From: Bryan Roessler (roessler_at_uab.edu)
Date: Thu Oct 29 2015 - 19:24:53 CDT
Hello,
I am having issues with getting my configuration file to work.
My configuration file has a simple line to set the input name for the
coordinate files from the directory name:
set INPUTNAME [basename [pwd]]
Is this disallowed?
Charm++: standalone mode (not using charmrun)
> Converse/Charm++ Commit ID:
> v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
> Warning> Randomization of stack pointer is turned on in kernel, thread
> migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space'
> as root to disable it, or try run with '+isomalloc_sync'.
> CharmLB> Load balancer assumes all CPUs are same.
> Charm++> Running on 1 unique compute nodes (56-way SMP).
> Charm++> cpu topology info is gathered in 0.024 seconds.
> Info: Built with CUDA version 6000
> Pe 41 physical rank 41 will use CUDA device of pe 48
> Did not find +devices i,j,k,... argument, using all
> Pe 6 physical rank 6 will use CUDA device of pe 16
> Pe 17 physical rank 17 will use CUDA device of pe 16
> Pe 3 physical rank 3 will use CUDA device of pe 16
> Pe 4 physical rank 4 will use CUDA device of pe 16
> Pe 0 physical rank 0 will use CUDA device of pe 16
> Pe 36 physical rank 36 will use CUDA device of pe 32
> Pe 52 physical rank 52 will use CUDA device of pe 48
> Pe 30 physical rank 30 will use CUDA device of pe 32
> Pe 15 physical rank 15 will use CUDA device of pe 16
> Info: NAMD 2.10 for Linux-x86_64-multicore-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 60601 for multicore-linux64-iccstatic
> Info: Built Tue Dec 9 15:36:34 CST 2014 by jim on despina.ks.uiuc.edu
> Pe 1 physical rank 1 will use CUDA device of pe 16
> Info: 1 NAMD 2.10 Linux-x86_64-multicore-CUDA 55
> phy145.physiology.uab.edu bryan
> Info: Running on 55 processors, 1 nodes, 1 physical nodes.
> Info: CPU topology information available.
> Pe 10 physical rank 10 will use CUDA device of pe 16
> Info: Charm++/Converse parallel runtime startup completed at 2.00478 s
> Pe 50 physical rank 50 will use CUDA device of pe 48
> Pe 40 physical rank 40 will use CUDA device of pe 48
> Pe 13 physical rank 13 will use CUDA device of pe 16
> Pe 42 physical rank 42 will use CUDA device of pe 48
> Pe 23 physical rank 23 will use CUDA device of pe 32
> Pe 5 physical rank 5 will use CUDA device of pe 16
> Pe 31 physical rank 31 will use CUDA device of pe 32
> Pe 33 physical rank 33 will use CUDA device of pe 32
> Pe 24 physical rank 24 will use CUDA device of pe 32
> Pe 38 physical rank 38 will use CUDA device of pe 48
> Pe 49 physical rank 49 will use CUDA device of pe 48
> Pe 8 physical rank 8 will use CUDA device of pe 16
> Pe 29 physical rank 29 will use CUDA device of pe 32
> Pe 34 physical rank 34 will use CUDA device of pe 32
> Pe 19 physical rank 19 will use CUDA device of pe 32
> Pe 11 physical rank 11 will use CUDA device of pe 16
> Pe 27 physical rank 27 will use CUDA device of pe 32
> Pe 25 physical rank 25 will use CUDA device of pe 32
> Pe 2 physical rank 2 will use CUDA device of pe 16
> Pe 14 physical rank 14 will use CUDA device of pe 16
> Pe 44 physical rank 44 will use CUDA device of pe 48
> Pe 37 physical rank 37 will use CUDA device of pe 48
> Pe 28 physical rank 28 will use CUDA device of pe 32
> Pe 35 physical rank 35 will use CUDA device of pe 32
