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Support ResourceAssignment interface for tMPI library builds.
2020-09-29
M
.
Eric
I
r
rgang
S
upport Resourc
e
As
s
ignme
n
t interface for tMPI library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Allow MP
I
-enable
d
clients to prov
i
de the library communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
I
r
r
gan
g
Us
e
MpiContextMan
a
ger to provid
e
MPI
c
o
mmunica
t
or
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
Irrgang
Relocate MpiContextMa
n
ager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrg
a
ng
Interface up
d
ates allowing client to provide MPI
communica
t
or
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
r
ic
Ir
r
gang
I
mpr
o
ve naming an
d
docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
r
i
c I
r
rgang
Document a Mdrun
n
er::BuilderImplementation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Irrgang
Remove outda
t
ed workaround
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
Refine the CMakeLists
.
txt fo
r
MPI g
m
xapi te
s
ts
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrgang
Clar
i
fy t_in
p
utrec a
l
location logic in runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
A
c
c
e
p
t Python versions highe
r
than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Remove conditional
f
o
r
C
M
ake < 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eri
c
Irrga
n
g
Allow more
granularity for public interfaces in bui
l
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric
Irrgan
g
P
r
ev
e
nt failed commandline_operation
f
r
om
publis
h
ing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Minor add
i
tion
s
t
o
g
mx
a
pi install
.
r
st
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric
Irrgang
Use imp
o
rtlib_res
o
urces
i
n
P
yth
o
n 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
I
rrgang
Normalize
d
ocker image na
m
e
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrg
a
ng
Fix some min
o
r t
y
pesetting issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
I
rr
g
ang
I
m
pro
v
e install do
c
s
l
inks
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Move sourc
e
s for libgm
x
api
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eri
c
I
rrgang
Remove d
i
sabled test for superseded f
e
ature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Er
i
c Irrgang
I
gnor
e
a
gener
a
t
e
d
f
i
le
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
E
ri
c
Irrgang
Begin moving instal
l
ed interface to `ap
i
/`
commit
|
commitdiff
|
tree
2020-07-10
M
.
E
ri
c
I
r
rgang
Fix l
i
bgro
m
acs CM
a
ke
t
a
rget i
n
stall sy
n
tax
.
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eri
c
Irrga
n
g
Add missing A
B
I h
e
ader
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
I
mpleme
n
t Simul
a
torBuilder
.
add() for
B
oxD
e
for
m
a
tio
n
Handle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irr
g
an
g
Use TopologyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irr
g
ang
Use IonSw
a
ppi
n
g param
e
ter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Use
C
enterOfMassPu
l
ling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrg
a
ng
U
s
e Repl
i
caExchang
e
mem
b
er instead of build() argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use SimulatorMo
d
ules
p
arameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrga
n
g
Use InteractiveMD SimulatorBuilder parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Le
g
acyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
C
onstra
i
nt
s
Param
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Move Profiling parameter out of
s
i
mulatorbuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
r
r
gang
U
s
e SimulatorE
n
v
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Im
p
lement rem
a
ining Simulator
B
uilder
.
a
d
d
() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
Inte
r
fac
e
for
r
emaining
S
i
mu
l
atorBuilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
SimulatorBuilder
.
add() for
StopHan
d
lerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrga
n
g
Imp
l
emen
t
Simu
l
at
o
rBu
i
lder
.
bu
i
ld()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Re
f
ormat pairs
.
c
p
p
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
ri
c
Irrgang
U
se Gr
o
macs::gmx tar
g
et
t
o hint
gmxapi te
s
ts
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgang
Remove workaround for gcc bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irrgang
Impr
o
ve pytest output handling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric I
r
rgang
C
o
mpartmentalize job
rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Improve us
a
ge
o
f
Python logging mo
d
ule
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric
I
rrgan
g
Rem
o
ve unused (and broken) image from D
o
ck
e
r
image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
D
ocker image bui
l
ds: simplify d
o
x
yge
n
ver
s
ion ha
n
dlin
g
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric I
r
rg
a
ng
Docke
r
i
mage builds: move
doxy
g
en handling to a
sep
a
rate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eri
c
I
rrg
a
ng
Extend MPI ensemb
l
e t
e
sting for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Enab
l
e MPI en
s
emble te
s
ting for
gmxapi
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
E
r
ic Irrgang
Enable MP
I
en
s
emble testi
n
g for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
E
r
i
c Irrgang
Nor
m
alize
gmxap
i
related rele
a
se
-
2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgang
Ma
k
e
s
u
re images h
a
ve /usr/b
i
n/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Upda
t
e docker
i
mag
e
build
scripts for master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Ir
r
gang
Make sur
e
CI
s
cript
can call
/
bin/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irrgang
M
inor c
l
ean
up
t
o bu
i
ldall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Irrgang
A
l
low ll
v
m o
p
t
ion already used in
b
ui
l
dall
.
