VMD-L Mailing List

From: Wang Yi (dexterwy_at_gmail.com)
Date: Wed Jul 18 2012 - 10:31:17 CDT

Actually, it didn't...
___________________________

Yi (Yves) Wang
Duke University

On 2012-7-18, at 上午11:23, John Stone wrote:

>
> Hi,
> Okay, I see your problem:
>> Invalid axes location: on
>
> You have errors in your .vmdrc or in the main .vmdrc (if you edited it)
> which are causing the Tcl interpreter to skip subsequent script evaluations.
> I think you need to look at your .vmdrc and any other scripts it calls and
> fix that problem. Once that is fixed, I would expect your problems to go
> away.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jul 18, 2012 at 11:17:52AM -0400, Wang Yi wrote:
>> That's a good idea and it helped me find the real problem:
>> not a single line of the script was executed by vmd.
>> I made a test script:
>> puts "Test"
>> set test_var [expr 1+100]
>> exit
>> Also got no output. The program started and exited "normally".
>> What also appears odd, is that the program finds 16 CPUs always. Probably
>> 8core+hyperthreading. But even after I submit the job as a single CPU job,
>> it still finds 16 CPUs.
>> ___________________________
>> Yi (Yves) Wang
>> Duke University
>>
>> On 2012-7-18, at a:,*aa**11:04, John Stone wrote:
>>
>> Hi,
>> I find it odd that you're not getting any output from the namdenergy
>> plugin in the console at all. If at the end of your script, you just
>> run "namdenergy" with no parameters, I would expect it to print out a
>> bunch of usage information to the console. What happens if you do that
>> on your cluster? Do you get any console output, or does it just return
>> as before?
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Wed, Jul 18, 2012 at 10:55:37AM -0400, Wang Yi wrote:
>>
>> Hi John,
>>
>> Thanks for your reply. Yes we have NAMD on the cluster. I invoked
>> the same
>>
>> binary executable file that we use to do routine NAMD simulations.
>> And
>>
>> what's odd is that there's no error message. The namdEnergy appears
>> to be
>>
>> version 1.3. I will try the latest version next. Here's all it gave
>> me:
>>
>> Thus no job control in this shell.
>>
>> ================================================
>>
>> JOB STARTED ON: Wed Jul 18 10:48:43 EDT 2012
>>
>> ================================================
>>
>> Machine: dbchem-n44.dscr.duke.local
>>
>> Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)
>>
>> Info) http://www.ks.uiuc.edu/Research/vmd/
>>
>> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>>
>> Info) Please include this reference in published work using VMD:
>>
>> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
>>
>> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
>>
>> Info) -------------------------------------------------------------
>>
>> Info) Multithreading available, 16 CPUs detected.
>>
>> Info) Free system memory: 30701MB (95%)
>>
>> Info) No CUDA accelerator devices available.
>>
>> Info) Dynamically loaded 2 plugins in directory:
>>
>> Info) /home/dbchem/yw34/lib/vmd/plugins/LINUXAMD64/molfile
>>
>> Invalid axes location: on
>>
>> Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)
>>
>> Info) Exiting normally.
>>
>> Here's the command to run VMD:
>>
>> vmd -dispdev text -e ~/bin/namd_intE.tcl -args /home/XXXXX/xxxx.psf
>>
>> /home/XXXXX/xxxx.dcd /home/XXXXX/par_all36_cgenff.prm
>>
>> /home/XXXXXX/namd/NAMD_2.8b1_Source_CentOS5/Linux-x86_64-g++/namd2
>>
>> /netscratch/yw34/namdEng /home/XXXXX/tmp3.eng
>>
>> All paths are absolute paths. And the same command runs fine when I
>> run it
>>
>> on the login terminal.
>>
>> Here's the content of namd_intE.tcl
>>
>> package require namdenergy
>>
>> set dcd_file_name [lindex $argv 1]
>>
>> set psf_file_name [lindex $argv 0]
>>
>> set par_file_name [lindex $argv 2]
>>
>> set bin_file_name [lindex $argv 3]
>>
>> set temp_file_prefix [lindex $argv 4]
>>
>> set output_file [lindex $argv 5]
>>
>> puts $argv
>>
>> mol load psf $psf_file_name dcd $dcd_file_name
>>
>> set host [atomselect top "resname CB7"]
>>
>> set guest [atomselect top "resname NC4"]
>>
>> namdenergy -vdw -elec -sel $host $guest -ofile $output_file -par
>>
>> $par_file_name -exe $bin_file_name -diel 1.0 -switch 16.0 -cutoff
>> 18.0
>>
>> -tempname $temp_file_prefix
>>
>> exit
>>
>> Thanks.
>>
>> ___________________________
>>
>> Yi (Yves) Wang
>>
>> Duke University
>>
>> On 2012-7-18, at a:,*aa**10:46, John Stone wrote:
>>
>> Hi,
>>
>> Do you have NAMD installed on your cluster? The namdenergy
>> plugin
>>
>> works
>>
>> by launching NAMD. If NAMD is either unavailable or has some
>> unexpected
>>
>> problem launching on the cluster, then the namdenergy plugin would
>> not
>>
>> succeed, however I would normally expect it to emit some kind of
>> warning
>>
>> or error messages to the VMD console or to the Tk console during
>> the
>>
>> attempted
>>
>> run. What output does namdenergy give you when you run it?
>>
>> Cheers,
>>
>> John Stone
>>
>> vmd_at_ks.uiuc.edu
>>
>> On Tue, Jul 17, 2012 at 11:28:06PM -0400, Wang Yi wrote:
>>
>> Dear VMD users,
>>
>> I was trying to use the text mode of VMD to calculate complex
>>
>> interaction
>>
>> energies from a series of long trajectories. I decided to
>> submit the
>>
>> job
>>
>> to the cluster and let it run in batch mode. But I found an
>>
>> interesting
>>
>> problem -- the "namdenergy" command doesn't run at all when I
>> run
>>
>> the job
>>
>> remotely.
>>
>> First, I did include "package require namdenergy".
>>
>> Secondly, the same tcl script, runs perfectly when I run it on
>> the
>>
>> command
>>
>> line of the login-terminal.
>>
>> Third, as long as the script is submitted to a remote computer
>> node,
>>
>> VMD
>>
>> seems to have skipped namdenergy. No error message, program
>> exited
>>
>> normally.
>>
>> Has anyone seen this kind of behavior before?
>>
>> Thanks.
>>
>> ___________________________
>>
>> Yi (Yves) Wang
>>
>> Duke University
>>
>> --
>>
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>
>> Beckman Institute for Advanced Science and Technology
>>
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>
>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078