> Pe 54 physical rank 54 will use CUDA device of pe 48
> Pe 7 physical rank 7 will use CUDA device of pe 16
> Pe 43 physical rank 43 will use CUDA device of pe 48
> Pe 26 physical rank 26 will use CUDA device of pe 32
> Pe 9 physical rank 9 will use CUDA device of pe 16
> Pe 46 physical rank 46 will use CUDA device of pe 48
> Pe 12 physical rank 12 will use CUDA device of pe 16
> Pe 51 physical rank 51 will use CUDA device of pe 48
> Pe 20 physical rank 20 will use CUDA device of pe 32
> Pe 18 physical rank 18 will use CUDA device of pe 16
> Pe 45 physical rank 45 will use CUDA device of pe 48
> Pe 53 physical rank 53 will use CUDA device of pe 48
> Pe 47 physical rank 47 will use CUDA device of pe 48
> Pe 22 physical rank 22 will use CUDA device of pe 32
> Pe 39 physical rank 39 will use CUDA device of pe 48
> Pe 21 physical rank 21 will use CUDA device of pe 32
> Pe 48 physical rank 48 binding to CUDA device 2 on
> phy145.physiology.uab.edu: 'GeForce GTX 980' Mem: 4095MB Rev: 5.2
> Pe 32 physical rank 32 binding to CUDA device 1 on
> phy145.physiology.uab.edu: 'GeForce GTX 980' Mem: 4095MB Rev: 5.2
> Pe 16 physical rank 16 binding to CUDA device 0 on
> phy145.physiology.uab.edu: 'GeForce GTX 980' Mem: 4095MB Rev: 5.2
> Info: 31.8125 MB of memory in use based on /proc/self/stat
> Info: Configuration file is sim.conf
> Info: Working in the current directory
> /home/bryan/Desktop/Jobs/15_10_29/ALL
> TCL: Suspending until startup complete.
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: basename
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> [0] Stack Traceback:
> [0:0] CmiAbort+0x5f [0xd8fd4f]
> [0:1] _Z8NAMD_diePKc+0x62 [0x66669a]
> [0:2] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0xa3
> [0xba88b1]
> [0:3] _ZN9NamdState14configListInitEP10ConfigList+0x3e6 [0xae7666]
> [0:4] _ZN9ScriptTcl9initcheckEv+0xb0 [0xb8012c]
> [0:5] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x36 [0xb7b0dc]
> [0:6] TclInvokeStringCommand+0x88 [0xe207e8]
> [0:7] [0xe23300]
> [0:8] [0xe246e6]
> [0:9] Tcl_EvalEx+0x16 [0xe24ec6]
> [0:10] Tcl_FSEvalFileEx+0x151 [0xe86cd1]
> [0:11] Tcl_EvalFile+0x2e [0xe86e8e]
> [0:12] _ZN9ScriptTcl4loadEPc+0x10 [0xb797bc]
> [0:13] _Z18after_backend_initiPPc+0x3e5 [0x66b3dd]
> [0:14] main+0x3a [0x66afc2]
> [0:15] __libc_start_main+0xf0 [0x7fd255a30700]
> [0:16] _ZNSt8ios_base4InitD1Ev+0x52 [0x5da58a]
> [0] Stack Traceback:
> [0:0] [0xd90b45]
> [0:1] CmiAbort+0x9d [0xd8fd8d]
> [0:2] _Z8NAMD_diePKc+0x62 [0x66669a]
> [0:3] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0xa3
> [0xba88b1]
> [0:4] _ZN9NamdState14configListInitEP10ConfigList+0x3e6 [0xae7666]
> [0:5] _ZN9ScriptTcl9initcheckEv+0xb0 [0xb8012c]
> [0:6] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x36 [0xb7b0dc]
> [0:7] TclInvokeStringCommand+0x88 [0xe207e8]
> [0:8] [0xe23300]
> [0:9] [0xe246e6]
> [0:10] Tcl_EvalEx+0x16 [0xe24ec6]
> [0:11] Tcl_FSEvalFileEx+0x151 [0xe86cd1]
> [0:12] Tcl_EvalFile+0x2e [0xe86e8e]
> [0:13] _ZN9ScriptTcl4loadEPc+0x10 [0xb797bc]
> [0:14] _Z18after_backend_initiPPc+0x3e5 [0x66b3dd]
> [0:15] main+0x3a [0x66afc2]
> [0:16] __libc_start_main+0xf0 [0x7fd255a30700]
> [0:17] _ZNSt8ios_base4InitD1Ev+0x52 [0x5da58a]
Thanks,
Bryan
*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
*uab.edu/cmdb <http://uab.edu/cmdb>*
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