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Update instructions in containers.rst
2020-12-04
M
.
Eric Irrgang
Add CI
j
o
bs for gmxapi 0
.
3
commit
|
commitdiff
|
tree
2020-12-04
M
.
Eric Irrgang
Up
d
ate ru
l
es for rel
e
ase-2
0
21
.
commit
|
commitdiff
|
tree
2020-12-04
M
.
Er
i
c Ir
r
gang
Sep
a
rate job
s
cript fi
l
es for gmxapi p
a
ckage
versions
.
commit
|
commitdiff
|
tree
2020-12-03
M
.
Eric Irrgang
I
mp
r
ove gmxapi C++ test coverage for faile
d
m
d
run
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eric Ir
r
gang
One a
r
gument pe
r
line for long functi
o
n signat
u
r
es
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Eric Irrgang
Look for the various p
o
s
sible name
s
of the gromacs
.
.
.
commit
|
commitdiff
|
tree
2020-11-20
M
.
Eric Irrg
a
ng
Creat
e
CM
a
ke targets for
each of the modules
.
commit
|
commitdiff
|
tree
2020-11-18
M
.
Eric Irrgang
Repla
c
e
gmxapi `erroro
u
tput` with `stderr` and `stdout`
commit
|
commitdiff
|
tree
2020-11-17
M
.
Eric Irrgang
Separ
a
te the
t
estutils
modu
l
e
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
E
ric I
r
rgang
gmxapi
versioning
update
s
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Er
i
c Irr
g
a
ng
Be mo
r
e explicit ab
o
ut
build-
t
ree-o
n
l
y
de
p
endencies
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Irrgang
Provi
d
e a catch-a
l
l
t
a
r
get fo
r
lib
r
a
ry modules
.
commit
|
commitdiff
|
tree
2020-11-12
M
.
Eric Irrgang
Provide common library h
e
aders throug
h
new CMake target
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
Eric Irrgang
H
elp clients find dependencies of im
p
orted CMake targets
.
commit
|
commitdiff
|
tree
2020-11-04
M
.
E
r
ic Irr
g
ang
E
stabli
s
h
`
api/`
as
the ho
m
e for
installed
h
eaders
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Er
i
c
Irrgang
R
e
m
o
ve a
n
unnecessary t
r
ansit
i
ve depend
e
ncy of imported
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrg
a
ng
Use the correct CI s
c
ript
for sample_restrai
n
t
j
o
bs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
No
r
mali
z
e FindMPI
h
ints
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric I
r
rgang
Clarify
b
e
h
a
v
io
r
of LegacyMdrunOptions
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrga
n
g
U
pdate
i
m
age
na
m
e
s in job def
i
n
i
t
i
ons
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Eric Irrgang
Tell gmxapi to look for MP
I
, when approp
r
i
a
t
e
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
Eric Irrgang
Update D
o
cke
r
i
m
a
g
e b
u
ild scripts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
E
r
ic
I
r
rgan
g
Use updated CI pipel
i
ne rules f
o
r Pyth
o
n pac
k
age test
s
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric
Irrg
a
n
g
Update gmxapi ver
s
i
on de
t
ails
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
Eric
Irrgang
Clarify the GMX_B
U
ILD_MDRUN_ONLY full
testing instructions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric Ir
r
gang
I
mprove
gmxPythonDis
c
overy
.
cmake
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric Irrgan
g
Don't override us
e
r provided CMAKE_OSX_D
E
PLOYMENT_T
A
RGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Er
i
c
I
rrga
n
g
H
an
d
le
g
mxapi tmpi
p
ara
m
et
e
rs better
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrgang
Let gm
x
api installat
i
on r
e
cord the GROMACS li
b
rary
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
Er
i
c Irr
g
ang
Use updated i
m
a
ges
f
or
Pyt
h
on CI jo
b
s
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Re
s
trict
gmxapi pyt
e
st tests to `-n
t
2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
E
r
ic I
r
rgang
Spe
c
ify OMP_NUM_T
H
READ
S
for Pyhon CI scr
i
pts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgan
g
Clar
i
fications
for ResourceA
s
signment int
e
rface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Er
i
c Ir
r
ga
n
g
Support
R
esourceA
s
signment interface for tMPI library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Allow MPI-enabled clients t
o
pr
o
vide th
e
library
c
o
m
munica
t
or
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Us
e
MpiCont
e
x
t
M
anager to provide M
P
I commun
i
cator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Relo
c
ate MpiContextMana
g
er
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Interfa
c
e u
p
d
ates allowing cl
i
e
nt
t
o provide MPI commu
n
i
cato
r
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric
Irrgang
Im
p
r
ove naming and docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
D
o
cument a Mdrun
n
er::BuilderImple
m
entation mem
b
er
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Er
i
c Irrg
a
ng
Re
m
o
v
e ou
t
d
ated wo
r
k
a
round
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
C
reate and use S
i
mulationInpu
t
module
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irr
g
an
g
Refine t
h
e CMakeLis
t
s
.
