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Improve gmxapi C++ test coverage for failed mdrun.
2020-12-03
M
.
Eric
I
rrgan
g
Improve gmxapi
C++ tes
t
coverage for
failed mdrun
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eric Irrgang
One argum
e
nt pe
r
line for long function
s
igna
t
u
res
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Eric
I
rrgang
Look for th
e
various po
s
s
i
ble na
m
es of
the gromac
s
.
.
.
commit
|
commitdiff
|
tree
2020-11-20
M
.
Eric Irrgang
Create
CMake targe
t
s for eac
h
of the module
s
.
commit
|
commitdiff
|
tree
2020-11-18
M
.
Eric Irr
g
a
ng
Repla
c
e gmxapi `e
r
r
o
routput` with `stderr` and `stdout`
commit
|
commitdiff
|
tree
2020-11-17
M
.
Eric Irrgang
Separate t
h
e testutils module
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
Eric Irrg
a
ng
gmxa
p
i ver
s
io
n
i
n
g updates
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Ir
r
gang
B
e
more expli
c
it a
b
out build-tree-o
n
ly depende
n
cie
s
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Ir
r
gang
Provi
d
e a
catch-all target fo
r
library
modules
.
commit
|
commitdiff
|
tree
2020-11-12
M
.
Eric
Irrgang
Provi
d
e
commo
n
l
i
brary headers throug
h
new CMake targ
e
t
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
Eric Ir
r
ga
n
g
Hel
p
c
lient
s
f
ind
d
e
p
endencies of imp
o
rted CMake
targets
.
commit
|
commitdiff
|
tree
2020-11-04
M
.
E
ric
I
r
rgang
Establish
`
a
p
i/`
as the
home
f
or installed he
a
ders
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eri
c
Irrgan
g
Remove an unne
c
essary transiti
v
e
dependency
o
f im
p
orted
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Use the correct C
I
script
f
or sample_restraint jobs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Er
i
c Irrgan
g
Normal
i
ze
FindMPI
hint
s
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
r
i
c Irrg
a
ng
C
l
arify behavior of Legacy
M
dru
n
Option
s
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Updat
e
image names in job definitions
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Eric Irrgang
Tell gmxapi t
o
l
o
ok for MPI, when appropriate
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
E
r
ic Irrgang
Update Docker image build scripts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Er
i
c Irr
g
an
g
Use upd
a
ted
C
I pip
e
line r
u
les fo
r
Python
p
a
c
kage te
s
ts
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric Irrgang
Update gmxapi version details
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
Eric Irrg
a
ng
Clarify the GM
X
_BUIL
D
_MDRUN_
O
NLY full testing in
s
tructions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric
I
r
r
gang
Improve gmxPy
t
hon
D
iscovery
.
cma
k
e
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric
I
rrgang
Don't overr
i
de use
r
provided CMAK
E
_
OSX_DEPLOYMEN
T
_
TARGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
E
r
ic Irrgan
g
Handle gmxapi tmpi parameters better
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrg
a
ng
Let gmxap
i
installatio
n
rec
o
rd the GROMA
C
S libr
a
ry
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
E
ri
c
Irrgang
U
s
e
u
p
d
a
ted images for Py
t
hon CI jobs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Rest
r
ict g
m
xapi p
y
te
s
t t
e
s
t
s to `-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrg
a
ng
Specify OMP_NUM_THREADS for Pyhon
CI scripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Clarif
i
cations for ResourceAss
i
gn
m
ent interface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
ric Irr
g
ang
Support
ResourceAss
i
gnment interface f
o
r
t
M
P
I libra
r
y
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irrgang
A
l
l
o
w
M
PI-
e
nabled
c
lients to pr
o
vide the l
i
brary c
o
mmunicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irrgan
g
Use MpiCont
e
xtManager to provide MPI com
m
unica
t
o
r
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
i
c Irrg
a
n
g
Relocate MpiContextMa
n
ager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irr
g
ang
Inter
f
ace updates allowing clien
t
t
o
pr
o
vide MPI communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
ric Irrg
a
n
g
Impr
o
ve namin
g
and docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric
I
rr
g
a
ng
Docume
n
t a Mdrunner::Build
e
rImple
m
entation me
m
ber
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Er
i
c Irrgang
Remove
outdated wo
r
karo
u
nd
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
Create and use Simulation
I
np
u
t module
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrg
a
ng
Refine t
h
e CMakeLis
t
s
.
txt
f
or MPI gmxa
p
i tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eric Irrgang
Ex
p
lic
i
tly include STL headers used
i
n t
e
st
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eric Irrgang
R
eplace
f
ilename-
b
ased initialization
f
unction
s
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrg
a
n
g
Cl
a
r
i
fy t_inputrec allocation log
i
c in runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrga
n
g
Us
e
a heap object for inputre
c
in gmx::Mdrunner::mdrunner()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Accept Python versions high
e
r than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric
I
rrgang
Remove conditional for
C
Mak
e
< 3
.
