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Clarify behavior of LegacyMdrunOptions.
2020-10-27
M
.
E
ric Irrgang
C
l
arif
y
beh
a
vio
r
of
L
egacyMdrunOptions
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Update im
a
ge name
s
i
n jo
b
defini
t
io
n
s
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
E
ric
I
rrgang
Tell gmxapi to look for MPI, whe
n
appropriate
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
Eric I
r
rg
a
ng
Update Docker
imag
e
bu
i
ld scripts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
E
ric I
r
rgang
Use updated C
I
pipeline rules for Python pack
a
ge tests
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
E
ric Irrgang
Update
gmxap
i
version
detai
l
s
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
Eri
c
I
r
r
g
ang
Cl
a
rify
th
e
GMX_BUIL
D
_MDRUN_ONLY fu
l
l testi
n
g instructions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric Irr
g
ang
Imp
r
ove gmxPytho
n
Disco
v
e
r
y
.
c
m
ake
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric
Irrgang
Don'
t
o
v
e
rride user pro
v
ided CMAKE_OSX
_
DEPLOY
M
ENT_TARGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrgan
g
Handle gmxapi tmpi paramet
e
rs better
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Ir
r
gan
g
Let gmxapi installation
r
ecord the
GROMACS library
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
Eric Irrgang
Use upd
a
ted images for Python CI
j
o
bs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Restri
c
t gmx
a
pi py
t
est tests to `-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgan
g
S
p
ecify
OMP
_
NUM_T
H
READS
f
or P
y
hon CI scripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Cla
r
ifi
c
ations for Resour
c
eAssignment int
e
rface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Sup
p
ort ResourceA
s
si
g
n
m
e
n
t
interface for tMPI
l
ib
r
ary
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
Irrgan
g
Al
l
ow MPI
-
enab
l
ed
c
l
ients to prov
i
de th
e
lib
r
ary communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eri
c
Irrgang
Use MpiContextManage
r
to prov
i
de MPI co
m
munic
a
tor
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
R
e
lo
c
ate MpiContext
M
anager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
I
rrgang
Interfac
e
updates
allo
w
ing client to p
r
ovide MPI communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
Improve
n
aming a
n
d docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
r
ic Irrga
n
g
Document a Md
r
un
n
e
r::Buil
d
er
I
mple
m
entation mem
b
er
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
E
ric Irrg
a
ng
Remov
e
o
utdated workaro
u
n
d
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Er
i
c I
r
rgang
Create and use SimulationInp
u
t
module
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
Refine
the CMak
e
Lists
.
t
xt for M
P
I gmxapi tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
E
r
ic Irrgang
Explic
i
t
ly include STL headers used in
te
s
t
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
E
r
ic Irrgang
Replace filenam
e
-based initializa
t
ion fu
n
c
t
ions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eri
c
Irrgang
Clarify
t
_
inputrec
allocation lo
g
ic in
r
unner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrgang
Use a heap object
for input
r
e
c
i
n gmx::Mdrunner::mdrun
n
e
r
()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric
I
rrg
a
ng
Accept
Python vers
i
ons hi
g
her t
h
an 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
E
r
ic Irrgang
Remove con
d
itional
f
o
r CMa
k
e <
3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eric Irrgang
Allo
w
more g
r
an
u
la
r
i
ty fo
r
publ
i
c interfaces in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Er
i
c Irrgang
Prevent failed comman
d
line_oper
a
tion from publis
h
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Min
o
r additions t
o
gmxapi install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric
I
rrgang
Use import
l
i
b
_r
e
sou
r
ces in Pytho
n
3
.
6 ima
g
es
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
ric I
r
rga
n
g
No
r
malize
docker ima
g
e
n
a
mes
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
F
ix
s
o
me
minor t
y
pesetting issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Ir
r
gang
Improve install docs
links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Move sources for
l
ib
g
mxa
p
i
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric
Irrgang
Remove di
s
abled test for superseded feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric
I
rrgang
Ignore a generated
fi
l
e
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
E
ric Irrgang
Use GMXAPI CM
a
ke optio
n
g
uard
f
or gmxapi target d
e
cla
r
ation
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eri
c
Irrga
n
g
B
e
g
in moving i
n
st
a
lled
interface to `api/
`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Er
i
c Irr
g
ang
Fix libgromacs CMake target insta
l
l syn
t
ax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric Irrgang
Fix l
i
b
g
rom
a
cs
C
M
ake targ
e
t install syntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Irrgang
Clean up simulatorbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric Irrgang
A
dd
m
issing ABI hea
d
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gan
g
Imple
m
ent SimulatorBuil
d
er
.
