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Support ResourceAssignment interface for tMPI library builds.
2020-09-29
M
.
Eric
I
rrgang
Support Res
o
urceA
s
sign
m
e
nt in
t
erface f
o
r t
M
P
I library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Ir
r
g
a
ng
A
l
low MPI-e
n
abled c
l
ients to
p
r
ovid
e
the
l
i
b
rary communicato
r
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irrgang
Use Mp
i
ContextManager
t
o
provide MP
I
co
m
muni
c
ator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Relo
c
a
te M
p
iCo
n
textManager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irr
g
ang
Inte
r
face updates al
l
o
wing client to pr
o
vide MPI communicat
o
r
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
Improve naming an
d
docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
Document a Mdrunner::BuilderImple
m
entation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Irrgang
Re
m
ove out
d
a
ted
w
orkaround
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
E
r
ic Ir
r
gang
Create
a
nd use Simul
a
t
i
on
I
nput module
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric I
r
r
gang
Re
f
i
ne the CMakeLists
.
txt f
o
r MPI g
m
xapi tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eri
c
I
r
r
gang
Explicitly include STL headers used i
n
test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
E
ric Ir
r
gang
Replace
filename-
b
ased initialization functi
o
ns
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric
Irrgang
Clarify
t
_
i
nput
r
ec allocat
i
on logi
c
in runner
.
c
pp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrgang
Use a
h
eap obj
e
ct
for inp
u
tr
e
c
in g
m
x::M
d
runner::
m
drunner()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
E
ric Ir
r
gang
A
ccept Python ve
r
si
o
ns higher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irr
g
ang
Remove conditional
for CMake < 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eric Irrga
n
g
A
llow more granularity for pu
b
lic
i
nterfaces in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Ir
r
gang
Prevent f
a
iled commandline_operation fr
o
m publis
h
ing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
r
ic
Ir
r
gang
Minor additions to gmxa
p
i install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
U
se im
p
ortl
i
b_resources in Py
t
hon
3
.
6 i
m
age
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric I
r
rgang
Normaliz
e
docker
image names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
r
i
c
I
r
rgang
F
i
x some minor typesetti
n
g issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
ric Irr
g
ang
Improve i
n
stall docs li
n
ks
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric I
r
rgang
M
o
ve s
o
urces for libg
m
xapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
R
emove
dis
a
bled
test
f
or superseded f
e
atur
e
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
ric
I
rr
g
a
ng
I
g
no
r
e
a generated
file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Ir
r
gang
Us
e
GMXAPI CMake
o
ptio
n
g
u
ard for gm
x
api
target
d
ec
l
aration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irrgang
Begin moving insta
l
led
i
nterface
t
o `api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Irrgang
Fix l
i
bgrom
a
cs CMake target ins
t
all synt
a
x
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric
Irrgang
Fix libgromacs CMak
e
target ins
t
all synt
a
x
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Irrga
n
g
Clean up
s
imulatorbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Er
i
c Irrgang
Add miss
i
n
g
ABI
header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
I
m
plement SimulatorBuilder
.
add() for BoxDeforma
t
ionHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Use Topology
D
ata
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
U
se IonSwa
p
ping para
m
e
ter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use CenterOfMassPullin
g
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
U
se ReplicaE
x
change member inst
e
ad of build() argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use SimulatorModules paramet
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Us
e
Interactive
M
D SimulatorBui
l
der parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
LegacyInp
u
t
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gan
g
U
se Con
s
traintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Move Profiling paramet
e
r out of simulatorbuilder
.
buil
d
(
)
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic I
r
rgan
g
Use Sim
u
l
a
t
orEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement remaining SimulatorBu
i
lder
.
add
(
)
m
ethods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Inte
r
face for
r
e
ma
i
ning Simulato
r
Builder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Ir
r
gang
Simu
l
a
tor
B
uilder
.
a
d
d
() for St
o
pHandlerBuilde
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Imple
m
ent S
i
mulatorBuilder
.
