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Update instructions in containers.rst
2020-12-04
M
.
Eric Irrgang
Add CI j
o
bs for
gm
x
api 0
.
3
commit
|
commitdiff
|
tree
2020-12-04
M
.
Eric Irrgang
Update rules for r
e
lease-2021
.
commit
|
commitdiff
|
tree
2020-12-04
M
.
Eric
I
rr
g
ang
Separ
a
t
e jo
b
script fi
l
es for
gm
x
api pac
k
age versions
.
commit
|
commitdiff
|
tree
2020-12-03
M
.
Eric
Irrgang
Improve gmx
a
pi C++ test coverage
for fail
e
d m
d
run
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eric Irrgang
O
n
e argumen
t
per line fo
r
long
f
unction
sig
n
atures
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Eric Irrgang
L
o
ok for
the various
p
ossible names
of the
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2020-11-20
M
.
Eric Irrgang
C
reat
e
C
Make targets for each of
the mo
d
ule
s
.
commit
|
commitdiff
|
tree
2020-11-18
M
.
Eric Ir
r
g
ang
Repla
c
e gmxapi `erroroutput`
w
i
th `stderr` and
`
stdout`
commit
|
commitdiff
|
tree
2020-11-17
M
.
Eric I
r
rgang
Sepa
r
ate the
testutils module
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
Eric Irrgang
gmxapi vers
i
o
n
ing upd
a
tes
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Irrga
n
g
Be more explicit
a
bo
u
t b
u
ild-tr
e
e-only dependencies
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Irrgang
Provide a catch-all target for
library
m
o
d
ules
.
commit
|
commitdiff
|
tree
2020-11-12
M
.
Eric Irrgang
Pr
o
vide c
o
mmon library
h
eaders th
r
o
u
gh new CMake
ta
r
get
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
E
ric I
r
r
g
an
g
Help clients fi
n
d depe
n
dencies of i
m
por
t
e
d
C
Make
targ
e
ts
.
commit
|
commitdiff
|
tree
2020-11-04
M
.
Eric Irrg
a
n
g
Establish `api/` as t
h
e home for inst
a
lled headers
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irrga
n
g
Remove
a
n unnecessary tr
a
n
s
itive depen
d
en
c
y of imp
o
rted
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Er
i
c
Irrgang
U
se the
correct CI script for sample_restraint jobs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Normalize FindMPI h
i
nts
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Cl
a
r
ify behavior
o
f
LegacyMd
r
unOptions
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
ric Irrgang
Update im
a
ge
n
a
mes in
j
ob definitions
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Eric Irrgan
g
Tel
l
gmx
a
pi to look fo
r
M
P
I, when appropriat
e
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
Eric I
r
rgang
U
pda
t
e
D
o
cker image build s
c
ripts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Eric Irrgang
U
s
e upda
t
ed CI pi
p
e
l
ine
rules
for Python package
test
s
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric Irr
g
ang
Update gmxapi versi
o
n details
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
E
r
i
c Irrgang
Clar
i
f
y the GMX_BUILD_MD
R
UN_ONLY
full t
e
sting inst
r
uctions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric Irrgang
I
mprove gmxPythonDiscovery
.
c
make
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric
I
rrg
a
ng
D
o
n't override user provided C
M
AKE_OS
X
_DEPLOY
M
ENT_TARGE
T
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrga
n
g
Handle
gmxapi tmpi parameters b
e
t
t
er
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrgang
Le
t
gmxap
i
installation record th
e
GR
O
MACS library
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
Er
i
c
Irrgang
Use
u
pdated images for
P
ython
C
I jobs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
R
e
s
tri
c
t gmx
a
pi pytest
tes
t
s to `-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric I
r
rgang
Specify OMP_NUM_THREADS for P
y
hon CI scripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
C
l
arificat
i
ons for Resour
c
eAssignment in
t
erface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irrgang
S
u
pport
Resour
c
e
A
ssig
n
ment interface for
t
MPI libra
r
y
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Allo
w
MPI
-
en
a
bled
clien
t
s to p
r
ovide the
library communic
a
tor
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
I
r
r
gang
U
se M
p
iContextManag
e
r to provide MPI communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Ir
r
gang
Re
l
ocate MpiContextManager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrg
a
ng
Inte
r
f
ace updates allowing
c
lien
t
to provi
d
e MPI communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Ir
r
g
ang
Improve n
a
ming and docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
ric Ir
r
gang
Doc
u
ment a
M
drunne
r
::B
u
ilderImplementation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
E
ric
I
r
r
gang
Remo
v
e out
d
ated workar
o
und
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Er
i
c
Irrgang
Create
and use
Simul
a
t
i
onInput module
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Er
i
c Irrgang
Refine the
C
MakeLists
.
