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GROMACS 2021 first beta release
2020-10-08
M
.
E
ric
I
r
rgang
C
l
a
r
ify
t
h
e GMX_BUILD_MDRUN_ONLY full testing instr
u
ctions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric
Irrg
a
ng
I
mprove gmxPythonDiscovery
.
cmake
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric Irrgang
D
o
n't
o
v
e
r
r
ide user pr
o
vided CMAKE_OSX_DEPLOYMENT_TARGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Ir
r
gang
Handle gmxapi tmpi parameters b
e
tter
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Er
i
c Irrgang
Let gmx
a
pi
instal
l
a
tion record
t
he GROM
A
CS library
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
Eric Irrgang
Use updated i
m
ag
e
s for Python
C
I
j
obs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
E
r
i
c Irrgang
Res
t
ric
t
gmxapi p
y
test test
s
to
`-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric I
r
rg
a
ng
Sp
e
cify OMP_NU
M
_THREADS for Pyh
o
n CI scripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic
Irrgang
Clari
f
i
c
ations for ResourceAs
s
ig
n
men
t
in
t
erfa
c
e
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Er
i
c
I
rrgang
S
u
p
port ResourceAssignment inter
f
ace for tM
P
I libr
a
ry
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Ir
r
g
a
ng
Allow MPI-enab
l
ed clients to provide the library c
o
m
mun
i
c
a
t
o
r
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irr
g
a
n
g
Use M
p
iCo
n
textManager to provide MPI communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric I
r
rgang
R
e
locate MpiConte
x
tM
a
n
a
ger
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Ir
r
gang
I
nterface upd
a
t
e
s a
l
lowing client to provide MPI com
m
unicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
I
mprove n
a
m
i
ng and doc
s
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrg
a
ng
Docum
e
nt a Mdrun
n
er::BuilderIm
p
lementation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Irrgang
R
emove outdated workaround
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrga
n
g
Create an
d
u
se SimulationInput
m
odul
e
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric I
r
rgang
Refine
t
he CMakeLis
t
s
.
txt f
o
r
MPI
g
mxapi tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eric Irrga
n
g
Explicitly include STL
h
eaders used in test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eri
c
I
rrgang
Replace
filename-based initializatio
n
func
t
ions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrgang
C
l
arify t_input
r
ec allocation
l
ogic
in runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric
I
rrgang
Use a
h
eap o
b
je
c
t fo
r
input
r
ec
i
n
g
mx::Mdrunn
e
r
:
:m
d
runner()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Ir
r
gan
g
Acc
e
pt Py
t
hon versio
n
s h
i
gher th
a
n 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
R
emove c
o
ndit
i
onal
f
o
r CMake <
3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eri
c
Ir
r
ga
n
g
All
o
w
more gr
a
nularity for public
i
nterfaces in buil
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Er
i
c
I
rrgang
Prevent failed comm
a
nd
l
ine_ope
r
a
ti
o
n from p
u
blish
i
ng
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
ric Irrgan
g
Minor ad
d
itions
to gmxapi install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Use importlib_resources in Python
3
.
6 ima
g
es
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrg
a
ng
Norm
a
lize docker
i
mage names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrga
n
g
Fix
some minor type
s
etting
i
ssues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Er
i
c Ir
r
gang
Imp
r
ove install
do
c
s links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrg
a
ng
Move sour
c
es f
o
r
lib
g
mx
a
p
i
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Er
i
c Irrga
n
g
Remove di
s
ab
l
e
d
test for s
u
perseded
f
eat
u
re
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Er
i
c Irrgang
Ignore
a
g
e
ner
a
ted fi
l
e
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Irr
g
ang
Use GMXAPI CMake o
p
tion
guard for gmxapi t
a
rget declaration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irrgang
Begin
moving install
e
d interface to
`
api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric
I
r
rgang
Fix libgromacs CMake target install syntax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
E
r
ic Ir
r
gang
Fix
l
ibgr
o
macs CMake targ
e
t install sy
n
t
a
x
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Irrga
n
g
C
lean up s
i
mulator
b
ui
l
der
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Er
i
c Irr
g
a
ng
Add miss
i
ng ABI he
a
d
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Implement S
i
mulatorBuilder
.
add()
f
or
B
oxDeformationHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
r
r
gang
Use
T
o
p
ologyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irr
g
ang
Us
e
IonSwa
p
p
i
ng par
a
m
ete
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Center
O
fM
a
ssP
u
lli
n
g
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric
Irrga
n
g
U
s
e ReplicaExchange
member instead
o
f
b
uild(
)
argum
e
nt
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
ng
Use
Simulat
o
rM
o
dul
e
s param
e
ter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
U
s
e
Interactiv
e
MD SimulatorBuilder pa
r
a
m
e
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Use
LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
Constrai
n
tsPa
r
am
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rg
a
n
g
M
ove Profi
l
ing param
e
ter out of
simulator
b
uilder
.
