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Update instructions in containers.rst
2020-12-04
M
.
Eri
c
I
rrgang
Add CI j
o
bs for gmxa
p
i 0
.
3
commit
|
commitdiff
|
tree
2020-12-04
M
.
E
ric
I
rrg
a
n
g
Upd
a
te rules for release-2021
.
commit
|
commitdiff
|
tree
2020-12-04
M
.
E
r
ic Irrg
a
ng
Separate
j
ob script fil
e
s f
o
r
g
mxapi
p
a
c
k
a
ge
versions
.
commit
|
commitdiff
|
tree
2020-12-03
M
.
Eric Irr
g
ang
Impro
v
e gmxap
i
C++ test c
o
verage
for
failed m
d
run
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eri
c
Irrgang
O
ne argument per l
i
ne f
o
r long function
s
ignatu
r
es
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Eric Irrgan
g
L
oo
k
for th
e
variou
s
possible names of the gromacs
.
.
.
commit
|
commitdiff
|
tree
2020-11-20
M
.
Eric Irrgang
Create CMake targets
f
or each of the m
o
dules
.
commit
|
commitdiff
|
tree
2020-11-18
M
.
Eric
Irrgang
Replace g
m
x
api
`
erroroutpu
t
` with `stderr` and
`
stdout`
commit
|
commitdiff
|
tree
2020-11-17
M
.
Eric
I
rrga
n
g
Separate the testutils module
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
Eric Irrgang
g
mxa
p
i versionin
g
upd
a
t
e
s
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Irrga
n
g
Be mo
r
e explicit
a
bout build
-
tree-only dependencies
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric I
r
rgang
Pr
o
vide a
c
atch-all tar
g
et for
library mod
u
le
s
.
commit
|
commitdiff
|
tree
2020-11-12
M
.
Eric Irrgang
Provide common library hea
d
ers t
h
r
o
u
gh new CMake
t
arget
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
E
ric Irrgang
H
e
l
p
cl
i
ents find dependencies of imported CMake targets
.
commit
|
commitdiff
|
tree
2020-11-04
M
.
Eric
Irrgang
Establish `a
p
i/` as the home
for in
s
talled headers
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irrg
a
ng
Remove an unnece
s
sa
r
y
transiti
v
e de
p
e
ndency of imported
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Use the corr
e
c
t
CI script for sample_restraint jobs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eri
c
Irrgang
Normalize
F
indMPI h
i
nts
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrg
a
n
g
Clarify behavior o
f
LegacyMdrunOpti
o
ns
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Updat
e
i
m
age n
a
mes in job
d
efinitions
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Eric Irr
g
ang
Tell gmxap
i
to look fo
r
MPI
,
when appropr
i
ate
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
Eric Irrgang
Update Docker image build
scripts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Eric Irrg
a
ng
U
s
e updated CI pipeline rules for Py
t
h
on
package tests
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Er
i
c Irrgang
Upda
t
e gm
x
a
pi version de
t
ails
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
Eric Irr
g
an
g
Clarif
y
t
h
e
G
M
X_BUI
L
D_MDR
U
N_ONLY full testing instru
c
tions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric Irrgang
Impro
v
e gmxPy
t
honDiscovery
.
c
m
a
k
e
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric
I
rrgang
Don't o
v
erride
user pr
o
v
ided
C
M
A
KE_O
S
X
_
DEPLOYM
E
N
T_T
A
RGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric
I
r
rgang
Handle gmxapi
t
m
p
i
p
arameters better
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrgang
Le
t
gm
x
api
i
nstallat
i
on
r
ecord the GR
O
MACS
library
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
E
r
ic Irrgang
U
s
e
u
p
dated
i
mages f
o
r Pyth
o
n
CI
j
obs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric I
r
r
gang
Restrict gmxapi pytest te
s
ts to `-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Specify OMP_NUM
_
THREADS for
Pyho
n
CI scripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic I
r
rga
n
g
Clari
f
ications f
o
r
Reso
u
r
ceAs
s
ignment in
t
e
rface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irrgang
Suppor
t
Res
o
urceAs
s
ignm
e
nt interface for
t
MPI library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eri
c
Irrgang
A
l
lo
w
MPI-e
n
abled clients to provi
d
e the library communica
t
or
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Use MpiContextMa
n
ager t
o
provide
MPI
c
ommunicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
I
rrgang
R
e
locat
e
MpiContextM
a
nager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Ir
r
gang
In
t
e
rface u
p
dat
e
s allo
w
ing cli
e
nt to provi
d
e
M
PI communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eri
c
I
r
rgang
Improve
n
aming and docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
Document a
M
drunn
e
r:
:
Buil
d
erImplementation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
E
ric Irrgang
Remove ou
t
dated wo
r
k
around
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric
I
rrgang
Crea
t
e and use S
i
mulatio
n
Input module
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
E
ric
I
r
rgang
Refine the CMake
L
is
t
s
.
