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Merge "Merge release-2019 into master"
2018-11-20
M
ark
A
brah
a
m
Merg
e
"Mer
g
e r
e
lease-
2
019
into master"
commit
|
commitdiff
|
tree
2018-11-14
Mark Abrah
a
m
F
ix Open
C
L
mdrun from insta
l
led
path
commit
|
commitdiff
|
tree
2018-11-11
Viacheslav Bol
n
ykh
Fi
x
ing segfault in parallel MiMiC QM/
M
M
runs
commit
|
commitdiff
|
tree
2018-11-08
Mark Abraham
Pr
a
gma w
a
rning suppressi
n
s for icc+windows
commit
|
commitdiff
|
tree
2018-11-07
Paul Bau
e
r
M
ark new cmake variables advanced
commit
|
commitdiff
|
tree
2018-11-07
Szilárd Páll
E
liminate macro tha
t
ex
p
ands to varia
b
le
i
n PME
G
PU
commit
|
commitdiff
|
tree
2018-11-07
Szilárd Páll
Ensure minimum exec width o
f
the PME OpenCL ke
r
nels
commit
|
commitdiff
|
tree
2018-11-07
Paul Bau
e
r
Add glob
a
l directory for simul
a
ti
o
n test inp
u
t
s
commit
|
commitdiff
|
tree
2018-11-06
Pau
l
Bauer
Fix wrong
b
ra
n
ch for regress
i
ontes
t
s
commit
|
commitdiff
|
tree
2018-11-05
M
ark
A
bra
h
am
Make PME OpenCL e
n
able
d
o
nly fo
r
AMD devices
commit
|
commitdiff
|
tree
2018-11-05
Paul Bau
e
r
Ma
k
e QM/MM cod
e
a
l
ways co
m
pile
commit
|
commitdiff
|
tree
2018-11-05
Alexey Shvetsov
Disable -
W
n
o
-
m
i
ssin
g
-pr
o
totype
s
commit
|
commitdiff
|
tree
2018-11-05
Paul Baue
r
G
ive mor
e
info whe
n
t
r
ying to build
manual
commit
|
commitdiff
|
tree
2018-11-01
Mark Abraham
D
i
sable ccache
b
y default
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Limit au
t
o assignment of
b
onde
d
s to GPUs
commit
|
commitdiff
|
tree
2018-10-31
Jonatha
n
Vincent
Add C
U
DA
bond
e
d kernel
s
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Corre
c
t VV integr
a
tor nstcalcenergy use
commit
|
commitdiff
|
tree
2018-10-30
Mark
A
braham
Im
p
rove ccache
i
mplemen
t
ation
commit
|
commitdiff
|
tree
2018-10-30
Paul
B
a
uer
Chang
e
Table of conten
t
s
depth
commit
|
commitdiff
|
tree
2018-10-30
Mark Ab
r
aham
Rename to GMX_OPENCL_
N
B
_
CL
U
STER
_
S
I
ZE
commit
|
commitdiff
|
tree
2018-10-26
Mark Abraham
Merge "Merg
e
branch
release-2
0
18 into release-
2
0
19
.
.
.
commit
|
commitdiff
|
tree
2018-10-26
Mark A
b
ra
h
a
m
Me
r
ge branch release
-
2
0
18 int
o
rel
e
ase-2019
commit
|
commitdiff
|
tree
2018-10-26
Berk Hess
Add missing m
a
ss term to deltaH
commit
|
commitdiff
|
tree
2018-10-25
Mark
Abraham
I
n
troduc
e
Arra
y
RefWi
t
hPa
d
di
n
g
commit
|
commitdiff
|
tree
2018-10-25
Paul Bauer
Chang
e
doc build
w
ithout
i
mage convers
i
on
commit
|
commitdiff
|
tree
2018-10-24
Pa
u
l Bauer
Fix MPI w/o MPI_I
N
_PLAC
E
commit
|
commitdiff
|
tree
2018-10-22
P
a
ul
B
auer
Prep
a
r
e
mas
t
er for 2020
commit
|
commitdiff
|
tree
2018-10-21
Berk He
s
s
F
i
x
m
drun start/en
d
time print
commit
|
commitdiff
|
tree
2018-10-19
M
.
