VMD-L Mailing List

From: TAE BUM LEE (taebumlee_at_gmail.com)
Date: Sun Dec 13 2009 - 12:23:03 CST

Hi,

 Here is my result for your tracking.

taebum_at_Aubie:~/Documents/NAMD-tutorial$ ls
1-1-build 2-1-rmsd 2-4-temp 2-7-echoes README
1-2-sphere 2-2-maxwell 2-5-spec-heat 3-1-pullcv common
1-3-box 2-3-energies 2-6-heat-diff 3-2-pullcf
taebum_at_Aubie:~/Documents/NAMD-tutorial$ cd 1-2-sphere/
taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$ ls
example-output ubq_ws_eq.dcd ubq_ws_eq.restart.vel.old
rmsd.dat ubq_ws_eq.log ubq_ws_eq.restart.xsc
rmsd.tcl ubq_ws_eq.restart.coor ubq_ws_eq.restart.xsc.old
ubq_ws_eq.conf ubq_ws_eq.restart.coor.old ubq_ws_eq.vel
ubq_ws_eq.coor ubq_ws_eq.restart.vel ubq_ws_eq.xsc
taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$ vmd
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
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, 2 CPUs detected.
Info) Free system memory: 721MB (72%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce FX 5700/AGP/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX PP PS GLSL(OVF)
Warning) GPU driver failed to compile shader:
Warning) /usr/local/lib/vmd/shaders/vmd
Warning) This GPU/driver is buggy, or doesn't fully implement GLSL.
Warning) Set environment variable VMDGLSLVERBOSE for more info.
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
vmd > Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
Info) Exiting normally.
taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$ vmd -debug
***
*** Running VMD in debugger, type 'run' at debugger prompt
***
GNU gdb (GDB) 7.0-ubuntu
Copyright (C) 2009 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html
>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "i486-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/local/lib/vmd/vmd_LINUX...(no debugging symbols
found)...done.
(gdb) run
Starting program: /usr/local/lib/vmd/vmd_LINUX
[Thread debugging using libthread_db enabled]
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
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, 2 CPUs detected.
Info) Free system memory: 659MB (65%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce FX 5700/AGP/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX PP PS GLSL(OVF)
Warning) GPU driver failed to compile shader:
Warning) /usr/local/lib/vmd/shaders/vmd
Warning) This GPU/driver is buggy, or doesn't fully implement GLSL.
Warning) Set environment variable VMDGLSLVERBOSE for more info.
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
vmd > psfplugin) Detected a Charmm31 PSF file
Info) Using plugin psf for structure file
/home/taebum/Documents/NAMD-tutorial/common/ubq_ws.psf
Info) Analyzing structure ...
Info) Atoms: 6682
Info) Bonds: 4871
Info) Angles: 4074 Dihedrals: 3293 Impropers: 204 Cross-terms: 74
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1893
Info) Waters: 1817
Info) Segments: 2
Info) Fragments: 1818 Protein: 1 Nucleic: 0
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file
/home/taebum/Documents/NAMD-tutorial/1-2-sphere/ubq_ws_eq.dcd
Info) Finished with coordinate file
/home/taebum/Documents/NAMD-tutorial/1-2-sphere/ubq_ws_eq.dcd.

