VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 24 2012 - 09:51:53 CDT

Vlad,
  I'm not sure how your configure script was out of date, but it's
likely that it was just a CVS sticky tag (which I explain below).
I'm glad that solved it. The issues you had with the other stuff
(vmdprefs, two missing .gif files) were because there were two
half-committed sets of changes in the plugin tree at the time
you were updating.

In general, doing a "cvs update -PAd" will help ensure that your
CVS tree is up to date, and there are no sticky tags set on a
particular version. If you do something like:
  cvs update -r vmd-1-8-7 configure
for example, that sets a so-called "sticky" tag, and if you just do a:
  cvs update
CVS will not update configure to the latest version, even though there is
a much newer version in the CVS tree. If you periodically
do a "cvs update -PAd" that will clear any old sticky tags and
ensure that you have all of the new directories and so on.
I always make it a habit to run a "cvs update -PAd" when I am
planning on working with the top of the tree and I'm not purposefully
working with a specific alternative CVS revision of some kind.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 24, 2012 at 02:15:31PM +0200, Vlad Cojocaru wrote:
> Dear John,
>
> Thanks a lot for the tip ... It looks as if the 2 lines you pointed out
> were missing in the configure script I was using and that's why the
> linking errors.
> This is strange because I checked out the configure file exactly at the
> same time with the rest of the code but since I've had a similar problem
> with the new plugin vmdprefs (which was also not present in my first
> checkout), I guess it is a limitation of the cvs checkout.
>
> Anyhow, now things work well, and indeed the problem with the jumping
> scroller disappeared, which is very nice.
>
> Maybe a nice option for the VMD CVS would be something like the "nightly
> builds" bundles of NAMD. Like this, we know we'd download a complete
> version of the CVS that should compile without troubles.
>
> Best wishes
> Vlad
>
>
> On 08/23/2012 04:41 PM, John Stone wrote:
> >Vlad,
> > I don't think there's any bug in the actual source code, as I can
> > compile
> >on several different versions of Linux and MacOS X, and multiple versions
> >of CUDA without any problems.
> >
> >Can you determine whether CUDAMarchingCubes.cu and CUDADispCmds.cu
> >were compiled on your machine? The errors you're getting are linkage
> >problems
> >that would result if CUDAMarchingCubes.cu and CUDADispCmds.cu were
> >not compiled for some reason. Is your "configure" script fully up to date?
> >This could happen if you tried to compile using an old "configure" script,
> >for example. The portion of the configure script that relates to CUDA
> >should look like this, note that CUDADispCmds.cu and CUDAMarchingCubes.cu
> >are in the list of source files, that's important:
> >
> >#######################
> ># OPTIONAL COMPONENT: NVIDIA CUDA GPU acceleration API
> ># This option enables the use of CUDA GPU acceleration functions.
> >#######################
> >$cuda_defines = "-DVMDCUDA -DMSMPOT_CUDA";
> >$cuda_dir = "";
> >$cuda_include = "";
> >$cuda_library = "";
> >$cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
> >@cuda_cc = ();
> >@cuda_cu = ('msmpot_cuda.cu',
> > 'msmpot_cuda_latcut.cu',
> > 'msmpot_cuda_shortrng.cu',
> > 'CUDABench.cu',
> > 'CUDAClearDevice.cu',
> > 'CUDADispCmds.cu',
> > 'CUDAMarchingCubes.cu',
> > 'CUDAMeasureRDF.cu',
> > 'CUDAOrbital.cu',
> > 'CUDAQuickSurf.cu',
> > 'CUDAUtil.cu',
> > 'CUDAVolCPotential.cu',
> > 'CUDAVolMapCreateILS.cu');
> >@cuda_ccpp = ();
> >@cuda_h = ('CUDAKernels.h');
> >@cuda_extra = ();
> >
> >
> >Cheers,
> > John
> >
> >On Thu, Aug 23, 2012 at 02:24:39PM +0200, Vlad Cojocaru wrote:
> >>Just in case this additional information may be useful:
> >>
> >>Compilation with gcc-4.6 and cuda-5.0.24 also fails with exactly the
> >>same error. So, it seems to me that here there is a code problem and not
> >>a compiler/cuda problem.
