From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Aug 07 2013 - 02:18:25 CDT
Hi,
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.
Aborted
I could totally run it on window with windows version of NAMD2.8
Do you have any idea of what might be wrong?
Tian
On Tue, Aug 6, 2013 at 10:57 AM, Norman Geist
<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] Im Auftrag
von Tian Li
Gesendet: Dienstag, 6. August 2013 15:36
An: 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:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
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
[0] Stack Traceback:
[0] _Z8NAMD_diePKc+0x65 [0x4a6c85]
[1] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x75
[0x71fbcd]
[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?
Thanks,
Tian
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