sh script
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Update
he
a
d
er
s
o
r
ting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
ric I
r
rgang
R
equire C++17
s
tand
a
r
d and STL feat
u
r
es
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric
Ir
r
ga
n
g
Apply
more granu
l
ar
C
Test time-out policy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Er
i
c
Irrgan
g
Note CUDA
bui
l
ds i
n
job
n
ames
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric
Irr
g
ang
Only set
GMX_PYTHON_PACKAG
E
=ON where needed
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Er
i
c Irrgan
g
Change def
a
ult CMake vers
i
on to 3
.
1
3
.
0 f
o
r CI i
m
ages
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Require CMake >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric Irrgang
E
x
plic
i
tl
y
s
et UTF
-
8 encoding for gmxapi CLI i
n
teraction
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric Ir
r
ga
n
g
A
voi
d
accide
n
tally initial
i
zing
pyenv in CI
i
mages
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
E
r
ic Irrg
a
n
g
Moc
k
hpccm import so
i
nfrastructure do
c
s build eas
i
ly
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irr
g
ang
Extract logic for when CI jobs e
x
e
c
ute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric I
r
r
g
ang
Normali
z
e some m
o
re job
n
a
mes
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Simplify archi
v
e
.
gitlab-c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Ir
r
gang
Rem
o
ve redunda
n
t jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Ir
r
gang
Fi
x
duplicate variables para
m
eter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrgang
A
d
d required Infrastruct
u
re for
G
itlab merg
e
s
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgan
g
Norma
l
ize
n
a
ming for gro
m
acs
b
uild
/
testin
g
jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Ir
r
gang
Remove
s
ome unnecessary indi
r
ection in job definitions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Consolidate
.
use-clangX
CI job mix-i
n
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c Irrgang
Cons
o
lidate
.
u
s
e-gccX CI job
mix-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Adopt CI
j
o
b
nami
n
g guidelines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgan
g
Normaliz
e
GitLab-CI *cac
h
e*
param
e
ter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge envir
o
nment supp
o
rt int
o
g
l
o
bal
.
gitla
b
-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irr
g
ang
Move
.
b
uild-template
.
yml definitions c
l
oser
t
o p
o
i
nt
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irrgang
Merge
*
-test-template
.
yml into
te
s
ting-matrix
.
gi
t
la
b
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
i
c Irrga
n
g
Merge
.
test-runn
e
r
-
t
emplate
.
yml into testing-matri
x
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge
.
test-s
c
rip
t
-
t
e
m
plate
.
y
m
l into test
i
ng-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rgang
Merge
.
regress
i
ontest-template
.
y
ml into archi
v
e co
n
f
i
g
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrg
a
ng
Consolidate d
o
cu
m
entation template
s
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
R
eorganize
r
elease templates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
ric
Ir
r
gan
g
Remo
v
e co
n
fusing and
du
p
licated variab
l
e
s
as
s
ignmen
t
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
Conso
l
i
dat
e
global mix-ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eri
c
Irrgang
[ci skip] Remove
i
n
direction for default tags parameter
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Ir
r
gang
[
ci skip] Reorg
a
nize
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
Doc
u
ment CI variable a
n
d rem
o
ve unused t
e
mplate
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
Disable
sphinx
.
ext
.
viewco
d
e
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
r
ic Irrgang
Add s
t
ub Varia
b
les
documentation to GitLa
b
CI
doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric Irrgang
Re
m
ove dup
l
icate
d
YAML k
e
y
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrg
a
ng
Add
do
c
ument
f
or containerization infr
a
structure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irr
g
a
n
g
Alphabetize list for readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eri
c
Ir
r
gang
Reforma
t
argument
s
for readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrga
n
g
D
e
f
in
e
an argparse parent
pa
r
s
er for cont
a
i
n
er image
.
.
.
commit
|
commitdiff
|
tree
next