee
m
u
M
u
r
t
ola
Basic support for trans
f
orming
KeyV
a
l
u
eTrees
commit
|
commitdiff
|
tree
2016-08-27
Teemu Murtola
Suppo
r
t Ke
y
ValueTree object
s
in refdata
commit
|
commitdiff
|
tree
2016-08-18
T
e
e
mu Murtola
C
h
eck for unus
e
d re
f
data val
u
es
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murtola
Gen
e
ri
c
s
t
r
uctur
e
d key-value tree f
o
r
o
ptio
n
s
commit
|
commitdiff
|
tree
2016-08-18
T
eemu Murtola
Support for no
n
-string option va
l
ue assignmen
t
commit
|
commitdiff
|
tree
2016-08-17
T
eemu
Murtola
Basic su
p
p
ort
for array-of-struc
t
s in options
commit
|
commitdiff
|
tree
2016-08-17
Te
e
mu Murto
l
a
G
enera
l
ize
and
s
i
m
plify option value storage
commit
|
commitdiff
|
tree
2016-08-17
Te
e
m
u
Murtola
Ge
n
eralize option section internals
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
Reimplement
s
ubsections in Opt
i
on
s
commit
|
commitdiff
|
tree
2016-08-04
Teemu Mur
t
ola
Fix/improve
doc links in templ
a
te/READ
M
E
commit
|
commitdiff
|
tree
2016-08-01
Teemu Murtola
Functio
n
to
s
plit delimited strings
commit
|
commitdiff
|
tree
2016-07-14
Teemu Murto
l
a
Use newe
r
gcc for
c
o
v
er
a
ge
commit
|
commitdiff
|
tree
2016-07-07
Teemu Murtol
a
Change ha
n
dlin
g
for mis
s
i
ng releng docs
commit
|
commitdiff
|
tree
2016-06-30
Te
e
mu M
u
r
tola
Extract string parsi
n
g routines to utility
commit
|
commitdiff
|
tree
2016-06-28
Teemu Mur
t
ol
a
Split up
compare
.
*
commit
|
commitdiff
|
tree
2016-06-27
Teemu Murtola
F
a
ctory for creating
t
_
inputr
e
c
commit
|
commitdiff
|
tree
2016-06-01
Te
e
mu Murt
o
la
Use C++ rep
l
a
c
ement
for
m
d_l
o
g
g
i
ng
.
*
commit
|
commitdiff
|
tree
2016-06-01
Te
e
mu Murtola
Bas
i
c C++ logg
i
ng
interf
a
ce
commit
|
commitdiff
|
tree
2016-05-31
T
e
emu Mu
r
t
o
la
Im
p
rove m
a
k
e_ndx he
l
p text
commit
|
commitdiff
|
tree
2016-05-25
Te
e
mu Mur
t
ola
S
u
pport for real MPI unit test
s
commit
|
commitdiff
|
tree
2016-05-24
T
e
emu Mu
r
tola
Tests
f
or single-
r
ank thread affin
i
ty setting
commit
|
commitdiff
|
tree
2016-05-21
Tee
m
u Murto
l
a
Pass number of local
threads to thread affinity
commit
|
commitdiff
|
tree
2016-05-21
T
eemu Murtola
Allow crea
t
i
n
g
mock Har
d
wa
r
eTo
p
o
logy
objects
commit
|
commitdiff
|
tree
2016-05-21
Teem
u
Murtola
Use only H
a
rdwareT
o
polo
g
y for thread affinity
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
Mer
g
e branch r
e
lease-2016
commit
|
commitdiff
|
tree
2016-05-21
T
e
emu
M
urtola
Bump version nu
m
b
ers
for 2017
d
evelo
p
ment
commit
|
commitdiff
|
tree
2016-05-17
T
eem
u
Murtola
Fix some
thread
a
ffinity
c
ases
commit
|
commitdiff
|
tree
2016-05-10
Tee
m
u Murtola
A
d
ditional Jenk
i
ns documentation
commit
|
commitdiff
|
tree
2016-05-10
Tee
m
u M
u
rtola
In
c
lud
e
r
e
l
eng documentation to
d
ev
e
loper gu
i
de
commit
|
commitdiff
|
tree
2016-05-08
Teemu Mur
t
ola
Support for Ope
n
CL CI builds
commit
|
commitdiff
|
tree
2016-05-05
Tee
m
u Murto
l
a
Merge branch release-5
-
1
commit
|
commitdiff
|
tree
2016-05-05
T
eemu Murtol
a
Ma
k
e
Sp
h
inx
build silent for
v
ersion 1
.
3+
commit
|
commitdiff
|
tree
2016-05-03
Teemu Murtola
Ma
r
k opti
o
nal input/ou
t
put files in gm
x
o
rder
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtola
Use Hard
w
a
r
e
T
opo
l
ogy to
s
et nthreads_hw_avail
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtola
R
e
move gmx_hw_in
f
o_t::nco
r
e
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Improve r
e
lease wo
r
kflow testing
commit
|
commitdiff
|
tree
2016-04-27
T
e
emu Murtola
D
isable multip
l
e ranks for non-MPI
u
nit
tests
commit
|
commitdiff
|
tree
2016-04-27
Teemu Mur
t
ola
Fi
x
issues
with failing thread affinity setting
commit
|
commitdiff
|
tree
2016-04-27
Te
e
mu Mu
r
t
o
la
Merge
"
Merge branch
r
elease-5
-
1"
commit
|
commitdiff
|
tree
2016-04-18
Teemu Murtola
Make th
r
ea
d
affi
n
ity failures always end up in log
commit
|
commitdiff
|
tree
2016-03-30
Tee
m
u Murtola
Make in
c
ludesorter
.
py
work with Doxygen 1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
Teemu M
u
r
t
ola
F
ix error reporting
f
or
d
ocumenta
t
ion build
commit
|
commitdiff
|
tree
2016-03-28
T
e
e
mu Murtola
M
o
r
e
sup
p
ort for release workflo
w
commit
|
commitdiff
|
tree
next