repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Look for the various possible names of the gromacs package.
2020-11-23
M
.
Eric Irrgang
Look for the various p
o
ssible names of the gr
o
mac
s
.
.
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irrgang
Remove
an unnecessary tr
a
ns
i
t
i
ve dependency of importe
d
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Er
i
c
Irrgang
Us
e
the corre
c
t
C
I s
c
ri
p
t for
s
ample
_
restraint jobs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Normalize F
i
ndMPI hi
n
ts
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgan
g
Clarify behav
i
or of Leg
a
cyMdrunOp
t
io
n
s
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric
Irrgang
Update image
names in job
definitions
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Eric Irr
g
ang
Tell
g
mxapi to look for M
P
I,
wh
e
n
a
ppropriate
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
Eric Irrg
a
ng
Update
Docker image b
u
il
d
scripts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Er
i
c Irrga
n
g
Us
e
updated CI pipeline ru
l
es for Pytho
n
package
tests
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric Irrgang
U
pdate gmxapi vers
i
on d
e
t
a
i
l
s
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
Eric Irrgang
Clar
i
fy the GMX_BUIL
D
_
M
D
RUN
_
ONLY
f
u
l
l testing i
n
structions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric
I
rrga
n
g
Impro
v
e gmxPytho
n
Di
s
c
o
very
.
c
m
ak
e
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric Irr
g
a
ng
Don't
o
v
erride user prov
i
d
e
d
CMAKE_OSX
_
DEPLOYME
N
T_TARGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric
Irrga
n
g
Handle g
m
xapi t
m
pi
parameters bette
r
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrg
a
n
g
Let gmx
a
pi installation record the GROMACS library
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
Er
i
c Irrgang
Use updated images
f
or Python CI jobs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrgang
Restri
c
t
gmxa
p
i pytest tests to `-nt
2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irr
g
ang
Specify OMP_N
U
M_THREADS
f
or
P
yh
o
n CI s
c
r
ipts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Clarific
a
t
ions for
R
esourceAssignment interface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
Irrgang
S
u
p
p
o
r
t Res
o
ur
c
eAssignment interface for tMPI libra
r
y
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Allow MPI-enab
l
ed clients to p
r
o
vide the l
i
b
rary communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Use Mpi
C
ontextM
a
nager to provid
e
M
PI comm
u
nicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irrgang
Reloca
t
e MpiContextMa
n
ager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irr
g
ang
Inte
r
fac
e
updates allowing client to provide MPI co
m
municator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
ric
Ir
r
gang
Im
p
r
ove n
a
m
ing and docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Er
i
c Irrgang
D
ocument a Mdrunn
e
r::Buil
d
erIm
p
lementation
m
e
m
b
er
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eri
c
Irrg
a
ng
R
emove outdated wor
k
around
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Er
i
c Irrgang
C
r
e
ate and us
e
SimulationI
n
put module
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
Refine t
h
e C
M
akeLi
s
ts
.
txt f
o
r
M
P
I gmxa
p
i
tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eri
c
Irrgang
E
xplicitl
y
i
nclude STL heade
r
s u
s
ed
in
t
est
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eric Ir
r
g
a
n
g
Repla
c
e filename-ba
s
ed initiali
z
atio
n
functi
o
ns
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrgang
Cl
a
rify t_inputrec allocatio
n
logic in runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
E
r
ic Irrgang
Use a he
a
p
object for in
p
u
t
rec in gmx::Mdrunn
e
r::mdrunner()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Accept P
y
t
hon vers
i
ons higher 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
.
E
r
ic Irrgang
A
l
low more
g
ranularity
f
or public
interfaces in bui
l
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Pr
e
vent faile
d
co
m
mandl
i
ne_o
p
erat
i
on fr
o
m publishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
ric Irr
g
ang
Min
o
r addit
i
ons to gmxapi install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Er
i
c Irrgang
Use importlib
_
r
e
sources
i
n Pytho
n
3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eri
c
I
rrgang
Nor
m
ali
z
e d
o
c
ker ima
g
e names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Fix some minor typesett
i
n
g issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgan
g
I
m
p
r
o
ve
i
n
stal
l
docs li
n
ks
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric
I
rrgang
Move
s
o
u
rces for l
i
bgmx
a
pi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
ric Irrg
a
ng
Remove
d
isabled
tes
t
f
or supers
e
ded
f
eatur
e
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ignore a g
e
nerated
file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Irrgang
U
s
e GMXAPI CMake option guard for gmxapi
target de
c
laratio
n
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irr
g
ang
B
e
gin
m
oving instal
l
ed
i
nterface to
`api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Ir
r
g
a
ng
Fix
l
ibgromacs CMa
k
e t
a
rget install syntax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Eric Irr
g
ang
Fix libgromacs CMake
t
arge
t
install
s
yntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Ir
r
gang
C
l
e
a
n
up simulatorbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric
Irrgang
Ad
d
m
i
s
s
i
ng
A
BI
h
ea
d
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric
I
r
rgang
I
m
p
l
emen
t
Sim
u
lato
r
Builder
.
