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Removed erronous manual variable handling
2018-11-29
Ma
r
k Abraham
R
e
moved
e
rronous manual variable
h
andling
commit
|
commitdiff
|
tree
2018-11-29
P
aul Baue
r
Fix ref
e
rence manual imag
e
sizes
commit
|
commitdiff
|
tree
2018-11-29
P
aul Bauer
Fix r
e
f
erence
manual doc build
commit
|
commitdiff
|
tree
2018-11-28
P
aul Bauer
Fix gcc-8 warnings
commit
|
commitdiff
|
tree
2018-11-28
Mark A
b
raham
Int
r
od
u
c
e
G
puB
o
nded
commit
|
commitdiff
|
tree
2018-11-27
Sz
i
l
á
rd
P
á
l
l
Add A
R
M
PL
s
upport to
a
d
min script
commit
|
commitdiff
|
tree
2018-11-27
Szilárd Páll
A
dd tweaks to su
p
port ARMPL f
o
r FF
T
s
commit
|
commitdiff
|
tree
2018-11-26
Paul
B
a
uer
Fix newline printing in -v output
commit
|
commitdiff
|
tree
2018-11-20
Mark
Abra
h
am
Parti
a
l revert o
f
"
Fi
x
ineffici
e
nt she
l
l
m
inimization"
commit
|
commitdiff
|
tree
2018-11-15
Paul Bauer
R
efine F
i
ndSphinx
commit
|
commitdiff
|
tree
2018-11-15
M
.
Eri
c
Irrga
n
g
Note GMX_
E
NABL
E
_
C
CACHE in build system docs
.
commit
|
commitdiff
|
tree
2018-11-15
Mark A
b
raham
Fix
checkpoint res
t
art o
f
tpr with infinite
st
e
p
count
commit
|
commitdiff
|
tree
2018-11-15
Paul B
a
u
er
Rework GMXAPI tests
commit
|
commitdiff
|
tree
2018-11-15
Mark Abr
a
ham
Rela
x
a
rbitrary tolerance on rer
u
n test
commit
|
commitdiff
|
tree
2018-11-14
Mar
k
Abraham
Fix
O
penCL m
d
run from insta
l
l
e
d p
a
t
h
commit
|
commitdiff
|
tree
2018-11-11
Viacheslav Bolnykh
Fixing segfault in parallel MiMiC QM/MM
runs
commit
|
commitdiff
|
tree
2018-11-11
David
v
an d
e
r
S
p
o
el
Fi
x
ent
r
o
py calcu
l
ation in gmx anaeig
commit
|
commitdiff
|
tree
2018-11-09
Dav
i
d
van der
S
poel
Change get_atom_in
d
ex to allow
m
ultiple molecul
e
s
.
commit
|
commitdiff
|
tree
2018-11-08
Paul Bauer
Issu
e
fatal error if checkpoint does not suit the
.
t
pr
commit
|
commitdiff
|
tree
2018-11-08
M
ar
k
Abraham
Pr
a
g
m
a warning suppr
e
ssins for icc+windows
commit
|
commitdiff
|
tree
2018-11-07
Pau
l
Bauer
Ma
r
k new cma
k
e v
a
ri
a
bles advanced
commit
|
commitdiff
|
tree
2018-11-07
Sz
i
l
á
rd Páll
E
liminate m
a
cro that
e
xpan
d
s to variable
i
n PME GPU
commit
|
commitdiff
|
tree
2018-11-07
Szilárd P
á
ll
E
n
sure minimu
m
exec
width
of t
h
e PME OpenCL k
e
rnels
commit
|
commitdiff
|
tree
2018-11-07
Paul
B
auer
Add global directory for sim
u
lat
i
on test
inputs
commit
|
commitdiff
|
tree
2018-11-06
Paul Bauer
Fix wrong
branch for
r
egressiontest
s
commit
|
commitdiff
|
tree
2018-11-05
Mark Abrah
a
m
M
ake PME OpenCL enabled only for
A
MD devic
e
s
commit
|
commitdiff
|
tree
2018-11-05
P
a
ul
B
aue
r
Make QM/MM code always
compile
commit
|
commitdiff
|
tree
2018-11-05
Alexey Shvetsov
D
i
sable -Wno-m
i
ssing-prototyp
e
s
commit
|
commitdiff
|
tree
2018-11-05
Pau
l
Bau
e
r
Give more in
f
o when trying to b
u
i
l
d manual
commit
|
commitdiff
|
tree
2018-11-01
Mark Abraham
Dis
a
b
l
e ccache b
y
d
e
fault
commit
|
commitdiff
|
tree
2018-10-31
Ber
k
H
ess
L
imit a
u
to assig
n
ment of bonded
s
to GPUs
commit
|
commitdiff
|
tree
2018-10-31
Jonathan Vin
c
ent
Add CUDA bonded kernels
commit
|
commitdiff
|
tree
2018-10-31
Be
r
k H
e
s
s
Work arou
n
d expanded ensemb
l
e issues
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
C
o
rrect V
V
integrator nstc
a
l
c
ene
r
gy use
commit
|
commitdiff
|
tree
2018-10-30
Mark Abraham
Improve
ccache
i
mpl
e
me
n
tat
i
on
commit
|
commitdiff
|
tree
2018-10-30
Paul Bauer
Ch
a
nge
Table of co
n
ten
t
s depth
commit
|
commitdiff
|
tree
2018-10-30
Mark Abraham
Rename to GMX_OPENCL
_
NB_CLUST
E
R_SIZE
commit
|
commitdiff
|
tree
2018-10-26
Mark Ab
r
aham
M
erge
"
Merge
b
r
a
n
ch release-20
1
8 into release-
2
019
.
