VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Mar 31 2013 - 13:14:38 CDT
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Hello:
With VMD for LINUXAMD64, version 1.9.2a20 (March 12, 2013), FFTK plugin,
from OptGeom, for a diatomic molecule, skipping charge optimization, I
tried CalcBonded OptBonded.
At RunOptimization, error
Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
FATAL ERROR: Please add +idlepoll to command line for proper performance.
[0] Stack Traceback:
[0:0] CmiAbort+0x70 [0xa6302d]
[0:1] _Z8NAMD_diePKc+0x4a [0x55e03a]
[0:2] _ZN7BackEnd4initEiPPc+0xd4 [0x565d84]
[0:3] main+0x10 [0x529190]
[0:4] __libc_start_main+0xfd [0x7fa6e82afead]
[0:5] [0x52bead]
[0] Stack Traceback:
[0:0] [0xa62598]
[0:1] CmiAbort+0xa5 [0xa63062]
[0:2] _Z8NAMD_diePKc+0x4a [0x55e03a]
[0:3] _ZN7BackEnd4initEiPPc+0xd4 [0x565d84]
[0:4] main+0x10 [0x529190]
[0:5] __libc_start_main+0xfd [0x7fa6e82afead]
[0:6] [0x52bead]
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Please add +idlepoll to command line for proper
performance.
Charm++ fatal error:
FATAL ERROR: Please add +idlepoll to command line for proper performance.
Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
FATAL ERROR: Please add +idlepoll to command line for proper performance.
[0] Stack Traceback:
[0:0] CmiAbort+0x70 [0xa6302d]
[0:1] _Z8NAMD_diePKc+0x4a [0x55e03a]
[0:2] _ZN7BackEnd4initEiPPc+0xd4 [0x565d84]
[0:3] main+0x10 [0x529190]
[0:4] __libc_start_main+0xfd [0x7fa6e82afead]
[0:5] [0x52bead]
[0] Stack Traceback:
[0:0] [0xa62598]
[0:1] CmiAbort+0xa5 [0xa63062]
[0:2] _Z8NAMD_diePKc+0x4a [0x55e03a]
[0:3] _ZN7BackEnd4initEiPPc+0xd4 [0x565d84]
[0:4] main+0x10 [0x529190]
[0:5] __libc_start_main+0xfd [0x7fa6e82afead]
[0:6] [0x52bead]
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Please add +idlepoll to command line for proper
performance.
Charm++ fatal error:
FATAL ERROR: Please add +idlepoll to command line for proper performance.
while executing
"::exec /opt/namd2.9-cuda4.0-plumed-1.3_2013-03-12/bin/namd2
min-bondangles.conf"
("eval" body line 1)
invoked from within
"eval ::exec [list $exec_path] [lrange $args 1 end]"
(procedure "::ExecTool::exec" line 14)
invoked from within
"::ExecTool::exec $namdbin $minName.conf"
(procedure "::ForceFieldToolKit::BondAngleOpt::optBondsAngles" line 68)
invoked from within
"$function $p0list"
(procedure "construct_initial_simplex" line 22)
invoked from within
"construct_initial_simplex [lindex $args 0] $scale"
(procedure "::Optimize::Opt0::handle" line 91)
invoked from within
"$opt initsimplex $baInitial $scale"
(procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line 320)
invoked from within
"::ForceFieldToolKit::BondAngleOpt::optimize"
(procedure "::ForceFieldToolKit::gui::baoptRunOpt" line 40)
invoked from within
"::ForceFieldToolKit::gui::baoptRunOpt "
invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt invoke "
invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt instate {pressed !disabled} {
.fftk_gui.hlf.nb.bondangleopt.runOpt state !pressed;
.fftk_gui.hlf.nb.bondangleopt...."
(command bound to event)
This is a CPU/GPU system (and the GPUs where activated before runopt) where
the command line is
charmrun $NAMD_HOME/bin/namd2 filename.conf +p(numver of CPUs) +idlepoll
With FFTK I simply added the full path to namd2 executable
Where to add the requested "+idlepoll"? If added after "namd" of the FFTK
line, the error is "namd2 binary not found"
I am following old directions for FFTK. Where to find a manual for current
version?
Thanks
francesco pietra
- Next message: JC Gumbart: "Re: FFTK bond optimization +idlepoll request"
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- Reply: JC Gumbart: "Re: FFTK bond optimization +idlepoll request"
- Reply: Josh Vermaas: "Re: FFTK bond optimization +idlepoll request"
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