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Update rules for release-2021.
2020-12-04
M
.
Eric Irrgang
Upd
a
te rules for release-2021
.
commit
|
commitdiff
|
tree
2020-12-04
M
.
E
ric Irrg
a
ng
S
eparate job scri
p
t
f
iles f
o
r
gmxap
i
package
v
e
rsions
.
commit
|
commitdiff
|
tree
2020-12-03
M
.
Eric Irrgang
Improve
g
mxapi C++
t
est co
v
e
r
age for faile
d
mdrun
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eric Irrgang
One arg
u
men
t
per lin
e
for long fu
n
ction signatures
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Eric Irr
g
ang
L
ook for
the
v
arious possible
names of t
h
e gromacs
.
.
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
E
r
ic
I
rrga
n
g
g
mxapi versi
o
n
i
ng updates
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Irrgang
Be m
o
re explicit ab
o
ut build
-
tree
-
only depe
n
d
e
n
c
ies
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
E
r
i
c Irrgan
g
Help cli
e
nts
f
ind d
e
pendencies of im
p
ort
e
d CMake
targ
e
ts
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric
I
r
rgang
Remov
e
an unneces
s
a
r
y
t
r
ansi
t
ive
d
ependen
c
y of imported
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
No
r
malize
F
indMPI hints
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
r
ic
I
r
rgang
Clarify
behavior of LegacyMdru
n
Opti
o
ns
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Er
i
c
I
r
r
gan
g
Tell
gmxapi to loo
k
f
or MPI,
wh
e
n appropriate
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Eric Irrgan
g
Us
e
upd
a
ted CI pipeline r
u
les for Pyt
h
on package
tes
t
s
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric Irr
g
ang
U
p
da
t
e gmxapi
ve
r
s
i
on
detai
l
s
.
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric
Irrgang
Don'
t
override user pr
o
vided CMAK
E
_OS
X
_DEPLOYMENT_TARGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrgang
Handl
e
gm
x
a
pi tmpi
parameters be
t
te
r
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrgang
L
e
t gmxap
i
installa
t
i
o
n record the
GROMACS l
i
brary
.
.
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Er
i
c Ir
r
g
an
g
Restri
c
t
g
mx
a
pi pytest tests to `-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Specify OMP_NUM_THR
E
ADS for Pyho
n
CI
scripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrga
n
g
C
larificat
i
ons f
o
r Re
s
ourceAs
s
ig
n
ment interface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric I
r
rgang
Support ResourceAs
s
ignme
n
t int
e
r
face for tMPI library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic
I
rrgang
A
l
low MPI-en
a
bled clients
to provide the
l
ibrary commu
n
i
c
ator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric I
r
rgan
g
Use MpiContextM
a
nager to pro
v
ide MPI commu
n
ic
a
t
or
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Relocate MpiCo
n
textManager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irr
g
ang
Interface
u
pd
a
t
e
s allowing client to provide
M
PI communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric
Ir
r
gang
Impr
o
ve naming and
docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
Document a
Mdrunner::Bui
l
der
I
mplementation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
E
r
i
c Ir
r
g
a
n
g
Remove ou
t
dated
work
a
round
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
E
ri
c
Irrgang
Refine
the
C
Make
L
i
s
ts
.
txt
for M
P
I gmxapi tests
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Er
i
c
Irrgang
Clarify t_inputr
e
c al
l
ocati
o
n
logic in runn
e
r
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
E
ric Irrgang
Accept
P
ython versio
n
s
h
igher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Rem
o
ve conditional for CMa
k
e < 3
.
1
2
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
E
ric Irrgang
Al
l
o
w m
o
r
e granularity fo
r
public interfaces in b
u
ild
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irr
g
ang
P
revent fail
e
d co
m
mandlin
e
_o
p
er
a
tion from p
u
blishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Minor add
i
t
io
n
s to
gmxapi
i
n
s
t
al
l
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Use importl
i
b_resources
in Python 3
.
6 image
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
ric
Irrgang
Normalize docker image names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Ir
r
gang
Fix some minor typesett
i
ng issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgan
g
Improve install docs
l
inks
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Mov
e
s
o
urces for
l
ibgm
x
api
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
r
ic Irrgang
Remove disabled test for super
s
eded feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ignore a g
e
nerated f
i
le
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irrgan
g
Beg
i
n moving installed int
e
rf
a
ce
t
o `api/`
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric Irrgang
Fix
l
ibgromac
s
CMake target ins
t
a
ll s
y
ntax
.
