From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Oct 29 2015 - 19:45:12 CDT
Basename isn't a variable how you've written it out, so it complains
about not being able to find it. Something like this would work,
assuming basename is set somewhere beforehand:
set INPUTNAME [pwd]$basename
You might also consider using format strings if its something weird.
Note that since pwd returns the absolute rather than relative path, it
also might not do what you want, and is why I reversed the order in the
command above.
-Josh Vermaas
On 10/29/2015 07:24 PM, Bryan Roessler wrote:
> 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/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_namd_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=fjuB-HfIXWQOCUw6_GdEqUGbaplZlEp2eOa62ILba30&s=oEGw9f7sSAuIWjzTkufLk-x3Od2D-BYAWuXzfpUGEU0&e=>
> 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
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__despina.ks.uiuc.edu&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=fjuB-HfIXWQOCUw6_GdEqUGbaplZlEp2eOa62ILba30&s=8LXfiWgNn21g-TnMzaFPv5S3jtXC7uUqYxt8fhZBeIU&e=>
> 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
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__phy145.physiology.uab.edu&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=fjuB-HfIXWQOCUw6_GdEqUGbaplZlEp2eOa62ILba30&s=IsHRl_dHw6tPDp6eN8ppw5n--EleY9k84TYlQbaAaJ4&e=>
> 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
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__phy145.physiology.uab.edu&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=fjuB-HfIXWQOCUw6_GdEqUGbaplZlEp2eOa62ILba30&s=IsHRl_dHw6tPDp6eN8ppw5n--EleY9k84TYlQbaAaJ4&e=>:
> 'GeForce GTX 980' Mem: 4095MB Rev: 5.2
> Pe 32 physical rank 32 binding to CUDA device 1 on
> phy145.physiology.uab.edu
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__phy145.physiology.uab.edu&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=fjuB-HfIXWQOCUw6_GdEqUGbaplZlEp2eOa62ILba30&s=IsHRl_dHw6tPDp6eN8ppw5n--EleY9k84TYlQbaAaJ4&e=>:
> 'GeForce GTX 980' Mem: 4095MB Rev: 5.2
> Pe 16 physical rank 16 binding to CUDA device 0 on
> phy145.physiology.uab.edu
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__phy145.physiology.uab.edu&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=fjuB-HfIXWQOCUw6_GdEqUGbaplZlEp2eOa62ILba30&s=IsHRl_dHw6tPDp6eN8ppw5n--EleY9k84TYlQbaAaJ4&e=>:
> '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
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__uab.edu_cmdb&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=fjuB-HfIXWQOCUw6_GdEqUGbaplZlEp2eOa62ILba30&s=1_bZXRyYvSLc5q03Ph5x19Ugz9Lf7guPLACNS01R_6I&e=>_*
> Knowledge that will change your world
>
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