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Work around memory leak in t_state
2016-10-15
Teemu Murtola
Work around memory le
a
k in t
_
state
commit
|
commitdiff
|
tree
2016-10-15
Teemu Murt
o
la
F
i
x
most me
m
ory le
a
ks rec
e
ntly int
r
oduced
commit
|
commitdiff
|
tree
2016-10-14
Teemu Murtola
Use gmx_mtop_t in
selections, part 3
commit
|
commitdiff
|
tree
2016-10-14
Teemu Mur
t
ola
Use
g
mx_
m
to
p
_t in s
e
lections, part 2
commit
|
commitdiff
|
tree
2016-10-13
Teem
u
Murtola
Use
gmx_m
t
op_t in selec
t
ions, part 2
commit
|
commitdiff
|
tree
2016-10-13
T
eemu M
u
rtola
Add b
a
c
k-mapping
to KeyValue
T
r
e
eTransform
commit
|
commitdiff
|
tree
2016-10-13
T
e
emu Murtola
Update
b
undled TNG
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murt
o
la
Getter for
m
apped paths from Key
V
a
l
ueTr
e
eTransform
commit
|
commitdiff
|
tree
2016-10-12
Teemu
M
urtol
a
Use gmx_mtop_
t
i
n sele
c
tions, par
t
1
commit
|
commitdiff
|
tree
2016-10-12
Teemu Murtola
Wrap sel
.
metho
d
ev
a
lu
a
t
io
n
parame
t
ers
to stru
c
t
commit
|
commitdiff
|
tree
2016-10-11
Teemu Murt
o
la
Sup
p
or
t
concurrent t_topology
and gmx_mtop_t use
commit
|
commitdiff
|
tree
2016-10-11
Teemu M
u
rtola
C
h
e
ck a
t
om
mass a
v
a
i
lab
i
lity
in selections
commit
|
commitdiff
|
tree
2016-10-05
Teemu
Murto
l
a
Support different key mat
c
hing in
K
e
y
ValueTreeTransform
commit
|
commitdiff
|
tree
2016-10-05
T
ee
m
u M
u
rtola
Merge "Merge b
r
anch r
e
lease-5-
1
into
r
elease-201
6
"
.
.
.
commit
|
commitdiff
|
tree
2016-09-24
T
e
emu Murto
l
a
Fi
x
d
e
fault nice le
v
el in mdrun
-
only bu
i
ld
commit
|
commitdiff
|
tree
2016-09-12
Teemu
Murto
l
a
Fix various mem
o
ry l
e
a
k
s
commit
|
commitdiff
|
tree
2016-09-07
Teemu Murtola
Clean up CTest t
e
s
t management
commit
|
commitdiff
|
tree
2016-08-30
Teemu Murtola
Ba
s
i
c suppo
r
t
f
or
tr
a
n
s
f
orm
i
ng KeyValueTree
s
commit
|
commitdiff
|
tree
2016-08-27
T
eemu Murtola
Support KeyValueTree
obje
c
ts in refdat
a
commit
|
commitdiff
|
tree
2016-08-18
Teem
u
Murtol
a
Ch
e
ck for unused refd
a
ta value
s
commit
|
commitdiff
|
tree
2016-08-18
Teemu
Murtola
Gene
r
i
c
structured
key-value tree for options
commit
|
commitdiff
|
tree
2016-08-18
Teem
u
M
u
r
t
ola
Support
f
or non-string option value as
s
i
gnm
e
nt
commit
|
commitdiff
|
tree
2016-08-17
T
eemu Murtola
Basic support f
o
r arr
a
y
-of-structs in optio
n
s
commit
|
commitdiff
|
tree
2016-08-17
Teemu Mur
t
ola
Generalize
a
nd simplify option valu
e
s
t
orage
commit
|
commitdiff
|
tree
2016-08-17
Teemu M
u
rtola
Generalize opti
o
n section interna
l
s
commit
|
commitdiff
|
tree
2016-08-17
Te
e
mu Murtola
R
eimplement su
b
s
ec
t
ion
s
in Option
s
commit
|
commitdiff
|
tree
2016-08-04
Teemu
M
urtol
a
Fix/improve doc links in templat
e
/README
commit
|
commitdiff
|
tree
2016-08-01
Te
e
mu Murt
o
la
Function t
o
split d
e
limited strings
commit
|
commitdiff
|
tree
2016-07-14
T
e
emu Murtola
U
se newer gcc for coverage
commit
|
commitdiff
|
tree
2016-07-07
Te
e
mu
M
urtola
Ch
a
nge
h
a
n
d
ling for missing
r
e
l
e
ng docs
commit
|
commitdiff
|
tree
2016-06-30
T
e
emu Murtola
Extract string parsing r
o
utines to u
t
i
lity
commit
|
commitdiff
|
tree
2016-06-28
T
e
emu Murtola
S
plit up compa
r
e
.
