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Move old neighborsearch code to C++
2015-07-08
Erik Lindahl
Move
old nei
g
h
bors
e
arch
code t
o
C+
+
commit
|
commitdiff
|
tree
2015-07-07
Teemu Murtol
a
Wrap use
s
of t
h
rea
d
_mpi/mutex
.
h
commit
|
commitdiff
|
tree
2015-07-04
Teemu Mu
r
tola
Bump
various ve
r
sion n
u
mb
e
r
s
commit
|
commitdiff
|
tree
2015-07-04
Tee
m
u Murto
l
a
Make some unit tests
u
se mo
c
k file
outp
u
t
commit
|
commitdiff
|
tree
2015-07-02
Tee
m
u M
u
rtola
Minor include sorting c
h
ang
e
s
commit
|
commitdiff
|
tree
2015-07-01
Teemu Murtol
a
C
l
ean up u
n
us
e
d code from
gmxfio
commit
|
commitdiff
|
tree
2015-06-30
Mark Abraham
Do
c
ument how to add a
n
d use NVML support
commit
|
commitdiff
|
tree
2015-06-30
Mark A
b
r
a
h
am
Avoid GPU data ra
c
e also w
i
th
O
penCL
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
e
nabled 1 PP
+
1 PME node
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Add checks
f
or inefficient resource usa
g
e
commit
|
commitdiff
|
tree
2015-06-30
Mark Abraham
A
dd support for flushing WDDM que
u
e
commit
|
commitdiff
|
tree
2015-06-29
M
a
rk Abraham
M
e
rge "Me
r
g
e b
r
an
c
h r
e
lease-5-0"
commit
|
commitdiff
|
tree
2015-06-29
Erik Lindahl
F
i
x OS
X openC
L
builds
commit
|
commitdiff
|
tree
2015-06-29
E
rik Lindahl
R
e
place funct
i
o
n
s deprecat
e
d in OpenCL 1
.
2
commit
|
commitdiff
|
tree
2015-06-29
Teemu
Murto
l
a
Only accept e
x
act
ma
t
c
h
es
for
sel
e
c
t
ion keywords
commit
|
commitdiff
|
tree
2015-06-29
a
nca
Impl
e
ment Op
e
nCL support
commit
|
commitdiff
|
tree
2015-06-29
M
a
rk
A
braham
A
d
d M
S
A
N
build type
commit
|
commitdiff
|
tree
2015-06-29
Eri
k
Lindahl
Fix bug remov
i
ng m
u
ltiple dihedr
a
l
s
i
n
main rtp ent
r
ies
commit
|
commitdiff
|
tree
2015-06-29
Teemu Mu
r
tola
Make some unit
tests sk
i
p fi
l
e
s
y
stem a
c
c
ess
commit
|
commitdiff
|
tree
2015-06-29
E
rik Lindahl
Removed
gmx pro
t
o
na
t
e
t
ool
commit
|
commitdiff
|
tree
2015-06-29
B
e
r
k
Hess
Imp
r
ove DLB+PME tun
i
ng with GPUs
commit
|
commitdiff
|
tree
2015-06-28
Erik Lindahl
Fix double
p
r
ecision reference SIMD and gcc bug
commit
|
commitdiff
|
tree
2015-06-28
E
rik Li
n
dahl
Fi
x
one e
r
ror and compiler warn
i
ngs wit
h
Cuda & clang-3
.
6
commit
|
commitdiff
|
tree
2015-06-28
Peter Ka
s
son
A
p
p
e
n
d
_pul
l
x_ and _pullf t
o
p
u
l
l files when -deffnm
.
.
.
commit
|
commitdiff
|
tree
2015-06-28
R
o
land S
c
hul
z
Remove unused cmak
e
files
commit
|
commitdiff
|
tree
2015-06-28
R
olan
d
Schu
l
z
Do
n
't u
s
e
che
c
k_lib
r
ary f
o
r libm
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk Hess
Improved the intra-GPU load balancing
commit
|
commitdiff
|
tree
2015-06-27
Sz
i
lard
Pal
l
Fix CU
D
A
a
rchitecture dependen
t
issues
commit
|
commitdiff
|
tree
2015-06-27
Erik Linda
h
l
Fix IBM VSX SIMD compi
l
es wit
h
xlc
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Re
d
uce
t
he
use of nbnxn_consts
.
h
commit
|
commitdiff
|
tree
2015-06-27
Berk
H
ess
Co
r
r
ected n
s
tcalclr/nstfep/nst_
r
epl_
e
x ch
e
cks
commit
|
commitdiff
|
tree
2015-06-27
Erik Lindahl
Merge "Merge release-5-0 in
t
o master"
commit
|
commitdiff
|
tree
2015-06-27
Teemu Murtola
Documen
t
tool changes in
5
.
