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Merge "Merge release-2019 into master"
2018-11-20
Mark A
b
raham
Merge
"Merge release-2
0
19 into mast
e
r"
commit
|
commitdiff
|
tree
2018-11-14
Mark Abraham
Fix
O
p
en
C
L mdr
u
n from installed path
commit
|
commitdiff
|
tree
2018-11-11
Viacheslav Bo
l
nykh
Fixing s
e
gfault
i
n parallel
M
iMiC QM/MM runs
commit
|
commitdiff
|
tree
2018-11-08
Mark Abraha
m
Pragma warning
suppressins for icc+windows
commit
|
commitdiff
|
tree
2018-11-07
P
a
ul B
a
uer
Mar
k
ne
w
cmake va
r
ia
b
les advanced
commit
|
commitdiff
|
tree
2018-11-07
S
z
ilárd Páll
Eliminate mac
r
o
that expand
s
to varia
b
le in PME GPU
commit
|
commitdiff
|
tree
2018-11-07
Szilárd Páll
Ensure min
i
mum exec width of the PME OpenC
L
ke
r
nels
commit
|
commitdiff
|
tree
2018-11-07
Paul Bauer
Add
g
lobal directory for sim
u
lation
tes
t
inputs
commit
|
commitdiff
|
tree
2018-11-06
Paul Bauer
Fix
wrong branch for regres
s
iontests
commit
|
commitdiff
|
tree
2018-11-05
Mark Abraham
Make PME
O
p
e
n
CL ena
b
led on
l
y for
AMD devices
commit
|
commitdiff
|
tree
2018-11-05
P
a
ul Bauer
Make QM/MM code
alw
a
ys
c
ompile
commit
|
commitdiff
|
tree
2018-11-05
Ale
x
ey S
h
vet
s
ov
Disable -Wno-missing-pro
t
otype
s
commit
|
commitdiff
|
tree
2018-11-05
P
a
ul
B
auer
G
i
ve more
info
w
hen trying to
b
uild
m
a
nual
commit
|
commitdiff
|
tree
2018-11-01
Mark
Abr
a
ham
Disable
c
cache by defaul
t
commit
|
commitdiff
|
tree
2018-10-31
Berk Hes
s
Limit aut
o
assignment
o
f bonde
d
s
to GPU
s
commit
|
commitdiff
|
tree
2018-10-31
Jonathan Vincent
Add CUDA bonded kerne
l
s
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Correct VV integr
a
t
o
r
n
stcalcene
r
gy use
commit
|
commitdiff
|
tree
2018-10-30
Mark Abraha
m
Improve ccache implementation
commit
|
commitdiff
|
tree
2018-10-30
Pa
u
l B
a
u
e
r
Change Table of contents dept
h
commit
|
commitdiff
|
tree
2018-10-30
Mar
k
Abraham
Rename
to
GMX_OPENCL_NB_CLUS
T
ER_SIZE
commit
|
commitdiff
|
tree
2018-10-26
Mark
A
b
rah
a
m
Merge "Mer
g
e branch r
e
lease-2018
into re
l
ease-2019
.
.
.
commit
|
commitdiff
|
tree
2018-10-26
Mark Abra
h
am
Merge branch relea
s
e-
2
018 into
r
elease-2019
commit
|
commitdiff
|
tree
2018-10-26
Berk Hess
Add mi
s
sing ma
s
s
term to
d
eltaH
commit
|
commitdiff
|
tree
2018-10-25
Mar
k
Ab
r
aham
Introd
u
ce ArrayRefWithP
a
dding
commit
|
commitdiff
|
tree
2018-10-25
P
a
ul Ba
u
er
C
h
ange doc build
witho
u
t image conversion
commit
|
commitdiff
|
tree
2018-10-24
Paul Bauer
Fix M
P
I
w
/o MPI_IN_PLACE
commit
|
commitdiff
|
tree
2018-10-22
Paul Bauer
Prepare master for 2020
commit
|
commitdiff
|
tree
2018-10-21
Berk Hess
Fix mdrun star
t
/end ti
m
e prin
t
commit
|
commitdiff
|
tree
2018-10-19
M
.
Eric
Irr
g
ang
Doc
u
mentatio
n
bug
in
gmxa
p
i/con
t
ext
.
h
commit
|
commitdiff
|
tree
2018-10-18
Berk Hess
A
d
d
env
.
var
.
to
d
isable update groups
commit
|
commitdiff
|
tree
2018-10-16
Mark
A
braham
Eliminated
t
_
ifu
n
c f
r
om t_interact
i
on_f
u
nction
commit
|
commitdiff
|
tree
2018-10-16
Magnus L
u
n
d
borg
Move gm
x
_ffparams_
t
t
o
for
c
efie
l
dparameters
commit
|
commitdiff
|
tree
2018-10-16
Mark Abrah
a
m
Task assignment for bonded int
e
ractio
n
s on CUDA GPUs
commit
|
commitdiff
|
tree
2018-10-16
Mark A
b
raham
Fix
compiler is
s
ues
commit
|
commitdiff
|
tree
2018-10-16
M
a
rk A
b
r
a
ham
Removed support
fo
r
NVIDIA CC 2
.
x devices (codena
m
e
.