*
commit
|
commitdiff
|
tree
2016-06-27
Teemu Murtola
Facto
r
y fo
r
c
re
a
tin
g
t_inp
u
trec
commit
|
commitdiff
|
tree
2016-06-01
T
e
emu Murtola
Use
C++ replacement fo
r
md_logging
.
*
commit
|
commitdiff
|
tree
2016-06-01
Teemu M
u
rtola
Basic C++ logging int
e
rfa
c
e
commit
|
commitdiff
|
tree
2016-05-31
Teem
u
Murt
o
la
Imp
r
ov
e
mak
e
_ndx he
l
p text
commit
|
commitdiff
|
tree
2016-05-25
Tee
m
u Murtola
Sup
p
o
rt
f
o
r real MPI
u
n
i
t tes
t
s
commit
|
commitdiff
|
tree
2016-05-24
Teemu
M
urto
l
a
T
e
st
s
for
sin
g
le-rank thre
a
d affi
n
i
t
y
setting
commit
|
commitdiff
|
tree
2016-05-21
T
e
emu Murtola
Pass number of l
o
cal threads to
thread aff
i
nity
commit
|
commitdiff
|
tree
2016-05-21
Teemu M
u
rto
l
a
Allow creat
i
ng mock HardwareTopology objects
commit
|
commitdiff
|
tree
2016-05-21
Teem
u
Murtola
Use only Hardware
T
o
p
ology for threa
d
a
ffinity
commit
|
commitdiff
|
tree
2016-05-21
Teemu Murtola
Merge br
a
nch rel
e
a
s
e
-201
6
commit
|
commitdiff
|
tree
2016-05-21
Teemu Mur
t
ola
Bu
m
p version
n
umbers
f
or 201
7
d
evelo
p
ment
commit
|
commitdiff
|
tree
2016-05-17
Tee
m
u Murtola
F
ix some thread affinity cases
commit
|
commitdiff
|
tree
2016-05-10
T
eemu Mu
r
tol
a
Ad
d
ition
a
l Jenkins documentatio
n
commit
|
commitdiff
|
tree
2016-05-10
T
e
emu
M
u
r
tola
Incl
u
de releng docum
e
nta
t
i
o
n to dev
e
loper guide
commit
|
commitdiff
|
tree
2016-05-08
Teemu Murtol
a
Sup
p
ort for OpenCL CI builds
commit
|
commitdiff
|
tree
2016-05-05
T
ee
m
u Murtola
Me
r
ge bran
c
h
rele
a
se-5-1
commit
|
commitdiff
|
tree
2016-05-05
T
eemu Murtola
Make Sphinx build silent
fo
r
version 1
.
3+
commit
|
commitdiff
|
tree
2016-05-03
Te
e
mu Murtola
M
a
r
k
optio
n
a
l
input/outp
u
t files
in
gmx
o
rder
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtola
Use Har
d
wareTopology to set nthreads_hw_avail
commit
|
commitdiff
|
tree
2016-04-28
Teemu Mu
r
tol
a
Remove gmx_hw
_
i
n
fo_
t
::ncore
commit
|
commitdiff
|
tree
2016-04-27
T
e
emu
Mu
r
tol
a
I
mprove re
l
ease workflow testing
commit
|
commitdiff
|
tree
2016-04-27
T
e
emu
Murtol
a
D
i
sable multiple
r
anks
for
n
on-MPI un
i
t tes
t
s
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Fix
issues with fai
l
i
ng thr
e
ad affinity setting
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtola
Merg
e
"Mer
g
e branch release-
5
-
1
"
commit
|
commitdiff
|
tree
2016-04-18
Te
e
m
u Murt
o
la
Make thread affin
i
ty failure
s
al
w
a
y
s end up in log
commit
|
commitdiff
|
tree
2016-03-30
Teemu Mur
t
o
l
a
M
ak
e
includ
e
sorter
.
py work with Doxy
g
en
1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtol
a
Fix erro
r
reporting for do
c
umentation
b
uild
commit
|
commitdiff
|
tree
2016-03-28
Teemu M
u
rtol
a
More support for rel
e
ase
w
o
rkflow
commit
|
commitdiff
|
tree
2016-03-26
Teemu
M
urtola
Ignore
e
mpty GM
X
LIB
commit
|
commitdiff
|
tree
2016-03-14
Tee
m
u Murtola
Add
t
ests
f
or empt
y
s
trin
g
s
i
n re
f
dat
a
commit
|
commitdiff
|
tree
2016-03-13
Teemu Murtola
S
upport replacing s
o
lvent in inse
r
t-mol
e
cules
commit
|
commitdiff
|
tree
2016-02-01
Teemu
M
u
rt
o
la
Handle p
d
bi
n
fo
i
n
AtomsBuilde
r
commit
|
commitdiff
|
tree
2016-01-28
T
e
emu Murtol
a
Update
build sc
r
i
pts to releng ch
a
nges
commit
|
commitdiff
|
tree
2016-01-24
Teemu Murtola
Document
l
i
m
itations
on 32-
b
it Linu
x
commit
|
commitdiff
|
tree
2016-01-12
T
e
e
m
u Murto
l
a
M
a
ke
G
MX_MP
I
alwa
y
s
d
efined
to 0/1
commit
|
commitdiff
|
tree
2016-01-12
T
eemu Murtola
M
ove flags out of
t
_
t
r
x
frame
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtol
a
Remove histori
c
a
l
tim
e
s from t_trx
f
rame
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtola
Support pass
i
ng tarbal
l
MD5
f
or webpa
g
e
b
uild
commit
|
commitdiff
|
tree
2016-01-12
Teemu Murtola
R
e
m
o
ve vmdplugin from t_trxframe
commit
|
commitdiff
|
tree
2016-01-11
Teem
u
Murtola
C
onv
e
rt more co
n
fig
.
