From: Patrick Yee (pyee_at_nd.edu)
Date: Tue Mar 30 2010 - 17:10:49 CDT
Hi NAMD users,
I'm trying to find the PMF of an ion pair in water using the ABF
method. I'm having problems with jobs crashing when I try running ABF
simulations. The jobs seem to crash when I submit them to a node with
multiple cores. However, if I try running NAMD as a background process
on my workstation, the job runs fine, though it takes about 10 times
as long to complete. Does anyone have any suggestions or know
potential problems with what I'm doing?
The abf.tcl script as well as the other ABF scripts are the same as
those found on http://www.ks.uiuc.edu/~char/tutorials/ABF/. The
equilibration of the system is fine, but adding the following causes
crashes when I submit jobs.
source ../../Tutorial-ABF/abf-1.8/abf.tcl
abf coordinate distance-com
abf abf1 {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
20 21 22 23 24 25}
abf abf2 {26 27 28 29 30 31 32 33 34 35 36 37 38 39 40}
abf ximin 0.05
abf ximax 15.95
abf dxi 0.2
abf fullSamples 4000
abf forceConst 12.0
abf writeXiFreq 10000
abf outfile abf_Bmim_Tf2N.abf
The error I get in my log file is:
TCL: can't use floating-point value as operand of "*"
FATAL ERROR: can't use floating-point value as operand of "*"
while executing
"expr {$retval + $term * $term}"
(procedure "veclength2" line 4)
invoked from within
"veclength2 $v"
(procedure "veclength" line 2)
invoked from within
"veclength $dr"
(in namespace eval "::ABF::ABFcoord" script line 4)
invoked from within
"namespace eval ABFcoord {
set dr [vecsub $coords($group2) $coords($group1)]
set r [veclength $dr]
set nv [vecnorm $dr] ;# unity vector group1 -> ..."
(procedure "ABFapply" line 5)
invoked from within
"ABFapply $F"
(in namespace eval "::ABF" script line 87)
invoked from within
"namespace eval ::ABF {
# First timestep : we don't have forces
if { $timestep == 0 } {
# must not be equal to $timestep - 1
set timeStored -2
..."
(procedure "calcforces" line 2)
invoked from within
"calcforces"
Stack Traceback:
[0] CmiAbort+0x4f [0x7eb405]
[1] _Z8NAMD_diePKc+0x62 [0x4b31e2]
[2] _ZN15GlobalMasterTcl9calculateEv+0x295 [0x65e723]
[3] _ZN12GlobalMaster11processDataEPiS0_P6VectorS2_S2_S0_S0_S2_S0_S0_S2_+0x71
[0x6524cd]
[4] _ZN18GlobalMasterServer11callClientsEv+0x43e [0x6564aa]
[5] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x6f7 [0x655b1b]
[6] _ZN10ComputeMgr21recvComputeGlobalDataEP20ComputeGlobalDataMsg+0x12
[0x52039a]
[7] _ZN18CkIndex_ComputeMgr48_call_recvComputeGlobalData_ComputeGlobalDataMsgEPvP10ComputeMgr+0xf
[0x520385]
[8] CkDeliverMessageFree+0x21 [0x786a6b]
[9] _Z15_processHandlerPvP11CkCoreState+0x455 [0x786075]
[10] CsdScheduleForever+0xa2 [0x7f18a2]
[11] CsdScheduler+0x1c [0x7f14a0]
[12] _ZN7BackEnd7suspendEv+0xb [0x4bab01]
[13] _ZN9ScriptTcl3runEPc+0x15b [0x6fbae5]
[14] main+0x21b [0x4b69c3]
[15] __libc_start_main+0xf4 [0x32b121d994]
[16] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b2b5a]
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