RE: NAMD Configuration file error

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Mar 07 2019 - 10:03:26 CST

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<http://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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