1
2
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Er
i
c I
r
rgang
Allow more g
r
an
u
l
a
ri
t
y for
p
ubl
i
c interfac
e
s in buil
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrga
n
g
Preve
n
t f
a
iled
comm
a
ndline_
o
p
e
rat
i
on f
r
om publishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
r
ic
Irrgan
g
Mino
r
additions to gmx
a
pi install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Ir
r
g
a
ng
U
s
e impo
r
tlib_re
s
ources
i
n
Python 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
r
ic Ir
r
ga
n
g
Nor
m
aliz
e
docker im
a
ge n
a
mes
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Ir
r
gang
Fix some minor typese
t
ting
issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Impro
v
e
inst
a
ll docs links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Er
i
c Irrgang
Mo
v
e s
o
ur
c
es for
l
ibgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric
I
r
rgang
Remove disabled test fo
r
superseded
feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
I
g
nore a
g
e
n
erated
file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
E
r
ic Ir
r
gang
Use GMXAPI CMake
option guard for
g
mxapi target de
c
larati
o
n
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
E
ric Irrgang
Begin mo
v
ing install
e
d interface to
`api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Irrgang
Fix li
b
gromac
s
CMake t
a
rge
t
install syntax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
E
r
ic Irrgang
Fix libgromacs CMake tar
g
et install syntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Irrgang
Cle
a
n up simulatorb
u
ilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
E
r
ic I
r
rgang
Add
missing ABI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c Irrgang
Impleme
n
t Simul
a
torBuilder
.
add() for B
o
xDeformationHa
n
d
le
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Use TopologyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rgang
Use
IonSwapping
p
arameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Use CenterOfMassP
u
llin
g
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
a
ng
Use Rep
l
icaExchange member i
n
stead o
f
bui
l
d()
a
rgumen
t
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irr
g
ang
Use SimulatorModules
paramet
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
U
se Interactive
M
D
Si
m
ulatorBuild
e
r
parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Use
C
on
s
trai
n
tsPar
a
m
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Mo
v
e
Profilin
g
paramet
e
r out of simula
t
orbuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Simula
t
orE
n
v
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Implement remaining
S
imulato
r
Builder
.
a
d
d() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
In
t
erfa
c
e for remaining SimulatorBuild
e
r
.
a
d
d() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic
I
rrgang
S
i
mul
a
torBuilder
.
a
dd() for StopH
a
ndlerBuilde
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrga
n
g
I
m
pl
e
m
ent SimulatorB
u
ilder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
r
ic I
r
r
g
an
g
Refo
r
mat pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric
Irr
g
ang
Use
Gromacs::g
m
x target
to
h
int
g
mxapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgang
R
emov
e
wo
r
karound for gcc bug
5
8265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
E
r
ic I
r
rgang
Impr
o
ve pytest output handling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Comp
a
r
t
mentalize job rul
e
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
I
mp
r
ove
usage of Pyth
o
n log
g
ing mod
u
l
e
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric
Irrgang
Handle arbitrary dox
y
gen versions in Docke
r
i
m
a
g
e
b
u
i
ld
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric
I
rrgan
g
Remov
e
unused
(an
d
broken) image from Docker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eri
c
I
rrgang
Doc
k
er im
a
ge
builds: simpl
i
fy doxygen versi
o
n handli
n
g
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker
i
mage bui
l
ds: move doxygen handling to a separa
t
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Ex
t
e
nd MPI ensemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric I
r
rgang
Enable MPI
e
nsem
b
l
e
testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
N
o
rmalize g
m
xapi related
r
elease-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric
I
rrgang
Reduce console
l
og outpu
t
from s
a
mple_restrain
t
t
ests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgang
Enable MPI ensemble testing for
gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric Irrgang
No
r
malize gmx
a
pi related
r
elease
-
2020 job lo
g
ic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric I
r
r
ga
n
g
Make sure
images ha
v
e
/usr/b
i
n/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
rgang
Up
d
ate docker image build scripts for master
branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irrgang
Make sure CI sc
r
ipt can
c
all /bin/env p
y
thon`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Min
o
r clean up to builda
l
l
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
rrgang
Allow
l
lvm
option already
u
sed in buildall
.
s
h
s
cript
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
Irrgang
Reduce
c
on
s
o
le log output fr
o
m sample_restrain
t
tes
t
s
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eric Irrgang
Refine
usage of *job:tags* parame
t
er
.
commit
|
commitdiff
|
tree
next