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Separate job script files for gmxapi package versions.
2020-05-24
P
aul Bau
e
r
Ad
d
conversion fro
m
n
e
w to leg
a
cy sy
m
tab
commit
|
commitdiff
|
tree
2020-05-24
Kevin Boyd
C
l
ean up grompp memory lea
k
s
in
r
otation and pull st
r
uctur
e
s
.
commit
|
commitdiff
|
tree
2020-05-24
Paul Ba
u
er
Avoi
d
parsing
o
f
fatale
r
ror
.
cpp
a
s lint failure
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgang
Enable MPI ensemble
testin
g
for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-22
Arte
m
Zh
m
u
r
ov
R
e
move
depe
n
dence
o
f
c
o
nstraints
on
t_m
d
atoms
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
Irrgang
Update docker image build scripts f
o
r
mast
e
r
branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
i
c Irrgang
M
a
ke
s
ure CI
script can call /bi
n
/env py
t
hon`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
rrgang
Minor c
l
ea
n
up to bui
l
dall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Allow llvm option already used in build
a
l
l
.
sh s
c
rip
t
.
commit
|
commitdiff
|
tree
2020-05-13
Pa
u
l
Bauer
F
ix c
h
eck sour
c
e error pa
r
sing
commit
|
commitdiff
|
tree
2020-05-11
Artem Zhmurov
U
n
ify C
U
DA a
n
d OpenCL lookup-table creation
commit
|
commitdiff
|
tree
2020-05-05
Artem
Zh
m
u
rov
U
n
ify
CUDA a
n
d
O
penCL lookup-table
c
reatio
n
commit
|
commitdiff
|
tree
2020-05-04
Paul
Ba
u
er
F
ix cmake e
r
ror:
M
ixed styles of target_link_libraries
.
.
.
commit
|
commitdiff
|
tree
2020-05-04
Artem Zhm
u
r
ov
Unify CUDA and OpenCL lookup-table crea
t
ion
commit
|
commitdiff
|
tree
2020-04-30
ejjordan
A
d
d EOF
n
ewli
n
e
s to eliminate c
o
mpiler warning
s
commit
|
commitdiff
|
tree
2020-04-30
ejj
o
rdan
Remove
cmake log
i
c that
i
s
ou
t
d
a
ted by requiring
c
make
.
.
.
commit
|
commitdiff
|
tree
2020-04-28
R
oland
Schulz
Add
c
l
a
n
g WA
commit
|
commitdiff
|
tree
2020-04-28
Roland Sch
u
l
z
Fix
MSVC 201
9
test failures
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhm
u
rov
Fix the removal of
C
OM ve
l
ocity in c
a
se
o
f GPU upda
t
e
commit
|
commitdiff
|
tree
2020-04-27
A
rtem
Zhmurov
Move PBC setup out of the launchKernel(
.
.
.
) in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-04-27
Paul Bauer
Fix seg
m
entatio
n
fault in
do_dssp
commit
|
commitdiff
|
tree
2020-04-25
Mar
k
Abr
a
ham
Move
configurati
o
n of glo
b
al headers
commit
|
commitdiff
|
tree
2020-04-25
Paul Baue
r
Fi
x
copyright header
commit
|
commitdiff
|
tree
2020-04-25
Roland Schul
z
Fix MSVC 2019 w
a
rnin
g
s
commit
|
commitdiff
|
tree
2020-04-23
Pau
l
Bauer
Use
b
ranch point
a
lso for
forma
t
and copyri
g
ht check
commit
|
commitdiff
|
tree
2020-04-23
Mark
A
braham
Mark HWLOC
c
make
c
ache variable
as advanced
commit
|
commitdiff
|
tree
2020-04-22
Pasc
a
l
Merz
Ma
k
e ini
t
_dires independent of t_c
o
mm
r
ec
commit
|
commitdiff
|
tree
2020-04-21
Mar
k
A
b
raham
F
ix warnings with c
l
ang 9
commit
|
commitdiff
|
tree
2020-04-20
A
rtem
Z
hmurov
Fix the
n
u
mber of s
t
eps
check when
c
heckpoint is load
e
d
commit
|
commitdiff
|
tree
2020-04-20
Pau
l
Bauer
Make tes
t
s check co
d
e for warnings same
as the main
.
.
.
commit
|
commitdiff
|
tree
2020-04-16
Artem
Zhmurov
Unify CUDA and Ope
n
CL lookup-tab
l
e crea
t
ion
commit
|
commitdiff
|
tree
2020-04-14
Pascal Mer
z
Make bond
e
d
i
nteraction c
h
eck
i
ng more
r
obust (m
o
dula
r
.
.