a
dd() f
o
r BoxDeformationHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irr
g
a
n
g
Use Top
o
logyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Use IonSwapping param
e
ter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
r
r
gang
Use CenterOfMassPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Use
R
eplicaExchan
g
e m
e
mber instead of buil
d
(
)
argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
U
se SimulatorModules para
m
eter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
U
se Inter
a
c
tiveMD Simul
a
torBuilder parame
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
Use LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
U
s
e Con
s
trai
n
tsPa
r
am
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rgang
Move Pr
o
filing parame
t
er out of sim
u
latorbui
l
der
.
build
(
)
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
U
s
e SimulatorEn
v
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
I
m
plement remaining SimulatorBuilder
.
add()
methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgan
g
In
t
erface for remaining Simulat
o
rBui
l
der
.
add() meth
o
ds
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgan
g
S
i
mulato
r
B
uilder
.
add()
f
or StopHandlerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement Sim
u
latorBuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric I
r
rgang
Reformat pair
s
.
cp
p
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eri
c
Irrgan
g
U
s
e Gro
m
acs::gmx target to hint gmxapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric
I
rrg
a
ng
Remove workaround for gcc bug
58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
E
r
ic Irrgang
I
m
prove pytest output ha
n
dling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eri
c
Irrgang
Compartmentalize jo
b
rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric
I
r
r
gan
g
Improve usage of Pytho
n
log
g
ing module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric I
r
rgang
H
andle
a
rbit
r
ary doxyge
n
version
s
in Docker
i
ma
g
e build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Re
m
o
v
e unused (and broken) ima
g
e from Docker im
a
g
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eri
c
Irr
g
a
ng
Docker
imag
e
builds: sim
p
l
i
f
y doxygen versio
n
handl
i
ng
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrg
a
n
g
D
o
c
k
er ima
g
e builds: move doxyge
n
handling to a
s
e
p
arate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
ic I
r
rgang
Ext
e
nd M
P
I ensemble testi
n
g
for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
i
c
Irrgan
g
E
n
ab
l
e MPI
e
nsemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgan
g
N
ormalize gmxapi
r
e
lated rele
a
se-2020 job lo
g
ic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric
I
r
rgang
Reduce
c
o
n
s
ole log output f
r
o
m
sample_restraint tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
E
r
i
c
Irrg
a
ng
Enable MPI ens
e
mble
t
esting
f
or gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric Irrg
a
n
g
Normalize gmxa
p
i related
release-20
2
0
j
o
b logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgan
g
Make su
r
e im
a
g
es have /usr/bi
n
/
pytho
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Irrgang
Update docker im
a
g
e buil
d
scr
i
p
t
s for master
branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
rrga
n
g
M
a
ke sure
C
I
s
c
ript
c
an
ca
l
l /b
i
n
/
e
nv python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
ang
Minor clea
n
up to b
u
il
d
all
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
Irrgang
A
llow llvm option
a
lready used in buildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
Irrg
a
ng
Re
d
uce cons
o
le lo
g
output
f
rom s
a
mple_restraint t
e
st
s
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Er
i
c Irr
g
an
g
Ref
i
n
e
usa
g
e of
*
job:t
a
gs* parameter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
r
ic
Irrgang
Update hea
d
er so
r
ting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Require C+
+
17 s
t
an
d
ard and STL features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irrgang
Apply
more granular CTest tim
e
-
out
policy
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric
Irrgang
Resolve stati
c
analyzer warni
n
gs from goo
g
le tests
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
E
r
ic Irr
g
ang
Avo
i
d temporary strings
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Ir
r
gang
N
o
te CUDA bu
i
ld
s
in job
nam
e
s
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Er
i
c
I
rrgang
U
pdate
bun
d
le
d
pybind
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Er
i
c Irrgang
Only
s
et GMX_P
Y
THON_PACKAG
E
=O
N
wh
e
re
n
ee
d
ed
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
Eric Irrgang
Use CMake
3
.
12+ fac
i
l
i
tie
s
for dete
c
tin
g
Python
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
E
r
ic Irrgang
Change defa
u
lt CMake version to 3
.
13
.
0 for CI
i
mages
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Re
q
u
i
re CMake >=3
.
1
3
.
commit
|
commitdiff
|
tree
next