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Allow MPI-enabled clients to provide the library communicator.
2020-09-29
M
.
Eric Irrgan
g
Allo
w
MPI-enabl
e
d
c
l
ients to pro
v
ide
the libr
a
ry co
m
mun
i
ca
t
or
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Er
i
c Irrga
n
g
Use MpiCont
e
xtManage
r
to provide MP
I
communicat
o
r
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Ir
r
gang
Relocate M
p
i
C
ontex
t
M
a
nager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Interface
u
pdates al
l
owing client
t
o provide MPI communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
r
ic Irrgang
Improve naming a
n
d docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
ric I
r
rg
a
ng
Documen
t
a
Mdru
n
ner:
:
Build
e
rImple
m
entatio
n
m
e
mber
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric
I
rrgang
Re
m
ove outda
t
e
d workaroun
d
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric I
r
rgang
Refin
e
the CMakeLists
.
t
x
t for MPI gmx
a
p
i
tests
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
E
r
i
c Irrgan
g
C
l
arify t_inp
u
trec
allocation logi
c
in ru
n
ner
.
c
p
p
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrga
n
g
Accept Python ve
r
sions
higher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Er
i
c I
r
rgang
Remov
e
c
o
nditional for
CMa
k
e < 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Er
i
c Irrgang
Allow more gran
u
l
a
rity for public interfac
e
s in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eri
c
I
r
rgang
Prevent failed commandl
i
ne_operation fr
o
m
p
ublish
i
ng
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric
Irrga
n
g
Minor additions to gmxapi
i
nstal
l
.
r
st
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
ric I
r
rga
n
g
Use importl
i
b
_
resources
i
n Python 3
.
6 imag
e
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
r
ic Irrgang
Norma
l
ize doc
k
er image names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
Irrgang
Fix some min
o
r typesetting issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
ric
Irrgang
Improve install docs links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eri
c
I
rrgang
Mo
v
e
s
o
urces f
o
r libgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Rem
o
v
e di
s
abled test for su
p
erseded
feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Er
i
c Irrgang
Ignore a generated f
i
l
e
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Er
i
c Irrgang
Begin movi
n
g installe
d
interfac
e
to `api/`
commit
|
commitdiff
|
tree
2020-07-10
M
.
E
ric Irrgang
Fix
l
ibgromacs CMake target ins
t
all syntax
.
commit
|
commitdiff
|
tree
2020-06-27
M
.
E
ri
c
Irrgan
g
A
d
d missing AB
I
head
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
I
m
plement SimulatorBuilde
r
.
add() for BoxD
e
formationHand
l
e
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Use Topo
l
og
y
Dat
a
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
I
o
nSwapping paramet
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use CenterOfMassPul
l
in
g
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Repli
c
aExchange
m
e
m
b
e
r
inst
e
ad o
f
b
u
ild() argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Use
Si
m
ulatorModules
p
arameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ri
c
Ir
r
gang
U
se I
n
ter
a
ctiveMD
S
i
mulatorBuilder parame
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgan
g
Us
e
Leg
a
c
yI
n
put
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
ng
Use Constra
i
nts
P
a
r
a
m
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c Irrgang
Move Pro
f
iling pa
r
am
e
ter
o
u
t of simulatorbuilder
.
bui
l
d()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
U
s
e Si
m
u
lat
o
rEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c Irrgan
g
Implement rema
i
n
ing Sim
u
latorBuilder
.
add(
)
methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Inte
r
f
ace for remaining
SimulatorB
u
ilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
Irrgang
SimulatorBuilder
.
a
d
d
() fo
r
Sto
p
Ha
n
dlerB
u
i
lder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Impleme
n
t
SimulatorBuilder
.
b
u
il
d
(
)
commit
|
commitdiff
|
tree
2020-06-22
M
.
Er
i
c
Irrgang
Re
f
ormat pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
ric I
r
rga
n
g
U
s
e
Gro
m
a
c
s::gmx target to hint gmxap
i
tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
E
ric Irrgang
Remove w
o
r
karound for gcc bug 5826
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Ir
r
g
a
ng
Improve pytest
output handli
n
g
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrga
n
g
Comp
a
rtmentalize job
r
u
les
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irr
g
ang
I
m
prove usage of Python logging module
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Remove unused (and broken) i
m
age from Docker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrga
n
g
Dock
e
r
image
builds: simplify doxyge
n
ver
s
ion handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker image builds: move doxygen handling to
a
separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Extend MPI
e
nsemble testin
g
f
o
r
gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrg
a
ng
E
nable M
P
I
e
nsemb
l
e testing for
gmxapi
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrga
n
g
Enable MPI ensemble t
e
st
i
ng f
o
r
gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric
I
rrg
a
ng
N
ormalize gmxapi relat
e
d release-202
0
job l
o
gic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eri
c
I
r
rgang
Make sur
e
image
s
h
ave /usr/bin/pytho
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
ang
Upda
t
e doc
k
er image
build
scripts for m
a
st
e
r
branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
ang
Make sure CI script c
a
n call /bin/env python
`
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Irr
g
ang
Mi
n
or clean up
t
o
build
a
ll
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irr
g
ang
Allow ll
v
m option already used in
b
uil
d
all
.
