VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun May 31 2015 - 17:51:52 CDT

Francesco,
  Add some code to the top and bottom of your bigdcd.tcl script to make sure
that it is actually loading correctly, e.g. like this:
  puts "loading bigdcd..."
[... to the end]
  puts "bigdcd loaded..."

If you see both messages, then it should have loaded the bigdcd.tcl
script correctly, and there shouldn't have been any errors. On the
other hand, if either or both are missing when you run, that would
indicate there's something going wrong there, and that would explain
why your later calls to the procs within bigdc are failing.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 30, 2015 at 07:30:29PM +0200, Francesco Pietra wrote:
> Hi John:
> actually, bigdcd.tcl is in the working directory. The same when working
> directly on my computer. I failed to mention that.
>
> In what I reported here, I was at a computing node. Thereafter I did the
> same at a graphical node, i.e., by raising a graphical terminal. Same
> problem.
>
> The cluster is
>
> Model: IBM NeXtScale
> Architecture: Linux Infiniband Cluster
>
> Nodes: 516Â
> Processors: 2 8-cores Intel Haswell 2.40 GHz per node
> Cores: 16 cores/node, 8256 cores in total
> GPU: 2 Intel Phi 7120p per node on 384 nodes  (768 in total)
> RAM: 128 GB/node, 8 GB/core
> Internal Network: Infiniband with 4x QDR switches
> Disk Space: 2.000 TB of local scratch
> Peak Performance: 1.000 TFlop/s (to be defined)
>
> Operating system: CentOS 7.0
>
> For remote visualization (graphical terminal)
> 3 nodes with Intel Xeon E5 2670 v2 @ 2.5Ghz, 128GB, 2 GPU Nvidia K40
> (different configurations available with different quantity of memory and
> number of cores)
>
> which I found to work nicely with both VMD and CHIMERA
> francesco
> On Sat, May 30, 2015 at 5:41 PM, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â It looks to me as through your script is failing to load bigdcd.tcl,
> and that is why it is aborting. I would suggest that you put the
> bigdcd.tcl script in the working directory, or that ou modify your code
> to use the full pathname to the bigdcd.tcl script.
>
> Cheers,
> Â John Stone
> Â [2]vmd_at_ks.uiuc.edu
>
> On Sat, May 30, 2015 at 05:19:32PM +0200, Francesco Pietra wrote:
> > Hello:
> >
> > I could calculate the radius of gyration on my computer (VMD 1.9.1)
> with
> > short, test files, following command
> >
> > vmd -e rgyr.tcl -dispdev none > rgyr_npt35.tx
> >
> > The same tlc script failed to perform on a long file at the computing
> > center, following commands
> >
> > module load profile/advanced vmd
> >
> > vmd -e rgyr.tcl -dispdev none > rgyr_npt35.txt
> >
> >
> >
> > The tlc script reads:
> >
> > # calculates radius of gyration using bigdcd
> >
> > # run with vmd in text mode
> > #
> >
> > source bigdcd.tcl
> >
> > proc gyration { frame } {
> >Â Â global ref sel all outfile
> >Â Â $all move [measure fit $ref $sel]
> >Â Â puts "$frame: [measure rgyr $sel]"
> >Â Â puts $outfile "[measure rgyr $sel]"
> >Â }
> > set mol [mol addfile XAN_O2-out_watbox_isotonic.pdb type pdb waitfor
> all]
> > set all [atomselect $mol all]
> > set ref [atomselect $mol "protein and backbone and noh" frame 0]
> > set sel [atomselect $mol "protein and backbone and noh"]
> > set outfile [open gyration.dat w]
> > bigdcd gyration dcd npt-35.dcd
> > bigdcd_wait
> > close $outfile
> >
> >
> > Permission for the tcl script
> >
> > -rw-r--r--
> >
> > I also tried by giving execute permission, although it should be
> unnecessary
> >
> > -rwxr-xr-x
> >
> >
> > The wrong rgyr_npt35.txt from the computing center reads:
> >
> > Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> > Info) [3]http://www.ks.uiuc.edu/Research/vmd/
> > Info) Email questions and bug reports to [4]vmd_at_ks.uiuc.edu
> > Info) Please include this reference in published work using VMD:
> > Info)Â Â Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > Info)Â Â Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > Info) -------------------------------------------------------------
> > Info) Multithreading available, 16 CPUs detected.
> > Info) Free system memory: 115938MB (90%)
> > Info) Creating CUDA device pool and initializing hardware...
> > Info) Detected 2 available CUDA accelerators:
> > Info) [0] Tesla K40m     15 SM_3.5 @ 0.75 GHz, 11GB RAM, KTO,
> AE2, ZCP
> > Info) [1] Tesla K40m     15 SM_3.5 @ 0.75 GHz, 11GB RAM, KTO,
> AE2, ZCP
> > Info) Detected 2 available TachyonL/OptiX ray tracing accelerators
> > Info) Dynamically loaded 2 plugins in directory:
> > Info)
> /cineca/prod/tools/vmd/1.9.2/binary/lib/vmd/plugins/LINUXAMD64/molfile
> > too many nested evaluations (infinite loop?)
> > Info) Using plugin pdb for structure file
> XAN_O2-out_watbox_isotonic.pdb
> > Info) Using plugin pdb for coordinates from file
> > XAN_O2-out_watbox_isotonic.pdb
> > Info) Determining bond structure from distance search ...
> > Info) Finished with coordinate file
> UOX_XAN_O2-out_watbox_isotonic.pdb.
> > Info) Analyzing structure ...
> > Info)Â Â Atoms: 187233
> > Info)Â Â Bonds: 131246
> > Info)Â Â Angles: 0Â Dihedrals: 0Â Impropers: 0Â Cross-terms: 0
> > Info)Â Â Bondtypes: 0Â Angletypes: 0Â Dihedraltypes: 0Â
> Impropertypes: 0
> > Info)Â Â Residues: 57547
> > Info)Â Â Waters: 56031
> > Info)Â Â Segments: 37
> > Info)Â Â Fragments: 56371Â Â Protein: 4Â Â Nucleic: 0
> > 0
> > atomselect0
> > atomselect1
> > atomselect2
> > file28
> > invalid command name "bigdcd"
> > invalid command name "bigdcd_wait"
> > vmd > Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> > Info) Exiting normally.
> >
> > I wonder whether
> > means that the plugins are not loaded.
> >
> >
> > The same failure was met with related tcl scripts for calculationg the
> > center of mass and the rmsd, both running correctly on my computer.
> >
> > Thanks for advice
> > francesco pietra
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [5]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: [6]217-244-3349
> [7]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/Research/vmd/
> 4. mailto:vmd_at_ks.uiuc.edu
> 5. http://www.ks.uiuc.edu/~johns/
> 6. file:///tmp/tel:217-244-3349
> 7. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center 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/