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Work around memory leak in t_state
2016-10-15
Teemu Murtola
Work around m
e
mory lea
k
in
t
_
st
a
t
e
commit
|
commitdiff
|
tree
2016-10-15
Teemu
M
u
rt
o
la
Fi
x
most m
e
m
o
ry leaks recently introdu
c
ed
commit
|
commitdiff
|
tree
2016-10-14
Teemu Murtola
Use gmx_mtop_
t
in sele
c
ti
o
ns, part 3
commit
|
commitdiff
|
tree
2016-10-14
Tee
m
u M
u
r
t
o
l
a
Use gmx_mto
p
_
t
in selections, part 2
commit
|
commitdiff
|
tree
2016-10-13
T
e
emu
M
urtola
Use
g
mx_mtop_t in selectio
n
s, p
a
rt 2
commit
|
commitdiff
|
tree
2016-10-13
Tee
m
u Murtola
Add
b
ack-map
p
ing to KeyValueTr
e
eTransform
commit
|
commitdiff
|
tree
2016-10-13
Teem
u
Murtola
Update bu
n
dled TNG
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Getter for mapped paths from
K
eyV
a
lueTreeTransform
commit
|
commitdiff
|
tree
2016-10-12
Teemu Murt
o
la
Use gmx_mtop
_
t in selections,
part 1
commit
|
commitdiff
|
tree
2016-10-12
Tee
m
u Murtola
Wrap sel
.
meth
o
d evalua
t
ion par
a
meters t
o
str
u
ct
commit
|
commitdiff
|
tree
2016-10-11
Teemu Murtola
Suppor
t
concurrent t_to
p
ology
a
nd gmx_mto
p
_t use
commit
|
commitdiff
|
tree
2016-10-11
T
e
e
mu
M
urtola
Check atom mass availability in s
e
lect
i
ons
commit
|
commitdiff
|
tree
2016-10-05
Teemu
M
u
rtola
S
u
pport different key matchi
n
g in KeyValueTre
e
T
r
a
nsfor
m
commit
|
commitdiff
|
tree
2016-10-05
Te
e
mu Murtola
M
e
rg
e
"Merge
b
ran
c
h r
e
lease-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
T
ee
m
u
Murtola
Fix defaul
t
nice le
v
el in
md
r
un-only bu
i
l
d
commit
|
commitdiff
|
tree
2016-09-12
T
eemu
Mu
r
tol
a
Fix
v
arious memory leaks
commit
|
commitdiff
|
tree
2016-09-07
T
eemu Murtola
Clean up CTe
s
t
test man
a
ge
m
ent
commit
|
commitdiff
|
tree
2016-08-30
Teemu Murt
o
la
Basic
s
upport f
o
r transformin
g
KeyValueTrees
commit
|
commitdiff
|
tree
2016-08-27
Teemu Mur
t
ola
Supp
o
rt
Key
V
a
l
ueTree o
b
jects in
re
f
d
ata
commit
|
commitdiff
|
tree
2016-08-18
Teemu
Murtola
C
heck for unused refda
t
a va
l
ues
commit
|
commitdiff
|
tree
2016-08-18
Teemu Murtola
G
e
n
eric
structured ke
y
-value t
r
ee for optio
n
s
commit
|
commitdiff
|
tree
2016-08-18
Teemu Mu
r
tola
Support for non-str
i
ng option value as
s
ignment
commit
|
commitdiff
|
tree
2016-08-17
Teemu
M
u
r
tola
Basic support for a
r
r
a
y-
o
f-structs in option
s
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murto
l
a
Generaliz
e
and simplify o
p
tion value storage
commit
|
commitdiff
|
tree
2016-08-17
T
e
e
m
u
M
urto
l
a
Generalize optio
n
s
ection internals
commit
|
commitdiff
|
tree
2016-08-17
Teemu Murtola
Reimpleme
n
t
subsectio
n
s in
O
p
t
io
n
s
commit
|
commitdiff
|
tree
2016-08-04
Teemu Murto
l
a
Fix
/
impr
o
ve doc l
i
n
k
s in
te
m
plate/README
commit
|
commitdiff
|
tree
2016-08-01
Te
e
m
u
M
u
r
tola
Function to
s
plit delimited strings
commit
|
commitdiff
|
tree
2016-07-14
Teem
u
Murtola
Use new
e
r gcc f
o
r coverage
commit
|
commitdiff
|
tree
2016-07-07
Teemu
M
u
rtola
Chan
g
e handling for missing releng
d
ocs
commit
|
commitdiff
|
tree
2016-06-30
T
e
emu Murtola
Extract string parsi
n
g routines
to
u
tility
commit
|
commitdiff
|
tree
2016-06-28
Teemu
M
urtola
S
p
lit up com
p
are
.
*
commit
|
commitdiff
|
tree
2016-06-27
T
e
emu Murt
o
la
F
actory for cre
a
ting t_inpu
t
rec
commit
|
commitdiff
|
tree
2016-06-01
T
e
emu Murtola
Use C++ r
e
p
lace
m
ent for md_loggin
g
.