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric I
r
rgang
A
dd
mis
s
i
n
g
A
BI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
I
rrga
n
g
Implement SimulatorB
u
ilder
.
add() for BoxDefo
r
mationHand
l
e
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Use TopologyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
an
g
Use
I
onSwapping para
m
e
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
r
rga
n
g
U
s
e C
e
nterOfMa
s
sPulli
n
g
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
Use
R
e
p
lic
a
Exchange
member instead of build() argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c Irrgang
Us
e
Simu
l
atorModules parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Inte
r
activ
e
MD S
i
mulatorB
u
il
d
er parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
Us
e
LegacyI
n
put
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
U
s
e ConstraintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Move Profiling parameter out of simulatorbui
l
der
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrg
a
ng
Use Simulator
E
nv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
I
r
rga
n
g
Imple
m
ent remaining S
i
mulatorBuilder
.
ad
d
(
)
methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgan
g
I
n
terface for remainin
g
SimulatorBuild
e
r
.
a
d
d()
methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
S
imulatorBuilder
.
add() for
S
t
opH
a
ndlerBu
i
lder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Implem
e
n
t Simu
l
atorBuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Ir
r
ga
n
g
Reformat pairs
.
c
pp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrga
n
g
U
se
G
romacs
:
:gmx
target t
o
hint gmxapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
E
r
i
c Irrgang
Rem
o
ve workaround for gcc bug 58
2
6
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Ir
r
gang
Improve
pytes
t
output han
d
ling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irr
g
ang
Compar
t
menta
l
ize job rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Improve
u
s
age
of
P
ython l
o
gging mod
u
le
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
R
e
m
ove u
n
used (an
d
broken
)
image from Doc
k
er image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric Irr
g
a
ng
Docker im
a
ge
b
u
ilds
:
simplify
d
o
x
ygen version handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrg
a
ng
Docker imag
e
b
u
ilds: move do
x
ygen handling to
a
sep
a
rate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
Irrgang
E
x
tend MPI ensem
b
le t
e
sting for gmxap
i
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eri
c
Irrg
a
ng
Enable M
P
I ensemb
l
e
t
esting f
o
r gmxa
p
i
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgang
Enable MPI ensembl
e
testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric Irrgang
Normalize gmxapi related rel
e
ase-2
0
20 job
l
ogic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgang
M
a
ke sure images
h
ave /usr/bin/py
t
h
o
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Update dock
e
r image build scripts for
m
aster branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrg
a
n
g
M
ake sure CI script
c
a
n
c
a
ll /bin/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
I
rrgang
Minor clean up to buildall
.
s
h
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Allow llvm o
p
ti
o
n
a
lready
used in buildall
.
sh s
c
ript
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
r
ic
I
r
rgang
Upd
a
te
header sort
i
ng
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Require C
+
+
1
7 stand
a
r
d
and
S
TL f
e
atures
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irr
g
ang
App
l
y mo
r
e granul
a
r CTest
t
ime-out policy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
E
ric Irrgang
Note
CUDA builds in job name
s
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irr
g
ang
O
n
ly
s
e
t
GMX_PYTHON_P
A
CKAGE=ON where needed
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Er
i
c Irrgang
C
h
ang
e
d
efault
C
Make v
e
rsion
t
o 3
.
13
.
0 for
C
I ima
g
es
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Er
i
c
I
r
rga
n
g
Require CMake >
=
3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
Er
i
c
Ir
r
g
a
ng
Explicitly set
U
TF-8 enc
o
ding for
g
mxapi
CL
I
inter
a
cti
o
n
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric Irrgang
Avo
i
d accide
n
tally initializ
i
ng
p
yenv in CI images
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Er
i
c Irrgang
Mock
h
pccm
i
mport so infras
t
ructure
d
o
cs
build eas
i
l
y
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Ext
r
act logic for
when CI
jobs
e
xecute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ri
c
Irrgang
N
o
rmali
z
e
some more job na
m
e
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Simpl
i
fy archive
.
g
i
tlab-ci
.
y
ml
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric
Irrgan
g
Remov
e
redundan
t
jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
rrgang
Fix duplic
a
te varia
b
les param
e
ter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c
Irrga
n
g
Add required In
f
ras
t
ructure
f
or Gi
t
lab m
e
rg
e
s
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Irrgang
Normalize na
m
ing fo
r
gromacs
b
uild/testing j
o
bs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric
I
rrgang
Remove s
o
me
u
nn
e
cess
a
ry
in
d
ire
c
tion in job de
f
in
i
tions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
g
ang
Co
n
solidate
.
use-clangX CI job m
i
x
-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
C
onsolid
a
te
.
u
s
e
-gccX CI
j
o
b
m
i
x-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
i
c Ir
r
gang
Ad
o
pt CI
j
o
b
naming g
u
i
d
e
li
n
e
s
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
I
r
rgang
Norm
a
lize GitLab-CI *cache
*
para
m
e
t
er
.
commit
|
commitdiff
|
tree
next