From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Nov 05 2014 - 02:54:43 CST
Hi Leili,
This is indeed a bug that is fixed in the current codebase. You can get the
fix by compiling the current CVS version of NAMD (or using a nightly
build), or downloading the updated colvars code from
https://github.com/colvars/colvars/ and recompiling.
I don't know if you actually need the colvar velocities for your analysis.
If not, an immediate workaround is to disable the "outputVelocity" option.
Best,
Jerome
On 5 November 2014 05:44, Leili Zhang <livingwater9986_at_gmail.com> wrote:
> Dear all:
>
> I recently compiled NAMD-2.10b1 for Linux-x86_64-MPI. I ran normal MD
> simulations perfectly fine with 16-128 cores of CPU. However when I tried
> to start metadynamics simulations, I got the following error messages:
>
> ...
> colvars: Collective variables biases initialized, 1 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables module initialized.
> colvars:
> ----------------------------------------------------------------------
> Info: Startup phase 10 took 0.015816 s, 381.293 MB of memory in use
> Info: Startup phase 11 took 0.000250816 s, 381.293 MB of memory in use
> Info: useSync: 1 useProxySync: 0
> Info: Startup phase 12 took 0.000249147 s, 381.293 MB of memory in use
> Info: Finished startup at 2.20578 s, 381.293 MB of memory in use
>
> TCL: Running for 10000000 steps
> colvars: Error: NAMD does not have yet a way to communicate atom
> velocities to the colvars.
> colvars: If this error message is unclear, try recompiling with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
> : Success
> [0] Stack Traceback:
> [0:0] _Z8NAMD_errPKc+0xde [0x61345e]
> [0:1] _ZN16colvarproxy_namd11fatal_errorERKSs+0x52 [0xa67232]
> [0:2] _ZN12colvarmodule4atom13read_velocityEv+0x2c [0xa631ac]
> [0:3] _ZN12colvarmodule10atom_group15read_velocitiesEv+0x1fc [0xa2d04c]
> [0:4] _ZN6colvar4calcEv+0x11a [0x9ee14a]
> [0:5] _ZN12colvarmodule4calcEv+0x55 [0x9bff85]
> [0:6] _ZN16colvarproxy_namd9calculateEv+0x5e2 [0xa64be2]
> [0:7]
> _ZN12GlobalMaster11processDataEPiS0_P6VectorS2_S2_PdS3_S0_S0_S2_S0_S0_S2_+0x6e
> [0x9979be]
> [0:8] _ZN18GlobalMasterServer11callClientsEv+0xcfc [0x99a48c]
> [0:9] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x67c
> [0x998eac]
> [0:10] _Z15_processHandlerPvP11CkCoreState+0x705 [0xcb5da5]
> [0:11] CsdScheduler+0x47d [0xe15bdd]
> [0:12] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x2c5 [0xba44d5]
> [0:13] TclInvokeStringCommand+0x88 [0xe712a8]
> [0:14] [0xe73ec7]
> [0:15] [0xe752e2]
> [0:16] Tcl_EvalEx+0x16 [0xe75b06]
> [0:17] Tcl_FSEvalFileEx+0x151 [0xed7cb1]
> [0:18] Tcl_EvalFile+0x2e [0xed7e6e]
> [0:19] _ZN9ScriptTcl4loadEPc+0xf [0xba126f]
> [0:20] main+0x3e7 [0x617ac7]
> [0:21] __libc_start_main+0xfd [0x300081ecdd]
> [0:22] [0x57ccf9]
>
> The input files worked also fine with NAMD-2.9 on, say, gordon cluster or
> stampede. Unfortunately I cannot successfully compile NAMD-2.9 on our
> current cluster after several tries. So I cannot say..
>
> Thanks in advance for any advices!
>
> Leili
>
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