> >>I noticed that thee file CUDAMarchingCubes.cu was modified in the last 2
> >>days, so I will wait until a stable version of this file will be
> >>available in the CVS before trying compilation again.
> >>
> >>Best wishes
> >>Vlad
> >>
> >>On 08/23/2012 10:00 AM, Vlad Cojocaru wrote:
> >>>Dear John,
> >>>
> >>>Just to let you know that the same error I reported below, appears
> >>>when I tried compiling the CVS code updated yesterday with cuda 4.0.17
> >>>and gcc 4.3.4
> >>>With exactly the same combination, vmd-19.1 compiled without any
> >>>problem shortly after its release.
> >>>
> >>>Also, sorry in my previous mail I forgot to send you the output of
> >>>"uname -a". Here it is
> >>>Linux kratos 3.1.10-1.16-desktop #1 SMP PREEMPT Wed Jun 27 05:21:40
> >>>UTC 2012 (d016078) x86_64 x86_64 x86_64 GNU/Linux
> >>>
> >>>And below is the error again:
> >>>
> >>>Best wishes
> >>>Vlad
> >>>
> >>>Stride.o: In function `ss_from_stride(DrawMolecule*)':
> >>>Stride.C:(.text+0x41): warning: the use of `tempnam' is dangerous,
> >>>better use `mkstemp'
> >>>CUDAQuickSurf.o: In function `CUDAQuickSurf::~CUDAQuickSurf()':
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x1d56):
> >>>undefined reference to `CUDAMarchingCubes::~CUDAMarchingCubes()'
> >>>CUDAQuickSurf.o: In function `CUDAQuickSurf::~CUDAQuickSurf()':
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x1da6):
> >>>undefined reference to `CUDAMarchingCubes::~CUDAMarchingCubes()'
> >>>CUDAQuickSurf.o: In function `CUDAQuickSurf::calc_surf(long, float
> >>>const*, float const*, int, float*, int*, float, float, float, float,
> >>>float, VMDDisplayList*)':
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x277a):
> >>>undefined reference to `CUDAMarchingCubes::~CUDAMarchingCubes()'
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2797):
> >>>undefined reference to `CUDAMarchingCubes::CUDAMarchingCubes()'
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x27b7):
> >>>undefined reference to `CUDAMarchingCubes::Initialize(uint3)'
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2c85):
> >>>undefined reference to `CUDAMarchingCubes::SetVolumeData(float*, float*,
> >>>uint3, float3, float3, bool)'
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2d3c):
> >>>undefined reference to `CUDAMarchingCubes::SetSubVolume(uint3, uint3)'
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2d64):
> >>>undefined reference to `CUDAMarchingCubes::computeIsosurface(float3*,
> >>>float3*, float3*, unsigned int)'
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2de2):
> >>>undefined reference to `DispCmdTriMesh::cuda_putdata(float const*, float
> >>>const*, float const*, int, VMDDisplayList*)'
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x30f2):
> >>>undefined reference to `DispCmdTriMesh::cuda_putdata(float const*, float
> >>>const*, float const*, int, VMDDisplayList*)'
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x35a3):
> >>>undefined reference to `CUDAMarchingCubes::CUDAMarchingCubes()'
> >>>tmpxft_000066ee_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x35c3):
> >>>undefined reference to `CUDAMarchingCubes::Initialize(uint3)'
> >>>collect2: ld returned 1 exit status
> >>>make: *** [vmd_LINUXAMD64] Error 1
> >>>
> >>>
> >>>On 08/22/2012 05:16 PM, Vlad Cojocaru wrote:
> >>>>Hi John,
> >>>>
> >>>>Here they are:
> >>>>
> >>>>gcc (SUSE Linux) 4.6.2
> >>>>Copyright (C) 2011 Free Software Foundation, Inc.