t
x
t f
o
r MPI gmxapi tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
E
ric
I
r
rgang
Explicitl
y
i
nclude STL headers used in t
e
st
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eric Irr
g
ang
R
eplace file
n
ame-
b
ased ini
t
i
a
lization functions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrg
a
ng
Clarify t_
i
npu
t
rec allocati
o
n l
o
gic in runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric I
r
rgang
Use a heap obj
e
c
t
for input
r
ec
i
n
gmx::Mdrunner
:
:m
d
r
u
nner()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Accept Python versions higher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrga
n
g
Remove condi
t
i
o
nal for CMa
k
e
< 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eric Ir
r
gan
g
Allow
m
ore granularity for public interfa
c
es in
buil
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric I
r
rgang
Prevent failed commandlin
e
_oper
a
tion from
publishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
M
inor addition
s
to gmxapi install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Use importl
i
b_resources i
n
Pytho
n
3
.
6
images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrga
n
g
Normaliz
e
d
o
cker im
a
ge names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Fix some
minor typese
t
ting issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
r
ic Irrgang
Improve
install
docs
l
inks
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Er
i
c
I
rrgan
g
Move
s
ources
f
o
r li
b
gmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Re
m
ove disabled test f
o
r superseded feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
r
ic I
r
rgang
Ig
n
ore a
g
en
e
rated
f
ile
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Irrgang
Use GM
X
AP
I
C
M
a
ke
opti
o
n gu
a
r
d for gmxapi
t
a
rget d
e
c
l
aration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
E
ric Irrgang
Be
g
in mo
v
ing
installed interface to `a
p
i
/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Irrgang
Fix libgromacs CMake
target ins
t
al
l
synt
a
x
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric Irrgang
Fix libgromacs CMake targ
e
t insta
l
l syntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
E
r
ic Irrgang
C
lea
n
u
p
s
i
m
u
l
a
torbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric Irrgang
A
dd
m
i
ssing ABI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement SimulatorBuilder
.
ad
d
() for BoxDeformat
i
onHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use TopologyDa
t
a
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
a
ng
Use IonSwapp
i
ng parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c I
r
rg
a
ng
Use Ce
n
terOfMas
s
Pul
l
ing
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use ReplicaExchange member instead of build()
a
rgument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Use SimulatorModules parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c
Irrgang
U
s
e In
t
eract
i
veMD Sim
u
latorBu
i
lder para
m
eter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
LegacyInp
u
t
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c Irrgang
Use Const
r
aintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Move
Profiling parameter out
o
f simulat
o
rbuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ri
c
Irrgan
g
Use Simul
a
torEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Impleme
n
t r
e
ma
i
ni
n
g Simulato
r
Builder
.
a
dd() method
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rg
a
ng
Interface for remai
n
i
n
g SimulatorBui
l
der
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
SimulatorBuilder
.
a
dd
(
) f
o
r Sto
p
Ha
n
dler
B
ui
l
der
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
I
m
ple
m
ent Si
m
ulatorBuilder
.
b
u
ild()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Reformat pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrg
a
n
g
Use
Gromacs::g
m
x target to hint gmxapi
tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgang
Remove workaround for gcc b
u
g 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
E
r
i
c Irrgang
Improve pytest o
u
tput handli
n
g
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
r
ic Irrg
a
ng
Compart
m
entalize job r
u
l
e
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrga
n
g
I
m
prove usage of
Pyt
h
on logging mo
d
u
le
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric Irrgang
H
a
ndle
a
rbi
t
rary do
x
y
g
en ver
s
ions in Do
c
ker image build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric Irr
g
a
ng
Remove unused (and broken)
i
mage from Docker i
m
age
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eri
c
Irr
g
ang
Doc
k
er image build
s
: si
m
pli
f
y do
x
ygen
version handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric Irrgang
Docker image b
u
ilds: move do
x
ygen handlin
g
to a
s
eparate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrga
n
g
Exte
n
d
MPI e
n
semble testi
n
g f
o
r
gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
ri
c
I
rrgang
Enable
MPI e
n
semble testing for gm
x
api
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric I
r
rgang
Normaliz
e
gmxapi related
release-2020
j
ob l
o
g
i
c
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
E
r
ic Irrg
a
ng
Red
u
ce
co
n
sole log o
u
tput from sam
p
le
_
restraint t
e
sts
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
E
ric Irrgang
Enable MPI ensemb
l
e
testing for g
m
xapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric I
r
rgang
N
ormali
z
e gmx
a
p
i related rele
a
se
-
20
2
0 job
l
ogic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irr
g
ang
Make s
u
re images h
a
v
e
/usr/bi
n
/
p
yt
h
on
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Irrgang
Update docke
r
image b
u
ild scripts
f
o
r master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Irrgang
M
a
ke sure
C
I
script can
ca
l
l
/bin/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Minor clean u
p
to
buildal
l
.
sh
commit
|
commitdiff
|
tree
next