txt for
MPI
g
mxapi tes
t
s
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eric Irrgang
Explicitly include STL head
e
r
s
used in test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Er
i
c
Irrgang
Replace filename-based ini
t
ialization
f
unctions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Er
i
c Ir
r
g
a
ng
Clar
i
fy t_inputrec allocati
o
n
l
og
i
c in ru
n
ner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrgang
Us
e
a heap ob
j
ect
f
o
r inputrec in gmx::Mdrunner::mdrun
n
er(
)
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Er
i
c
I
rrg
a
ng
Accept Python versio
n
s higher tha
n
3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
E
ri
c
Irrgang
Remove
c
o
nditional for CMake < 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eri
c
Irrgang
Allow more granularit
y
for public
i
n
t
erfa
c
es
i
n build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eri
c
Irrgang
Preven
t
failed commandli
n
e_opera
t
ion from pub
l
i
shing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric
I
r
r
gang
Mi
n
or additions to gmxapi install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
r
ic I
r
rgang
U
se imp
o
rtlib_r
e
sources in Python 3
.
6
i
mages
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eri
c
Irrga
n
g
N
o
rmal
i
ze
docker i
m
a
g
e names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Fix some minor typeset
t
ing issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Er
i
c Irrgang
Improve install docs
l
inks
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric
Irrgang
Move
sources for libgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrga
n
g
Rem
o
ve disabled test for super
s
eded feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Ir
r
g
ang
Ignore
a generated file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Irrgan
g
Use
G
M
XAPI CMake option guar
d
for
gmxapi ta
r
get
d
ecla
r
ation
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irrga
n
g
Begin moving
i
nstal
l
ed
i
nterf
a
ce to `
a
pi/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Irrga
n
g
Fix libgromacs C
M
ak
e
ta
r
get install
s
y
n
t
a
x
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric Irrgang
Fix libgrom
a
cs CMake t
a
rge
t
install s
y
ntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
E
ric
Irrg
a
n
g
Clean up simulatorbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
E
ric I
r
rgang
Add missing ABI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrg
a
n
g
Imple
m
ent Sim
u
lat
o
rBuilder
.
add()
f
or Bo
x
DeformationHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
Irrgang
Use Top
o
logyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Use
IonSwa
p
pi
n
g
paramete
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Ce
n
terOfMassPull
i
n
g
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgan
g
Use R
e
plicaE
x
change memb
e
r in
s
tead of
buil
d
() argume
n
t
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrg
a
ng
Us
e
SimulatorModules paramet
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
U
se Int
e
ractiveMD SimulatorBuilder paramete
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
U
s
e
L
e
g
acyInp
u
t
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rga
n
g
Use ConstraintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Move Profiling parameter out
of simulat
o
r
builde
r
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
r
gan
g
Use Simu
l
atorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
I
m
p
leme
n
t rem
a
ining
S
imulatorBu
i
l
der
.
add() me
t
hods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrg
a
ng
Inte
r
f
a
ce fo
r
remaini
n
g
SimulatorBuilder
.
add() me
t
hods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Simula
t
o
r
Builder
.
add() fo
r
S
t
opH
a
nd
l
erB
u
i
lder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c
Irrgang
Imple
m
ent Simu
l
ato
r
Bu
i
lder
.
build(
)
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
r
ic I
r
rga
n
g
Reformat
pairs
.
cp
p
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrga
n
g
Use Gromacs::gmx tar
g
et to hin
t
gmxapi test
s
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Er
i
c Irrgang
Rem
o
ve wo
r
ka
r
o
und
f
or gc
c
bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
E
ric Irrgang
Im
p
rove pyte
s
t
output handling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgan
g
Compartme
n
talize j
o
b rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Er
i
c Ir
r
g
ang
Improve us
a
ge of Python
l
ogging module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
E
r
i
c
I
r
rgang
Handle arbit
r
ar
y
doxygen versions in
D
ocker
image build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irr
g
ang
R
e
m
o
ve unused (
a
n
d
broken)
im
a
ge
from Docke
r
i
m
age
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric
I
rrgang
Docker image builds:
simplify doxy
g
en version
h
a
n
dli
n
g
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker image builds: m
o
ve
d
oxygen handl
i
ng to a
s
e
p
arate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
Irrgang
Ex
t
end MPI ensemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Enable M
P
I e
n
s
e
mble testing for gmx
a
p
i
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Normalize gmxapi rel
a
ted r
e
lea
s
e-2020
j
ob logi
c
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
E
r
ic Ir
r
gang
Reduce consol
e
log output from sample_restrai
n
t tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric
I
rr
g
ang
Ena
b
le
MPI ensemble t
e
s
ting for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric
Irrgang
Normali
z
e gmxa
p
i rela
t
ed release-2020
job
l
ogic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
E
ric Irrga
n
g
Make sure images have /usr/bin/p
y
thon
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
rrgang
Updat
e
docker image build scripts
f
or master
b
ranch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrga
n
g
M
ake sure CI scrip
t
can
c
all /bin/env pyth
o
n`
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Ir
r
gang
Minor clean up to buildall
.
sh
commit
|
commitdiff
|
tree
next