VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Jun 01 2015 - 01:49:30 CDT

Hi John:
Following your last suggestion, now I see bigdcd loading and loaded, while
rmsd.tcl centermass.tcl and rgyr.tcl work fine with all my dcd files at
the IBM cluster. However, I must say that I have now used a fresh copy of
bigdcd.tcl, so that I can't rule out that what I used before was a
corrupted file (although, at the naked eye, it contained all that it
should).

thanks a lot

francesco

On Mon, Jun 1, 2015 at 12:51 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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: 516Ā
> > 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 Ā (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,
> > Ā It looks to me as through your script is failing to load
> bigdcd.tcl,
> > and that is why it is aborting.Ā 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,
> > Ā John Stone
> > Ā [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 } {
> > >Ā Ā global ref sel all outfile
> > >Ā Ā $all move [measure fit $ref $sel]
> > >Ā Ā puts "$frame: [measure rgyr $sel]"
> > >Ā Ā puts $outfile "[measure rgyr $sel]"
> > >Ā }
> > > 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)Ā Ā Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > > Info)Ā Ā 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 K40mĀ Ā Ā Ā Ā 15 SM_3.5 @ 0.75 GHz, 11GB RAM,
> KTO,
> > AE2, ZCP
> > > Info) [1] Tesla K40mĀ Ā Ā Ā Ā 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)Ā Ā Atoms: 187233
> > > Info)Ā Ā Bonds: 131246
> > > Info)Ā Ā Angles: 0Ā Dihedrals: 0Ā Impropers: 0Ā Cross-terms:
> 0
> > > Info)Ā Ā Bondtypes: 0Ā Angletypes: 0Ā Dihedraltypes: 0Ā
> > Impropertypes: 0
> > > Info)Ā Ā Residues: 57547
> > > Info)Ā Ā Waters: 56031
> > > Info)Ā Ā Segments: 37
> > > Info)Ā Ā Fragments: 56371Ā Ā Protein: 4Ā Ā 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/Ā Ā Ā Ā Ā Ā 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/
>