Eri
c
Irrga
n
g
Document
a
tio
n
bug in
gm
x
api/context
.
h
commit
|
commitdiff
|
tree
2018-10-18
Berk
Hess
Add
env
.
var
.
to disa
b
le
u
pdat
e
groups
commit
|
commitdiff
|
tree
2018-10-16
Mark Abraham
Elimin
a
ted t_ifunc from t_interaction_function
commit
|
commitdiff
|
tree
2018-10-16
M
agnus Lundborg
Move gmx_ffpara
m
s_t
to forcef
i
e
l
dparameters
commit
|
commitdiff
|
tree
2018-10-16
M
ark Abraham
Task
a
ssignment f
o
r bonded interact
i
o
ns on CUDA GPUs
commit
|
commitdiff
|
tree
2018-10-16
Mark Abraham
Fix com
p
i
l
er is
s
ue
s
commit
|
commitdiff
|
tree
2018-10-16
M
a
rk Ab
r
aham
Remo
v
ed support for
N
VIDIA CC 2
.
x devices (codename
.
.
.
commit
|
commitdiff
|
tree
2018-10-15
Ma
r
k Abraha
m
Cr
e
ate ExclusionBlocks
commit
|
commitdiff
|
tree
2018-10-15
M
a
rk
A
braham
D
e
-duplicating mdr
u
n
s
etu
p
commit
|
commitdiff
|
tree
2018-10-15
M
a
g
n
us Lundborg
E
n
able output of average pull
f
orce a
n
d p
o
sitio
n
s
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Er
i
c
Irrgang
R
esolve
s
ome lin
t
er
warning
s
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric
Irrgang
Test signal
i
ng facility
through se
s
sion resources
.
commit
|
commitdiff
|
tree
2018-10-14
S
z
ilárd Pá
l
l
Modernize OpenCL m
e
mory alloc
a
tion flags
commit
|
commitdiff
|
tree
2018-10-14
M
.
E
r
i
c
Irrga
n
g
Clean up gmxap
i
testsupport output
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Er
i
c Irr
g
ang
gmxapi::UsageError
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric
I
rrgang
Allow API access to simulation
s
ig
n
als
.
commit
|
commitdiff
|
tree
2018-10-13
Ale
k
sei Iupinov
Add and
e
nable PME
O
penCL
commit
|
commitdiff
|
tree
2018-10-12
M
.
E
r
ic Irrgang
Add API for addi
n
g MDModules
/
Rest
r
aints
.
commit
|
commitdiff
|
tree
2018-10-12
B
e
rk
H
e
ss
I
m
plement
assigni
n
g
b
o
ndeds
to the
GPU
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Irrgang
Add re
s
tr
a
ints framework
.
commit
|
commitdiff
|
tree
2018-10-12
Viache
s
lav Bo
l
nykh
I
m
p
lemented QM/MM workflow inside cor
e
GROMA
C
S
commit
|
commitdiff
|
tree
2018-10-12
Mark Abraham
Exclude gmxapi
s
our
c
e fil
e
s fr
o
m
include
s
orting
commit
|
commitdiff
|
tree
2018-10-11
D
avi
d
van der
S
poel
R
einstat
e
d quasi
h
armonic entropy calculat
i
on in
gmx
.
.
.
commit
|
commitdiff
|
tree
2018-10-11
M
.
Er
i
c Irrgang
Ad
d
gmxa
p
i::Sess
i
on
.
commit
|
commitdiff
|
tree
2018-10-11
Mark Abraham
Fi
x
PaddedVector issues
commit
|
commitdiff
|
tree
2018-10-11
Paul Bauer
Add
s
h
o
r
t
security
notice
commit
|
commitdiff
|
tree
2018-10-10
Paul Bauer
Inc
l
ude do
i
str
i
ngs from zenod
o
during rel
e
ase
commit
|
commitdiff
|
tree
2018-10-10
M
.
E
r
i
c
Irrgang
gmxap
i
expects position i
n
dependent c
o
de
.
commit
|
commitdiff
|
tree
2018-10-10
Szil
á
rd Páll
Swap custom OpenCL mem
s
et kernel f
o
r clEnque
u
eFill
B
u
f
fer
commit
|
commitdiff
|
tree
2018-10-09
Szil
á
rd Páll
U
pdate regr
e
ssi
o
n
test ref
t
o download
commit
|
commitdiff
|
tree
2018-10-09
Viac
h
es
l
a
v
Bolnykh
Implem
e
nt
e
d changes to preprocess
o
r to work with MiMi
C
.
.
