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Improve gmxapi C++ test coverage for failed mdrun.
2020-12-03
M
.
Eric Irrgang
Improve
g
mxapi
C
++
t
est
cove
r
ag
e
for failed mdrun
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eric I
r
rg
a
ng
O
n
e arg
u
ment per line for long function sig
n
a
t
u
res
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Er
i
c Irrgang
Look for the various poss
i
ble nam
e
s o
f
the
gromacs
.
.
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
Eric Irrgang
gmxapi
v
e
rsioning upd
a
t
es
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Ir
r
gang
Be mo
r
e explicit a
b
out build-tree-only dependencies
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
Er
i
c Irrga
n
g
Help
clients find
d
epend
e
ncies
o
f import
e
d CMake
targe
t
s
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irrg
a
ng
R
e
m
o
ve a
n
u
nnecessary transitive
d
e
pendency of imported
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric
Irrga
n
g
Nor
m
ali
z
e
F
ind
M
PI hin
t
s
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
ric
I
rrga
n
g
Clarify
b
e
ha
v
ior of LegacyMdr
u
nOptions
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Eri
c
Ir
r
gang
Tell gm
x
api to look for MPI, when appro
p
ria
t
e
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Eric Irrgang
Use
updated CI
pipeline
r
ul
e
s for Python
p
a
ckage tests
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric Irrgang
Upd
a
te g
m
xapi
v
e
r
s
i
on detail
s
.
commit
|
commitdiff
|
tree
2020-10-05
M
.
E
ric Irrgang
D
o
n
't overri
d
e
user
p
ro
v
i
d
ed CMA
K
E_OSX_
D
EPLO
Y
M
E
NT_
T
ARGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
E
r
ic Irrgang
H
a
ndle gmxapi tm
p
i param
e
ters better
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irr
g
a
n
g
L
et gmxapi installation reco
r
d the GRO
M
ACS
l
ibrary
.
.
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Er
i
c I
r
rgang
Restrict gmxapi pytest tests to `-
n
t
2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Er
i
c
I
rr
g
an
g
Spe
c
if
y
OM
P
_NUM_THREADS for Py
h
on CI scripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Er
i
c
Irrgang
Clarifi
c
ati
o
ns for R
e
so
u
rceAssignment interf
a
ce
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Er
i
c Irrgang
Support
R
eso
u
rceAssig
n
m
e
nt interface for tMP
I
l
i
br
a
ry
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Al
l
ow
MPI-
e
nabled clients to
p
rovide
t
he library communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
I
rrga
n
g
Use Mp
i
ContextManager
to provide MPI communica
t
or
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrga
n
g
Relocate
MpiContextM
a
nag
e
r
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrg
a
ng
Interfa
c
e updates al
l
owing client to provide MP
I
communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
Imp
r
ov
e
naming and
d
ocs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
Docum
e
nt a Mdrunner::BuilderImplementation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Irrgang
Remove outda
t
ed
w
ork
a
round
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
Refine
t
he CMakeLists
.
txt
f
or MPI gmxapi tests
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irr
g
ang
Clarify
t_inputrec allo
c
ation
log
i
c in r
u
n
ne
r
.
c
p
p
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
E
ric
Ir
r
g
a
n
g
A
c
cept P
y
thon
vers
i
o
ns h
i
g
her than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Remove
conditional for CMake < 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eric Irrgang
A
l
low more
g
ra
n
ula
r
ity
f
or public interfaces in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Prevent failed comm
a
ndline_operation
f
rom pu
b
lishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Er
i
c
Irrgang
M
i
nor additions to g
m
x
api i
n
stall
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric
Irrgang
Use importl
i
b_reso
u
rce
s
in
Python 3
.
6
images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
r
ic
Irrgang
Normalize docker
i
mage names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
I
r
r
gang
Fix som
e
minor type
s
ettin
g
issue
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
r
ic Irr
g
ang
Improve
insta
l
l docs links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
ric Irrga
n
g
Move sources for
libgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eri
c
Irr
g
ang
R
emove disabled
t
e
s
t for
supers
e
ded f
e
atur
e
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ignore a
g
enerated file
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irr
g
ang
B
e
gin
m
oving installed i
n
terface to
`api/`
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric I
r
rgan
g
Fix libgromacs CMak
e
target install syntax
.
commit
|
commitdiff
|
tree
2020-06-27
M
.