build(
)
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eri
c
Irrgang
Ref
o
rmat pair
s
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Use Grom
a
cs::gmx ta
r
get to h
i
n
t gmxapi test
s
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrg
a
ng
Remove wor
k
around
f
or gcc bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irrgang
Improve pyte
s
t
outpu
t
handling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
ric Irrga
n
g
C
o
mpart
m
entalize job rul
e
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irr
g
ang
I
mprove usa
g
e of Python log
g
ing module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
E
r
i
c Irrg
a
n
g
Handle arbitrary do
x
ygen v
e
rsion
s
in Doc
k
er
image build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Remove unused (
a
nd
broken) image from D
o
c
k
er imag
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
D
ocker ima
g
e bu
i
l
d
s: simpli
f
y dox
y
gen ve
r
sion h
a
ndling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irr
g
ang
Doc
k
er ima
g
e
bui
l
ds: mo
v
e
doxyg
e
n handling to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Ir
r
g
a
ng
Extend
M
PI en
s
emble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrg
a
ng
Enable MP
I
e
nsemble testing for gm
x
a
pi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
I
rrg
a
ng
Normalize gmxapi related relea
s
e-2020 job
l
ogic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric Irrgang
Reduce console log
output from
sample_restraint tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgan
g
Enable MPI e
n
sem
b
le testi
n
g for
g
m
x
api
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Er
i
c Irrgang
Normalize
gmx
a
pi r
e
l
a
t
e
d rele
a
s
e-2020
j
ob log
i
c
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
E
r
i
c Irrga
n
g
Make
s
u
r
e
i
m
a
ges ha
v
e
/usr/bin/pyt
h
on
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Update do
c
ker im
a
ge build
s
cripts f
o
r master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Mak
e
sure CI script can call /b
i
n/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Minor clean up
t
o buildall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrg
a
ng
Al
l
ow llvm
opt
i
on al
r
ea
d
y u
s
ed in b
u
il
d
all
.
sh script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Irrgang
R
e
duce console log output
f
rom sample_
r
e
s
t
ra
i
nt tests
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eric Irrg
a
ng
Re
f
ine usa
g
e of
*
j
o
b:tags
*
param
e
ter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrg
a
ng
Update header
sor
t
ing
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Er
i
c Irrgang
R
equire C++1
7
standard and STL features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Er
i
c
Irrgan
g
Ap
p
ly
m
ore granular
C
Test time
-
out
policy
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eri
c
I
rrgang
Resolve static ana
l
yzer warn
i
ngs
f
rom
g
o
ogle tests
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric I
r
rgang
A
v
o
id tem
p
o
r
ary s
t
rin
g
s
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Ir
r
gang
No
t
e CUDA build
s
i
n
j
o
b nam
e
s
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrga
n
g
Update b
u
ndled
p
y
bind
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrga
n
g
Only set GMX_P
Y
THON_PACKAGE=ON where ne
e
ded
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
Eric Irrgang
Use CMake 3
.
12+ facilities
f
or d
e
tecti
n
g Pyth
o
n
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Er
i
c Irrgang
Change
d
efault CMak
e
version to 3
.
13
.
0
f
o
r CI i
m
ages
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgan
g
Require CMake >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric I
r
rga
n
g
Fix invalid gitlab-
c
i
.
ym
l
commit
|
commitdiff
|
tree
2020-04-09
M
.
E
r
ic
I
r
rga
n
g
Allow useful CI to run
i
n f
o
rks
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric Irrga
n
g
E
xplicitly set UT
F
-8
e
ncoding for gmxapi C
L
I intera
c
tion
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
E
ric
I
rrgang
P
r
e
pare Pytho
n
e
n
vironments f
o
r Git
L
ab CI p
i
peline
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
E
r
ic
Ir
r
gang
I
mprove gmxapi Pytho
n
package dep
e
nd
e
ncy resol
u
tio
n
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irrga
n
g
P
r
une change-mana
g
ement
.
rst
and update links
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
Eric
Ir
r
gan
g
Mod
e
rnize some
P
ython s
u
bprocess call
s
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric Ir
r
gan
g
Avoid accidental
l
y init
i
alizing
pyen
v
in CI images
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric
Irrg
a
ng
Prepare Python environment
s
for G
i
t
L
ab CI
p
ipeline
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric
I
rrgang
Update s
c
ripts for all of the request
e
d pre-commi
t
.
.
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Irr
g
ang
Require Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric
I
r
r
g
a
ng
Co
m
partmen
t
al
i
ze
hpccm build stage
s
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric Irrgang
Be fri
e
ndlier w
.
r
.
t
.
l
i
nkc
h
ecke
r
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
E
ric Irrgang
Mock hpccm import so
infrastructure d
o
cs bu
i
ld e
a
sily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrga
n
g
E
xtract logic for when CI jobs execut
e
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrg
a
n
g
Normalize some
more job names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Simp
l
ify archive
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric I
r
rgan
g
Remove redundant jo
b
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irrgang
Fix duplicate var
i
ables paramete
r
.
commit
|
commitdiff
|
tree
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