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Merge branch 'master' of git.gromacs.org:gromacs
2010-07-26
Sander Pronk
M
e
rge
branch 'master
'
of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-26
Sander Pronk
Ad
d
ed s
u
pport for
W
indow
s
_fseeki64
.
commit
|
commitdiff
|
tree
2010-07-26
Sa
n
d
e
r Pro
n
k
Windows fixes
.
commit
|
commitdiff
|
tree
2010-07-26
San
d
er
P
ro
n
k
Merg
e
b
r
anch 'master
'
of git
.
grom
a
cs
.
or
g
:
g
romacs
commit
|
commitdiff
|
tree
2010-07-26
S
and
e
r Pronk
Fixe
d
more thread_mpi installation issu
e
s
.
commit
|
commitdiff
|
tree
2010-07-26
Sander
Pro
n
k
Merge branch 'mast
e
r' of git
.
grom
a
cs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-07-26
Sander
P
ronk
Fixed thread_mpi distributio
n
issues
.
commit
|
commitdiff
|
tree
2010-07-26
Sa
n
der P
r
onk
Merge
b
r
anch 'master' of git
.
grom
a
c
s
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-07-26
Sander Pronk
Fix
e
d faulty commit
.
commit
|
commitdiff
|
tree
2010-07-26
Sa
n
der Pronk
Remove
d
redunda
n
t header fi
l
es
from
t
hread_mpi
.
commit
|
commitdiff
|
tree
2010-07-25
Sander Pronk
Removed extraneo
u
s
argu
m
en
t
from filter_ter()
.
commit
|
commitdiff
|
tree
2010-07-24
Sander Pronk
New
.
edr file forma
t
: n
o
w supports blocks of arbitrary
.
.
.
commit
|
commitdiff
|
tree
2010-07-22
Sander Pronk
S
mall
bu
g
fix for previous comm
i
t
.
commit
|
commitdiff
|
tree
2010-07-22
Sande
r
Pronk
Serialized access to FOR
T
RAN binding
s
of gromacs's
.
.
.
commit
|
commitdiff
|
tree
2010-07-22
San
d
er P
r
onk
Ov
e
rlinking issue
s
with 3d pa
r
ty
t
ools
f
ixed for
autotoo
l
s
.
commit
|
commitdiff
|
tree
2010-07-21
S
ander Pron
k
R
e
moved reference to orig
.
h in thread_
m
p
i
Makefil
e
.
am
commit
|
commitdiff
|
tree
2010-07-21
Sander Pronk
thread_mpi hea
d
e
r
files ar
e
now in sync with
so
u
rce
.
.
.
commit
|
commitdiff
|
tree
2010-07-20
S
ander Pronk
Sm
a
ll
C syntax f
i
x
.
commit
|
commitdiff
|
tree
2010-07-06
Sander Pronk
M
i
no
r
Windows thread fixes
.
commit
|
commitdiff
|
tree
2010-07-05
Sander Pronk
Added option to
ingore f
s
ync f
a
ilures
.
commit
|
commitdiff
|
tree
2010-07-05
San
d
er Pronk
More th
r
ead_mpi fixe
s
.
commit
|
commitdiff
|
tree
2010-07-05
Sa
n
der Pronk
Added missin
g
incl
u
d
e
files in thread_m
p
i
commit
|
commitdiff
|
tree
2010-07-05
Sander Pronk
Fix
e
d thread_
m
p
i hea
d
e
r
installs
.
commit
|
commitdiff
|
tree
2010-07-05
Sander
P
ronk
Fixed h
e
ader file
s
to be able to link 3d party code
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Sand
e
r Pronk
Fix
e
d m
i
ssing pr
o
totyp
e
in ge
n
born
.
c
commit
|
commitdiff
|
tree
2010-07-02
Sander Pron
k
SSE fix for incor
r
ect cast; f
i
xe
s
bug 441
.
commit
|
commitdiff
|
tree
2010-07-02
Sand
e
r Pronk
more cflags
.
commit
|
commitdiff
|
tree
2010-07-02
Sander P
r
o
n
k
more cflags
.
commit
|
commitdiff
|
tree
2010-07-01
Sa
n
der Pronk
Ad
d
e
d p
a
thscale cflags
.
commit
|
commitdiff
|
tree
2010-07-01
Sander Pronk
Auto
m
at
i
c CFL
A
GS in C
M
ak
e
f
or PGI, xlc compile
r
s
.
commit
|
commitdiff
|
tree
2010-07-01
San
d
er Pronk
More
t
hr
e
ad s
a
fety fixes in gm
x
lib
.
commit
|
commitdiff
|
tree
2010-06-30
S
a
nder Pronk
N
o
w
s
e
t
s the r
i
ght FLAGS
variables wit
h
CMake
.
commit
|
commitdiff
|
tree
2010-06-30
Sander Pro
n
k
Streamlined CFLAGS te
s
ting in cmake
.
commit
|
commitdiff
|
tree
2010-06-30
Sander
P
r
onk
Added tes
t
for MSVC _al
i
gned_malloc
.
commit
|
commitdiff
|
tree
2010-06-30
Sander P
r
onk
C90 fixes in qm
_
orca
.
c, fixed line endings to
UNI
X
.