.
commit
|
commitdiff
|
tree
2018-10-09
Mar
k
Abraham
Fix
D
om
d
ecOptions
defa
u
lt
commit
|
commitdiff
|
tree
2018-10-09
R
ol
a
nd S
c
hulz
Fix MSAN errors
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
Enable update groups
commit
|
commitdiff
|
tree
2018-10-08
Szilárd
Páll
Tweak F
i
ndFFTW AP
I
checks
commit
|
commitdiff
|
tree
2018-10-08
S
zilárd Páll
Fix
c
l
ang-6 warnings
commit
|
commitdiff
|
tree
2018-10-08
Rol
a
nd Schu
l
z
OCL: A
d
d
const
t
o function argu
m
e
nts
commit
|
commitdiff
|
tree
2018-10-08
Roland
S
chulz
Ad
d
OCL kernel t
a
r
get
commit
|
commitdiff
|
tree
2018-10-08
Ma
r
k Abraham
Disable FPE
explicitly for
TP
I
for
c
e c
a
lculation
commit
|
commitdiff
|
tree
2018-10-08
Szilárd P
á
ll
R
e
place some
NULL
wi
t
h n
u
llptr in
C
U
DA code
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
Imp
l
ement Pad
d
e
dVe
c
t
o
r
commit
|
commitdiff
|
tree
2018-10-08
Paul B
a
uer
Workaround
f
or ICC
p
o
sts
u
b
mit bug
commit
|
commitdiff
|
tree
2018-10-08
M
a
r
k Abraham
More upd
a
te
s
to te
s
t mat
r
ix
commit
|
commitdiff
|
tree
2018-10-08
Mark
Abraham
Fix
m
ak
e
tes
t
commit
|
commitdiff
|
tree
2018-10-07
Mar
k
Abr
a
ham
Test
with g
c
c 8 and cu
d
a 1
0
commit
|
commitdiff
|
tree
2018-10-05
Mark Abraham
Check l
o
g and
o
ther files di
f
ferently
d
u
r
i
n
g appending
.
.
.
commit
|
commitdiff
|
tree
2018-10-05
Berk He
s
s
Add
u
pdat
e
gr
o
ups to DD ato
m
displacement
commit
|
commitdiff
|
tree
2018-10-05
Mark
Ab
r
aham
Change to t
e
st T
S
A
N
wit
h
c
l
ang and libomp
commit
|
commitdiff
|
tree
2018-10-05
R
o
l
a
n
d
Schulz
OCL: Make vari
a
bles
co
n
st
commit
|
commitdiff
|
tree
2018-10-05
M
.
Eric Irr
g
ang
Add gmxapi::S
y
stem
.
commit
|
commitdiff
|
tree
2018-10-05
Szilárd Pá
l
l
Update test matrices with new G
P
U specifiers
commit
|
commitdiff
|
tree
2018-10-04
Berk Hess
Make AVX2 p
a
ss TSAN
commit
|
commitdiff
|
tree
2018-10-04
M
a
r
k
Abraham
Extract helper functions for preparing for appending
commit
|
commitdiff
|
tree
2018-10-04
M
a
r
k
Abraham
S
i
mplif
y
E
M
u
s
age of mdebin
commit
|
commitdiff
|
tree
2018-10-03
Mark Abraham
Use f
a
st returns i
n
md5 computation
commit
|
commitdiff
|
tree
2018-10-03
Magn
u
s Lundborg
Allow using COM of previous step as P
B
C
reference
commit
|
commitdiff
|
tree
2018-10-03
Mark Abrah
a
m
Add end-to
-
en
d
tests of
e
nergy m
i
nimization
commit
|
commitdiff
|
tree
2018-10-03
Paul Bauer
Disable GMX
A
PI when only b
u
ilding
m
drun
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric Irrgang
Add gmxapi::Context
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric Irrgang
Move mdrun mainFunction
t
o
client c
o
de
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric
Irrgang
Add test data for
g
mxapi
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eri
c
Irr
g
ang
Add
gmxapi
e
xcept
i
ons
.
commit
|
commitdiff
|
tree
2018-10-02
Paul Bauer
Fix inc
l
ude for
m
atting in gmxapi
commit
|
commitdiff
|
tree
2018-10-02
Roland
S
ch
u
lz
U
se subgroup
s
huff
l
e for
r
e
duct
i
on
commit
|
commitdiff
|
tree
2018-10-02
Berk Hess
Up
d
a
te
D
D cutoff
s
f
or update groups
commit
|
commitdiff
|
tree
2018-10-02
M
a
rk Abraham
R
educe md
r
un tests using group s
c
heme
commit
|
commitdiff
|
tree
2018-10-01
Mark Abraham
Fix gc
c
-8 warnings abo
u
t stri
n
g
s
commit
|
commitdiff
|
tree
2018-10-01
Paul Bauer
Change get_
a
tom
_
i
nde
x
to ret
u
rn int
commit
|
commitdiff
|
tree
2018-10-01
Mar
k
Abraham
Add release
note
s
for
r
emoving non
-
reproducible
aspects
commit
|
commitdiff
|
tree
2018-10-01
Ma
r
k Ab
r
aham
Tests for md5 computation on
o
pen f
i
l
es
commit
|
commitdiff
|
tree
2018-09-29
Mark Abraham
Stop ICC ICE
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Add UpdateGr
o
upsCog to
DD
commit
|
commitdiff
|
tree
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