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Update instructions in containers.rst
2020-12-04
M
.
Er
i
c Ir
r
gang
Add CI j
o
bs
for g
m
x
api 0
.
3
commit
|
commitdiff
|
tree
2020-12-04
M
.
Eric Irrgang
Updat
e
r
ules for r
e
lea
s
e-2021
.
commit
|
commitdiff
|
tree
2020-12-04
M
.
E
ric Ir
r
g
ang
S
e
parat
e
job scrip
t
f
i
les for gmx
a
pi package versions
.
commit
|
commitdiff
|
tree
2020-12-03
M
.
Eric Irrgang
Improve gm
x
api C++ te
s
t covera
g
e f
o
r failed mdrun
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eric Irr
g
ang
One argument
p
er
line for long functi
o
n s
i
gnatures
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Eric Irrga
n
g
Look for
t
h
e various
p
o
ssible
names of the gromacs
.
.
.
commit
|
commitdiff
|
tree
2020-11-20
M
.
E
r
i
c Ir
r
ga
n
g
Create
CMake targets for each of the modules
.
commit
|
commitdiff
|
tree
2020-11-18
M
.
Eric Irrgang
Rep
l
ace gmxapi `er
r
oroutput` wit
h
`stder
r
`
and `stdout`
commit
|
commitdiff
|
tree
2020-11-17
M
.
Eric Irrgang
S
eparate the testutils mo
d
ule
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
Eric
I
rrgang
gmx
a
p
i versio
n
i
ng up
d
ates
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric
Irrg
a
ng
Be more explicit
a
b
o
u
t
bu
i
ld-tree-onl
y
dependencies
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Irrga
n
g
Provide a ca
t
ch-all target for
l
i
b
rary modules
.
commit
|
commitdiff
|
tree
2020-11-12
M
.
Er
i
c Ir
r
gan
g
Provi
d
e common l
i
brary
headers through new C
M
ake
tar
g
et
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
Eric Irrgang
Help clie
n
ts find d
e
pe
n
dencies of i
m
por
t
ed CMake targ
e
t
s
.
commit
|
commitdiff
|
tree
2020-11-04
M
.
Eric Irr
g
ang
Estab
l
ish
`api/` as
the ho
m
e for installed
h
eaders
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irr
g
ang
R
emov
e
a
n u
n
necessary trans
i
tive
dependency of im
p
orte
d
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Er
i
c Irrgang
Use the correct CI scr
i
pt for
s
ample_
r
estraint jobs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgan
g
N
o
rmal
i
ze FindM
P
I hints
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric I
r
rgang
Clarify b
e
h
a
v
ior of Lega
c
yMdru
n
Options
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irr
g
a
n
g
Update image names
in job de
f
i
ni
t
i
ons
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Er
i
c
Irrgang
Tell
g
mxapi to
l
o
o
k
for MPI,
w
hen appropriate
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
E
r
i
c Irrgang
Update Docker image build scripts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
E
ric Ir
r
gang
Use up
d
ated CI pip
e
line
r
ules for P
y
thon package te
s
ts
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric Irrgang
Update gmx
a
pi
v
e
rsio
n
details
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
Eric Ir
r
gang
Clarify the
G
MX_BUILD_MD
R
UN_ONL
Y
full
testing instructions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric I
r
r
g
a
n
g
Improve gmxPyt
h
onDiscov
e
ry
.
cmake
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric Irrgang
Don'
t
override user p
r
ovid
e
d CMAKE_O
S
X
_
DEPLO
Y
MENT_T
A
RGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irr
g
ang
Handle
gmxap
i
tmp
i
p
a
r
a
m
e
t
ers
better
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric
I
rrgang
Let
g
m
x
api installatio
n
r
e
cord th
e
G
ROMACS library
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
Eri
c
Irrg
a
ng
Use updated images for Python CI
j
obs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Restrict
g
mxapi pyt
e
st tests to
`-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Specif
y
O
M
P
_
NUM_THREADS
f
o
r
Pyhon CI scr
i
p
t
s
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
I
rrgan
g
Cl
a
rifications
f
or Resou
r
ce
A
ssignme
n
t
i
nterface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irr
g
a
n
g
Support Re
s
o
u
rc
e
Assignment i
n
terface f
o
r tMPI library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
Irrgang
Allo
w
M
P
I
-
enabled cli
e
nts to pro
v
ide the
l
i
brary communica
t
or
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrga
n
g
Use M
p
i
ContextManage
r
to p
r
ovid
e
MP
I
commun
i
ca
t
or
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Relocate MpiContextManager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
ric Irrgang
I
nte
r
f
a
ce updates allowing
cl
i
e
n
t to provide MPI com
m
unicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric
I
r
rgang
Improve
namin
g
a
n
d
d
ocs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
r
i
c
Irrgang
D
o
cument
a Mdru
n
ner::Builder
I
mplementation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Ir
r
gang
Remove outdated workaro
u
nd
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
Create and use SimulationInput module
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric I
r
r
g
an
g
Refine the CMakeLis
t
s
.