.
.
commit
|
commitdiff
|
tree
2018-10-15
Mark Abr
a
ha
m
C
reate Exclusio
n
Blocks
commit
|
commitdiff
|
tree
2018-10-15
Mar
k
Abrah
a
m
De-duplica
t
i
n
g
mdr
u
n setu
p
commit
|
commitdiff
|
tree
2018-10-15
Magnus Lu
n
d
b
org
Enable output of average pull force and positi
o
ns
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eri
c
Irrgang
Re
s
olve some
linter warnings
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Er
i
c
I
r
rgang
T
e
s
t
signali
n
g faci
l
ity through
s
ession resour
c
es
.
commit
|
commitdiff
|
tree
2018-10-14
Szi
l
árd Páll
Mode
r
niz
e
Ope
n
CL memory alloc
a
ti
o
n
f
lags
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric
I
rrgang
Cle
a
n u
p
gmxapi
t
e
s
t
support output
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
E
r
ic Irrgang
gmxapi::Usa
g
eErr
o
r
commit
|
commitdiff
|
tree
2018-10-14
M
.
E
r
i
c
I
r
rgang
Allow API a
c
c
e
s
s
to simulat
i
on signa
l
s
.
commit
|
commitdiff
|
tree
2018-10-13
A
l
ek
s
e
i Iupinov
A
d
d a
n
d
e
nable PME OpenCL
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Irrga
n
g
Add API for adding MDModules / Restraint
s
.
commit
|
commitdiff
|
tree
2018-10-12
Berk Hess
Implement assigning bondeds to the GPU
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Irrgang
A
dd re
s
train
t
s
f
r
ame
w
o
r
k
.
commit
|
commitdiff
|
tree
2018-10-12
Viacheslav Bolnykh
I
mplemented QM/MM wo
r
kfl
o
w inside core GROMACS
commit
|
commitdiff
|
tree
2018-10-12
Mark Abraham
Exc
l
ude gmxapi
s
o
u
rc
e
f
i
l
e
s
from incl
u
de sorting
commit
|
commitdiff
|
tree
2018-10-11
Da
v
id v
a
n der Spoel
R
einstated
quasih
a
r
monic entro
p
y
c
a
lculation in gmx
.
.
.
commit
|
commitdiff
|
tree
2018-10-11
M
.
Eric Irrgang
Add gmxapi
:
:
S
ession
.
commit
|
commitdiff
|
tree
2018-10-11
Mark
A
b
r
aham
F
i
x
PaddedVector issues
commit
|
commitdiff
|
tree
2018-10-11
Paul
Bauer
Add short s
e
cur
i
t
y
notic
e
commit
|
commitdiff
|
tree
2018-10-10
P
a
ul Bauer
Incl
u
de doi strings
f
rom zenodo during rele
a
se
commit
|
commitdiff
|
tree
2018-10-10
M
.
Eri
c
Irrgang
gmxapi e
x
pects position independent code
.
commit
|
commitdiff
|
tree
2018-10-10
Szilárd Páll
Swap custom
OpenCL memset kernel for
c
lEnqueueFillBuffer
commit
|
commitdiff
|
tree
2018-10-09
Szilárd Páll
Update
regressiont
e
st ref to
download
commit
|
commitdiff
|
tree
2018-10-09
Viach
e
s
l
av B
o
lnykh
Impl
e
mented cha
n
ges to prepro
c
essor to w
o
r
k
w
ith MiMiC
.
.
.