> >>>>This is free software; see the source for copying conditions. There
> >>>>is NO
> >>>>warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> >>>>PURPOSE.
> >>>>
> >>>>g++ (SUSE Linux) 4.6.2
> >>>>Copyright (C) 2011 Free Software Foundation, Inc.
> >>>>This is free software; see the source for copying conditions. There
> >>>>is NO
> >>>>warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> >>>>PURPOSE.
> >>>>
> >>>>nvcc: NVIDIA (R) Cuda compiler driver
> >>>>Copyright (c) 2005-2012 NVIDIA Corporation
> >>>>Built on Thu_Apr__5_00:24:31_PDT_2012
> >>>>Cuda compilation tools, release 4.2, V0.2.1221
> >>>>
> >>>>Best,
> >>>>Vlad
> >>>>
> >>>>
> >>>>On 08/22/2012 05:12 PM, John Stone wrote:
> >>>>>Vlad,
> >>>>> I've never seen that error before. I've been compiling VMD with
> >>>>>CUDA 4.0 and with the latest CUDA 5.0 release candidate, but I
> >>>>>haven't ever tried with version 4.2.9. Can you email me the output
> >>>>>you get from:
> >>>>> uname -a
> >>>>> gcc --version
> >>>>> g++ --version
> >>>>> nvcc --version
> >>>>>
> >>>>>Cheers,
> >>>>> John
> >>>>>
> >>>>>On Wed, Aug 22, 2012 at 04:49:16PM +0200, Vlad Cojocaru wrote:
> >>>>>>Thanks John,
> >>>>>>
> >>>>>>I read through the VMD CVS documentation and I realized that this a
> >>>>>>new
> >>>>>>plugin .. I retrieved it and not the plugins built properly.
> >>>>>>However, I have another problem, which seems to be related to CUDA.
> >>>>>>When
> >>>>>>I build VMD, I get the error below. I am using cuda 4.2.9.
> >>>>>>
> >>>>>>Best,
> >>>>>>Vlad
> >>>>>>
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2820):
> >>>>>>
> >>>>>>undefined reference to `CUDAMarchingCubes::~CUDAMarchingCubes()'
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x283d):
> >>>>>>
> >>>>>>undefined reference to `CUDAMarchingCubes::CUDAMarchingCubes()'
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2858):
> >>>>>>
> >>>>>>undefined reference to `CUDAMarchingCubes::Initialize(uint3)'
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2cc4):
> >>>>>>
> >>>>>>undefined reference to `CUDAMarchingCubes::SetVolumeData(float*,
> >>>>>>float*,
> >>>>>>uint3, float3, float3, bool)'
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2d6d):
> >>>>>>
> >>>>>>undefined reference to `CUDAMarchingCubes::SetSubVolume(uint3, uint3)'
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2d8d):
> >>>>>>
> >>>>>>undefined reference to `CUDAMarchingCubes::computeIsosurface(float3*,
> >>>>>>float3*, float3*, unsigned int)'
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x2e01):
> >>>>>>
> >>>>>>undefined reference to `DispCmdTriMesh::cuda_putdata(float const*,
> >>>>>>float
> >>>>>>const*, float const*, int, VMDDisplayList*)'
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x30de):
> >>>>>>
> >>>>>>undefined reference to `DispCmdTriMesh::cuda_putdata(float const*,
> >>>>>>float
> >>>>>>const*, float const*, int, VMDDisplayList*)'
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x33af):
> >>>>>>
> >>>>>>undefined reference to `CUDAMarchingCubes::CUDAMarchingCubes()'
> >>>>>>tmpxft_00000c64_00000000-6_CUDAQuickSurf.compute_20.cudafe1.cpp:(.text+0x33ca):
> >>>>>>
> >>>>>>undefined reference to `CUDAMarchingCubes::Initialize(uint3)'
> >>>>>>collect2: ld returned 1 exit status
> >>>>>>make: *** [vmd_LINUXAMD64] Error 1
> >>>>>>
> >>>>>>On 08/22/2012 04:34 PM, John Stone wrote:
> >>>>>>>Vlad,
> >>>>>>> Please try doing a "cvs update -PAd" in the top level plugins
> >>>>>>>directory
> >>>>>>>to make sure you get the new vmdprefs plugin. That should solve
> >>>>>>>the error
> >>>>>>>you got below.