E
r
ic Irrgang
Add missing ABI
h
ead
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement Simul
a
torBuilder
.
ad
d
()
f
o
r
BoxDeforma
t
ionH
a
ndle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Topolo
g
yData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ri
c
Irrgang
Use IonS
w
apping parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Ir
r
gang
Use CenterOfMassPullin
g
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgan
g
Use ReplicaExchang
e
m
ember instead
o
f build() arg
u
ment
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use SimulatorModules parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
a
ng
Use Int
e
ractiveMD Simula
t
o
r
Builder par
a
mete
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrga
n
g
Use LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rgang
U
s
e Co
n
straintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Move Profi
l
ing par
a
met
e
r
out of simulatorbuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Sim
u
lato
r
Env
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
I
rrgang
Implement remaining Simula
t
o
rBuilder
.
a
dd() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c Irrgang
Interface for remaining
S
imu
l
atorBui
l
der
.
a
dd() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
SimulatorBuilder
.
add()
f
o
r
StopHandlerBuilde
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgan
g
Implem
e
nt SimulatorBu
i
lder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Er
i
c Ir
r
ga
n
g
R
e
for
m
at pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
r
ic
I
rrgan
g
Use Gromacs:
:
gmx target
to
hint gmxapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgang
Remove wo
r
karound for gcc bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eri
c
Irrgang
Improve pytest output handling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Compart
m
en
t
aliz
e
job
rul
e
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric I
r
rgan
g
Improve usage of
Pytho
n
logging mod
u
le
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Remove u
n
used (and br
o
k
e
n)
image from Docker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Ir
r
gang
Docker
i
m
ag
e
b
u
ilds
:
s
i
mplify doxygen
version handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric
Irr
g
ang
Docker i
m
age
builds: move doxygen handling to a sepa
r
at
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrg
a
ng
Extend MPI ensemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Enable
M
P
I
e
nsemble
t
esti
n
g
f
or gmxapi
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eri
c
Ir
r
ga
n
g
Enab
l
e
MP
I
e
nsemble te
s
ting for gmx
a
pi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
E
ric Irr
g
ang
Normalize
gmxapi
relat
e
d releas
e
-2020
j
o
b
logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgang
Mak
e
sure images have /usr/bin/pytho
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
Irrgang
Update docker imag
e
bu
i
l
d
scripts for master br
a
nch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
Irrgang
Mak
e
sure CI script can
c
a
l
l /bin/
e
n
v
python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Irrga
n
g
M
i
n
o
r clean up to buildal
l
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
r
r
gang
Allo
w
llvm option
alread
y
used in buildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
U
p
d
ate
h
eader
sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrg
a
ng
Require C++17
st
a
ndard and STL features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Er
i
c Irrg
a
ng
Ap
p
ly more
g
r
a
n
u
lar
CTest time-ou
t
policy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Irrg
a
ng
N
o
te CUDA
builds in job names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric
I
rrgang
Only se
t
GMX_
P
YTHON_PACKAGE=
O
N where needed
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric Irrgang
Change de
f
ault CMake vers
i
o
n to 3
.
13
.
0 for CI images
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Require CMake
>
=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
Er
i
c
I
r
rgang
Explicitly se
t
UTF-
8
en
c
o
ding for
g
mxapi CLI interacti
o
n
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric Irrgang
Avoid acci
d
entally initi
a
lizi
n
g pyenv in CI ima
g
es
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eri
c
I
rrgang
Mock hpcc
m
import so infrastructu
r
e docs bui
l
d e
a
sily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Extrac
t
logic f
o
r
w
he
n
CI jobs execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrgan
g
Normalize some mor
e
job names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic
Irr
g
a
ng
Sim
p
lify archive
.
git
l
a
b
-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic
Irrgang
Remove red
u
nd
a
nt job
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c
I
r
rga
n
g
F
i
x du
p
licate variables parameter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c Irrg
a
ng
Add required Infrastructure
f
or Gitlab merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Nor
m
alize na
m
ing
for grom
a
cs build/testing
j
ob
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrgang
Remove some un
n
ecessa
r
y in
d
ir
e
ction
i
n job de
f
initi
o
ns
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrg
a
ng
Cons
o
lida
t
e
.
use-cl
a
ngX CI
j
ob
mi
x
-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric
I
r
rgang
Consol
i
date
.
u
s
e-
g
ccX
CI job mix-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Ir
r
gang
Ad
o
pt
CI
j
ob naming guidel
i
nes
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irrgang
Normalize GitLab-
C
I
*cache* parameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge e
n
vironment s
u
ppor
t
in
t
o
global
.
g
i
tlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Ir
r
gang
M
o
ve
.
b
u
i
l
d-t
e
mpla
t
e
.
yml
d
efinition
s
closer t
o
p
o
int
.
.
.
commit
|
commitdiff
|
tree
next