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Specify OMP_NUM_THREADS for Pyhon CI scripts.
2020-09-30
M
.
E
r
ic Irrga
n
g
Sp
e
c
i
f
y
OMP
_
N
U
M_THREADS for Pyhon CI scr
i
pts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Er
i
c Irrgang
Clar
i
fications for Reso
u
rceA
s
signm
e
nt inte
r
face
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eri
c
Irrgang
Support
ResourceAssignment i
n
terf
a
ce for t
M
PI library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Allow MPI-e
n
abl
e
d clients
t
o
provide the library communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
ric Irrg
a
ng
U
se MpiConte
x
tMana
g
er to provide MPI c
o
mm
u
n
i
cator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
Irrgang
Relocate M
p
iCont
e
x
t
M
anage
r
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eri
c
Irrgang
In
t
erface
updates allowing client to provide MP
I
communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irr
g
ang
Improve nami
n
g and docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric
I
rrg
a
ng
D
o
cument a
Mdru
n
ner::Bui
l
derImple
m
e
ntation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric
I
r
r
g
ang
Remo
v
e
o
u
t
da
t
e
d workaround
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
E
r
ic Irrgang
Create
a
nd u
s
e
S
i
m
ula
t
i
o
n
Input m
o
dule
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eri
c
Irrgang
Ref
i
ne
the CMakeLists
.
tx
t
for M
P
I
gm
x
api tes
t
s
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
E
ric Irr
g
an
g
Exp
l
icitly include STL headers us
e
d in test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eri
c
Irrgang
Replac
e
filename-based initi
a
l
ization functions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Er
i
c
I
rr
g
ang
Clarify t
_
input
r
e
c
alloca
t
ion
l
ogic in runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Er
i
c Irrg
a
ng
Use a
h
eap o
b
ject for
inputrec in gmx::M
d
runner::
m
dr
u
nne
r
()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrga
n
g
A
c
c
e
pt Python vers
i
o
ns hi
g
her
th
a
n
3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Er
i
c
Irrgang
Remove co
n
ditional fo
r
CMake < 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Er
i
c Irrgan
g
Al
l
ow more granularity for
pu
b
lic interfaces in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Prevent failed commandline_operatio
n
f
r
om pu
b
l
ishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric
Irrgan
g
Min
o
r additions to gm
x
api install
.
r
st
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Ir
r
gang
Use im
p
ortli
b
_res
o
ur
c
e
s in Python 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eri
c
Irrgang
Normaliz
e
do
c
ker image names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Ir
r
g
a
ng
Fix some minor types
e
tting is
s
ues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgan
g
Imp
r
ove install docs link
s
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Move s
o
u
r
c
es for
l
ibgmx
a
pi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Ir
r
gang
Re
m
ove disab
l
ed
test
for superseded feat
u
re
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ig
n
ore a
g
e
n
erated
fi
l
e
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Irrgang
Use
GMXAPI CMa
k
e
opti
o
n
guard
f
or gmxapi targ
e
t declaration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
E
ric Irrga
n
g
Begin moving in
s
talled
i
nt
e
rface
t
o
`
api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Irr
g
ang
Fix libgro
m
acs
C
Make
t
arg
e
t install syn
t
a
x
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eri
c
Irrgang
Fix libgromacs CMake targ
e
t inst
a
l
l sy
n
tax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
E
r
i
c Irrgang
C
lean up simulat
o
rbu
i
lde
r
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric
I
r
rgang
Add missing ABI hea
d
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Implement SimulatorBu
i
l
d
er
.
add(
)
fo
r
B
o
xDe
f
ormat
i
onHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c I
r
rgang
U
se
Topolog
y
Da
t
a
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use IonSwapping parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic
I
rrgang
Use CenterOfM
a
ssPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrg
a
ng
U
se ReplicaExchan
g
e m
e
mber instead of build
(
) argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgan
g
Use SimulatorModules param
e
ter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
ng
Use In
t
e
ractiv
e
MD Simulat
o
rBui
l
der
parame
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Constrain
t
sParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irr
g
ang
Move Pro
f
ili
n
g
par
a
meter out o
f
simulator
b
uilder
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Use Si
m
ulator
E
nv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement remaining S
i
mulatorBuil
d
e
r
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Interfac
e
for
r
emaining SimulatorBuilde
r
.
ad
d
()
m
eth
o
ds
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
SimulatorBui
l
de
r
.
a
dd() for
StopHandler
B
u
ilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrga
n
g
Impleme
n
t
S
imulatorBuilde
r
.