1
commit
|
commitdiff
|
tree
2015-06-26
E
r
ik Li
n
d
a
hl
Fix compi
l
e issues on K computer
commit
|
commitdiff
|
tree
2015-06-26
Be
r
k Hess
Fixed Verlet buf
f
e
r
issue with 2-wide SIMD
commit
|
commitdiff
|
tree
2015-06-26
E
r
i
k
L
i
n
d
a
h
l
Fix buffer size iss
u
es
i
n
string dat
a
base
commit
|
commitdiff
|
tree
2015-06-26
Mark Abraham
F
i
x
mdrun -confo
u
t
somet
i
mes
affecting
f
inal
.
edr
f
rame
commit
|
commitdiff
|
tree
2015-06-25
Berk Hess
Intermolecular bonded
i
nteraction supp
o
rt added
commit
|
commitdiff
|
tree
2015-06-25
Szilard Pall
Add missi
n
g m
a
c
r
o undef i
n
C
UDA NB kernel
commit
|
commitdiff
|
tree
2015-06-25
Rola
n
d Schulz
Fix Wundef warnin
g
s
commit
|
commitdiff
|
tree
2015-06-25
T
e
emu M
u
rtola
Mo
v
e d
o
cumentation on tool chang
e
s
f
rom wiki
commit
|
commitdiff
|
tree
2015-06-25
Mar
k
Ab
r
aham
Merge "Merge release-5
-
0 into master"
commit
|
commitdiff
|
tree
2015-06-25
Berk H
e
ss
Reen
a
b
led SIMD
k
ernels
without c
u
t
-
of
f
s
commit
|
commitdiff
|
tree
2015-06-24
Erik Lindahl
Avoid accessi
n
g
h
a
ckblocks fo
r
x2to
p
commit
|
commitdiff
|
tree
2015-06-24
Magnus Lu
n
dbo
r
g
Update h
e
ad
e
r when append
i
ng to TNG fil
e
.
commit
|
commitdiff
|
tree
2015-06-24
Berk H
e
ss
GPU Ewald ta
b
l
e
kern
e
l now
u
ses CPU spacing
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Avoid G
P
U
s
ele
c
t
ion
wi
t
h GPU emu
l
ation
commit
|
commitdiff
|
tree
2015-06-24
Berk Hes
s
Minor reformatting of
SIMD mis
m
atch message
commit
|
commitdiff
|
tree
2015-06-24
Berk He
s
s
Add sugar
to
p
rint empty line in printBinaryInfo
r
m
a
tion
commit
|
commitdiff
|
tree
2015-06-23
E
r
i
k
L
in
d
ahl
Upda
t
ed physica
l
c
o
nstan
t
s fro
m
N
I
ST 201
0
C
O
DATA
commit
|
commitdiff
|
tree
2015-06-23
E
rik
Lindahl
Removed buggy -smooth hack in
hb
o
nd
m
odule
commit
|
commitdiff
|
tree
2015-06-22
Ber
k
Hess
Up
d
ate launch configurat
i
on for physical
n
odes
commit
|
commitdiff
|
tree
2015-06-22
Roland Schulz
F
ix
GMX_
A
LI
G
NMENT for
M
SVC 20
1
2 and 2013
commit
|
commitdiff
|
tree
2015-06-22
B
e
r
k
H
e
ss
Avoid fp exception
s
in pair sear
c
h
debug
commit
|
commitdiff
|
tree
2015-06-22
Erik
L
in
d
ah
l
Fix compile
r
w
a
rnings in cmake tests
commit
|
commitdiff
|
tree
2015-06-22
Erik Lindahl
Us
e
MPI
_
T
HREAD_FUNNELED when available
commit
|
commitdiff
|
tree
2015-06-22
Rolan
d
Sc
h
ulz
F
ix cm
a
ke 3
.
1 w
a
r
ning
s
with MSVC
commit
|
commitdiff
|
tree
2015-06-22
E
r
i
k
Linda
h
l
Fix segfault in rando
m
access XTC searching
commit
|
commitdiff
|
tree
2015-06-22
Erik Lindahl
Fix argument
o
r
der error for g_rmsdist
commit
|
commitdiff
|
tree
2015-06-22
Erik Lindahl
Fix
gro e
r
ro
r
s
wit
h
PDB insert
i
on codes
commit
|
commitdiff
|
tree
2015-06-22
Berk He
s
s
Replaced hardware t
h
reads by logical
cores in
output
commit
|
commitdiff
|
tree
2015-06-21
Szilard Pall
fix
CPU co
r
e oversubsc
r
iption detection
commit
|
commitdiff
|
tree
2015-06-20
E
r
ik Lin
d
ahl
Upda
t
ed docs f
o
r g_gyrate
commit
|
commitdiff
|
tree
2015-06-20
E
r
ik Lindahl
Fi
x
pote
n
tial buffer overflow in pdb
2
g
m
x
commit
|
commitdiff
|
tree
2015-06-20
Erik Li
n
dahl
Di
s
al
l
ow infinite epsilon w
i
th
PME or GB
.
commit
|
commitdiff
|
tree
2015-06-20
Erik Lin
d
a
h
l
Remove GMX
_
MAX_MPI_THR
E
A
DS
commit
|
commitdiff
|
tree
2015-06-20
Erik
Linda
h
l
Fix reproducib
i
l
ity bug in fft5d
commit
|
commitdiff
|
tree
2015-06-20
Er
i
k Lindahl
H
a
n
d
le multidir/mul
t
isi
m
with single argument correctly
commit
|
commitdiff
|
tree
2015-06-18
B
e
rk H
e
ss
Reduced
t
h
e cost of the pull communication
commit
|
commitdiff
|
tree
2015-06-18
Mark
A
br
a
h
a
m
Fix typo in GMX_B
U
ILD_
O
WN_FFTW message
commit
|
commitdiff
|
tree
2015-06-17
Teemu Mu
r
tola
Minor clean up for refdata
.
