From: Belkin, Maxim (mbelkin_at_illinois.edu)
Date: Tue Nov 03 2015 - 10:53:53 CST
Hm... I’d use something like:
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: Tue Dec 27 2016 - 23:21:30 CST
set INPUTFILE [file tail [pwd]]
Maxim
On Oct 29, 2015, at 20:06, Bryan Roessler <roessler_at_uab.edu<mailto:roessler_at_uab.edu>> wrote:
Thanks guys, I figured out a workaround just as you posted.
Josh, the basename is a shell command, not a variable. For whatever reason it will return the correct result but not store it in the variable. I am guessing that Axel's answer is the likely culprit.
Both of your answers will be helpful moving forward.
Thanks again,
Bryan
Bryan Roessler | Graduate Research Assistant
UAB | The University of Alabama at Birmingham
uab.edu/cmdb<http://uab.edu/cmdb>
Knowledge that will change your world
On Thu, Oct 29, 2015 at 7:45 PM, Josh Vermaas <vermaas2_at_illinois.edu<mailto:vermaas2_at_illinois.edu>> wrote:
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/
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