From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Aug 07 2013 - 03:04:23 CDT
I experienced similar problem, convert just NAMD configuration file and
colvars configuration file using program dos2unix
(http://sourceforge.net/projects/dos2unix/). Likely that colvar module
in Linux version simply cannot recognize end of lines as ascribed by
dos (i.e. Windows).
On 8/7/2013 9:18 AM, Norman Geist wrote:
> 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.
> Norman Geist.
> *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
> Hello Dr.Geist,
> 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
> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
> 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:*owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>
> [mailto: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
> *An:* namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> *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
> ERROR: colvarsConfig
> ERROR: colvars
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>  Stack Traceback:
>  _Z8NAMD_diePKc+0x65 [0x4a6c85]
>  _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x75
>  _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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