From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Fri Jan 22 2010 - 14:28:30 CST
We have a problem most probably in colvar module using Linux
(self)compiled 2.7b2 on MPI. Linux error is printed bellow; while
exactly the same input proceeds smoothly under win dual core
processor. Colvar configuration file is attached. All suggestions are
highly appreciated, thanks a lot in advance
Branko
colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 20090807.
colvars: Error: boolean values only are allowed for "analysis".
colvars: If this error message is unclear, try recompile with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
[0] Stack Traceback:
[0] CmiAbort+0x25 [0xa605e5]
[1] _Z8NAMD_diePKc+0x72 [0x4ea0b2]
[2] _ZN16colvarproxy_namd11fatal_errorERKSs+0x70 [0x8574c0]
[3] _ZN12colvarmodule11fatal_errorERKSs+0x13 [0x7d4093]
[4] _ZN11colvarparse10get_keyvalERKSsPKcRbRKbNS_10Parse_ModeE+0x89e
[0x7de4de]
[5] _ZN12colvarmoduleC1EPKcP11colvarproxy+0x603 [0x7ca823]
[6] _ZN16colvarproxy_namdC1Ev+0x364 [0x853484]
[7] _ZN10ComputeMgr14createComputesEP10ComputeMap+0x361 [0x55a851]
[8] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x269 [0x8cdff9]
[9] CkDeliverMessageFree+0x25 [0x9f8945]
[10] _Z15_processHandlerPvP11CkCoreState+0x529 [0x9f7f39]
[11] CsdScheduleForever+0x48 [0xa63a18]
[12] CsdScheduler+0x25 [0xa63ad5]
[13] _ZN7BackEnd7suspendEv+0xb [0x4f493b]
[14] _ZN9ScriptTcl3runEPc+0x10e [0x93ac4e]
[15] main+0x26a [0x4eea6a]
[16] __libc_start_main+0xf4 [0x397341d994]
[17] _ZNSt8ios_base4InitD1Ev+0x39 [0x4e9829]
p0_27470: p4_error: : 1
p0_27470: (10.734375) net_send: could not write to fd=4, errno = 32
colvarsTrajFrequency 1
colvarsRestartFrequency 10000
analysis on
colvar {
name d
lowerBoundary 2.98
upperBoundary 9.82
width 0.01
distance {
group1 {
atomnumbers 1 3 5
}
group2 {
atomnumbers 16 17 18
}
}
}
colvar {
name gyration
lowerBoundary 3.90
upperBoundary 4.94
width 0.01
gyration {
atoms {
atomNumbers 7 8 9 10 11 12 13 14 15 19 20 21 22 23 24 25 26
}
}
}
abf {
colvars d gyration
fullSamples 500
hideJacobian no
outputFreq 1000
applyBias yes
}
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