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Separate job script files for gmxapi package versions.
2020-12-04
M
.
Eric
I
rrgan
g
Separate
j
ob script fi
l
es for gmxa
p
i p
a
ckage
versions
.
commit
|
commitdiff
|
tree
2020-12-03
M
.
Eric Irrgan
g
Im
p
rove gmxapi
C
++
t
est coverage for f
a
ile
d
mdru
n
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eric Irrgang
O
n
e ar
g
ument
per
l
ine for long function signatures
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
E
ric Irrg
a
ng
L
ook
f
or t
h
e v
a
r
ious possible names of the gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2020-11-20
M
.
E
r
ic
Irrgan
g
Cr
e
ate CMake targets
for each of
the mod
u
le
s
.
commit
|
commitdiff
|
tree
2020-11-18
M
.
E
ric
Irrgang
R
e
p
l
a
ce gmxapi `
e
r
r
or
o
utput` with `stderr` a
n
d `stdout`
commit
|
commitdiff
|
tree
2020-11-17
M
.
Eri
c
Irr
g
ang
Separate the testutils module
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
Eric Irr
g
a
ng
g
mxapi ver
s
i
o
n
i
ng updates
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
E
ric
I
rrgang
Be mo
r
e explicit ab
o
ut build-tree-only de
p
endencies
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eri
c
Irrg
a
ng
Provide a catch-all
t
arge
t
f
o
r
library m
o
dules
.
commit
|
commitdiff
|
tree
2020-11-12
M
.
Eric
Irrg
a
ng
Provide commo
n
library headers thr
o
ugh new CMake target
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
Eric Irrgang
Hel
p
clients
fi
n
d de
p
endencie
s
of imported CMake t
a
rgets
.
commit
|
commitdiff
|
tree
2020-11-04
M
.
Er
i
c
Irr
g
a
n
g
E
stablis
h
`api/` as the home for ins
t
alled headers
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irrgan
g
Remove
an unne
c
essary
trans
i
tive dependency of im
p
orted
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Use th
e
correct
CI s
c
ript
f
or sample_restrai
n
t jobs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric I
r
r
g
ang
N
or
m
a
lize FindMPI
h
ints
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
C
larify behavior of
L
egacyMdrunOptions
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
ric Irrgan
g
U
p
dat
e
image names in job definitions
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Eric Ir
r
gang
T
e
ll
gmxapi to look
f
or
M
PI, when appropr
i
ate
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
Eric Irr
g
ang
Update Docker ima
g
e
build s
c
ripts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
E
ric
I
rrgang
Use upd
a
ted CI p
i
pe
l
ine rules f
o
r Python
p
ackage tests
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric Irrgang
Up
d
ate gmxa
p
i version details
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
Eric Irr
g
ang
Clarify the GMX_BUI
L
D_MDRUN_ONLY fu
l
l tes
t
i
n
g in
s
tructi
o
n
s
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric Irrgang
Improve
g
m
x
PythonDiscovery
.
cmake
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric Irrgang
Don'
t
overrid
e
u
s
er
p
rovided CMAK
E
_
O
SX_DEPLOYMENT_TARGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrgang
Hand
l
e
gmxapi t
m
p
i
parame
t
ers better
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
E
r
ic Ir
r
g
a
ng
Le
t
gmxapi installat
i
on
r
e
co
r
d the GROMACS libr
a
r
y
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
Eric Irrgang
U
se up
d
a
t
e
d images for P
y
t
h
on CI
jo
b
s
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Restr
i
ct gmxapi pytest
t
est
s
to `-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Ir
r
gang
S
p
ecify
OMP_NU
M
_T
H
READ
S
fo
r
Pyhon
CI
s
c
ripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
C
l
ar
i
ficat
i
ons
for ResourceAss
i
gnm
e
nt i
n
terface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Er
i
c Irrgang
Sup
p
ort ResourceA
s
s
i
gnment interface for
t
MPI
library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irrgan
g
Allow
M
P
I-enab
l
ed c
l
i
e
nts to pr
o
v
i
de
the library comm
u
nicat
o
r
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eri
c
I
rrgang
Use MpiC
o
ntextManager to provide MPI commun
i
cator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eri
c
Irrga
n
g
R
eloc
a
te
Mpi
C
ontextManager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrg
a
ng
Interface updates a
l
lowin
g
client to pr
o
vide
M
PI commun
i
cato
r
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
Imp
r
ove
naming and docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eri
c
Irrgang
Docume
n
t a Mdrunner::Build
e
rImpl
e
m
e
ntatio
n
me
m
ber
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eri
c
I
r
rgang
Remove
o
utd
a
te
d
workaround
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
C
r
eate and
u
se SimulationInput mo
d
ul
e
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eri
c
Irrgang
R
e
f
i
ne the
C
MakeLists
.
txt fo
r
MPI gmxapi
t
e
sts
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
E
r
i
c
Irrgang
Explicitly in
c
lude STL
hea
d
ers used
i
n
t
e
s
t
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eric Irrgang
R
eplace filename-bas
e
d initialization
functi
o
ns
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
E
ric Ir
r
gang
Cl
a
rif
y
t_inpu
t
rec allocation l
o
gic i
n
runner
.
