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Document a Mdrunner::BuilderImplementation member.
2020-09-18
M
.
Er
i
c Irrgang
Document a
Mdrunn
e
r::Build
e
rImplementation
me
m
ber
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Irr
g
ang
Re
m
ov
e
outdated wor
k
around
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric I
r
r
g
ang
Create
and use SimulationInput m
o
du
l
e
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric
I
rrgang
Refi
n
e the
C
MakeLists
.
txt for MPI
g
m
x
api test
s
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eri
c
I
r
r
gang
E
x
plicitly
i
nclude STL headers used in
t
e
s
t
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eric Irrgang
Replace
f
ilena
m
e-b
a
sed initialization functions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
E
r
ic Irr
g
ang
Clarify
t_inputrec a
l
location logic in
r
unner
.
c
p
p
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric
I
rrgang
Use a heap object for inpu
t
rec
i
n gmx::Mdr
u
nner::mdrunn
e
r
()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
A
ccept Pyth
o
n versions hi
g
her th
a
n 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Remove condition
a
l for CMake < 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Er
i
c Irrgang
Allow m
o
re granularity
f
or pub
l
ic interfaces
in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
P
r
event f
a
ile
d
comm
a
ndlin
e
_opera
t
ion from publishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrg
a
ng
Minor additions to gmxapi install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgan
g
Use
i
m
p
ortlib_resource
s
i
n
Python 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
Irrgang
Normalize dock
e
r image names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Fix some minor typesettin
g
issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
I
rrgang
Improve
ins
t
a
l
l doc
s
l
inks
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
ric
I
rrg
a
ng
Mo
v
e sources for l
i
bgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Ir
r
ga
n
g
Remove disa
b
l
ed test for sup
e
rs
e
d
e
d fe
a
tu
r
e
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrga
n
g
Ignore a genera
t
ed
f
i
l
e
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric I
r
rgang
Use GMXAPI CMake option guard for gmxapi targe
t
declaration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric
I
r
rgang
Beg
i
n moving
i
n
s
talled
i
nterfa
c
e to `api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Irrgang
Fix libgromacs CMake targe
t
instal
l
s
y
nt
a
x
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
E
ric Irr
g
ang
Fix
l
i
b
gromacs CMake target install synta
x
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Irrgang
Clean up simulat
o
rbui
l
der
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric Irrgang
Add missing
A
BI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement SimulatorBu
i
lder
.
add() for BoxDeformation
H
andle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irr
g
ang
Use To
p
o
l
o
g
yDat
a
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use IonS
w
apping par
a
meter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c
Irrgang
Use
C
e
nterOfMassPullin
g
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Repli
c
aExc
h
a
n
ge member inst
e
ad o
f
build() argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Us
e
Sim
u
latorMod
u
l
es parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c I
r
rgang
U
s
e Interactive
M
D SimulatorBu
i
lder p
a
r
ameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
I
r
rgang
U
se LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric I
r
r
gang
Use ConstraintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Ir
r
gang
Move P
r
ofiling
p
ar
a
met
e
r
out
of simulat
o
rbuil
d
er
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
S
imulatorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgan
g
Impleme
n
t remaining S
i
m
ulator
B
uilder
.
add() me
t
hods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Inte
r
face for remai
n
i
n
g
Simu
l
atorB
u
ilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irr
g
an
g
S
i
mu
l
atorBuilder
.