*
commit
|
commitdiff
|
tree
2016-06-01
Teemu Mu
r
t
ola
Bas
i
c C+
+
logging
i
nt
e
rface
commit
|
commitdiff
|
tree
2016-05-31
Teemu
M
urt
o
la
I
m
p
r
ove make_ndx hel
p
text
commit
|
commitdiff
|
tree
2016-05-25
Teemu
M
u
rtol
a
S
up
p
ort for real MPI uni
t
tests
commit
|
commitdiff
|
tree
2016-05-24
T
e
e
m
u Mu
r
t
o
l
a
T
es
t
s fo
r
sin
g
l
e-rank
t
hread affi
n
ity setting
commit
|
commitdiff
|
tree
2016-05-21
Te
e
mu
Murtola
Pass num
b
e
r
of l
o
cal threads
to
t
hread affinity
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murt
o
l
a
Allow creating
m
ock Hard
w
areTopology o
b
jects
commit
|
commitdiff
|
tree
2016-05-21
Teemu
M
u
r
tol
a
Use only Hardwar
e
T
o
p
ology
for thread af
f
i
n
ity
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
Merge branch re
l
ease
-
2
016
commit
|
commitdiff
|
tree
2016-05-21
T
eemu
Mu
r
tola
B
ump version numbers f
o
r
2
01
7
dev
e
lo
p
ment
commit
|
commitdiff
|
tree
2016-05-17
Teemu M
u
r
to
l
a
F
i
x som
e
thr
e
ad
af
f
inity cases
commit
|
commitdiff
|
tree
2016-05-10
T
e
e
m
u
Murtol
a
A
ddit
i
onal
J
en
k
ins doc
u
m
en
t
ation
commit
|
commitdiff
|
tree
2016-05-10
Teemu
M
urtola
I
n
c
lude releng
d
ocumentation to de
v
eloper guide
commit
|
commitdiff
|
tree
2016-05-08
T
e
emu Murto
l
a
S
u
p
port for Op
e
nC
L
CI bui
l
ds
commit
|
commitdiff
|
tree
2016-05-05
Teemu M
u
rtola
M
erge branc
h
r
elease-5-
1
commit
|
commitdiff
|
tree
2016-05-05
Teemu Murtola
Make Sphi
n
x build
s
i
len
t
for
vers
i
on
1
.
3+
commit
|
commitdiff
|
tree
2016-05-03
T
e
emu Murtola
M
a
rk optional inp
u
t/output files
i
n gmx
order
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtola
Us
e
Hardw
a
reTopology to set nthreads_hw_avail
commit
|
commitdiff
|
tree
2016-04-28
T
e
e
m
u
Mu
r
t
o
l
a
Rem
o
ve
g
mx_hw_in
f
o_t::ncore
commit
|
commitdiff
|
tree
2016-04-27
T
e
e
m
u
Mu
r
tola
Improve release
workflow testing
commit
|
commitdiff
|
tree
2016-04-27
T
eemu Mur
t
ol
a
Disable
m
ultiple ra
n
ks fo
r
non
-
MPI uni
t
t
ests
commit
|
commitdiff
|
tree
2016-04-27
Teem
u
Murtola
Fix
i
ssues with failing
t
hread
a
f
fini
t
y
se
t
ting
commit
|
commitdiff
|
tree
2016-04-27
Teem
u
Murtol
a
Merge "Merg
e
b
ranc
h
release
-
5-1
"
commit
|
commitdiff
|
tree
2016-04-18
Teemu Murtola
M
a
k
e
t
h
read a
f
finity f
a
ilures always end u
p
in l
o
g
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtola
M
ake in
c
l
u
desorter
.
py
w
o
r
k with Doxygen
1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
Teem
u
Murtola
F
i
x
error reporting for documentation build
commit
|
commitdiff
|
tree
2016-03-28
Teemu
M
urto
l
a
More support
f
or relea
s
e workflow
commit
|
commitdiff
|
tree
2016-03-26
Teemu Murtola
I
gnore
e
mpt
y
GMXLIB
commit
|
commitdiff
|
tree
2016-03-14
Teemu Mur
t
ola
A
d
d
t
ests for
e
mpty
s
t
r
ings
in r
e
fda
t
a
commit
|
commitdiff
|
tree
2016-03-13
Teemu Murto
l
a
Support repl
a
cing solvent i
n
i
n
sert-m
o
lecules
commit
|
commitdiff
|
tree
2016-02-01
Teemu Mu
r
tola
Handle
pdbinf
o
in A
t
omsBui
l
der
commit
|
commitdiff
|
tree
2016-01-28
T
eemu Murtola
Upd
a
t
e
build scripts
t
o rele
n
g changes
commit
|
commitdiff
|
tree
2016-01-24
Teemu
Murtola
Document
l
i
mitations on 32-b
i
t
L
inux
commit
|
commitdiff
|
tree
2016-01-12
T
e
emu Murtola
Make GMX
_
MPI always def
i
ned to
0
/
1
commit
|
commitdiff
|
tree
2016-01-12
T
eemu
M
u
r
tola
Move flags
o
u
t of t_trx
f
rame
commit
|
commitdiff
|
tree
2016-01-12
T
e
emu Murtola
Rem
o
v
e
historica
l
t
im
e
s from t
_
tr
x
frame
commit
|
commitdiff
|
tree
2016-01-12
T
e
e
m
u Mu
r
tola
Support passing
tarball MD5 for webpage build
commit
|
commitdiff
|
tree
2016-01-12
Tee
m
u Mur
t
ola
R
emov
e
v
mdplugin
from t_trxframe
commit
|
commitdiff
|
tree
2016-01-11
Teemu
M
u
rtola
C
onvert mo
r
e config
.