txt for MPI gmxapi tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eric I
r
rgang
Explicit
l
y inc
l
ud
e
S
T
L he
a
ders used in test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Er
i
c Irrgang
Repl
a
ce
f
i
le
n
ame
-
based ini
t
ialization functions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Er
i
c Irrga
n
g
C
larify t_inputrec allocation logic in run
n
er
.
cp
p
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric I
r
r
gang
U
s
e a
h
eap object for inputrec in gmx::Mdrunner::mdr
u
nner()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Er
i
c Irrgan
g
Accept Python versions higher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgan
g
Remove cond
i
ti
o
nal fo
r
CMak
e
< 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
E
r
ic
Irrgang
Allow more gra
n
u
l
a
r
ity for pub
l
i
c in
t
erfaces in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
r
ic
Irrgang
Prevent fail
e
d comm
a
ndli
n
e_operati
o
n
fro
m
publishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Mi
n
or additions to gmxapi install
.
rs
t
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eri
c
Irrgang
Use
i
m
p
ort
l
ib
_
resources in
P
y
thon 3
.
6 i
m
ages
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Ir
r
g
a
ng
Norm
a
lize d
o
cker image
names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
F
i
x some
min
o
r
t
y
p
esett
i
ng issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eri
c
Irrg
a
ng
Improve
i
n
stall d
o
cs links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric
Irrgang
Move sources for libgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eri
c
Irrgan
g
R
e
move
d
isabled test
for superseded
f
ea
t
ure
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ignore
a generated file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Er
i
c
Irrgang
Use
G
MXAP
I
CMa
k
e option gu
a
rd for gmxapi
t
a
rget declara
t
ion
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric
I
rr
g
ang
Begin mov
i
ng installed interface to `api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric
I
r
rgang
Fix libgr
o
macs CMake target i
n
s
t
all
s
y
ntax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric Irrga
n
g
Fix libgromacs
C
Ma
k
e target i
n
st
a
ll synta
x
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Irrgang
Clean up simulatorbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Er
i
c Irrgang
Ad
d
m
issing
A
BI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rr
g
ang
Implement Si
m
u
l
a
to
r
Bui
l
der
.
add() for BoxDeformat
i
onH
a
n
d
le
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Us
e
T
opologyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rgang
U
s
e IonS
w
apping p
a
rameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
n
g
Use Ce
n
terOfM
a
ssPul
l
ing
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
I
rrgang
Use
Replica
E
xchan
g
e memb
e
r
i
nstead of
b
uild() argumen
t
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Sim
u
latorModule
s
paramete
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrg
a
ng
Us
e
In
t
e
r
a
ctiveMD
Simu
l
atorBuil
d
er par
a
meter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Use LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrga
n
g
Use Cons
t
raintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Move
P
rofil
i
ng pa
r
a
meter out of simulatorbuild
e
r
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Use Simu
l
a
torEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
ng
Implement remaining SimulatorBuild
e
r
.
add()
m
ethods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Interface
f
o
r re
m
aining
Si
m
ul
a
tor
B
uilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
n
g
SimulatorBuild
e
r
.
a
d
d() fo
r
St
o
pHandlerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrg
a
ng
I
mple
m
e
nt Simu
l
ato
r
Builder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
r
i
c Irrgang
Reformat pairs
.
c
p
p
commit
|
commitdiff
|
tree
2020-06-22
M
.
Er
i
c Irrgang
Use Gromacs::gmx
t
arget
t
o h
i
nt
g
mxapi
t
ests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric I
r
r
g
ang
Re
m
ove wo
r
karound for gc
c
bug
58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric I
r
r
g
a
ng
I
m
prov
e
pytest ou
t
put handli
n
g
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
ric
Irrgang
Co
m
partme
n
t
a
liz
e
job rule
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eri
c
Irrgang
Improv
e
u
s
age of
P
yt
h
on
logging
m
o
d
ule
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric Irrgang
Handle arbitrary dox
y
g
e
n versions i
n
Docker ima
g
e build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irr
g
ang
Remove unu
s
ed (
a
nd broken) image from D
o
cker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Er
i
c
I
rrgang
Docker image builds: simplify doxygen versi
o
n handli
n
g
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker ima
g
e b
u
ilds: move
d
oxygen
handling
t
o a se
p
a
rat
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
I
r
rgang
E
x
t
e
nd MPI ensemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
ic Irrgang
E
n
able M
P
I ensemble testing for gm
x
a
pi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
Irrga
n
g
No
r
malize gmxap
i
related
r
elease
-
2020 job
l
o
gic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric
Irrgang
Reduce c
o
nsole
log
o
utput f
r
om
sample_restrai
n
t tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric
Irrgang
Enable
MPI ense
m
b
le te
s
ting for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Er
i
c Irrgang
Normaliz
e
gmxapi related
r
elease-2020 job
l
ogic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgang
Make sure im
a
ges ha
v
e /usr/b
i
n/pytho
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
Irr
g
a
n
g
Update docker ima
g
e build
s
cri
p
ts for
m
aster branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Make sure CI script can ca
l
l
/bin/env py
t
h
on`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
rgang
M
in
o
r clean up to bui
l
d
a
l
l
.
s
h
commit
|
commitdiff
|
tree
next