From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Mar 31 2013 - 14:13:41 CDT

Good point, I've run into this too when using the GPU version of NAMD on my desktop (for autoimd). The immediate solution would be to edit the fftk code to add the +idlepoll to the command. But given that minimization is not reliable with the GPU version of NAMD anyway, can you install the CPU-only version as well and point fftk to that?

On Mar 31, 2013, at 2:14 PM, Francesco Pietra wrote:

> 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
>
>