VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Apr 01 2013 - 00:45:20 CDT

There’s no installation. Just download the appropriate binary for your system.

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Francesco Pietra
Sent: Monday, April 01, 2013 1:39 AM
To: Josh Vermaas; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: FFTK bond optimization +idlepoll request

 

Hi Josh:

I intended to add to my post that I was already aware (though I forgot it when posting) that, even if the way is found to place "+idlepoll" correctly, the error would result that there are too few threads for the simulation to run. In my experience, such simulations could not at all be carried out (see for example the "tests' accompanying the plugin "plumed". Then, I found your kind advice....

I am not familiar with installing namd for a single cpu (and I have to find a suitable machine to do that) but I'try.

Thanks again

francesco

 

On Sun, Mar 31, 2013 at 9:14 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

Hi Francesco,

The easy solution is just to get a second namd binary that is CPU only, and point to that one when using FFTK. For typical molecule parameterizations where the number of atoms is less than 100, the merits of using a GPU-accelerated version of NAMD (or even using more than 1 CPU) are questionable. The speedup simply isn't there (and may actually be slower), as the number of interactions that need to be computed is low relative to the overhead of splitting the work up. So don't worry about it, and pick up a simpler binary.

-Josh Vermaas

 

On 03/31/2013 01:14 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