> >>>>>>>
> >>>>>>>Cheers,
> >>>>>>> John Stone
> >>>>>>> vmd_at_ks.uiuc.edu
> >>>>>>>
> >>>>>>>On Wed, Aug 22, 2012 at 11:41:21AM +0200, Vlad Cojocaru wrote:
> >>>>>>>>Thanks John,
> >>>>>>>>
> >>>>>>>>I updated the CVS but now I get other missing directory error
> >>>>>>>>(see below):
> >>>>>>>>
> >>>>>>>>Best,
> >>>>>>>>Vlad
> >>>>>>>>
> >>>>>>>>Copying volutil 1.3 files to
> >>>>>>>>Copying vmddebug 1.0 files to
> >>>>>>>>/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/vmddebug1.0
> >>>>>>>>
> >>>>>>>>Copying vmdmovie 1.9 files to
> >>>>>>>>/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/vmdmovie1.9
> >>>>>>>>
> >>>>>>>>/bin/sh: line 0: cd: vmdprefs: No such file or directory
> >>>>>>>>make: *** [distrib] Error 1
> >>>>>>>>
> >>>>>>>>On 08/21/2012 06:06 PM, Vlad Cojocaru wrote:
> >>>>>>>>>Dear all,
> >>>>>>>>>
> >>>>>>>>>I am trying to compile the vmd cvs code downloaded today and while
> >>>>>>>>>building the plugins, I get the error below (build script also
> >>>>>>>>>provided below).
> >>>>>>>>>It looks as if some gif files are missing .... Does anybody
> >>>>>>>>>know how
> >>>>>>>>>to fix this ?
> >>>>>>>>>
> >>>>>>>>>Thanks
> >>>>>>>>>Vlad
> >>>>>>>>>
> >>>>>>>>>----------------script used to build plugins ----------------
> >>>>>>>>>#!/bin/bash
> >>>>>>>>>
> >>>>>>>>>export TCLINC="-I/usr/include"
> >>>>>>>>>export TCLLIB="-L/usr/lib64"
> >>>>>>>>>
> >>>>>>>>>export NETCDFINC="-I/usr/include"
> >>>>>>>>>export NETCDFLIB="-I/usr/lib64"
> >>>>>>>>>
> >>>>>>>>>make clean
> >>>>>>>>>make LINUXAMD64 TCLINC=$TCLINC TCLLIB=$TCLLIB NETCDFINC=$NETCDFINC
> >>>>>>>>>NETCDFLIB=$NETCDFLIB 2>&1 | tee make.log
> >>>>>>>>>export PLUGINDIR="/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins"
> >>>>>>>>>make distrib 2>&1 | tee make_distrib.log
> >>>>>>>>>
> >>>>>>>>>exit
> >>>>>>>>>
> >>>>>>>>>-----------------error--------------------
> >>>>>>>>>Copying molfile plugins to
> >>>>>>>>>/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins destination area
> >>>>>>>>> abinitplugin.so ...
> >>>>>>>>> biomoccaplugin.so ...
> >>>>>>>>> cpmdplugin.so ...
> >>>>>>>>> psfplugin.so ...
> >>>>>>>>> pdbplugin.so ...
> >>>>>>>>> dcdplugin.so ...
> >>>>>>>>> babelplugin.so ...
