From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat May 30 2015 - 12:30:29 CDT

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*: 516
*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 <johns_at_ks.uiuc.edu> wrote:

> Hi,
> 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,
> John Stone
> 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 } {
> > global ref sel all outfile
> > $all move [measure fit $ref $sel]
> > puts "$frame: [measure rgyr $sel]"
> > puts $outfile "[measure rgyr $sel]"
> > }
> > 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) 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: 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) Atoms: 187233
> > Info) Bonds: 131246
> > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > Info) Residues: 57547
> > Info) Waters: 56031
> > Info) Segments: 37
> > Info) Fragments: 56371 Protein: 4 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>