From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Aug 07 2013 - 02:18:25 CDT
if you can run the same simulation in windows, and as I don't expect that
the commands differ between windows and linux, it might be a problem with
the encoding of the files. Try "dos2unix" on all your textfiles (pdb,
namdconfig,psf etc.) and see if it works then.
Von: Tian Li [mailto:litian543_at_gmail.com]
Gesendet: Dienstag, 6. August 2013 23:07
An: Norman Geist
Betreff: Re: namd-l: Colvar cannot be ran on supercomputer newton
I downloaded NAMD2.8 and installed on Newton, once I run the simulation, it
shows error like following:
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
Charm++ fatal error:
FATAL ERROR: Error in the collective variables module: exiting.
I could totally run it on window with windows version of NAMD2.8
Do you have any idea of what might be wrong?
On Tue, Aug 6, 2013 at 10:57 AM, Norman Geist
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.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 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 http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
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
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
 Stack Traceback:
 _Z8NAMD_diePKc+0x65 [0x4a6c85]
 _ZN9NamdState14configListInitEP10ConfigList+0x342 [0x6a2e28]
 _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x1bf [0x6fda1b]
 TclInvokeStringCommand+0x69 [0x2abac496f589]
 TclEvalObjvInternal+0x2f3 [0x2abac4970c73]
 Tcl_EvalEx+0x38b [0x2abac497116b]
 Tcl_FSEvalFile+0x217 [0x2abac49b4167]
 Tcl_EvalFile+0x2f [0x2abac49b424f]
 _ZN9ScriptTcl3runEPc+0x13 [0x6fa049]
 main+0x240 [0x4aa2b8]
 __libc_start_main+0xf4 [0x2abac67a2994]
 _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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