.
.
commit
|
commitdiff
|
tree
2010-06-29
Sander Pronk
Bug fi
x
for the previous commit
commit
|
commitdiff
|
tree
2010-06-29
San
d
er Pronk
Sim
p
lified ali
g
n
e
d mallocs and fre
e
s
.
commit
|
commitdiff
|
tree
2010-06-29
Sander Pronk
Merge
branch 'master' of git
.
gromacs
.
org:g
r
o
m
a
cs
commit
|
commitdiff
|
tree
2010-06-29
Sander Pronk
Made aligned_mallo
c
thread safe
.
commit
|
commitdiff
|
tree
2010-06-27
Sander Pronk
m
in
o
r thread mpi
f
ix f
o
r C++
.
commit
|
commitdiff
|
tree
2010-06-24
S
ander Pronk
XDR file I/O is now thread
safe
.
commit
|
commitdiff
|
tree
2010-06-22
Sander Pro
n
k
More C90 fi
x
es
in
memb
e
d
.
commit
|
commitdiff
|
tree
2010-06-22
Sa
n
der Pronk
C
9
0
f
ixes
.
commit
|
commitdiff
|
tree
2010-06-22
Sander Pronk
vmdio error m
e
ssage
f
ix
.
commit
|
commitdiff
|
tree
2010-06-22
Sander
P
ronk
Most (if not
all) file
op
e
r
atio
n
s are now thread safe
.
commit
|
commitdiff
|
tree
2010-06-15
Sander Pronk
Fixed
return values for
M
PI_Comm_compare
i
n thread_mpi
.
commit
|
commitdiff
|
tree
2010-06-14
Sander Pronk
Ad
d
ed MPI_Comm_com
p
are() t
o
threa
d
_mpi
.
commit
|
commitdiff
|
tree
2010-06-12
Sander Pronk
More C90 p
e
dantry
.
commit
|
commitdiff
|
tree
2010-06-11
Sander Pr
o
n
k
Fixed anot
h
er
batch of //
comments
.
commit
|
commitdiff
|
tree
2010-06-11
S
a
nder Pronk
Remove
d
r
eference
s
to M
P
I_Wtim
e
(
) for
w
hen MPI is not
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
Sander
P
ronk
M
e
r
g
e branch 'master
'
of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-11
Sand
e
r Pron
k
Point
e
r ari
t
hmetic
bu
g
fix in mshift
.
c
commit
|
commitdiff
|
tree
2010-06-11
Sa
n
de
r
Pronk
Fixed an
allocation error during thread sp
a
w
n
s
.
commit
|
commitdiff
|
tree
2010-06-11
Sa
n
d
e
r P
r
onk
Aut
o
m
atic C
flags for icc with cmake
.
commit
|
commitdiff
|
tree
2010-06-11
Sander Pronk
x86 asse
m
bly fix in
t
hre
a
d sync atomics
.
commit
|
commitdiff
|
tree
2010-06-11
S
a
nder P
r
onk
Merge
b
ranch '
t
hr
e
adspawn'
commit
|
commitdiff
|
tree
2010-06-11
S
a
nder Pronk
Cleaned
up
c
o
de that determines thread number
.
commit
|
commitdiff
|
tree
2010-06-11
San
d
er
Pronk
Removed
-s
t
d=gnu99 from CXX
F
LA
G
S for C+
+
.
commit
|
commitdiff
|
tree
2010-06-11
Sa
n
der Pronk
Number of threads is now also de
t
e
r
min
e
d by system
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Sander Pronk
cmake counterpart to David's binary renamings
.
commit
|
commitdiff
|
tree
2010-06-09
Sander Pronk
cma
k
e
b
ug fixes: now com
p
iles with cmake 2
.
6
.
0
.
commit
|
commitdiff
|
tree
2010-06-09
Sander Pronk
A
utomatic compiler flags a
s
sembly/sse kernel
s
with
.
.
.
commit
|
commitdiff
|
tree
2010-06-06
S
ander Pronk
Pre
v
io
u
s ch
e
ckpoint's won't be overwr
i
tte
n
by
n
ewer
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Sander Pronk
C
h
eck
p
ointing is now slightly more relia
b
l
y d
o
ne to
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
San
d
er
Pr
o
nk
Bug
f
i
x
es - now
c
o
mpi
l
e
s on Wi
n
dows
.
commit
|
commitdiff
|
tree
2010-06-01
Sander
P
ronk
Fixed warnings, incl
u
d
ing so
m
e that were almo
s
t certainly
.
.