commit
|
commitdiff
|
tree
2018-10-09
Mark Abraham
F
i
x Do
m
d
e
c
O
ptions default
commit
|
commitdiff
|
tree
2018-10-09
Roland
Sc
h
u
l
z
Fix MSAN errors
commit
|
commitdiff
|
tree
2018-10-08
Berk Hes
s
E
nab
l
e updat
e
grou
p
s
commit
|
commitdiff
|
tree
2018-10-08
Szilárd Páll
Tweak F
i
ndFF
T
W API checks
commit
|
commitdiff
|
tree
2018-10-08
Szilárd Páll
Fix
c
lang-6 warnings
commit
|
commitdiff
|
tree
2018-10-08
R
ola
n
d S
c
hulz
OCL: Add
c
ons
t
to funct
i
on arguments
commit
|
commitdiff
|
tree
2018-10-08
Roland Schulz
Add OCL k
e
rnel target
commit
|
commitdiff
|
tree
2018-10-08
M
ark Abraham
Disable
FPE explicitly
f
o
r
TPI force calcula
t
ion
commit
|
commitdiff
|
tree
2018-10-08
Szilá
r
d Pá
l
l
Re
p
la
c
e some NULL
w
ith nullptr in CUDA code
commit
|
commitdiff
|
tree
2018-10-08
Mark Abr
a
h
am
Imp
l
ement PaddedVec
t
or
commit
|
commitdiff
|
tree
2018-10-08
Paul B
a
uer
Wo
r
karound for
I
CC
postsubmit b
u
g
commit
|
commitdiff
|
tree
2018-10-08
Mark A
b
raham
Mor
e
updates to test
m
a
t
rix
commit
|
commitdiff
|
tree
2018-10-08
Mark Ab
r
ah
a
m
Fix make test
commit
|
commitdiff
|
tree
2018-10-07
Mark
A
b
raha
m
T
e
st with gcc 8 and
c
u
d
a 10
commit
|
commitdiff
|
tree
2018-10-05
Mark Abraham
Check lo
g
and other fil
e
s differen
t
ly
durin
g
ap
p
e
nding
.
.
.
commit
|
commitdiff
|
tree
2018-10-05
Berk H
e
s
s
Add update grou
p
s to DD ato
m
displaceme
n
t
commit
|
commitdiff
|
tree
2018-10-05
Mark
A
braham
Change t
o
test TSAN wit
h
clang an
d
l
ibomp
commit
|
commitdiff
|
tree
2018-10-05
Roland
S
c
hulz
OCL: Make
v
ariables const
commit
|
commitdiff
|
tree
2018-10-05
M
.
Eric Irrgang
Add gmxapi:
:
Syste
m
.
commit
|
commitdiff
|
tree
2018-10-05
Sz
i
lárd
Páll
Update test ma
t
rice
s
with new GPU spec
i
fi
e
rs
commit
|
commitdiff
|
tree
2018-10-04
Berk He
s
s
Make AVX2 pass TSAN
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
E
x
t
r
act h
e
lper functions for
p
repari
n
g fo
r
appending
commit
|
commitdiff
|
tree
2018-10-04
Mark
A
brah
a
m
Simpl
i
f
y EM usage of
m
deb
i
n
commit
|
commitdiff
|
tree
2018-10-03
Mark Abraham
U
se fas
t
r
e
t
u
rns
i
n md5 comput
a
tio
n
commit
|
commitdiff
|
tree
2018-10-03
Magnus
Lund
b
org
A
llow
using COM of p
r
evio
u
s
s
te
p
as
P
BC re
f
er
e
nce
commit
|
commitdiff
|
tree
2018-10-03
Mar
k
Abraham
A
d
d end-
t
o-en
d
te
s
ts
o
f
e
nerg
y
m
ini
m
izat
i
on
commit
|
commitdiff
|
tree
2018-10-03
Paul Baue
r
Disable GMXAPI whe
n
o
n
ly building mdrun
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric Irrgang
A
d
d gmxa
p
i::Con
t
e
x
t
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric
Irrgang
Mo
v
e mdrun mainFunction to cl
i
en
t
code
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Er
i
c
I
rrgang
Add t
e
st data f
o
r gmxap
i
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
E
r
ic Irr
g
ang
Add
gmxap
i
exceptions
.
commit
|
commitdiff
|
tree
2018-10-02
Paul Baue
r
F
ix i
n
c
l
ude format
t
ing in gmxapi
commit
|
commitdiff
|
tree
2018-10-02
Roland Schulz
Use subgroup
shuffle for
r
eduction
commit
|
commitdiff
|
tree
2018-10-02
Ber
k
H
e
ss
Update DD cutoffs for up
d
ate gr
o
u
p
s
commit
|
commitdiff
|
tree
2018-10-02
Mark Abra
h
am
Re
d
uce mdrun test
s
using group scheme
commit
|
commitdiff
|
tree
2018-10-01
Mark Abraham
F
ix gcc
-
8
w
arnings about st
r
ings
commit
|
commitdiff
|
tree
2018-10-01
P
aul B
a
u
e
r
Change get_atom_index to return i
n
t
commit
|
commitdiff
|
tree
2018-10-01
Mar
k
Abraham
A
dd release
notes for removing non-re
p
r
o
ducible
aspects
commit
|
commitdiff
|
tree
2018-10-01
Mark
A
brah
a
m
Tests for
md5
computation on open file
s
commit
|
commitdiff
|
tree
2018-09-29
Ma
r
k Abraha
m
S
t
op ICC ICE
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Add Upd
a
teGroupsCog
t
o
D
D
commit
|
commitdiff
|
tree
next