a
d
d() for BoxDeformationHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Use Topo
l
ogyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
I
onSwapping parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use CenterOfMas
s
Pu
l
ling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Use Repli
c
aEx
c
h
a
nge m
e
mber
i
nste
a
d of build() a
r
gument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
S
imulator
M
o
d
ul
e
s parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric I
r
rgang
U
se Interacti
v
eMD Sim
u
la
t
orB
u
ilder parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Leg
a
cy
I
nput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgan
g
U
s
e Con
s
traintsPa
r
am
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Move Profili
n
g
param
e
ter out
of
simulato
r
builder
.
b
u
ild()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use SimulatorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Implement rem
a
ining Si
m
u
l
a
t
orBuilder
.
add()
m
ethods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Interface for remaining Simula
t
orBuilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
I
rrgang
Simu
l
ator
B
uilder
.
add() for S
t
o
pHan
d
lerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrg
a
ng
Imp
l
ement
S
i
m
u
l
ator
B
uilder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
ric I
r
rgang
Reformat p
a
irs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Ir
r
g
a
ng
Use Gromacs
:
:gmx
t
arge
t
to hint gmxa
p
i tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
E
r
ic Irrg
a
ng
R
e
move worka
r
ound for gcc bug 5826
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irrgang
Imp
r
o
v
e
pytest
outpu
t
hand
l
ing
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eri
c
I
r
rgang
Comp
a
rtm
e
nta
l
ize job
rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
r
ic Irrgang
Improve
u
sag
e
of Python l
o
g
g
i
n
g module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
E
r
ic Irrgang
Ha
n
dle a
r
bit
r
a
ry
d
oxygen versions in Docker image bui
l
d
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eri
c
Irrgang
Remove unused
(
and
b
roken) image from D
o
c
ker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docke
r
i
m
age bui
l
ds: simplif
y
doxygen version h
a
ndling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eri
c
Irrga
n
g
Doc
k
er imag
e
builds: move doxy
g
e
n ha
n
dling to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Extend MPI ensem
b
le
t
esting for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Er
i
c Irrgang
En
a
b
le MPI ensemble testing for gmx
a
pi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Norm
a
lize gmxapi
r
elat
e
d
relea
s
e-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Er
i
c
Irrgang
Reduce
console log out
p
ut from samp
l
e_restr
a
i
nt tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgang
Enable MPI ensem
b
l
e
t
est
i
n
g
for gmxap
i
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric Irrgang
Nor
m
alize gmxa
p
i r
e
lated release-2020 job l
o
gic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrga
n
g
Make sure images h
a
ve /u
s
r/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
Irrgan
g
Upda
t
e docke
r
image b
u
ild scripts for master b
r
a
nch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
ang
Make s
u
re
CI scrip
t
can
c
a
l
l
/bin/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Minor clean up
to buildall
.
s
h
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
rrgang
Al
l
o
w llv
m
o
p
tion alrea
d
y us
e
d in builda
l
l
.
sh script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
Irrga
n
g
Reduce console lo
g
outpu
t
from sa
m
p
le_re
s
traint tests
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eric Irrg
a
ng
R
efine u
s
a
g
e of *job:tags* par
a
meter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
r
i
c
Irrgan
g
U
p
d
ate header sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Er
i
c Irrgang
Require C
+
+17
s
t
andard and STL
f
eatures
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irrgang
Apply more granular C
T
e
s
t
time-out polic
y
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric Ir
r
ga
n
g
Res
o
l
v
e static analyzer
warnin
g
s
fr
o
m google tests
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric Irr
g
ang
Avoid temporar
y
string
s
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
E
r
ic Irrga
n
g
N
ote CUDA builds i
n
job names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eri
c
Ir
r
g
a
ng
Update bundle
d
pybind
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
E
ric Irrgang
O
n
ly s
e
t GMX_PYTHON
_
P
A
C
K
A
GE=ON whe
r
e nee
d
ed
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
Eric
I
rrgang
U
s
e CMake 3
.
1
2
+ facilities for detecting P
y
t
hon
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric I
r
r
gang
C
h
ange default CMak
e
ver
s
io
n
to 3
.
13
.
0 for CI
i
m
a
g
e
s
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrg
a
ng
Require CMake >=
3
.
13
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Fix invalid g
i
tl
a
b-ci
.
yml
commit
|
commitdiff
|
tree
2020-04-09
M
.
E
ric Irr
g
ang
Allow usef
u
l
C
I to run in
f
orks
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric
I
r
r
gang
E
x
plicitly
s
et UTF-8
encoding
f
or g
m
xapi CLI interaction
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eric Irrg
a
ng
Prepare Python environments
for
Gi
t
Lab CI pipe
l
ine
.
commit
|
commitdiff
|
tree
next