Colvars Errors to restart
Closed this issue · 2 comments
groponp commented
Dear developers,
I'm Experience a error:
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: REPLICA 0 FATAL ERROR: Error in the collective variables module (see above for details)
Charm++ fatal error:
REPLICA 0 FATAL ERROR: Error in the collective variables module (see above for details)
/var/spool/slurmd/job7212033/slurm_script: line 46: 1476773 Aborted ${namd3}/namd3 +p 16 --GPUresident on +setcpuaffinity +devices 0,1,2,3 metad${run}.confg > metad${run}.out
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: REPLICA 0 FATAL ERROR: Error in the collective variables module (see above for details)In particular the error say me to review above to details but I don't found theses details in the same file.
My configuration is :
colvarsTrajFrequency 500
colvar {
name r
width 0.1 # Mesmo do que CHARMM-GUI and também BFEE2. Não considere lower/upperWall.
lowerboundary 9.6 # O valor é zero, porque a diferencia de distanciaentre os dímeros é 0.0.
upperboundary 53.6 # O valor máximo para evaluar o PMF.
expandboundaries on
distance {
forceNoPBC yes
group1 {
atomsFile P1.pdb # PROB.
atomsCol B
atomsColValue 1.0
}
group2 {
atomsFile P2.pdb # PROA.
atomsCol B
atomsColValue 1.0
}
}
}
harmonicWalls {
name WTMetaD-Walls
colvars r
lowerWalls 9.6 # lowerboundary.
upperWalls 53.6 # upperboundary.
lowerWallConstant 10.0 # Força mesma como em charmm-gui.
upperWallConstant 10.0 # Força mesma como em charmm-gui.
}
abf {
name ABF-Distance
colvars r
fullSamples 10000 # FullSamples mesmo como BFFE2.
hideJacobian # Exclui a entropia geométrica. so para distance e distanceXY.
# fonte: https://github.com/Colvars/colvars/issues/367
historyfreq 500 # Salva o free energy gradient, sampling histograma e PMF no mesmo arquivo.
}Review the log from namd I get this:
CL: Original numsteps 250000000 will be ignored.
TCL: Running for 33513000 steps
colvars: Updating NAMD interface:
colvars: Warning: enabling wrapAll can lead to inconsistent results for Colvars calculations: please disable wrapAll, as is the default option in NAMD.
colvars: updating atomic data (0 atoms).
colvars: updating group data (2 scalable groups, 68 atoms in total).
colvars: updating grid object data (0 grid objects in total).
colvars: updating target temperature (T = 310 K).
colvars: Current simulation parameters: initial step = 216487000, integration timestep = 2
colvars: Updating atomic parameters (masses, charges, etc).
colvars: Re-initialized atom group for variable "r":0/0. 10 atoms: total mass = 120.11, total charge = 0.4.
colvars: Re-initialized atom group for variable "r":0/1. 58 atoms: total mass = 696.638, total charge = 3.56.
colvars: The restart output state file will be "md5.restart.colvars.state".
colvars: Error: the calculated value of colvar "r":
colvars: 63.1712
colvars: differs greatly from the value last read from the state file:
colvars: 26.1999
colvars: Possible causes are changes in configuration, wrong state file, or how PBC wrapping is handled.
FATAL ERROR: Error in the collective variables module (see above for details)
[0] Stack Traceback:
[0:0] namd3 0x1100458 CmiAbortHelper(char const*, char const*, char const*, int, int)
[0:1] namd3 0x110055d
[0:2] namd3 0x7b7543
[0:3] namd3 0xf218aa colvarmodule::error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)
[0:4] namd3 0xe2c7fc colvar::collect_cvc_values()
[0:5] namd3 0xe2d630 colvar::collect_cvc_data()
[0:6] namd3 0xf213a4 colvarmodule::calc_colvars()
[0:7] namd3 0xf268a0 colvarmodule::calc()
[0:8] namd3 0xac5973 colvarproxy_namd::calculate()
[0:9] namd3 0xaa0fb2 GlobalMaster::processData(int*, int*, Vector*, Vector*, Vector*, double*, double*, Vector*, Vector*, int*, int*, double*, double*, int*, int*, Vector*, int*, int*, Vector*)
[0:10] namd3 0xaa4b9c GlobalMasterServer::callClients()
[0:11] namd3 0xaa6773 GlobalMasterServer::recvData(ComputeGlobalDataMsg*)
[0:12] namd3 0x87392f ComputeMgr::sendComputeGlobalData(ComputeGlobalDataMsg*)
[0:13] namd3 0x851cb4 ComputeGlobal::sendData()
[0:14] namd3 0x854748 ComputeGlobal::recvResults(ComputeGlobalResultsMsg*)
[0:15] namd3 0x8533eb ComputeGlobal::doWork()
[0:16] namd3 0xc1c16b
[0:17] namd3 0xc39184 Sequencer::integrate_CUDA_SOA(int)
[0:18] namd3 0xc3975a Sequencer::algorithm()
[0:19] namd3 0x10c1fb5 CthStartThread
[0:20] namd3 0x10c21ff make_fcontext
[0] Stack Traceback:
[0:0] namd3 0x10ff32e
[0:1] namd3 0x11003ce LrtsAbort(char const*)
[0:2] namd3 0x1100460 CmiAbortHelper(char const*, char const*, char const*, int, int)
[0:3] namd3 0x110055d
[0:4] namd3 0x7b7543
[0:5] namd3 0xf218aa colvarmodule::error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)
[0:6] namd3 0xe2c7fc colvar::collect_cvc_values()
[0:7] namd3 0xe2d630 colvar::collect_cvc_data()
[0:8] namd3 0xf213a4 colvarmodule::calc_colvars()
[0:9] namd3 0xf268a0 colvarmodule::calc()
[0:10] namd3 0xac5973 colvarproxy_namd::calculate()
[0:11] namd3 0xaa0fb2 GlobalMaster::processData(int*, int*, Vector*, Vector*, Vector*, double*, double*, Vector*, Vector*, int*, int*, double*, double*, int*, int*, Vector*, int*, int*, Vector*)
[0:12] namd3 0xaa4b9c GlobalMasterServer::callClients()
[0:13] namd3 0xaa6773 GlobalMasterServer::recvData(ComputeGlobalDataMsg*)
[0:14] namd3 0x87392f ComputeMgr::sendComputeGlobalData(ComputeGlobalDataMsg*)
[0:15] namd3 0x851cb4 ComputeGlobal::sendData()
[0:16] namd3 0x854748 ComputeGlobal::recvResults(ComputeGlobalResultsMsg*)
[0:17] namd3 0x8533eb ComputeGlobal::doWork()
[0:18] namd3 0xc1c16b
[0:19] namd3 0xc39184 Sequencer::integrate_CUDA_SOA(int)
[0:20] namd3 0xc3975a Sequencer::algorithm()
[0:21] namd3 0x10c1fb5 CthStartThread
[0:22] namd3 0x10c21ff make_fcontextThis error is present after restart my simulation from 5th o 6th times , I don't have idea as fix it. Please I need help.
jhenin commented
Hi, the output messages that you pasted include two separate warnings about PBC wrapping. Have you checked that this is not the cause of the problem?
groponp commented
Hi Prof Jerome, I have been let off the wrap All option, and it is running ok now. Thanks so much.