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Use MpiContextManager to provide MPI communicator.
2020-09-29
M
.
Eric
I
r
rgang
Use MpiCont
e
xtManager to prov
i
de
MPI c
o
mmunicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
I
rr
g
ang
Relocate MpiContex
t
Mana
g
e
r
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Inter
f
ace update
s
al
l
owing client to pro
v
ide
MPI communicat
o
r
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrg
a
n
g
Improve
n
aming and docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
D
ocument a Mdrunner::Build
e
rImplementation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Ir
r
gang
Rem
o
ve outdated workaro
u
nd
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
E
r
i
c Ir
r
gan
g
Refin
e
the CMakeLists
.
txt for MPI
gm
x
api tests
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrgang
Clar
i
fy t_inputrec alloc
a
tion logi
c
in run
n
er
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Accept Python versions higher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgan
g
Re
m
o
v
e co
n
ditional for CM
a
k
e
<
3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Er
i
c Irrgang
Allow more granularity for public interfaces in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrg
a
ng
Preve
n
t
f
a
i
l
e
d commandline_operation from publishin
g
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrga
n
g
M
inor additions
t
o gmxapi insta
l
l
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
r
ic Irrgang
Use i
m
port
l
ib_resourc
e
s in Py
t
hon 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Er
i
c Irrgang
Normali
z
e docker image names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
I
rrgang
Fix
s
ome minor typesetting
issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
I
m
pro
v
e
install
docs l
i
nk
s
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irr
g
ang
Mov
e
sources for libg
m
xapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Er
i
c
Irrgang
Remo
v
e disabled
t
est for supers
e
de
d
feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrg
a
ng
Ignore a genera
t
ed fil
e
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irr
g
ang
Begin moving
i
n
stalled
i
nterface to `api/`
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric Irrgang
Fix libgroma
c
s
CMake target i
n
stall syntax
.
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric Irrgang
Add missing A
B
I header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Imple
m
ent
Si
m
ulato
r
Build
e
r
.
add() for BoxDeformationHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Use TopologyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c
Irrgang
Use IonSwapping param
e
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use C
e
nterOfMassP
u
l
ling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irr
g
ang
U
se R
e
pl
i
c
aE
x
cha
n
ge me
m
b
e
r i
n
stead of build() argum
e
nt
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrg
a
n
g
Use SimulatorM
o
dules
paramete
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Ir
r
gang
Use I
n
teractiveMD
S
i
m
ulato
r
Bu
i
lder parame
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Use LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irr
g
ang
Us
e
C
o
n
stra
i
ntsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rgang
Move Prof
i
li
n
g
p
a
rameter
out of
s
im
u
latorbuilder
.
b
u
il
d
()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
Simula
t
orEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement remaining SimulatorB
u
i
l
der
.
add() meth
o
d
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Interface for remaining Sim
u
l
atorBuilder
.
a
dd
(
) methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
SimulatorBuilder
.
add() f
o
r
StopHa
n
dlerBuild
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
I
m
plemen
t
SimulatorBuild
e
r
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Reform
a
t pa
i
r
s
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Use Gr
o
macs::g
m
x
t
ar
g
et to hin
t
gmxapi test
s
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgang
Remove workaround for gcc bug
5
8265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eri
c
Irrgang
Improve pytest output handl
i
ng
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric
I
rrgang
C
o
mpart
m
entaliz
e
jo
b
rul
e
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eri
c
I
rrgang
Imp
r
ove usage
o
f
P
y
t
hon logging modul
e
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric Irrgang
Rem
o
ve unused (and
broken) image from Docker imag
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Ir
r
gang
Docker
ima
g
e
builds: simpli
f
y
dox
y
gen
v
ersion h
a
ndling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
r
ic Irr
g
ang
Docker ima
g
e builds
:
m
o
v
e
d
oxygen handling to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eri
c
Irrgang
Extend MPI ensemb
l
e testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
ic Irrgang
Enable MPI ensemble
t
es
t
ing for
g
m
xa
p
i
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Er
i
c
Irrgang
Enable
M
P
I ensemble testing
for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric Irrga
n
g
N
o
rmalize g
m
xapi
related
r
eleas
e
-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric
I
rrga
n
g
Ma
k
e
sure images h
a
ve /
u
sr/bin/pytho
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
U
p
date docke
r
i
mage build scripts for master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c
I
rrgang
Make su
r
e CI
s
cript can call /b
i
n/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Mi
n
or
cl
e
an
u
p to buildall
.
