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Clarify the GMX_BUILD_MDRUN_ONLY full testing instructions.
2020-10-08
M
.
Eric I
r
rgang
C
larify the GMX_
B
UILD
_
MDRUN_ONLY
f
ull testing instructi
o
ns
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric Irrgang
Improve gmx
P
ythonDi
s
co
v
e
ry
.
c
m
a
k
e
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric
Irrg
a
ng
D
o
n'
t
override
u
ser provided CMAKE_OSX_DEPLO
Y
ME
N
T_TARGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrgang
Han
d
le
g
mxapi
t
mpi
p
aramet
e
rs bet
t
e
r
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric I
r
rg
a
ng
L
e
t
gmxapi
i
nstallation r
e
co
r
d the GROMACS libr
a
ry
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
Eric Irrgang
Use updated images for Pyt
h
o
n
C
I jobs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrga
n
g
Restrict gmxapi pytest
tests to `-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Specify OM
P
_NUM_THREADS
for Pyhon CI script
s
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
ric Irrga
n
g
Clarifica
t
ions for ResourceAssignment interfa
c
e
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrga
n
g
Support ResourceAssignm
e
n
t
interface fo
r
tMPI librar
y
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irr
g
ang
Allow MPI-e
n
ab
l
ed
c
li
e
nts t
o
provide the libra
r
y communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgan
g
Use
M
piC
o
n
t
ext
M
a
n
age
r
to
p
rovide MP
I
communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
Irrgan
g
Reloc
a
t
e
MpiC
o
nt
e
xt
M
anager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
I
nterface updates allowi
n
g client to
prov
i
de MPI
c
o
mmunicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
I
m
prove n
a
ming and
d
o
c
s
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Er
i
c Irrgang
Doc
u
me
n
t a Mdr
u
nner::Build
e
rImplemen
t
atio
n
member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric I
r
r
g
a
ng
Remove outdated worka
r
ound
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
Create and use Simul
a
ti
o
nInput module
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
E
ric I
r
rgang
Refine th
e
CMake
L
ists
.
t
x
t
f
o
r
MPI gmxa
p
i tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eric Irrgang
Explicitly includ
e
S
TL
headers used in test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eric
Irrg
a
n
g
Replace filen
a
me-ba
s
ed
i
n
i
tiali
z
ation func
t
i
o
ns
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Ir
r
gang
Clarify t_inputrec all
o
cati
o
n logi
c
i
n runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric
Irr
g
ang
Us
e
a
h
eap objec
t
for in
p
utrec
i
n gmx::Mdrun
n
e
r
:
:mdrunner()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Accept Pytho
n
versions h
i
gher th
a
n 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
R
emo
v
e conditional
f
or CMake <
3
.
1
2
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eric Irrgang
Allow more granulari
t
y for
publ
i
c interfaces in bui
l
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
ric
Irrgang
Prevent fa
i
led comma
n
d
l
ine_operat
i
o
n from publishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
r
ic Ir
r
gang
Minor
additions to
g
mxa
p
i ins
t
all
.
rs
t
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric I
r
rg
a
n
g
Use importlib_resources
i
n Python 3
.
6
i
m
a
ges
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irr
g
ang
Norm
a
li
z
e
docker
i
m
a
ge
names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irr
g
ang
Fix some minor typ
e
setti
n
g issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
I
m
prove in
s
tall docs links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrga
n
g
Move source
s
f
o
r
l
ib
g
mxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Remove d
i
s
able
d
test for supersed
e
d feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ignore
a gen
e
rated
f
ile
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric
Irrgang
Use
GMXAPI CMak
e
option
g
u
ard f
o
r gmxapi targe
t
d
eclaration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Ir
r
ga
n
g
Begin moving ins
t
al
l
ed
i
nterfac
e
t
o `api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Irr
g
a
ng
Fix libgro
m
a
c
s CMake target inst
a
l
l
syntax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric Irrg
a
n
g
F
ix libgrom
a
cs
CMake target install syntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Irrgang
Cle
a
n up s
i
m
u
l
a
torbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric Irrgang
A
d
d missing
A
B
I
h
e
a
der
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
n
g
Implement Sim
u
lator
B
uilder
.
add() f
o
r B
o
xDefo
r
mationHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgan
g
Use TopologyDat
a
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use IonSwapping
parame
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
a
n
g
Use CenterOfMassPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
Use Repli
c
aExchang
e
m
ember
i
nstead of bu
i
l
d() argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
Irrgang
Use S
i
mulatorModule
s
parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Interac
t
i
veMD Simulator
B
uilder parame
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
U
se Legac
y
Inpu
t
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rg
a
ng
Use Constra
i
n
tsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
g
a
ng
Move Prof
i
ling pa
r
ameter out of simulatorbuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irr
g
an
g
U
se Simula
t
orEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Implement remaining SimulatorBuilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Int
e
rface for r
e
maini
n
g
S
i
m
ulatorBui
l
der
.
