Re: NAMD Configuration file error

From: 김민재 (kjh950429_at_gmail.com)
Date: Thu Mar 07 2019 - 10:23:14 CST

Thanks!
Line 26 contained some syntactical errors, and job started running after I
deleted the errors.

On Fri, Mar 8, 2019 at 1:03 AM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> In that directory, what do you get when you grep for the ++++? Or what is
> on line 26 of 1ca2_min.conf like the error message is telling you? I've
> never seen this before, so I suspect its something you added into your
> configuration file by mistake that is confusing the parser.
>
> -Josh
>
>
>
> On 2019-03-06 23:35:44-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Hi everyone
> I am trying run a MD simulation on namd (a single node operation on a
> supercomputer.) However, I keep getting the following two error messages:
> Charm++: standalone mode (not using charmrun)
> Converse/Charm++ Commit ID:
> v6.8.2-0-g26d4bd8-namd-charm-6.8.2-build-2018-Jan-11-30463
> Warning> Randomization of virtual memory (ASLR) is turned on in the
> kernel, thread migration may not work! Run 'echo 0 >
> /proc/sys/kernel/randomize_va_space' as root to disable it, or try running
> with '+isomalloc_sync'.
> Warning> net-* deprecated (Charm >= 6.8.0), please use verbs-*
> Charm++> scheduler running in netpoll mode.
> Charm++ communication thread will sleep due to single-process run.
> CharmLB> Load balancer assumes all CPUs are same.
> Charm++> cpu affinity enabled.
> Charm++> Running on 1 unique compute nodes (32-way SMP).
> Charm++> cpu topology info is gathered in 0.001 seconds.
> Info: Built with CUDA version 9010
> Did not find +devices i,j,k,... argument, using all
> Pe 5 physical rank 5 will use CUDA device of pe 4
> Pe 7 physical rank 7 will use CUDA device of pe 8
> Pe 11 physical rank 11 will use CUDA device of pe 12
> Pe 1 physical rank 1 will use CUDA device of pe 2
> Pe 6 physical rank 6 will use CUDA device of pe 4
> Pe 0 physical rank 0 will use CUDA device of pe 2
> Pe 9 physical rank 9 will use CUDA device of pe 8
> Pe 3 physical rank 3 will use CUDA device of pe 2
> Pe 13 physical rank 13 will use CUDA device of pe 12
> Pe 10 physical rank 10 will use CUDA device of pe 8
> Pe 12 physical rank 12 binding to CUDA device 3 on c37.chundoong: 'GeForce
> GTX 1080' Mem: 8119MB Rev: 6.1 PCI: 0:84:0
> Pe 2 physical rank 2 binding to CUDA device 0 on c37.chundoong: 'GeForce
> GTX 1080' Mem: 8119MB Rev: 6.1 PCI: 0:2:0
> Pe 8 physical rank 8 binding to CUDA device 2 on c37.chundoong: 'GeForce
> GTX 1080' Mem: 8119MB Rev: 6.1 PCI: 0:83:0
> Pe 4 physical rank 4 binding to CUDA device 1 on c37.chundoong: 'GeForce
> GTX 1080' Mem: 8119MB Rev: 6.1 PCI: 0:3:0
> Info: NAMD 2.13 for Linux-x86_64-ibverbs-smp-CUDA
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: for updates, documentation, and support information.
> 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 60800 for
> net-linux-x86_64-ibverbs-smp-iccstatic
> Info: Built Fri Nov 9 14:45:54 CST 2018 by jim on ganymede.ks.uiuc.edu
> Info: 1 NAMD 2.13 Linux-x86_64-ibverbs-smp-CUDA 14 c37.chundoong
> user330
> Info: Running on 14 processors, 1 nodes, 1 physical nodes.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 2.84055 s
> CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level
> notification) but not using node-level queue
> Info: 1239.88 MB of memory in use based on /proc/self/stat
> Info: Configuration file is ./1ca2_min.conf
> Info: Changed directory to .
> TCL: tried before startup to read config file parameter that was not set
> FATAL ERROR: tried before startup to read config file parameter that was
> not set
> while executing
> "++++"
> (file "1ca2_min.conf" line 26)
> [0] Stack Traceback:
> [0:0] [0x4fc92c]
> [0:1] [0x519450]
> [0:2] __libc_start_main+0xf5 [0x7fed1e106b15]
> [0:3] [0x4124e9]
> [0] Stack Traceback:
> [0:0] [0x4fc92c]
> [0:1] [0x519450]
> [0:2] __libc_start_main+0xf5 [0x7fed1e106b15]
> [0:3] [0x4124e9]
> Abort (core dumped)
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
> Process name: [[10251,1],0]
> Exit code: 134
> --------------------------------------------------------------------------
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: tried before startup to read config file parameter
> that was not set
> while executing
> "++++"
> (file "1ca2_min.conf" line 26)
> Charm++ fatal error:
> FATAL ERROR: tried before startup to read config file parameter that was
> not set
> while executing
> "++++"
> (file "1ca2_min.conf" line 26)
> The bash script that I am running is: ./dir/namd2 +p14 +setcpuaffiinity
> ./config
> I am running the job in the same directory that my configuration file is
> in. How can I resolve this error?
> Thanks
>
>

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