From: Tian Li (litian543_at_gmail.com)
Date: Tue Aug 06 2013 - 08:35:44 CDT
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
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:32 CST