add()
methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Simulato
r
B
u
ilder
.
add()
f
or StopHand
l
erBuil
d
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Imple
m
e
nt Simula
t
orBuilder
.
bu
i
ld()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Reformat p
a
i
rs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Use Gromacs::gmx tar
g
e
t to
hint
g
m
xapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric I
r
r
g
ang
Remove w
o
rkar
o
und for gcc bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric
I
rrgang
Improve pyt
e
st
output handling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
C
ompartmentalize job rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eri
c
Ir
r
g
ang
Im
p
ro
v
e usage of Python
loggi
n
g
m
odule
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
E
ric Irrgang
H
andle
arbitrary dox
y
ge
n
v
ersions in Doc
k
er image
b
u
ild
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Remove unused (and broken) image from Docker
imag
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric
I
r
r
gan
g
Docker ima
g
e builds: simplify doxygen v
e
rsion handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eri
c
Irrg
a
ng
Docker
i
mage builds
:
move doxy
g
en handlin
g
t
o
a
se
p
ar
a
te
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
I
rrgang
E
x
t
e
nd M
P
I ensemble
testing for gm
x
a
pi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
I
rrgang
Enable MPI ensemb
l
e testing for g
m
xapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Normalize gmx
a
pi related release-2020
j
o
b
logic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric Irrgang
Reduce console
log output from sa
m
ple_restr
a
i
n
t tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
E
r
i
c Ir
r
gang
En
a
ble MPI ensemble testing for
g
mxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric Ir
r
gang
N
o
rmalize
g
mxapi related release
-
202
0
job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Er
i
c Irrg
a
ng
Make sure imag
e
s have /usr/bin/
p
yt
h
on
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Update docker image build scripts for master
b
ranch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
ang
Make sure CI script ca
n
c
a
l
l
/bi
n
/
e
nv p
y
thon`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
rr
g
ang
Minor clean up to build
a
l
l
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
rg
a
ng
A
llow llvm
o
p
t
ion
alre
a
d
y used in buildall
.
sh
script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
R
e
duce
c
o
n
s
ole log out
p
ut fr
o
m sample_r
e
st
r
aint
t
ests
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eri
c
Irrga
n
g
R
e
fine u
s
ag
e
o
f *job:tags* parameter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Update he
a
der sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
r
ic Irrg
a
ng
Require C++17 s
t
andard an
d
STL
f
ea
t
ures
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eri
c
Irrgang
Apply mor
e
granular CTest time-out policy
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric Ir
r
gang
Resolve static analyzer
warnings from google tests
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
E
ric Irrgang
Avoid
t
emp
o
rary s
t
r
ings
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Irr
g
ang
Note CUDA b
u
i
lds i
n
jo
b
names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrgan
g
Updat
e
bundled
p
y
bind
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrgang
Only se
t
GMX_PYTHON_PACKAGE=ON where
needed
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
Eric
I
rrgang
Use CM
a
ke 3
.
12+
facilities for de
t
ec
t
ing Py
t
hon
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric Ir
r
g
ang
Change d
e
fault CMake v
e
rsion to 3
.
13
.
0 fo
r
CI images
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric I
r
rgang
Require
CMake >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irr
g
a
ng
Fix
inval
i
d gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-04-09
M
.
E
r
i
c Irrgang
All
o
w usefu
l
CI to r
u
n in
f
o
rks
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric
I
r
rgang
E
xpli
c
itly set UTF-8 enc
o
din
g
fo
r
gmxapi CLI interaction
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eric I
r
rgang
Prepare
P
yth
o
n env
i
ro
n
ment
s
for
G
it
L
a
b CI pipe
l
in
e
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
E
r
ic Irrgang
I
m
pro
v
e gmxapi
P
ython package depen
d
enc
y
reso
l
ution
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irrga
n
g
Prune chang
e
-management
.
rst and
update
links
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
E
r
ic Ir
r
gang
Modernize some Pyt
h
on subproce
s
s call
s
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric Irr
g
ang
Av
o
id
accidenta
l
ly initia
l
iz
i
ng pyenv in CI im
a
ges
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrga
n
g
Prepare Python env
i
ronments for Gi
t
La
b
CI
p
ipeline
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eri
c
Ir
r
g
a
ng
Updat
e
scripts for a
l
l of the requested
p
re-commit
.
.
.
commit
|
commitdiff
|
tree
next