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Avoid parsing of fatalerror.cpp as lint failure
2020-05-24
Paul Bauer
Avoid pa
r
sing o
f
fatalerror
.
cpp as li
n
t fai
l
u
r
e
commit
|
commitdiff
|
tree
2020-05-22
Artem Zhmurov
Rem
o
ve dependence of const
r
ai
n
ts on t_md
a
tom
s
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Upda
t
e
d
ocker image build
s
cripts for master
branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
rgang
Make
sur
e
CI script can call /bin/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Ir
r
gang
M
i
nor clean up to buildall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irrgang
A
l
low llvm optio
n
already used in buildall
.
s
h
scr
i
pt
.
commit
|
commitdiff
|
tree
2020-05-13
Paul B
a
uer
F
i
x check
s
o
ur
c
e
e
rror parsing
commit
|
commitdiff
|
tree
2020-05-11
Artem
Zhmur
o
v
Unify
C
U
DA a
n
d
OpenCL lookup-table creat
i
on
commit
|
commitdiff
|
tree
2020-05-05
Artem Zh
m
u
rov
U
n
i
fy CUDA and OpenCL lookup-ta
b
l
e cre
a
tion
commit
|
commitdiff
|
tree
2020-05-04
Pau
l
Ba
u
er
Fix cmake error: Mixe
d
styles
o
f target_link
_
lib
r
aries
.
.
.
commit
|
commitdiff
|
tree
2020-05-04
Artem Zhmurov
Un
i
fy
C
U
D
A and Ope
n
CL lookup-table creation
commit
|
commitdiff
|
tree
2020-04-30
ejjor
d
a
n
Add EOF newlines to eliminate c
o
mpil
e
r warnings
commit
|
commitdiff
|
tree
2020-04-30
e
j
jordan
Remove
c
make logic that is outdate
d
by requiring cmake
.
.
.
commit
|
commitdiff
|
tree
2020-04-28
Roland S
c
hulz
Add cl
a
ng WA
commit
|
commitdiff
|
tree
2020-04-28
R
o
land Sc
h
ulz
Fix MSVC 2019 test failures
commit
|
commitdiff
|
tree
2020-04-27
A
r
tem Zhmurov
Fix the r
e
moval of COM
v
elocity in
c
ase of GPU update
commit
|
commitdiff
|
tree
2020-04-27
Artem
Z
hm
u
r
o
v
Move PBC se
t
up
o
u
t of
t
he
l
aunchKerne
l
(
.
.
.
) in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-04-27
Paul
B
auer
F
i
x seg
m
entat
i
on faul
t
in do_dssp
commit
|
commitdiff
|
tree
2020-04-25
Mar
k
Abraham
Move
c
onfi
g
u
r
ation of
g
l
obal heade
r
s
commit
|
commitdiff
|
tree
2020-04-25
Paul Bauer
Fix
c
opyright he
a
der
commit
|
commitdiff
|
tree
2020-04-25
Roland Schulz
Fix MSVC 2019 warn
i
ngs
commit
|
commitdiff
|
tree
2020-04-23
Paul Bauer
Use branch
p
oint also f
o
r format
and copyright check
commit
|
commitdiff
|
tree
2020-04-23
Mark Abraham
Mark HWLOC cmake cac
h
e variab
l
e as advance
d
commit
|
commitdiff
|
tree
2020-04-22
P
a
s
cal Merz
Make init_dire
s
indep
e
ndent
of t_commre
c
commit
|
commitdiff
|
tree
2020-04-21
Mar
k
Abraham
Fix warnings
w
i
th
clang 9
commit
|
commitdiff
|
tree
2020-04-20
Ar
t
em Z
h
murov
Fi
x
the numbe
r
of steps ch
e
ck when checkpoint i
s
loaded
commit
|
commitdiff
|
tree
2020-04-20
Pau
l
Bauer
M
a
k
e te
s
ts check code for
w
arnings same as
t
he main
.
.
.
commit
|
commitdiff
|
tree
2020-04-16
Artem
Zhmurov
Unify CUDA
and OpenCL lookup-table creation
commit
|
commitdiff
|
tree
2020-04-14
Pas
c
al Merz
Mak
e
bonded interac
t
ion ch
e
cking m
o
re rob
u
st (m
o
dular
.
.
.
commit
|
commitdiff
|
tree
2020-04-13
M
ark A
b
raham
Fix warnings for no-mpi build
commit
|
commitdiff
|
tree
2020-04-12
M
ark Abraham
Re
m
ove
d
unu
s
ed variable in force
t
able generation
commit
|
commitdiff
|
tree
2020-04-11
Paul
Bau
e
r
Add Imag
e
fo
r
GCC 7 and A
M
D
Ope
n
C
L
commit
|
commitdiff
|
tree
2020-04-07
M
a
rk
A
braham
Replace EnumOption with Enumera
t
ionA
r
rayOp
t
i
on
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eric Ir
r
g
ang
Prepare Python environ
m
ents for GitLab CI
p
ip
e
line
.
commit
|
commitdiff
|
tree
2020-04-07
Pascal M
e
rz
Make global topology constant in
energyOutput
.
printAnnealing
.
