From: Wang Yi (dexterwy_at_gmail.com)
Date: Wed Jul 18 2012 - 10:17:52 CDT

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 上午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