cp
p
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric I
r
rgang
U
s
e a heap object
for i
n
putrec
i
n gmx::Mdrunner::mdrunner()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eri
c
Irrgang
A
c
cept Pyth
o
n
versions hig
h
er than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
E
r
ic
I
rr
g
ang
Re
m
ove conditio
n
al for CMake
<
3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eric Irr
g
an
g
Allow
more granularity for public interfaces i
n
buil
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Er
i
c Irrgang
Prevent failed commandline_operation
f
rom publish
i
ng
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
M
i
n
or additi
o
ns to gmxapi install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric
Irrgang
U
se i
m
port
l
ib_resources in Pyt
h
on 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
ric Irrgang
No
r
mal
i
z
e
docker im
a
ge
names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
I
rrgang
F
i
x some
m
inor type
s
etting
issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Improve
install docs
l
inks
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
r
ic
I
rrgang
Move sou
r
ces for libgmx
a
pi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrga
n
g
Remove disable
d
test for superseded
f
e
a
ture
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric
Irr
g
ang
Ig
n
ore a gen
e
rated file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric
Ir
r
ga
n
g
U
se
GMXAPI CMake option guard for gm
x
api t
a
rget declaration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irr
g
ang
B
e
gin moving install
e
d
interface to `api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric
I
rrgang
Fix libgro
m
a
c
s CMa
k
e ta
r
get install sy
n
tax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Er
i
c Irrgang
Fix libgroma
c
s CMake
targ
e
t
ins
t
a
ll
syntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Irrgang
Cl
e
an up s
i
mulato
r
b
u
il
d
er
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
E
r
ic Irr
g
ang
Add
miss
i
ng ABI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Ir
r
g
a
ng
Implement S
i
mula
t
o
r
B
uilder
.
add() for BoxDeformationHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Us
e
TopologyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
U
s
e I
o
n
S
wapping p
a
rameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric
Ir
r
gang
Use CenterOfMassPullin
g
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Use Re
p
licaExchange m
e
m
b
er instead
o
f
b
uild() argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic
Irrga
n
g
Use SimulatorModules pa
r
ame
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Intera
c
tiveMD Simu
l
at
o
rBuilder parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
Us
e
Legacy
I
nput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic I
r
rgang
Use C
o
nstr
a
i
n
ts
P
a
ram
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rr
g
ang
M
o
v
e Profiling parame
t
e
r
ou
t
of simulato
r
bui
l
der
.
buil
d
()
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Use
S
imulatorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgan
g
Impl
e
ment r
e
maining Si
m
ulatorBuilder
.
a
dd(
)
metho
d
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Interface
f
o
r
rem
a
ining SimulatorBuilder
.
a
d
d() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgan
g
SimulatorBuil
d
er
.
add() for StopHandlerBuilde
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Impleme
n
t S
i
mulatorBu
i
l
d
er
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irr
g
a
n
g
R
eformat p
a
irs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
U
se Gromac
s
::gmx target
to hint gmxa
p
i tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
E
r
i
c Irrgang
Remove wo
r
karound for
gcc bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irr
g
a
ng
Im
p
ro
v
e pytest output
h
andling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
ric Ir
r
gan
g
C
o
mpartmentalize j
o
b rul
e
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Er
i
c Irrgang
Impro
v
e usage
o
f Python loggi
n
g mo
d
ule
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric Irrgang
Handle arbi
t
rary d
o
x
ygen versions in Docker i
m
age build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irr
g
a
n
g
R
e
move u
n
use
d
(and brok
e
n) image fr
o
m Docker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Ir
r
gang
Docker image builds: simpli
f
y
do
x
y
g
en ve
r
sion
h
andling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
D
o
cker image bui
l
ds: move doxyg
e
n handling t
o
a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Extend MP
I
e
nse
m
ble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Enab
l
e MPI
en
s
emble
testing
f
o
r
gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
ic Irrg
a
ng
Normali
z
e gmxap
i
related release-2020
j
ob
l
ogic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric
I
rrgang
Reduce
c
o
nsole log
outp
u
t from sample_restra
i
nt test
s
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgang
Enable MP
I
en
s
emble testing
for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
E
ric Irrg
a
ng
No
r
m
a
lize gm
x
api related release-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgang
Make
sure images have /u
s
r/bin/p
y
th
o
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Updat
e
doc
k
er image build scri
p
ts for master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Irrgang
Ma
k
e
sure C
I
s
c
ript can call /bin/env pyt
h
on`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
Irrgang
Min
o
r clean up to b
u
il
d
all
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Allow l
l
v
m
option already
u
s
e
d in buildal
l
.
s
h
sc
r
ipt
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Reduce console l
o
g out
p
u
t
f
rom samp
l
e
_rest
r
ai
n
t t
e
sts
.
commit
|
commitdiff
|
tree
next