.
.
commit
|
commitdiff
|
tree
2020-04-06
Be
r
k
Hess
Move
f
o
r
ce
b
uffer resi
z
ing to mdsetup
commit
|
commitdiff
|
tree
2020-04-06
P
a
scal Merz
Make bonded interaction c
h
ecking more
r
obust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Ir
r
gang
Improve gmxapi Python package
d
e
pendency resolution
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
E
r
i
c
Irrgang
Prune cha
n
ge-management
.
rst and update li
n
ks
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric
I
rr
g
ang
Prepare P
y
thon
envi
r
onments f
o
r
G
itLab CI pip
e
line
.
commit
|
commitdiff
|
tree
2020-03-30
Mark Abraham
Set buff
e
rs appropriate
l
y so
.
xpm files
c
an be read
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Ir
r
gang
Requi
r
e Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-23
A
rtem Zhmurov
Introdu
c
e Dev
i
c
e
Stream
M
anager
commit
|
commitdiff
|
tree
2020-03-21
Paul Ba
u
er
Add
Documentation build
t
o script
commit
|
commitdiff
|
tree
2020-03-19
Paul Bauer
Add script to generate CI Docker
files
commit
|
commitdiff
|
tree
2020-03-19
Art
e
m Zhmurov
Pa
s
s DeviceContext instead
o
f GP
U
runtim
e
data
w
he
n
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irr
g
an
g
Add stub V
a
ri
a
bl
e
s docu
m
entati
o
n to Gi
t
Lab CI d
o
c
.
commit
|
commitdiff
|
tree
2020-03-17
Berk Hess
Disable Ewald d
i
p
ole correctio
n
without DD
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c
I
rrg
a
ng
D
e
fine an argparse parent parser for container im
a
ge
.
.
.
commit
|
commitdiff
|
tree
2020-03-14
M
ar
k
Abra
h
am
Mov
e
testing c
o
de to test direc
t
ory
commit
|
commitdiff
|
tree
2020-03-12
Gilles Gou
a
i
l
lardet
grompp: fix
the -re
f
<file> option
commit
|
commitdiff
|
tree
2020-03-10
Artem Zh
m
urov
Use in
i
t(
.
.
) function
t
o build Devic
e
Context
commit
|
commitdiff
|
tree
2020-03-07
Berk Hess
Make shake work without graph
commit
|
commitdiff
|
tree
2020-03-04
M
ark Ab
r
aham
Imp
r
o
ve
T
P
I
handling
commit
|
commitdiff
|
tree
2020-03-02
B
e
rk Hess
Fix
c
en
t
er
o
f
ma
s
s motion rem
o
val with frozen atoms
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmurov
Updat
e
t
he
mes
s
a
g
e on wheth
e
r upda
t
e an
d
constr
a
in
t
s
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Paul Bauer
Remove fro
z
en
atoms from VC
M
groups
commit
|
commitdiff
|
tree
2020-02-27
P
asc
a
l Merz
Loo
s
e
n
gmxapi st
o
p
s
ignal
e
r test
commit
|
commitdiff
|
tree
2020-02-27
Pascal Mer
z
E
x
tract and expose funct
i
on
t
o determine w
h
e
t
her molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Szilárd Páll
Rem
o
ve out
d
at
e
d PME-GPU l
i
mitatio
n
in user guide
commit
|
commitdiff
|
tree
2020-02-25
Magnus Lundborg
Fix out o
f
sy
n
c checkpoint fil
e
s in simul
a
tions
s
h
aring
.
.
.