> >>>>>>>>> gromacsplugin.so ...
> >>>>>>>>> parmplugin.so ...
> >>>>>>>>> crdplugin.so ...
> >>>>>>>>> namdbinplugin.so ...
> >>>>>>>>> binposplugin.so ...
> >>>>>>>>> graspplugin.so ...
> >>>>>>>>> msmsplugin.so ...
> >>>>>>>>> stlplugin.so ...
> >>>>>>>>> offplugin.so ...
> >>>>>>>>> cubeplugin.so ...
> >>>>>>>>> edmplugin.so ...
> >>>>>>>>> ccp4plugin.so ...
> >>>>>>>>> dsn6plugin.so ...
> >>>>>>>>> brixplugin.so ...
> >>>>>>>>> pltplugin.so ...
> >>>>>>>>> raster3dplugin.so ...
> >>>>>>>>> parm7plugin.so ...
> >>>>>>>>> rst7plugin.so ...
> >>>>>>>>> tinkerplugin.so ...
> >>>>>>>>> uhbdplugin.so ...
> >>>>>>>>> vaspchgcarplugin.so ...
> >>>>>>>>> vaspparchgplugin.so ...
> >>>>>>>>> vaspposcarplugin.so ...
> >>>>>>>>> vaspoutcarplugin.so ...
> >>>>>>>>> vaspxdatcarplugin.so ...
> >>>>>>>>> vaspxmlplugin.so ...
> >>>>>>>>> dlpolyplugin.so ...
> >>>>>>>>> lammpsplugin.so ...
> >>>>>>>>> vtfplugin.so ...
> >>>>>>>>> xyzplugin.so ...
> >>>>>>>>> corplugin.so ...
> >>>>>>>>> moldenplugin.so ...
> >>>>>>>>> phiplugin.so ...
> >>>>>>>>> pbeqplugin.so ...
> >>>>>>>>> grdplugin.so ...
> >>>>>>>>> situsplugin.so ...
> >>>>>>>>> dxplugin.so ...
> >>>>>>>>> spiderplugin.so ...
> >>>>>>>>> mapplugin.so ...
> >>>>>>>>> avsplugin.so ...
> >>>>>>>>> fs4plugin.so ...
> >>>>>>>>> pqrplugin.so ...
> >>>>>>>>> mol2plugin.so ...
> >>>>>>>>> gridplugin.so ...
> >>>>>>>>> carplugin.so ...
> >>>>>>>>> mdfplugin.so ...
> >>>>>>>>> gamessplugin.so ...
> >>>>>>>>> xsfplugin.so ...
> >>>>>>>>> bgfplugin.so ...
> >>>>>>>>> xbgfplugin.so ...
> >>>>>>>>> jsplugin.so ...
> >>>>>>>>> dtrplugin.so ...
> >>>>>>>>> maeffplugin.so ...
> >>>>>>>>> basissetplugin.so ...
> >>>>>>>>> webpdbplugin.so ...
> >>>>>>>>> netcdfplugin.so ...
> >>>>>>>>> hoomdplugin.so ...
> >>>>>>>>> dmsplugin.so ...
> >>>>>>>>> libmolfile_plugin.a ...
> >>>>>>>>> libmolfile_plugin.h ...
> >>>>>>>>> libmolfile_plugin.lib ...
> >>>>>>>>> libmolfile_plugin.h ...
> >>>>>>>>>Copying apbsrun 1.3 files to
> >>>>>>>>>/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/apbsrun1.3
> >>>>>>>>>
> >>>>>>>>>Copying atomedit 1.0 files to
> >>>>>>>>>/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/atomedit1.0
> >>>>>>>>>
> >>>>>>>>>This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
> >>>>>>>>>restricted \write18 enabled.