h de
f
ines
to 0/1
commit
|
commitdiff
|
tree
2016-01-10
Teemu Mu
r
t
o
la
Supp
o
rt trajectory analysis w
i
t
h
a
ny atom
subset
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murtola
S
upp
o
rt frames with a
t
om
subsets
i
n selections
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murtola
S
upport arbitr
a
ry subset traject
o
ries in p
o
scalc
.
*
commit
|
commitdiff
|
tree
2016-01-10
Te
e
mu Murtola
Make file names in fatal error
messages more robust
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murtola
Do not warn about missing OpenMP w
i
th GMX_GPU=OFF
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murtola
More co
n
fig
.
h m
a
cros to 0
/
1
commit
|
commitdiff
|
tree
2016-01-10
Teem
u
M
u
rtola
Convert some
c
onfig
.
h ma
c
ros t
o
u
s
e
0/1
commit
|
commitdiff
|
tree
2016-01-05
Teemu Murtola
U
p
d
ate packagi
n
g
build
commit
|
commitdiff
|
tree
2015-12-31
Tee
m
u Murtola
Report us
e
d d
e
fi
n
es in
check
-
s
ource
commit
|
commitdiff
|
tree
2015-12-29
T
e
emu Mu
r
tola
Pac
k
a
ging build script
f
or
w
eb sit
e
commit
|
commitdiff
|
tree
2015-12-29
Teemu Murtola
Reduce inputrec
.
h
d
ependencies
commit
|
commitdiff
|
tree
2015-12-27
T
e
emu Murtola
Improve t
e
x
t
w
ritin
g
in h
e
lp
outpu
t
commit
|
commitdiff
|
tree
2015-12-27
Tee
m
u
M
u
rtola
Sour
c
e packagi
n
g
w
i
th
n
ew releng
commit
|
commitdiff
|
tree
2015-12-27
T
e
emu Murtola
Further vec
.
h clean
u
p
commit
|
commitdiff
|
tree
2015-12-26
Teemu Murtola
C
l
ean
u
p
vec
.
h
commit
|
commitdiff
|
tree
2015-12-24
Teem
u
M
u
r
t
ola
Ad
d
functionalit
y
to TextWriter
commit
|
commitdiff
|
tree
2015-12-20
T
e
emu Murtol
a
Fix mos
t
w
a
rnin
g
s
w
ith Doxygen 1
.
8
.
10
commit
|
commitdiff
|
tree
2015-12-19
Teem
u
Murt
o
la
Update versioning for
new s
c
heme
commit
|
commitdiff
|
tree
2015-12-16
Teemu Murt
o
la
Move calcgrid
.
* to f
f
t/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murto
l
a
Move main
.
*, s
p
litter
.
*
,
g
mx
_
om
p
_nthreads
.
* to
m
dlib
commit
|
commitdiff
|
tree
2015-12-15
Teemu
M
urto
l
a
Move readinp
.
*
a
nd wa
r
n
inp
.
* to fileio/
commit
|
commitdiff
|
tree
2015-12-15
Tee
m
u Murtola
Move
ha
r
d
wa
r
e d
e
te
c
tion to hardware/
commit
|
commitdiff
|
tree
2015-12-15
Te
e
mu Mu
r
tol
a
Move some mdrun c
o
de ou
t
of gmxlib/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
Move gpu_utils
etc
.
out
o
f gmxlib
commit
|
commitdiff
|
tree
2015-12-14
Teemu Murtola
Install base
v
ersion
.
h
commit
|
commitdiff
|
tree
2015-12-12
Teemu Murtola
C
r
eate separate module for traject
o
r
y d
a
ta
commit
|
commitdiff
|
tree
2015-12-12
Teemu Murtola
Move di
s
re
.
* and
o
r
ir
e
s
.
* to listed-forces/
commit
|
commitdiff
|
tree
2015-12-12
T
e
emu M
u
r
tola
Move i
f
unc
.
* to topology/
commit
|
commitdiff
|
tree
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