add() for
S
topHand
l
erBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Impl
e
ment Sim
u
la
t
orBuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric I
r
rgang
Reformat pair
s
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irr
g
ang
Use Gromacs
:
:gmx target to hint
gmxapi
t
ests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgang
Remov
e
workaround for gcc bug 5
8
2
6
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Er
i
c Irrgang
Impr
o
ve pytes
t
output hand
l
i
n
g
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
r
ic Irrgang
Compartm
e
n
talize job rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
ric I
r
rgang
Imp
r
ove usa
g
e of Python
l
ogging module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eri
c
Irrgang
Handle arbitr
a
ry doxygen versions in
D
ocker
i
mag
e
build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Ir
r
ga
n
g
Remove unus
e
d
(
and
b
roken
)
image from Docke
r
imag
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
r
ic Irrgang
Docker ima
g
e builds: sim
p
lif
y
doxygen
v
e
rsion han
d
li
n
g
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric
I
r
r
g
ang
D
o
cker image
buil
d
s:
move doxyg
e
n
h
andling to a s
e
par
a
te
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eri
c
Irrgang
Exten
d
MPI ens
e
mble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Enable
MPI ensembl
e
t
esti
n
g
for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Normalize
g
mxapi related
release-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
E
ric I
r
rgang
Reduce c
o
nsole log output
f
rom sample_re
s
traint tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irr
g
ang
Enable MPI
e
nsemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric Irrgang
Norma
l
i
z
e
gmx
a
pi related r
e
lease-2020
j
ob logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrga
n
g
Make sure
i
mages
have /
u
sr/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Update docker image build scri
p
ts for master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
Irrgan
g
Make su
r
e
C
I
s
c
r
ipt can
c
a
ll /bin/en
v
pytho
n
`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Mino
r
cl
e
an up to b
u
i
l
d
all
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Ir
r
gang
Allow llvm option a
l
r
e
a
d
y
used in buildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrga
n
g
Reduce c
o
ns
o
le l
o
g ou
t
put from sam
p
le_restr
a
int tests
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eric Irrgang
R
efine usa
g
e of *job:tags* p
a
r
ameter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric
Irrgang
Up
d
ate
h
eader
s
orti
n
g
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Er
i
c Irrga
n
g
Require
C++17 standard and
S
TL
f
eatures
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Ir
r
gang
Apply more granular CTest t
i
me-out policy
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric Irrgang
R
e
solve stat
i
c analy
z
er
warnings from
g
oogle
t
ests
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
E
r
ic Irrgang
Avoid tempora
r
y
string
s
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eri
c
I
r
rgang
Note
CUDA builds in job names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Er
i
c Irrgang
Upd
a
te bundl
e
d pybind
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrgang
O
n
l
y set GMX_PYTHON_PACKAGE=ON where needed
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
E
r
ic Irrgang
Use CMa
k
e 3
.
1
2
+ facilitie
s
for
detecti
n
g
P
ython
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric I
r
rga
n
g
Change default
C
Make version to
3
.
13
.
0 for CI images
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric I
r
rgang
Requi
r
e CMake >=3
.
1
3
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Fix i
n
valid gi
t
lab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-04-09
M
.
Eric Irrgang
All
o
w
useful
CI to run in forks
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric I
r
rgang
Expl
i
c
i
tly set
U
T
F
-8 encoding for gmx
a
pi CL
I
interaction
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eri
c
Irrgang
P
repare P
y
tho
n
environment
s
for Gi
t
Lab
CI
p
ip
e
line
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Er
i
c Irr
g
ang
I
mpro
v
e gmxapi
P
y
t
h
o
n package dependency
r
e
solutio
n
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Er
i
c Irrgang
Pru
n
e
change-management
.
rst and update links
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
Eric Irrgang
Modernize
s
ome Pyth
o
n
subprocess call
s
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
E
r
ic
Irrgang
Avoid
a
c
c
ide
n
tall
y
initializi
n
g
pye
n
v in CI images
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgang
Prepare Python en
v
i
ronments for G
i
tLab C
I
pipeli
n
e
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrg
a
ng
Update s
c
ripts fo
r
all of the requested pre-commi
t
.
.
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Ir
r
gang
Require Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric
I
rrga
n
g
Comp
a
r
tment
a
liz
e
hpccm build s
t
a
g
es
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric Irrgang
B
e friendlier
w
.
r
.
t
.
linkch
e
c
ker
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Er
i
c Irr
g
a
ng
Mock hpccm import so infrastru
c
ture
d
ocs b
u
ild ea
s
ily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Extract logic for when CI
jobs ex
e
cute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
N
ormalize some more job names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
S
i
mplify archive
.
g
itlab
-
ci
.
yml
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgan
g
Re
m
ove
redundant jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgan
g
F
ix
dupl
i
cate variables
paramete
r
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Irr
g
a
n
g
Add required In
f
rastructure fo
r
G
itlab merg
e
s
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
gan
g
N
o
rma
l
iz
e
naming for
g
romacs build/testing
jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Remove som
e
unnecess
a
r
y
indirectio
n
i
n job definitions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
rrgang
Consolidate
.
u
s
e-
c
l
a
ng
X
C
I
job
mix-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
ga
n
g
Consolidate
.
use-gccX
C
I
job mix-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
ic Irrgang
Adopt
C
I
job namin
g
g
u
i
d
elines
.
commit
|
commitdiff
|
tree
next