sh
s
cri
p
t
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Upda
t
e head
e
r
s
o
r
ting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Requ
i
re C++17 stand
a
rd and
S
TL features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric
I
rrga
n
g
Apply more
g
ranular CTest time-out polic
y
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric
I
r
r
gang
Note CUDA builds in job
names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Er
i
c Irrgang
Onl
y
set GM
X
_PYTHON_PAC
K
AGE=ON
where
n
e
eded
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Er
i
c Irrgang
Change
d
efault C
M
ake
v
ersio
n
to 3
.
13
.
0 for CI images
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Require CMake >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric
Irrgang
Explicitly set UT
F
-8 e
n
c
odi
n
g
f
or
g
mxa
p
i CLI inte
r
act
i
o
n
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric
Irrgang
Avoid accidental
l
y initializ
i
n
g
p
ye
n
v in CI
i
mages
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eric Irrgang
Mock hpccm import so infrastructure docs
bu
i
ld easily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Irrgang
Extract logic for when CI jo
b
s execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Normal
i
ze
some more j
o
b
n
a
mes
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Irr
g
an
g
Simpli
f
y archive
.
gitla
b
-
c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
rrgang
Re
m
ove
r
edundant
jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Irrgang
F
i
x d
u
p
licate variab
l
es parameter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrgang
Add r
e
quired Infrastruc
t
u
re fo
r
Gitlab me
r
ges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
rrgang
Norma
l
ize nam
i
ng for gro
m
ac
s
bui
l
d/tes
t
ing jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrg
a
ng
R
emove s
o
me unn
e
cessa
r
y
indirection in job
d
e
fin
i
tions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irr
g
a
n
g
Con
s
olidate
.
use-clangX CI job mix-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
C
o
nsolidate
.
use-
g
ccX CI job
m
i
x
-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
ric Irrgang
Adop
t
CI job na
m
ing guideli
n
es
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
Irrgang
Normali
z
e GitLab-CI *c
a
che* par
a
meter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
M
e
rge environment suppo
r
t into gl
o
bal
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
ric Irrgang
Move
.
bu
i
ld-template
.
y
m
l
d
efiniti
o
n
s
closer to
point
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irr
g
ang
M
erge
*-test-tem
p
late
.
y
m
l into
testing-matr
i
x
.
g
i
t
lab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irr
g
a
n
g
Merge
.
test-run
n
er-t
e
mplate
.
yml i
n
to testing-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge
.
test-scri
p
t-template
.
yml
i
nto
t
esting-matri
x
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irrgang
Merge
.
regressiontest-temp
l
a
t
e
.
yml
i
nto archi
v
e co
n
fig
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Ir
r
gang
Cons
o
lidat
e
do
c
um
e
ntat
i
on templ
a
tes
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c
I
r
rgang
Reorganiz
e
re
l
ea
s
e templates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
ric Irr
g
ang
R
emove confusin
g
and dup
l
icated varia
b
l
e
s
a
ss
i
gnment
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric
I
rrga
n
g
Co
n
solidate globa
l
mix-i
n
s
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irr
g
ang
[ci skip]
R
emove indirection for de
f
aul
t
tags parameter
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrg
a
ng
[
c
i ski
p
] Reo
r
g
a
nize
.
gitlab-ci
.
ym
l
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
ric Irrg
a
ng
Document CI v
a
riable a
n
d remov
e
unused templa
t
e
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
ric Irrgang
Disable sphi
n
x
.
ext
.
viewcode
commit
|
commitdiff
|
tree
2020-03-18
M
.
Er
i
c Irrgang
A
d
d stu
b
V
a
ri
a
bles doc
u
m
e
ntation to GitLab C
I
doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric
I
rrgang
Remov
e
d
uplic
a
ted YAML key
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
ic Irrgang
A
dd docume
n
t for contai
n
e
ri
z
at
i
on infrastructure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Ir
r
gang
Al
p
h
a
betize list for rea
d
a
b
ility
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
ric
I
r
r
g
an
g
Ref
o
rmat ar
g
uments for readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Define an argpar
s
e p
a
rent pars
e
r
for con
t
ainer i
m
age
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric
Irr
g
ang
Build MPI
i
n Dock
e
rfile
.
commit
|
commitdiff
|
tree
next