From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Aug 07 2013 - 11:25:38 CDT
Convert also NAMD configuration file, i.e. file in which all
instructions for NAMD run is given. Some more comments. Why you did not
use some more recent versions of NAMD (both Windows and Linux), the last
stable is 2.9 It is possible that you definition of colvars is not
compatible with more recent version or (more likely) vice versa. See
On 8/7/2013 5:47 PM, Tian Li wrote:
> Sorry, I think the problems back. any other files I need to convert? I
> just simply dos2unix the colvar configuration file.
> On Wed, Aug 7, 2013 at 10:03 AM, Tian Li <litian543_at_gmail.com
> <mailto:litian543_at_gmail.com>> wrote:
> Hey Branko,
> I converted the colvar configuration file, it works! Thanks a lot!
> On Wed, Aug 7, 2013 at 4:04 AM, Branko <bdrakuli_at_chem.bg.ac.rs
> <mailto:bdrakuli_at_chem.bg.ac.rs>> wrote:
> 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
>> 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.
>> <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
>> 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]
>>  _ZN9NamdState14configListInitEP10ConfigList+0x342
>>  _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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