.
.
commit
|
commitdiff
|
tree
2018-10-26
Mark Abraham
M
erge branch rel
e
as
e
-2018 into release-2019
commit
|
commitdiff
|
tree
2018-10-26
Berk
Hess
Add
m
i
s
si
n
g
m
a
s
s
t
erm to
d
elt
a
H
commit
|
commitdiff
|
tree
2018-10-25
Mark Abraham
Int
r
o
d
uce ArrayR
e
fWithPadding
commit
|
commitdiff
|
tree
2018-10-25
Paul Bauer
Chan
g
e
d
o
c
b
uild without
imag
e
conversion
commit
|
commitdiff
|
tree
2018-10-24
Paul Bauer
Fix
MPI
w
/o MPI_IN
_
PLACE
commit
|
commitdiff
|
tree
2018-10-21
Berk H
e
ss
Fix mdrun
sta
r
t/end time
p
rint
commit
|
commitdiff
|
tree
2018-10-19
M
.
E
ric
I
rrg
a
ng
D
ocumentat
i
on bu
g
in gmx
a
pi/context
.
h
commit
|
commitdiff
|
tree
2018-10-18
Berk Hess
Add env
.
var
.
to dis
a
bl
e
up
d
ate
groups
commit
|
commitdiff
|
tree
2018-10-16
Mark Abraham
Eliminated t_ifunc
from
t
_in
t
er
a
c
t
ion_func
t
ion
commit
|
commitdiff
|
tree
2018-10-16
Ma
g
nus L
u
ndborg
Move
gmx_ffpara
m
s
_
t to
f
orcefiel
d
paramet
e
rs
commit
|
commitdiff
|
tree
2018-10-16
Mark
A
b
raham
Ta
s
k assignmen
t
f
o
r
bon
d
e
d
i
n
teractions on CUDA GPUs
commit
|
commitdiff
|
tree
2018-10-16
M
ark Abraham
Fix compiler
issues
commit
|
commitdiff
|
tree
2018-10-16
Mark
A
brah
a
m
Remov
e
d support for NVIDIA CC 2
.
x devices (c
o
dename
.
.
.
commit
|
commitdiff
|
tree
2018-10-15
Mark
Abrah
a
m
Create Ex
c
lus
i
o
nBlocks
commit
|
commitdiff
|
tree
2018-10-15
Ma
r
k Abraham
De-duplicating mdrun setup
commit
|
commitdiff
|
tree
2018-10-15
Magn
u
s Lundb
o
rg
Ena
b
le outp
u
t of av
e
rage pull force and positi
o
ns
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Irrgang
Resol
v
e some linter warnin
g
s
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric I
r
rgang
Test signaling facil
i
ty through sess
i
on resou
r
ces
.
commit
|
commitdiff
|
tree
2018-10-14
Szilárd Páll
Modernize O
p
enCL memory allo
c
ation flags
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric I
r
r
g
a
n
g
Clean up gmxapi tes
t
support
output
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric
I
rrgang
gmxapi::UsageError
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric
I
r
rgang
Allow API acces
s
to
simulation signals
.
commit
|
commitdiff
|
tree
2018-10-13
Alek
s
ei Iup
i
no
v
A
d
d
and enab
l
e PME
OpenCL
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eri
c
Irrgang
Add API
for add
i
n
g MD
M
odules / Restrai
n
ts
.
commit
|
commitdiff
|
tree
2018-10-12
Berk
H
e
ss
Implement assignin
g
bondeds to the G
P
U
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Irrgang
A
d
d restraints
f
ramework
.
commit
|
commitdiff
|
tree
2018-10-12
V
i
acheslav Bolnykh
Implemen
t
e
d
Q
M
/
MM
w
o
rkflow in
s
ide core GROM
A
CS
commit
|
commitdiff
|
tree
2018-10-12
Mark
A
braham
E
x
clude gmxap
i
s
ource
files from
inclu
d
e sort
i
ng
commit
|
commitdiff
|
tree
2018-10-11
Da
v
id van
d
er Spoel
Reinst
a
t
e
d qu
a
siharmonic e
n
tropy calculation in gm
x
.