*
commit
|
commitdiff
|
tree
2015-06-17
Teemu Murtola
Improve lo
g
ic f
o
r au
t
oma
t
ic s
e
le
c
tion names
commit
|
commitdiff
|
tree
2015-06-17
B
e
rk Hess
Refactored pull data structu
r
e
s
commit
|
commitdiff
|
tree
2015-06-16
Mark Abrah
a
m
Stop
p
e
o
p
le ins
t
alling into the
bui
l
d tree
commit
|
commitdiff
|
tree
2015-06-16
Erik Lindahl
Fi
x
CUDA v
e
rsion info in NVML
a
pplicatio
n
clock
warning
commit
|
commitdiff
|
tree
2015-06-16
E
r
i
k Lin
d
ahl
Add membrane embedding docs
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Added missing DD
cycl
e
counting
commit
|
commitdiff
|
tree
2015-06-16
Erik Lindahl
Updated FFT
W
recom
m
endations i
n
in
s
tall-guide
.
commit
|
commitdiff
|
tree
2015-06-16
M
ark Ab
r
a
h
am
M
o
ve c
o
de
f
or managing
m
dru
n
-
c
p
i an
d
-append
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Automat
e
d t
h
e -gpu_id o
p
t
ion
commit
|
commitdiff
|
tree
2015-06-16
Erik Lindahl
Fix segfault with time
r
r
ese
t
a
n
d
-nb
cpu
commit
|
commitdiff
|
tree
2015-06-16
Erik Lin
d
a
hl
Avo
i
d wa
r
n
ing abo
u
t affinity on Blue Gene, reduce w
a
rni
n
gs
commit
|
commitdiff
|
tree
2015-06-16
Mark Abraham
Fix pairs_
n
b not recog
n
ized
as part of molecu
l
e
t
ype
commit
|
commitdiff
|
tree
2015-06-16
Mark
A
braham
Add unit
tests for Array
R
ef
commit
|
commitdiff
|
tree
2015-06-16
Roland Schulz
Fix warning in unc
r
usti
f
y
commit
|
commitdiff
|
tree
2015-06-15
Er
i
k Lindahl
Fix OS X FFTW build failures
i
ntrodu
c
e
d
86a772
commit
|
commitdiff
|
tree
2015-06-15
Erik Lindahl
Fi
x
ed SIMD de
t
ection and flags common for IBM archs
commit
|
commitdiff
|
tree
2015-06-13
Berk Hess
Hard
w
a
re r
e
p
o
rting now c
o
vers
a
ll nodes
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtola
Up
d
a
te help output
commit
|
commitdiff
|
tree
2015-06-12
Te
e
mu Murt
o
la
Initial do
c
s for Jenkins integration
commit
|
commitdiff
|
tree
2015-06-12
Teemu
M
urtola
Initial build
s
y
stem
d
ocumenta
t
i
o
n
in dev guide
commit
|
commitdiff
|
tree
2015-06-12
Tee
m
u Murtol
a
Imp
r
ove Jenkins docs
bui
l
d
commit
|
commitdiff
|
tree
2015-06-11
Mark Abraham
Me
r
ge "Merg
e
b
ranch release-4-6 in
t
o release-5-0" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-06-11
M
a
r
k
A
br
a
ham
Handl
e
timing better
i
n
Jenki
n
s
commit
|
commitdiff
|
tree
2015-06-11
Teem
u
Murtola
Script for Jenkins d
o
cumen
t
at
i
on build
commit
|
commitdiff
|
tree
2015-06-11
Mark Abraham
Clean up vsite i
n
teraction clean-u
p
code
commit
|
commitdiff
|
tree
2015-06-09
Ma
r
k
Ab
r
a
ham
Docu
m
e
nt limit
a
tions of
t
rjconv
-
dump
commit
|
commitdiff
|
tree
2015-06-09
Teem
u
Murtola
Misc
.
i
mp
r
ovements to
docs build s
y
stem
commit
|
commitdiff
|
tree
2015-06-09
Teemu Murtol
a
Im
p
r
ove user
g
u
i
d
e
t
e
xt for command line interfac
e
commit
|
commitdiff
|
tree
2015-06-07
Erik Lindahl
F
ix out-of-r
a
nge integer litera
l
s for t
h
re
e
f
ry
commit
|
commitdiff
|
tree
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