Program received signal SIGSEGV, Segmentation fault.
0x00575f43 in strlen () from /lib/tls/i686/cmov/libc.so.6
(gdb) where
#0 0x00575f43 in strlen () from /lib/tls/i686/cmov/libc.so.6
#1 0x0819a0eb in ParseTree::eval_key(atomparser_node*, int, int*) ()
#2 0x0819ba25 in ParseTree::evaluate(int, int*) ()
#3 0x080f05cc in AtomSel::change(char const*, DrawMolecule*) ()
#4 0x080f1aa2 in atomsel_custom_singleword(void*, int, int*) ()
#5 0x0819b53c in ParseTree::eval(atomparser_node*, int, int*) ()
#6 0x0819b2b2 in ParseTree::eval(atomparser_node*, int, int*) ()
#7 0x0819ba25 in ParseTree::evaluate(int, int*) ()
#8 0x080f05cc in AtomSel::change(char const*, DrawMolecule*) ()
#9 0x080f1aa2 in atomsel_custom_singleword(void*, int, int*) ()
#10 0x0819b53c in ParseTree::eval(atomparser_node*, int, int*) ()
---Type <return> to continue, or q <return> to quit---
#11 0x0819b33d in ParseTree::eval(atomparser_node*, int, int*) ()
#12 0x0819ba25 in ParseTree::evaluate(int, int*) ()
#13 0x080f05cc in AtomSel::change(char const*, DrawMolecule*) ()
#14 0x081f800d in ?? ()
#15 0x083693d2 in TclInvokeStringCommand ()
#16 0x0836c2ad in ?? ()
#17 0x0836d713 in ?? ()
#18 0x083ed72e in ?? ()
#19 0x0836d578 in ?? ()
#20 0x0836dc9e in Tcl_EvalEx ()
#21 0x083d9663 in Tcl_FSEvalFileEx ()
---Type <return> to continue, or q <return> to quit---
#22 0x0837f4ca in ?? ()
#23 0x0836c2ad in ?? ()
#24 0x083b5050 in ?? ()
#25 0x083bcc4a in ?? ()
#26 0x0836de40 in TclEvalObjEx ()
#27 0x083f7828 in ?? ()
#28 0x0836c2ad in ?? ()
#29 0x083b5050 in ?? ()
#30 0x083bcc4a in ?? ()
#31 0x0836de40 in TclEvalObjEx ()
#32 0x0836e11b in Tcl_EvalObjEx ()
---Type <return> to continue, or q <return> to quit---
#33 0x083c5535 in ?? ()
#34 0x083c8753 in ?? ()
#35 0x0836c2ad in ?? ()
#36 0x083b5050 in ?? ()
#37 0x083f882e in TclObjInterpProcCore ()
#38 0x083f8a72 in TclObjInterpProc ()
#39 0x0836c2ad in ?? ()
#40 0x0836c4c9 in Tcl_EvalObjv ()
#41 0x083c4f36 in ?? ()
#42 0x0836c2ad in ?? ()
#43 0x0836c4c9 in Tcl_EvalObjv ()
---Type <return> to continue, or q <return> to quit---
#44 0x083c4f36 in ?? ()
#45 0x0836c2ad in ?? ()
#46 0x083b5050 in ?? ()
#47 0x083f882e in TclObjInterpProcCore ()
#48 0x083f8a72 in TclObjInterpProc ()
#49 0x0836c2ad in ?? ()
#50 0x083b5050 in ?? ()
#51 0x083f882e in TclObjInterpProcCore ()
#52 0x083f8a72 in TclObjInterpProc ()
#53 0x0836c2ad in ?? ()
#54 0x0836d713 in ?? ()
---Type <return> to continue, or q <return> to quit---
#55 0x0836dc9e in Tcl_EvalEx ()
#56 0x08336f02 in Tk_BindEvent ()
#57 0x08339328 in TkBindEventProc ()
#58 0x08340962 in Tk_HandleEvent ()
#59 0x0834112f in ?? ()
#60 0x083e7e80 in Tcl_ServiceEvent ()
#61 0x083e81b0 in Tcl_DoOneEvent ()
#62 0x0820d792 in TclTextInterp::doTkUpdate() ()
#63 0x081ccbe8 in UIText::check_event() ()
#64 0x0811022c in CommandQueue::check_events() ()
#65 0x081cdf22 in VMDApp::VMDupdate(int) ()
---Type <return> to continue, or q <return> to quit---
#66 0x081f72d5 in main ()

