AW: Colvar cannot be ran on supercomputer newton

From: Norman Geist (
Date: Tue Aug 06 2013 - 09:57:32 CDT

Hi Tian,


I suppose that the colvar configuration syntax has changed since NAMD 2.6.
That having said, you need to switch to a newer Version of NAMD. If you have
problems getting the newer version itself to run, post what error you get
exactly, so we can help you at this point.


Norman Geist.


Von: [] Im Auftrag
von Tian Li
Gesendet: Dienstag, 6. August 2013 15:36
Betreff: namd-l: Colvar cannot be ran on supercomputer newton


Dear NAMD users,

I want to use SMD to explore the pathway of a channel, using colvar to
restrain the atom in the xy plane, I ran my configuration file on my
computer using NAMD 2.8 multicore 32, it seems working fine. However, when I
use supercomputer newton, the error shows up. The NAMD in the supercomputer
is 2.6-mpi, the .log file shows as following:

Charm++> Running on MPI version: 2.1 multi-thread support: MPI_THREAD_SINGLE
(max supported: MPI_THREAD_SINGLE)
Charm warning> Randomization of stack pointer is turned on in Kernel, run
'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it. Thread
migration may not work!
Charm++> cpu topology info is being gathered.
Charm++> 2 unique compute nodes detected.
Info: NAMD 2.6 for Linux-amd64-MPI
Info: Please visit
Info: and send feedback or bug reports to
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Based on Charm++/Converse 60102 for mpi-linux-x86_64
Info: Built Mon Jul 19 16:55:57 EDT 2010 by gragghia on admin.local
Info: 1 NAMD 2.6 Linux-amd64-MPI 36 chi14 tli10
Info: Running on 36 processors.
Info: 3320 kB of memory in use.
Info: Memory usage based on sbrk
Info: Configuration file is 71smd01.conf
TCL: Suspending until startup complete.
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: colvarsConfig
ERROR: colvars
[0] Stack Traceback:
  [0] _Z8NAMD_diePKc+0x65 [0x4a6c85]
  [1] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x75
  [2] _ZN9NamdState14configListInitEP10ConfigList+0x342 [0x6a2e28]
  [3] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x1bf [0x6fda1b]
  [4] TclInvokeStringCommand+0x69 [0x2abac496f589]
  [5] TclEvalObjvInternal+0x2f3 [0x2abac4970c73]
  [6] Tcl_EvalEx+0x38b [0x2abac497116b]
  [7] Tcl_FSEvalFile+0x217 [0x2abac49b4167]
  [8] Tcl_EvalFile+0x2f [0x2abac49b424f]
  [9] _ZN9ScriptTcl3runEPc+0x13 [0x6fa049]
  [10] main+0x240 [0x4aa2b8]
  [11] __libc_start_main+0xf4 [0x2abac67a2994]
  [12] _ZNSt8ios_base4InitD1Ev+0x39 [0x4a62c9]

p.s. I also tried the new installed 2.9, the NAMD doesn't even run.

If anyone had such experience before?




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