h defines to
0/1
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murtola
Suppo
r
t trajectory analysis with
a
ny a
t
om subset
commit
|
commitdiff
|
tree
2016-01-10
Te
e
mu
M
urtola
S
upport
f
r
a
mes
w
ith atom subsets in selections
commit
|
commitdiff
|
tree
2016-01-10
Te
e
mu M
u
rtola
S
u
pport
arbitrary subset tr
a
ject
o
ries in poscalc
.
*
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murto
l
a
Make fi
l
e names i
n
fatal er
r
or messages mo
r
e
r
obust
commit
|
commitdiff
|
tree
2016-01-10
Teemu Murt
o
la
Do not warn about missin
g
Op
e
nMP wi
t
h GMX_GPU=OFF
commit
|
commitdiff
|
tree
2016-01-10
Tee
m
u Mu
r
tola
More c
o
nfig
.
h macro
s
to 0/
1
commit
|
commitdiff
|
tree
2016-01-10
T
eemu M
u
rtola
Convert
som
e
config
.
h macros to use 0
/
1
commit
|
commitdiff
|
tree
2016-01-05
Teem
u
Murtola
Update
packagi
n
g build
commit
|
commitdiff
|
tree
2015-12-31
Tee
m
u Mur
t
ola
Repor
t
used
d
efine
s
in check-source
commit
|
commitdiff
|
tree
2015-12-29
Teemu Murtola
P
a
ckaging build scri
p
t for web site
commit
|
commitdiff
|
tree
2015-12-29
T
eemu Murtola
Reduce in
p
u
t
r
ec
.
h depe
n
d
e
n
c
ie
s
commit
|
commitdiff
|
tree
2015-12-27
Tee
m
u Murtola
Imp
r
ove text
writing in
h
elp
output
commit
|
commitdiff
|
tree
2015-12-27
Teem
u
Mu
r
tola
S
o
urce packaging with new releng
commit
|
commitdiff
|
tree
2015-12-27
Teemu Mur
t
ola
Further vec
.
h cleanup
commit
|
commitdiff
|
tree
2015-12-26
T
e
e
mu Murt
o
la
Cle
a
n u
p
ve
c
.
h
commit
|
commitdiff
|
tree
2015-12-24
Teemu Murtola
Add functionality to Tex
t
Writer
commit
|
commitdiff
|
tree
2015-12-20
Teem
u
Murtol
a
F
i
x
most
warnings with
D
o
xyge
n
1
.
8
.
10
commit
|
commitdiff
|
tree
2015-12-19
Teemu Mur
t
ola
Updat
e
versi
o
ning f
o
r new s
c
h
eme
commit
|
commitdiff
|
tree
2015-12-16
Teemu Mur
t
ola
Mo
v
e calcgrid
.
* to fft/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
Move main
.
*, splitt
e
r
.
*, gmx_omp_nthreads
.
*
to mdlib
commit
|
commitdiff
|
tree
2015-12-15
Teemu M
u
rtola
Mov
e
r
eadi
n
p
.
* and warn
i
np
.
* t
o
f
i
leio/
commit
|
commitdiff
|
tree
2015-12-15
Teemu M
u
rto
l
a
Move h
a
rdware detectio
n
to h
a
rdware/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Mur
t
ola
Move some mdrun code out of gmxlib/
commit
|
commitdiff
|
tree
2015-12-15
Teemu Murtola
Move gpu_utils etc
.
out
o
f
g
mxlib
commit
|
commitdiff
|
tree
2015-12-14
T
eemu M
u
rtola
Inst
a
ll baseversion
.
h
commit
|
commitdiff
|
tree
2015-12-12
Teemu Murtola
Create se
p
arate module for
t
rajector
y
d
a
ta
commit
|
commitdiff
|
tree
2015-12-12
Teemu Murto
l
a
Move disre
.
*
a
nd
orires
.
* to listed-forces/
commit
|
commitdiff
|
tree
2015-12-12
Te
e
mu Murtola
Move ifunc
.
* to topology/
commit
|
commitdiff
|
tree
next