Regards,
TaeBum

2009/12/11 John Stone <johns_at_ks.uiuc.edu>

> Hi,
> Interesting. I suspect that the locale may be giving you problems
> for some reason, though I'm not sure why it would have any effect on
> the DCD reader plugin. Can you do me a favor and run VMD like this
> on your linux machine: vmd -debug
> That will start up gdb and from there you should be able to type "run"
> and then go through the same steps that caused you trouble previously.
> Once you get to the point where the crash occurs, type the command "where"
> into gdb, and email me the results you get. If I can figure out what's
> going on there, I might be able to give you a new plugin that fixes your
> problem.
>
> Another temporary solution for you to try is to change your
> internationalization settings to English or the "C" locale, and see
> if the problem goes away or not.
>
> Regarding background/batch processing, yes, in fact you can run VMD
> without any graphics/GUI shell in a text-only mode, and even in a
> non-interactive batch type mode. This is described in the VMD User's
> guide. Let me know if you have more questions about that.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Dec 10, 2009 at 05:42:04PM -0600, TAE BUM LEE wrote:
> > Hi,
> > The size of DCD is 784K. Physical memory is 1GB while swap memory is
> 3GB.
> > My machine has a support for Korean language and my desktop setting is
> for
> > Korean.
> > Isn't there anyway to do rmsd.tcl in background mode(command mode)? It
> is
> > not necessary to me to do in GUI mode for RMSD.dat file.
> > Regards,
> > TaeBum
> >
> > 2009/12/10 John Stone <johns_at_ks.uiuc.edu>
> >
> > Hi,
> > How large is the DCD file that you're attempting to load?
> > I'm wondering if you are running out of memory when you load
> > the DCD file. Another thought I had is that it's conceivable your
> > DCD file is corrupted in some way, but I wouldn't expect the
> behavior
> > you're seeing. How much memory does your other machine have?
> > Do you have either machine set for a non-US locale
> > (internationalization)?
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> > On Wed, Dec 09, 2009 at 04:37:42PM -0600, TAE BUM LEE wrote:
> > > Hi,
> > > I am doing tutorial from NAMD-tutorial pdf file. For rmsd
> analysis
> > after
> > > MD simulation of ubiquitin protein, I try to do call psf and
> dcd
> > followed
> > > by source rmsd.tcl in Tk console. The VMD windows are collapsed
> > abruptly
> > > with segmentation fault error message.
> > > The generated rmsd.dat doesn't have any data in it.
> > > My computer system is Ubuntu 9.10. However, the same situation
> > happen in
> > > my macbook (Intel mac with OSX 10.5).
> > > Does anybody know the solution for this error?
> > > FYI, I attach the terminal message as a scrapbook below.
> > > Thanks,
> > > TaeBum
> > > taebum_at_Aubie:~/Documents/NAMD-tutorial$ ls
> > > 1-1-build 2-1-rmsd 2-4-temp 2-7-echoes common
> > > 1-2-sphere 2-2-maxwell 2-5-spec-heat 3-1-pullcv README
> > > 1-3-box 2-3-energies 2-6-heat-diff 3-2-pullcf
> > > taebum_at_Aubie:~/Documents/NAMD-tutorial$ cd 1-2-sphere/
> > > taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$ ls
> > > example-output ubq_ws_eq.dcd ubq_ws_eq.restart.vel.old
> > > rmsd.dat ubq_ws_eq.log ubq_ws_eq.restart.xsc
> > > rmsd.tcl ubq_ws_eq.restart.coor ubq_ws_eq.restart.xsc.old
> > > ubq_ws_eq.conf ubq_ws_eq.restart.coor.old ubq_ws_eq.vel
> > > ubq_ws_eq.coor ubq_ws_eq.restart.vel ubq_ws_eq.xsc
> > > taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$ vmd
> > > Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
> > > 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, 2 CPUs detected.
> > > Info) Free system memory: 635MB (63%)
> > > Info) No CUDA accelerator devices available.
> > > Warning) Detected X11 'Composite' extension: if incorrect
> display
> > occurs
> > > Warning) try disabling this optional X server feature.
> > > Info) OpenGL renderer: GeForce FX 5700/AGP/SSE2
> > > Info) Features: STENCIL MSAA(4) MDE CVA MTX PP PS GLSL(OVF)
> > > Warning) GPU driver failed to compile shader:
> > > Warning) /usr/local/lib/vmd/shaders/vmd
> > > Warning) This GPU/driver is buggy, or doesn't fully implement
> GLSL.
> > > Warning) Set environment variable VMDGLSLVERBOSE for more info.
> > > Info) GLSL rendering mode is NOT available.
> > > Info) Textures: 2-D (4096x4096), 3-D (512x512x512),
> Multitexture
> > (4)
> > > vmd > psfplugin) Detected a Charmm31 PSF file
> > > Info) Using plugin psf for structure file
> > > /home/taebum/Documents/NAMD-tutorial/common/ubq_ws.psf
> > > Info) Analyzing structure ...
> > > Info) Atoms: 6682
> > > Info) Bonds: 4871
> > > Info) Angles: 4074 Dihedrals: 3293 Impropers: 204
> > Cross-terms: 74
> > > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0
> > Impropertypes: 0
> > > Info) Residues: 1893
> > > Info) Waters: 1817
> > > Info) Segments: 2
> > > Info) Fragments: 1818 Protein: 1 Nucleic: 0
> > > dcdplugin) detected standard 32-bit DCD file of native
> endianness
> > > dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> > > Info) Using plugin dcd for coordinates from file
> > > /home/taebum/Documents/NAMD-tutorial/1-2-sphere/ubq_ws_eq.dcd
> > > Info) Finished with coordinate file
> > > /home/taebum/Documents/NAMD-tutorial/1-2-sphere/ubq_ws_eq.dcd.
> > > Segmentation fault
> > > taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$ cat
> rmsd.dat
> > > taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$
> > > ########################################
> > > TAE BUM LEE
> > > Dept. Chem. & Biochem
> > > Auburn Univ. AL. 36849
> > > TEL.: 334-844-6912
> > > e-mail: taebumlee_at_gmail.com
> > > ########################################
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
> > --
> > ########################################
> > TAE BUM LEE
> > Dept. Chem. & Biochem
> > Auburn Univ. AL. 36849
> > TEL.: 334-844-6912
> > e-mail: taebumlee_at_gmail.com
> > ########################################
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
########################################
TAE BUM LEE
Dept. Chem. & Biochem
Auburn Univ. AL. 36849
TEL.: 334-844-6912
e-mail: taebumlee_at_gmail.com
########################################