bui
l
d(
)
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Simulator
E
n
v
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
ng
Implement remainin
g
Simul
a
torBuilder
.
add() meth
o
ds
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
g
ang
Inte
r
face
f
or remaining
S
im
u
latorBuild
e
r
.
add()
m
eth
o
d
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
S
imulatorBu
i
l
d
er
.
add(
)
f
or S
t
o
p
Handler
B
uilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Impleme
n
t Simul
a
torBuilder
.
buil
d
(
)
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eri
c
Irrg
a
ng
Refor
m
a
t
pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgan
g
Use
G
romacs
:
:g
m
x tar
g
et
t
o
hint gmxapi te
s
ts
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
E
ric
Irrgang
Rem
o
ve wor
k
a
r
ound
f
or g
c
c
b
ug
5
8265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric
Irrgang
Improve
p
ytest o
u
tput
handli
n
g
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric
I
rrgang
Compartmentalize job rul
e
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrg
a
ng
Improve usage
o
f Python lo
g
ging
module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Er
i
c
I
rrg
a
ng
Handle arbi
t
rary doxygen versions in Doc
k
er im
a
ge
build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
r
ic Irr
g
a
ng
Remove
u
nused
(and broke
n
) i
m
a
g
e
from Docke
r
image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irr
g
ang
D
o
c
ker
i
mage build
s
:
s
implify doxy
g
en version handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
D
ocker
i
mage bu
i
lds: move doxygen h
a
n
dli
n
g to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
E
xtend MPI ens
e
mble
testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Enable MPI ensemble
testing fo
r
gmxa
p
i
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Normalize
g
mxapi
relat
e
d release-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric Irrg
a
ng
Reduce consol
e
log out
p
u
t from sample_restraint test
s
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgang
Enabl
e
MPI ens
e
mble testi
n
g for g
m
xap
i
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
E
r
ic
I
rrgang
Normal
i
ze
gmxapi
r
e
l
a
t
ed release-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgang
Make su
r
e im
a
ges
h
ave /usr/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Ir
r
gang
Update do
c
ker i
m
age bui
l
d scripts for master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Ir
r
gang
Ma
k
e su
r
e C
I
script can call /bin/
e
nv python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irrgang
Minor clean
u
p to bu
i
ld
a
l
l
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irrgan
g
Allo
w
llvm option al
r
eady used in bu
i
lda
l
l
.
s
h
s
c
ript
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
R
e
duce con
s
ol
e
l
og out
p
ut f
r
om s
a
mple_
r
estra
i
nt
te
s
ts
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Er
i
c Irrg
a
ng
Re
f
ine usa
g
e of *job:tags
*
parameter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Update header sort
i
ng
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Er
i
c
Irrgang
Requi
r
e C++17 standard and
S
T
L features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Er
i
c I
r
rgang
Appl
y
more granul
a
r CTest
time-out
p
olic
y
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
E
r
i
c Irrgang
Resolve static
a
n
aly
z
er war
n
ings fro
m
google tests
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric Irrg
a
ng
Avoid temporary strin
g
s
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric I
r
rgang
Note
C
UDA buil
d
s in j
o
b
names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
E
r
ic Irrga
n
g
Upd
a
te bundle
d
p
y
bi
n
d
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
E
r
ic I
r
r
gang
Only
s
et GMX_PYTHON_PACKA
G
E=ON
w
here needed
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
Eric
I
rrgang
Us
e
CMak
e
3
.
12+ fa
c
ilities for
detecting Python
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric I
r
r
gang
Change def
a
ult C
M
ake version to 3
.
13
.
0 for CI
i
mages
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric
I
rrgang
Require
C
Make >=
3
.
1
3
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Fix inva
l
id gitl
a
b-ci
.
yml
commit
|
commitdiff
|
tree
2020-04-09
M
.
E
r
ic Irrgang
Allow usefu
l
CI to run in forks
commit
|
commitdiff
|
tree
2020-04-08
M
.
E
ric Irrgang
E
xplicitly se
t
UTF-8 encoding for gmxa
p
i
CLI
interacti
o
n
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eric
I
rrgan
g
Prepare Python environments for GitLab CI pipeline
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irrgang
Im
p
r
o
ve gmxapi Python package dependency r
e
s
o
lution
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Er
i
c Irrga
n
g
Prune change
-
management
.
rst and updat
e
links
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
E
r
ic Irrg
a
n
g
Modernize some
Pyth
o
n subprocess calls
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric Irrgang
Avoid acciden
t
ally initializi
n
g pyen
v
in CI images
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrg
a
n
g
Prepar
e
Pyth
o
n environments for GitLab CI
p
ipeline
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgang
Update
s
cripts for all of the
r
equested pre-
c
ommi
t
.
.
.
commit
|
commitdiff
|
tree
next