commit
|
commitdiff
|
tree
2020-02-24
Paul Bauer
Fix
c
l
a
n
g-6 image template
commit
|
commitdiff
|
tree
2020-02-20
Art
e
m Zh
m
urov
Use CUDA float3
vecto
r
type instead of
f
vec
in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
P
a
ul
Ba
u
er
Workaround for Git
l
ab
archive s
i
z
e
commit
|
commitdiff
|
tree
2020-01-29
Magnus Lundborg
M
ore S
I
MD prepa
r
at
i
on
s
in
t
he
FE calculat
i
ons
commit
|
commitdiff
|
tree
2020-01-29
Paul
Bauer
Add rep
l
acement for symbol table
commit
|
commitdiff
|
tree
2020-01-27
M
ark
A
b
rah
a
m
Remove elemen
t
-size member fi
e
lds
commit
|
commitdiff
|
tree
2020-01-27
Mark Abraham
Ma
k
e Nb
n
xnGpu class with
c
onst
r
u
c
t
o
r
commit
|
commitdiff
|
tree
2020-01-24
Szi
l
á
r
d Páll
Add
tar
g
et for of
f
line PME OpenCL compilatio
n
commit
|
commitdiff
|
tree
2020-01-24
Magnus Lundbo
r
g
Removed S
C
RPower
48 from FEP ke
r
n
e
l
commit
|
commitdiff
|
tree
2020-01-17
Mark Abraham
R
egu
l
a
r
ize nbnxm
m
o
dule doxygen
commit
|
commitdiff
|
tree
2020-01-17
Paul
B
auer
Fix bad link
in deve
l
oper docs
commit
|
commitdiff
|
tree
2020-01-17
Be
r
k
Hess
Add
c
heck for she
l
l
s
and GPU up
d
ate
commit
|
commitdiff
|
tree
2020-01-13
Pa
u
l Bau
e
r
Re
v
ert
"
E
xclude bu
i
ld-
s
ystem files from
C
Pack"
commit
|
commitdiff
|
tree
2020-01-13
Christo
p
h
J
unghans
gmxManageM
P
I
.
c
ma
k
e:
c
onvert MPI
F
LAGS to lists
commit
|
commitdiff
|
tree
2020-01-09
Ma
r
k Abraham
Clean up ewald module
internals
commit
|
commitdiff
|
tree
2020-01-09
Mark Abr
a
ham
Split lines wit
h
many copyrig
h
t
years
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eri
c
Irr
g
ang
Remove t
r
ansitional links for online gmx
a
pi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
Pau
l
B
a
uer
GROMACS 2
0
20 release
commit
|
commitdiff
|
tree
2020-01-01
Er
i
k Lindahl
Add link to pape
r
explaining GROMOS twi
n
-
r
ange issues
.
commit
|
commitdiff
|
tree
2019-12-31
Ma
r
k Abraham
Avoid 386 O3 cod
e
g
en bug even more
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
I
n
form
u
ser
w
hy forcing
G
PU update i
s
not p
o
ssible
commit
|
commitdiff
|
tree
2019-12-31
A
r
tem Zhmurov
Add
d
e
scription of GMX_FORCE
_
UPDATE_DEFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Fix gpuupdate matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmurov
Cha
n
ge th
e
behavior of
t
h
e GPU u
p
date
U
I
commit
|
commitdiff
|
tree
2019-12-28
Mark Abr
a
ham
Merge "Merge
o
ri
g
in
/
release-2019 into rele
a
se-2020
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Paul Bauer
Re
m
ove me
m
bed from features
commit
|
commitdiff
|
tree
2019-12-28
Mark Abraham
Rem
o
v
e
support for ARM
v
7
commit
|
commitdiff
|
tree
2019-12-28
M
a
r
k
A
braham
Stop testing
A
R
M
v7
commit
|
commitdiff
|
tree
2019-12-20
Sz
i
lárd Páll
Enable buffer op
s
when
G
MX_GPU_DD
_
COMMS
i
s s
e
t
commit
|
commitdiff
|
tree
2019-12-19
Paul Bauer
F
ix
r
egre
s
s
iontests failing with ct
e
st
commit
|
commitdiff
|
tree
2019-12-18
Paul Ba
u
er
Igno
r
e
b
uild host f
o
r
C
I
builds
commit
|
commitdiff
|
tree
2019-12-17
Mar
k
Abraham
F
i
x t
h
at
tests i
n
tended f
o
r multiple ranks run
t
hat way
commit
|
commitdiff
|
tree
2019-12-16
Szilá
r
d
P
á
ll
Fix the GPU bonded stream w
i
th 1 PP + 1 PME rank
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
Us
e
ListOfLists in
gmx_
m
top_t and gmx_localtop_
t
commit
|
commitdiff
|
tree
2019-12-15
Christian Blau
Fix densityfitting s
t
alling
and energ
i
es
commit
|
commitdiff
|
tree
2019-12-14
Mark Abraham
Simpli
f
y
gmxapi RPATH ha
n
dling
commit
|
commitdiff
|
tree
2019-12-12
Ma
r
k Abra
h
am
Merge
"
Merge bra
n
c
h 'origin
/
relea
s
e-2020'
into mast
e
r"
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
Allow
using GPU upd
a
te wi
t
h DD and update g
r
ou
p
s
commit
|
commitdiff
|
tree
2019-12-11
Mark
Abraham
Document DOMAI
N
DECO
M
P(
c
r) co
r
r
e
c
t
ly
commit
|
commitdiff
|
tree
next