.
commit
|
commitdiff
|
tree
2010-05-31
San
d
er Pronk
Removed 'i
n
line
'
keyword for
xlc o
n
linux atomics
.
commit
|
commitdiff
|
tree
2010-05-16
Sander Pro
n
k
Fixed further
b
uild is
s
ues in geminate
.
c
commit
|
commitdiff
|
tree
2010-05-14
Sander Pronk
CMake fix
e
s
.
commit
|
commitdiff
|
tree
2010-05-14
Sand
e
r
P
ronk
Si
m
plified error check for fsync(
)
.
commit
|
commitdiff
|
tree
2010-05-13
S
ander Pronk
fsync
(
) return value is checked
.
commit
|
commitdiff
|
tree
2010-05-13
Sander Pronk
Turned
of
f
fsy
n
c for
FAHCORE
.
commit
|
commitdiff
|
tree
2010-05-13
Sa
n
der Pronk
Checkpoints
n
ow call
fsync()
on
a
ll o
p
en output fi
l
e
s
.
commit
|
commitdiff
|
tree
2010-05-12
Sa
n
der Pronk
Merge branch 'master' of git
.
gr
o
ma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-12
Sander Pr
o
nk
Now d
o
es some
t
hing use
f
ul
with the
USR1 sign
a
l
.
commit
|
commitdiff
|
tree
2010-05-11
Sander
P
ro
n
k
Merge br
a
nch '
m
ast
e
r'
o
f
g
it
.
gromacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-05-11
S
an
d
e
r Pronk
Further
c
h
a
nges to the signal
handling
.
commit
|
commitdiff
|
tree
2010-05-10
Sa
n
de
r
Pronk
M
e
rge branch 'm
a
ster' of
git@git
.
gro
m
acs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-05-10
Sander P
r
o
nk
Made g
m
x
_
tu
n
e_pme wo
r
k w
i
t
h
threaded mdru
n
.
commit
|
commitdiff
|
tree
2010-05-10
Sander
P
ronk
open
m
m fix f
o
r last
commit
commit
|
commitdiff
|
tree
2010-05-10
S
a
n
der Pronk
Cleaned up
s
ign
a
l handling code
.
commit
|
commitdiff
|
tree
2010-05-10
Sander Pronk
R
e
stored
p
r
oper signal
ha
n
dling when PME no
d
e
s are
.
.
.
commit
|
commitdiff
|
tree
2010-05-07
Sander Pronk
F
i
xed
a
n uninitialized variable in p
m
e
.
c (solve_pme_yzx)
.
commit
|
commitdiff
|
tree
2010-05-04
Sander Pronk
cm
a
ke equiv
a
lent
to p
r
ev
i
ous
c
ommit
.
commit
|
commitdiff
|
tree
2010-05-04
Sander Pronk
Added c
h
e
c
k for new compiler opt
i
on in gc
c
4
.
5 to
c
ontrol
.
.
.
commit
|
commitdiff
|
tree
2010-04-27
Sander Pr
o
nk
thread_mpi m
e
mory usage is no
w
less excessive
commit
|
commitdiff
|
tree
2010-04-12
S
a
nder Pronk
Fixed g_
m
sd
to print results
w
ith significan
t
digits
.
.
.
commit
|
commitdiff
|
tree
2010-04-02
Sander Pronk
C
l
eaned up the
mdrun/ma
i
n
.
c
t
hread code a
little more
.
commit
|
commitdiff
|
tree
2010-04-02
S
a
n
der Pronk
Fixed
checkpoint
co
n
t
in
u
ati
o
n
bug for thread-para
l
l
el
.
.
.
commit
|
commitdiff
|
tree
2010-04-01
San
d
er Pronk
Changed/fi
x
ed g_msd to
remove the center of
m
a
s
s
moti
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-03-25
Sander Pro
n
k
Fixed a pot
e
ntial memory c
o
herence issu
e
with t
h
re
a
d
.
.
.
commit
|
commitdiff
|
tree
2010-03-22
S
an
d
er Pron
k
Clearer
t
hread error message
.
commit
|
commitdiff
|
tree
2010-03-21
Sander Pr
o
nk
Auto
-
can
c
e
l
s thre
a
d
s for non-
p
arallel int
e
grators
.
commit
|
commitdiff
|
tree
2010-03-19
Sander
Pronk
Added makefile
.
am
t
o install ch
a
rmm force field
d
ata
.
commit
|
commitdiff
|
tree
2010-03-17
San
d
er Pronk
Fixed p
o
tential race condition in m
u
tex
/
cond_var/barrier
.
.
.
commit
|
commitdiff
|
tree
2010-03-15
Sa
n
der Pronk
S
ome windows fix
e
s
in thread_mpi
commit
|
commitdiff
|
tree
2010-03-15
Sa
n
der Pr
o
nk
Now auto-detects
the
number of hardw
a
re
t
hreads and
.
.
.
commit
|
commitdiff
|
tree
2010-03-07
Sander
P
ronk
Fi
x
ed MPI reduce ops M
P
I_MA
X
and MPI_MIN f
o
r thread_mpi
.
commit
|
commitdiff
|
tree
2010-03-05
S
a
nder P
r
onk
Re-fixed sm
a
l
l bug in genver
s
io
n
.
sh again
.
commit
|
commitdiff
|
tree
2010-03-05
Sander Pronk
M
e
r
g
e branch
'master' of git@git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
next