.
commit
|
commitdiff
|
tree
2020-04-13
Mar
k
Abraham
F
ix warnings for no-mpi build
commit
|
commitdiff
|
tree
2020-04-12
Mark Abra
h
am
Removed unused va
r
iab
l
e in force table genera
t
ion
commit
|
commitdiff
|
tree
2020-04-11
Pa
u
l Bauer
Add Image for GCC 7 and AMD O
p
e
n
CL
commit
|
commitdiff
|
tree
2020-04-07
Mark Abraham
Replace EnumOption w
i
th
Enumeration
A
rrayOption
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eric
Irrgang
Prepare Pytho
n
en
v
ironments for GitLa
b
CI pipe
l
ine
.
commit
|
commitdiff
|
tree
2020-04-07
Pascal Merz
Make global topology constant in energyOut
p
ut
.
printAnne
a
lin
g
.
.
.
commit
|
commitdiff
|
tree
2020-04-06
Berk Hess
Move force
buffer r
e
sizing
t
o
m
dset
u
p
commit
|
commitdiff
|
tree
2020-04-06
Pasca
l
Merz
Make bo
n
d
e
d
inte
r
action ch
e
cki
n
g more robust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
E
ri
c
Irr
g
an
g
Improve gmx
a
pi P
y
thon package d
e
pendency resolut
i
o
n
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Ir
r
ga
n
g
Prune
c
ha
n
ge-ma
n
agement
.
rst and update links
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgang
P
r
ep
a
re Python
environments for GitL
a
b
C
I pipeli
n
e
.
commit
|
commitdiff
|
tree
2020-03-30
Mar
k
A
br
a
h
am
Set buffers a
p
propriately so
.
xpm files can
b
e read
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Irr
g
ang
Re
q
u
i
r
e
Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-23
Artem Zhmurov
I
n
t
r
oduce De
v
i
ceStreamManager
commit
|
commitdiff
|
tree
2020-03-21
Pau
l
B
auer
Add D
o
cumen
t
ation buil
d
to script
commit
|
commitdiff
|
tree
2020-03-19
Paul B
a
u
e
r
Add script
to generate C
I
Docker files
commit
|
commitdiff
|
tree
2020-03-19
Artem Zh
m
u
rov
Pass DeviceCont
e
xt instead of GPU runtim
e
data when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irr
g
a
n
g
Ad
d
st
u
b V
a
riables documentation to GitLa
b
CI doc
.
commit
|
commitdiff
|
tree
2020-03-17
B
erk
Hess
D
i
s
able
Ewald dipole
correction without DD
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric I
r
rgang
Define an
argparse parent p
a
rser fo
r
c
ontainer image
.
.
.
commit
|
commitdiff
|
tree
2020-03-14
Mark
A
br
a
ham
Move testing code to test directo
r
y
commit
|
commitdiff
|
tree
2020-03-12
Gi
l
les Gouaillardet
gr
o
mpp: fix the -ref <f
i
l
e> option
commit
|
commitdiff
|
tree
2020-03-10
Artem Zhm
u
rov
Use
i
nit(
.
.
) fu
n
ction to build Devic
e
Co
n
tex
t
commit
|
commitdiff
|
tree
2020-03-07
Berk Hess
Make shak
e
work with
o
ut g
r
a
p
h
commit
|
commitdiff
|
tree
2020-03-04
Mark Ab
r
aham
I
m
p
r
o
ve TP
I
handli
n
g
commit
|
commitdiff
|
tree
2020-03-02
B
e
rk Hess
Fix cent
e
r
of ma
s
s motio
n
removal with frozen ato
m
s
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmurov
Up
d
ate the message on wheth
e
r up
d
ate and const
r
ai
n
t
s
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
P
a
ul Bauer
Remove
f
roz
e
n
a
t
oms fro
m
VCM groups
commit
|
commitdiff
|
tree
2020-02-27
Pas
c
al Merz
Loosen gmx
a
pi
st
o
psign
a
ler test
commit
|
commitdiff
|
tree
2020-02-27
Pascal
M
erz
E
xtract and expose functio
n
to
d
e
termine whether molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Szilárd Pál
l
Remove o
u
t
d
ated PME-GPU li
m
itati
o
n i
n
us
e
r guide
commit
|
commitdiff
|
tree
2020-02-25
Magnu
s
Lundborg
F
ix out of sync checkpoint files in simulations sharing
.
.