build(
)
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
r
i
c I
r
rgang
R
ef
o
rmat pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
ric Ir
r
ga
n
g
Use Gromacs
:
:gm
x
target to hi
n
t
gmxapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eri
c
Irrga
n
g
Remove workar
o
und for gcc bug
582
6
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
E
r
ic Irrg
a
ng
Im
p
rove pytest output handling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
r
ic
I
rrgang
Compa
r
tme
n
talize job rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Improve usage of Python logging module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Er
i
c
Irrgang
Han
d
le arbitrary
d
o
xygen versions
i
n
D
oc
k
er image build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Remove unused (
a
n
d
broken) image from Docker ima
g
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Er
i
c I
r
rgang
D
o
cker im
a
ge builds: simplify
doxy
g
en versio
n
handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric Irrgang
Dock
e
r image builds: move doxy
g
en han
d
ling to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irr
g
a
ng
E
xtend
MPI e
n
sembl
e
testi
n
g
for gm
x
api
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
ric Irrgang
Enabl
e
MPI
en
s
emble t
e
st
i
ng for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
ric
Ir
r
ga
n
g
Normalize
g
mx
a
pi rel
a
t
e
d release
-
202
0
job logic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric Irrga
n
g
Reduce co
n
sole log output from sample_restraint
tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Er
i
c Irr
g
a
n
g
Enable MPI
ens
e
mble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
E
r
i
c
I
rrgang
No
r
malize g
m
x
api related release-2020 job
lo
g
i
c
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric
I
rrgang
Make sure images have /usr/bin/pyt
h
on
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
Irrgan
g
Upd
a
te
d
ocke
r
i
m
age bui
l
d scripts fo
r
master b
r
anch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
rgan
g
Make su
r
e C
I
script can
call /bin/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Irrgang
Min
o
r clean up to builda
l
l
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Irr
g
ang
All
o
w
llvm option
already used
in
b
uildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Irrgang
Redu
c
e
console
log output from sample_restraint tests
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eric I
r
rgang
R
efine usage of
*
job:t
a
gs
*
parameter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric I
r
rgang
Upd
a
te h
e
ader sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
r
ic I
r
rgang
Require C++17 standard and STL fea
t
u
r
es
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
E
r
ic Irrgang
Apply
more g
r
anular CTest ti
m
e-out po
l
icy
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric Irrgang
Resolve
s
tatic analyzer warnings fr
o
m
goo
g
le tests
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
E
r
i
c Irrgang
Avoid t
e
mporar
y
st
r
i
n
gs
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Ir
r
gang
N
ote
CUDA buil
d
s in job names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eri
c
I
r
rgang
Update
b
undled pybind
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric
I
rrgang
Only set GMX_PYT
H
O
N_P
A
CKAGE=O
N
where
n
eeded
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
E
r
i
c
I
r
r
gang
Use CMake 3
.
12+ faci
l
ities for detect
i
n
g Python
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric Irrgang
Ch
a
nge
d
efau
l
t CMake version to 3
.
1
3
.
0
for CI imag
e
s
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
E
ric Ir
r
gang
R
eq
u
ire CMake >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Ir
r
g
ang
F
ix invalid git
l
ab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-04-09
M
.
E
ric Irrgang
Allow useful CI t
o
run in forks
commit
|
commitdiff
|
tree
2020-04-08
M
.
Er
i
c Irrgang
Explici
t
ly s
e
t
U
TF-8 encoding for gmxapi
C
LI interaction
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eric Irrgang
Prepare
P
y
thon e
n
v
i
ronments fo
r
GitLab
C
I p
i
peline
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irrgang
Improve
g
m
x
api Python package dependency resolu
t
i
on
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eri
c
Irrgang
Prune chang
e
-
m
anagement
.
rst
a
nd update links
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
Eric Irrgang
Modernize some Python
subprocess calls
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric
I
rrgang
Avoid accidentally
initiali
z
ing pyenv i
n
C
I images
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric
Irrgang
Pre
p
are Python env
i
ronments for GitLab CI pipeline
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrga
n
g
Update scripts for
all of t
h
e
r
equested
pre-commit
.
.
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Irrgang
Require Pyth
o
n
3
.
6
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric Irrga
n
g
Compart
m
e
ntalize hpccm build
s
tages
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
E
ric Irrgang
B
e
friendlier w
.
r
.
t
.
linkchecker
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
E
r
ic Irrgang
Mock h
p
ccm import so
inf
r
as
t
ructure docs bui
l
d easily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric I
r
rgang
Extr
a
ct logic for w
h
e
n CI j
o
bs execu
t
e
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrg
a
ng
Normalize s
o
me mor
e
job names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irrga
n
g
Simplify
a
rchive
.
gitlab-c
i
.
yml
commit
|
commitdiff
|
tree
next