s
h
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Ir
r
gang
Al
l
ow llvm option
a
lre
a
dy
u
sed in buil
d
all
.
s
h
s
cri
p
t
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
U
p
date header sort
i
ng
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Er
i
c Irr
g
ang
R
e
q
uire C++17 standar
d
an
d
STL fea
t
ures
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
E
r
i
c Irrgang
A
pply
m
o
re gra
n
ula
r
CTest t
i
me-out
p
olicy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Irrgang
Note CUDA builds in
job names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
E
ric Ir
r
gang
On
l
y
s
et
G
M
X_PYTHON_
P
A
C
KAGE
=
O
N
where ne
e
ded
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric Irrgang
Change default
C
M
ake version to 3
.
1
3
.
0 for CI images
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Require CMake >=3
.
1
3
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric Irrg
a
ng
Expli
c
itly set U
T
F-8 encoding
f
o
r gmxapi CLI interaction
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric Irrgang
A
void accidentall
y
initializ
i
ng
p
y
env in CI images
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
E
r
i
c
I
r
rgang
Mock h
p
c
c
m impo
r
t s
o
infrastructure docs
b
uild easily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrgang
Extract lo
g
ic
for wh
e
n CI jobs execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
gang
N
o
rmalize some more
j
ob names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrg
a
ng
Simplify archive
.
g
itl
a
b-
c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrga
n
g
Remove redundant job
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Fix
d
uplicate variables para
m
eter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic
I
rrgang
Add
r
e
q
u
ired Infrastructure for G
i
t
l
a
b merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrg
a
ng
Norm
a
lize
n
aming
for gromac
s
build/testin
g
jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgan
g
Remove some unnec
e
ssary indirection
i
n job defin
i
tions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrgang
Consolidate
.
use-clangX CI jo
b
mix-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
r
r
gang
Consoli
d
ate
.
u
se-g
c
c
X
CI j
o
b mix
-
in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
I
r
rgang
Adopt
C
I
job nam
i
ng g
u
ideli
n
es
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Normalize
GitLab-CI *cache*
para
m
eter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rgang
Mer
g
e
environ
m
ent support
i
nt
o
global
.
g
i
tlab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
ic Irrg
a
n
g
Move
.
b
u
ild-template
.
yml
d
efinitions closer to
p
oi
n
t
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merg
e
*-test-templat
e
.
ym
l
into testing-matrix
.
gitlab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge
.
test-runner-templa
t
e
.
yml i
n
to te
s
ting-matr
i
x
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rgang
M
erge
.
test-script-tem
p
late
.
yml into te
s
t
in
g
-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrg
a
ng
Merge
.
regression
t
est-template
.
ym
l
into
a
r
c
hive config
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Co
n
solidat
e
documentatio
n
templ
a
tes
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
ric
Irrgang
Reorga
n
ize release templates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eri
c
Irrgang
Remove conf
u
s
ing and du
p
lica
t
ed variables assignm
e
nt
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eri
c
Irr
g
an
g
C
onsolidat
e
gl
o
b
al mix
-
ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irr
g
ang
[ci skip]
R
e
move indirection fo
r
default tags p
a
r
a
meter
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
[ci
s
k
ip] Reorganize
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric
Ir
r
gang
D
o
c
u
ment CI variable and
r
emove unus
e
d template
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
ric I
r
rgang
D
isable sphinx
.
ext
.
v
iewc
o
de
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
r
ic Irrgang
Add stub Variable
s
documentation to GitLa
b
CI
d
oc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric Irrgang
Remove
d
uplicated Y
A
ML key
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c Irrgang
Add document for cont
a
ine
r
izati
o
n infrastructure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrga
n
g
Alphabetize list for readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric
I
rrgang
Re
f
ormat argumen
t
s
f
or r
e
adab
i
lit
y
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Define an argparse parent parser for
co
n
tainer im
a
g
e
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Ir
r
gan
g
Build MP
I
i
n
Dockerfi
l
e
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Er
i
c
I
rrgang
Merge
c
o
nf
.
py
and
con
f
-vars
.
py
.
commit
|
commitdiff
|
tree
next