.
commit
|
commitdiff
|
tree
2020-02-24
P
aul Bau
e
r
Fix
c
lang-6 image
t
emp
l
ate
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmurov
Use CUDA flo
a
t3 vector
type instead of f
v
ec in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Paul Bauer
W
o
rkaround for Gi
t
lab archive size
commit
|
commitdiff
|
tree
2020-01-29
Magnus L
u
n
d
borg
More
S
IMD preparatio
n
s in the FE calculations
commit
|
commitdiff
|
tree
2020-01-29
Paul B
a
uer
Add repl
a
cemen
t
f
o
r symb
o
l table
commit
|
commitdiff
|
tree
2020-01-27
Mar
k
Abra
h
am
Remove
element-siz
e
mem
b
er fiel
d
s
commit
|
commitdiff
|
tree
2020-01-27
Mark
A
braham
Make NbnxnGpu class
w
ith
con
s
t
r
uc
t
or
commit
|
commitdiff
|
tree
2020-01-24
Szilárd P
á
ll
Add target
for offline
PME OpenCL com
p
i
l
ation
commit
|
commitdiff
|
tree
2020-01-24
M
a
g
n
us Lundborg
Remo
v
e
d
SC RPower 48 fro
m
FEP
k
erne
l
commit
|
commitdiff
|
tree
2020-01-17
Mark A
b
raham
Regular
i
ze
nbnxm module doxygen
commit
|
commitdiff
|
tree
2020-01-17
Paul Bauer
Fi
x
bad link i
n
d
e
veloper docs
commit
|
commitdiff
|
tree
2020-01-17
Be
r
k Hes
s
Add check for shells and GPU u
p
date
commit
|
commitdiff
|
tree
2020-01-13
Paul Bauer
Revert
"Exclude bu
i
ld-system files from CP
a
c
k"
commit
|
commitdiff
|
tree
2020-01-13
Christoph
J
unghans
g
mxManageMPI
.
cma
k
e: conver
t
MPI FLAGS to list
s
commit
|
commitdiff
|
tree
2020-01-09
Mark Abraham
Clean up ewald modul
e
internals
commit
|
commitdiff
|
tree
2020-01-09
Mar
k
Abraham
Spli
t
lines wi
t
h many copyright yea
r
s
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric Irrgang
Remove transit
i
on
a
l links for online gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
Pau
l
B
a
u
er
GROMA
C
S 202
0
r
e
l
e
ase
commit
|
commitdiff
|
tree
2020-01-01
Erik Lindahl
Add link to pap
e
r
explaining GROMOS t
w
i
n-range issues
.
commit
|
commitdiff
|
tree
2019-12-31
M
ark Abra
h
am
Avoi
d
3
8
6 O3 co
d
egen bug even mor
e
commit
|
commitdiff
|
tree
2019-12-31
Artem
Z
hm
u
rov
I
n
form user why f
o
rcing
G
PU
u
pdate i
s
not possi
b
l
e
commit
|
commitdiff
|
tree
2019-12-31
Artem
Z
h
murov
Add descr
i
pti
o
n of
G
MX_FO
R
CE_UPDATE_DEFAULT_GPU
d
ev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Arte
m
Zhm
u
rov
F
ix gpuupdate
m
atrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmurov
Change the
b
ehavior of the GPU updat
e
UI
commit
|
commitdiff
|
tree
2019-12-28
M
a
r
k
Ab
r
aham
M
erge "Merge o
r
igi
n
/
re
l
ease-2019 into rel
e
ase-2020
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Paul Bauer
Remove membed fr
o
m features
commit
|
commitdiff
|
tree
2019-12-28
Ma
r
k Abra
h
am
R
emove support for
A
R
Mv7
commit
|
commitdiff
|
tree
2019-12-28
Mark Abraham
St
o
p
testing A
R
Mv7
commit
|
commitdiff
|
tree
2019-12-20
S
z
ilárd Páll
Enable buffer
o
ps whe
n
GMX_GP
U
_DD_
C
OMMS is set
commit
|
commitdiff
|
tree
2019-12-19
Paul Bauer
Fi
x
regressionte
s
ts failing with ctest
commit
|
commitdiff
|
tree
2019-12-18
Paul Bauer
I
gn
o
re build hos
t
for CI
builds
commit
|
commitdiff
|
tree
2019-12-17
Mark Ab
r
aham
Fix that tests intend
e
d fo
r
m
u
ltiple rank
s
run that way
commit
|
commitdiff
|
tree
2019-12-16
Szilárd Páll
Fix the
G
PU bond
e
d stream with 1 PP +
1 PME rank
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
U
se
L
istOfLists in gmx_mtop_t and g
m
x_l
o
calto
p
_t
commit
|
commitdiff
|
tree
2019-12-15
C
hristian Blau
Fix densityfittin
g
stalling and energie
s
commit
|
commitdiff
|
tree
2019-12-14
Mark
Abraham
Sim
p
lify gmxapi
R
P
A
TH handling
commit
|
commitdiff
|
tree
next