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tools
mrdna
Commits
d488dd39
Commit
d488dd39
authored
Aug 30, 2017
by
cmaffeo2
Browse files
Ordered GPUs according to PCI_BUS_ID in arbd/namd calls
parent
06fa752c
Changes
4
Hide whitespace changes
Inline
Side-by-side
atomicModel.py
View file @
d488dd39
...
...
@@ -1466,6 +1466,8 @@ if {$nLast == 0} {
## $bindir/charmrun +p$procs $bindir/namd2 +netpoll +idlepoll +devices $gpus $config &> $log
gpus
=
','
.
join
([
str
(
gpu
)
for
gpu
in
gpus
])
# cmd = (charmrun, "+p%d" % numprocs, namd, '+netpoll',
env
=
os
.
environ
.
copy
()
env
[
"CUDA_DEVICE_ORDER"
]
=
"PCI_BUS_ID"
cmd
=
(
namd
,
"+ppn"
,
numprocs
,
'+netpoll'
,
'+idlepoll'
,
...
...
@@ -1476,4 +1478,4 @@ if {$nLast == 0} {
logfile
=
"%s/%s.log"
%
(
outputDirectory
,
outputPrefix
)
print
(
"Running NAMD with: %s >& %s"
%
(
" "
.
join
(
cmd
),
logfile
)
)
with
open
(
logfile
,
'w'
)
as
fh
:
subprocess
.
call
(
cmd
,
stdout
=
fh
,
stderr
=
subprocess
.
STDOUT
)
subprocess
.
call
(
cmd
,
env
=
env
,
stdout
=
fh
,
stderr
=
subprocess
.
STDOUT
)
beadModel.py
View file @
d488dd39
...
...
@@ -315,6 +315,9 @@ class beadModel():
self
.
writePsf
(
outputPrefix
+
".psf"
)
self
.
writeArbdFiles
(
outputPrefix
,
numSteps
=
numSteps
,
timestep
=
timestep
)
env
=
os
.
environ
.
copy
()
env
[
"CUDA_DEVICE_ORDER"
]
=
"PCI_BUS_ID"
## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
# cmd = "%s -g %d %s.bd %s/%s" % (arbd, gpu, outputPrefix, outputDirectory, outputPrefix)
# cmd = (arbd, (-g %d %s.bd %s/%s" % (gpu, outputPrefix, outputDirectory, outputPrefix))
...
...
@@ -322,7 +325,7 @@ class beadModel():
cmd
=
tuple
(
str
(
x
)
for
x
in
cmd
)
print
(
"Running ARBD with: %s"
%
" "
.
join
(
cmd
))
process
=
subprocess
.
Popen
(
cmd
,
stdout
=
subprocess
.
PIPE
,
universal_newlines
=
True
)
process
=
subprocess
.
Popen
(
cmd
,
env
=
env
,
stdout
=
subprocess
.
PIPE
,
universal_newlines
=
True
)
for
line
in
process
.
stdout
:
# for line in iter(process.stdout.readline, b''):
sys
.
stdout
.
write
(
line
)
...
...
beadModelTwist.py
View file @
d488dd39
...
...
@@ -384,6 +384,9 @@ class beadModelTwist():
self
.
writePsf
(
outputPrefix
+
".psf"
)
self
.
writeArbdFiles
(
outputPrefix
,
numSteps
=
numSteps
,
timestep
=
timestep
)
env
=
os
.
environ
.
copy
()
env
[
"CUDA_DEVICE_ORDER"
]
=
"PCI_BUS_ID"
## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
# cmd = "%s -g %d %s.bd %s/%s" % (arbd, gpu, outputPrefix, outputDirectory, outputPrefix)
# cmd = (arbd, (-g %d %s.bd %s/%s" % (gpu, outputPrefix, outputDirectory, outputPrefix))
...
...
@@ -391,7 +394,7 @@ class beadModelTwist():
cmd
=
tuple
(
str
(
x
)
for
x
in
cmd
)
print
(
"Running ARBD with: %s"
%
" "
.
join
(
cmd
))
process
=
subprocess
.
Popen
(
cmd
,
stdout
=
subprocess
.
PIPE
,
universal_newlines
=
True
)
process
=
subprocess
.
Popen
(
cmd
,
env
=
env
,
stdout
=
subprocess
.
PIPE
,
universal_newlines
=
True
)
for
line
in
process
.
stdout
:
# for line in iter(process.stdout.readline, b''):
sys
.
stdout
.
write
(
line
)
...
...
run.py
View file @
d488dd39
...
...
@@ -52,6 +52,7 @@ def readAvgArbdCoords(psf,pdb,dcd,rmsdThreshold=3.5):
# r0 = ref.xyz[0,ids,:]
r0
=
sel
.
xyz
[
-
1
,
ids
,:]
t
=
-
1
# in case dcd_frames < 3
for
t
in
range
(
len
(
sel
.
xyz
)
-
2
,
-
1
,
-
1
):
# print(t)
R
,
comA
,
comB
=
minimizeRmsd
(
sel
.
xyz
[
t
,
ids
,:],
r0
)
...
...
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