txt for MPI gmxapi
t
ests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
E
r
i
c
Ir
r
g
a
ng
Explicitly
i
nclude STL headers used in test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eric Irrgang
Replace filen
a
me
-
based
i
n
i
tializ
a
ti
o
n functions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrgang
Clarify t_inputrec
a
ll
o
cation logi
c
in runn
e
r
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrgang
Use a heap obje
c
t fo
r
i
npu
t
rec in gmx::Mdrunner::mdrun
n
er(
)
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Accept Python versions
hi
g
he
r
than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Remove con
d
itional
f
o
r
CMake <
3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eric I
r
rgang
Allow more granularity
for public interfaces in bu
i
l
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Pre
v
e
n
t fa
i
l
ed
commandl
i
n
e
_operati
o
n from publishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Mino
r
additio
n
s to gmx
a
pi
i
nstall
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Use i
m
p
o
rtlib_reso
u
rces in P
y
thon 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrg
a
ng
Normal
i
ze docker i
m
a
g
e
names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric I
r
rgang
Fix so
m
e
m
inor typ
e
settin
g
issu
e
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
ric Irrgang
I
m
prove install docs links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
r
ic Irrga
n
g
M
ove sources for
l
ibgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
r
ic Irrg
a
ng
Remove disabled
test for superseded feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgan
g
Ignore a generated file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
E
r
ic Ir
r
g
ang
U
s
e GMXAPI CMake option guard for gmx
a
pi target de
c
la
r
ation
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
E
r
ic Ir
r
gang
Begin moving installed
i
nte
r
fa
c
e
t
o `api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric
I
r
rgang
Fix libgromacs C
M
a
k
e tar
g
et instal
l
synt
a
x
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eri
c
Irrgang
Fix libg
r
omacs CMa
k
e
t
ar
g
et install syntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
E
r
ic Irrgang
Clean up simulatorbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric Irrga
n
g
Add mis
s
i
n
g ABI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Imp
l
ement
S
imulator
B
uilder
.
add() for Bo
x
De
f
ormati
o
nHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Use
T
opologyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
ng
Use I
o
nSw
a
pping parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Use
Center
O
fMassPu
l
ling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
U
se ReplicaExcha
n
ge member instead of build() argum
e
nt
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Use SimulatorModules para
m
eter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgan
g
Use Interactive
M
D
SimulatorBuilder parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Use Le
g
ac
y
I
nput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Use ConstraintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgan
g
Move Pro
f
ilin
g
parameter out of simulator
b
u
i
l
d
er
.
bu
i
ld()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Use
S
im
u
l
a
torEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
I
mplement remaining Simulato
r
Builder
.
add
(
)
m
et
h
ods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
Interfac
e
for remaining SimulatorBuilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Simula
t
o
r
Builder
.
add() for Stop
H
andlerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
I
mplement Si
m
ulatorBuilde
r
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irr
g
a
n
g
Reformat
p
airs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Er
i
c Irrgang
Use Gromacs::gm
x
targe
t
t
o
hint gmxap
i
tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric
I
rrgang
Remov
e
work
a
round for gcc b
u
g 58
2
6
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eri
c
Irrgan
g
Impro
v
e pytes
t
output
h
and
l
ing
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Compartm
e
ntalize j
o
b rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
I
mprove usage of Python
logg
i
ng module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric
Irrgan
g
H
a
ndle arbit
r
ary do
x
ygen
ver
s
ions in Dock
e
r image bu
i
ld
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
r
ic Irrgang
Remove unuse
d
(and bro
k
en
)
i
mage
f
r
om Docker
i
mag
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eri
c
Irrg
a
ng
D
o
c
k
e
r image bu
i
lds:
simplify d
o
xy
g
en
version handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric Ir
r
g
a
ng
Doc
k
er image builds
:
m
o
v
e doxyg
e
n handl
i
ng to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Extend MPI ensemb
l
e tes
t
ing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
I
rrgang
Enable MPI ensemble tes
t
ing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irr
g
ang
Normalize gm
x
api re
l
a
t
ed rele
a
se-20
2
0 j
o
b logic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric Irrgang
Red
u
ce con
s
ole
log output from samp
l
e_restr
a
int tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eri
c
I
r
rg
a
n
g
Enable MP
I
e
nsemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eri
c
Ir
r
gang
Normalize
gmxapi relat
e
d release-2020 job lo
g
ic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric I
r
r
gang
Make sur
e
images ha
v
e
/
usr/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Update docker ima
g
e bui
l
d scripts f
o
r
master bra
n
ch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrga
n
g
M
a
ke sure CI sc
r
ipt ca
n
call /
b
i
n/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irrgang
Mi
n
or clea
n
up t
o
buildall
.
sh
commit
|
commitdiff
|
tree
next