.
.
commit
|
commitdiff
|
tree
2018-10-11
M
.
Eric Irrgang
A
d
d gm
x
a
pi::Ses
s
ion
.
commit
|
commitdiff
|
tree
2018-10-11
Mark
Ab
r
aham
Fix
Padded
V
ector issues
commit
|
commitdiff
|
tree
2018-10-11
Paul Bauer
Add
s
h
or
t
s
ecurity notice
commit
|
commitdiff
|
tree
2018-10-10
Pa
u
l
Bauer
I
n
c
lu
d
e doi stri
n
gs from zenodo dur
i
ng
rele
a
se
commit
|
commitdiff
|
tree
2018-10-10
M
.
Eric
Irrgang
gmxapi expec
t
s position i
n
dependent code
.
commit
|
commitdiff
|
tree
2018-10-10
Szilárd Páll
Swap custo
m
OpenCL m
e
mset kern
e
l for clE
n
q
u
eue
F
ill
B
uffer
commit
|
commitdiff
|
tree
2018-10-09
Szilárd P
á
l
l
Update regressiontest ref to downloa
d
commit
|
commitdiff
|
tree
2018-10-09
Viacheslav Bolnykh
I
m
p
l
emente
d
ch
a
nges to
prepro
c
essor to work with MiMiC
.
.
.
commit
|
commitdiff
|
tree
2018-10-09
Mark Abraham
Fix
Do
m
decOptio
n
s defa
u
lt
commit
|
commitdiff
|
tree
2018-10-09
R
o
land Schulz
Fix MSAN errors
commit
|
commitdiff
|
tree
2018-10-08
Ber
k
H
e
ss
Enable update grou
p
s
commit
|
commitdiff
|
tree
2018-10-08
Szilárd Páll
Tw
e
ak Find
F
FTW AP
I
checks
commit
|
commitdiff
|
tree
2018-10-08
Szilár
d
Pál
l
Fix clang-6 w
a
rnings
commit
|
commitdiff
|
tree
2018-10-08
Roland Schulz
OCL
:
Add
c
onst
to function a
r
gume
n
t
s
commit
|
commitdiff
|
tree
2018-10-08
R
o
lan
d
S
c
hulz
Add OC
L
kernel targe
t
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
Disable FPE e
x
plicitly for TPI force c
a
lcula
t
ion
commit
|
commitdiff
|
tree
2018-10-08
Szil
á
rd Páll
Repl
a
ce
some NULL with nullptr in CUDA code
commit
|
commitdiff
|
tree
2018-10-08
M
a
rk
A
braham
Implem
e
nt
PaddedVe
c
tor
commit
|
commitdiff
|
tree
2018-10-08
Paul
Baue
r
Worka
r
ound fo
r
IC
C
p
ostsubmit
bug
commit
|
commitdiff
|
tree
2018-10-08
Mark Abr
a
ham
More updates to test
m
atrix
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
F
ix
m
ake
t
e
st
commit
|
commitdiff
|
tree
2018-10-07
M
a
rk Abrah
a
m
Tes
t
with gcc 8 an
d
cuda 10
commit
|
commitdiff
|
tree
2018-10-05
Mark Abra
h
am
Check lo
g
and other fil
e
s di
f
f
e
r
e
n
t
l
y
d
uring appending
.
.
.
commit
|
commitdiff
|
tree
2018-10-05
Berk Hess
Add u
p
d
a
te g
r
oups to DD ato
m
displa
c
ement
commit
|
commitdiff
|
tree
2018-10-05
Mark Abra
h
am
Change t
o
t
e
st
TS
A
N wit
h
cl
a
ng and li
b
omp
commit
|
commitdiff
|
tree
2018-10-05
Roland Schu
l
z
O
CL: Ma
k
e variable
s
const
commit
|
commitdiff
|
tree
2018-10-05
M
.
Eric Irrgang
Add
g
mx
a
pi::System
.
commit
|
commitdiff
|
tree
2018-10-05
Szilárd Páll
Update test
m
a
t
rices with new G
P
U speci
f
iers
commit
|
commitdiff
|
tree
2018-10-04
Berk Hess
M
a
ke AVX
2
pass
T
SAN
commit
|
commitdiff
|
tree
2018-10-04
Mark Abra
h
am
Extract helper func
t
ions for prep
a
ring for a
p
pending
commit
|
commitdiff
|
tree
2018-10-04
Ma
r
k
A
braham
S
implify
E
M usage
o
f mdebin
commit
|
commitdiff
|
tree
2018-10-03
Mark Abrah
a
m
U
se fast returns
in md5
c
o
m
p
ut
a
tion
commit
|
commitdiff
|
tree
2018-10-03
Magn
u
s
Lundborg
Allow using COM of
pr
e
vious step
a
s PBC reference
commit
|
commitdiff
|
tree
next