> >>>>>>>>>entering extended mode
> >>>>>>>>>(./ug.tex
> >>>>>>>>>LaTeX2e <2009/09/24>
> >>>>>>>>>Babel <v3.8l> and hyphenation patterns for english, dumylang,
> >>>>>>>>>nohyphenation, ge
> >>>>>>>>>rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek,
> >>>>>>>>>ibycus, arabi
> >>>>>>>>>c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian,
> >>>>>>>>>czech, danis
> >>>>>>>>>h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic,
> >>>>>>>>>farsi, finnis
> >>>>>>>>>h, french, galician, german, ngerman, swissgerman, monogreek,
> >>>>>>>>>greek,
> >>>>>>>>>hungarian,
> >>>>>>>>>icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam,
> >>>>>>>>>marathi, or
> >>>>>>>>>iya, panjabi, tamil, telugu, indonesian, interlingua, irish,
> >>>>>>>>>italian,
> >>>>>>>>>kurmanji,
> >>>>>>>>>lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal,
> >>>>>>>>>nynorsk, pol
> >>>>>>>>>ish, portuguese, romanian, russian, sanskrit, serbian, serbianc,
> >>>>>>>>>slovak, sloven
> >>>>>>>>>ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian,
> >>>>>>>>>welsh, loaded
> >>>>>>>>>.
> >>>>>>>>>(/usr/share/texmf/tex/latex/base/article.cls
> >>>>>>>>>Document Class: article 2007/10/19 v1.4h Standard LaTeX document
> >>>>>>>>>class
> >>>>>>>>>(/usr/share/texmf/tex/latex/base/size10.clo))
> >>>>>>>>>(/usr/share/texmf/tex/latex/graphics/graphicx.sty
> >>>>>>>>>(/usr/share/texmf/tex/latex/graphics/keyval.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/graphics/graphics.sty
> >>>>>>>>>(/usr/share/texmf/tex/latex/graphics/trig.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/latexconfig/graphics.cfg)
> >>>>>>>>>(/usr/share/texmf/tex/latex/pdftex-def/pdftex.def
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/infwarerr.sty)
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty))))
> >>>>>>>>>(/usr/lib/texmf/tex/latex/html/html.sty
> >>>>>>>>>(/usr/share/texmf/tex/latex/hyperref/hyperref.sty
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/hobsub-hyperref.sty
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/hobsub-generic.sty))
> >>>>>>>>>(/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
> >>>>>>>>>(/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg)
> >>>>>>>>>(/usr/share/texmf/tex/latex/url/url.sty))
> >>>>>>>>>
> >>>>>>>>>Package hyperref Message: Driver (autodetected): hpdftex.
> >>>>>>>>>
> >>>>>>>>>(/usr/share/texmf/tex/latex/hyperref/hpdftex.def
> >>>>>>>>>(/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.sty)))
> >>>>>>>>>(./ug_macros.tex)
> >>>>>>>>>No file ug.aux.
> >>>>>>>>>(/usr/share/texmf/tex/context/base/supp-pdf.mkii
> >>>>>>>>>[Loading MPS to PDF converter (version 2006.09.02).]
> >>>>>>>>>) (/usr/share/texmf/tex/latex/oberdiek/epstopdf-base.sty
> >>>>>>>>>(/usr/share/texmf/tex/latex/oberdiek/grfext.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/latexconfig/epstopdf-sys.cfg))
> >>>>>>>>>(/usr/share/texmf/tex/latex/hyperref/nameref.sty
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/gettitlestring.sty))
> >>>>>>>>>(./ug_title.tex)
> >>>>>>>>>[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2]
> >>>>>>>>>(./ug_text.tex
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 10--11
> >>>>>>>>>
> >>>>>>>>>(/usr/share/texmf/tex/latex/base/omscmr.fd)
> >>>>>>>>><autoimd-diagram.pdf, id=19, 301.125pt x 288.07625pt>
> >>>>>>>>><use autoimd-diagram.pdf>
> >>>>>>>>>
> >>>>>>>>>LaTeX Warning: Reference `fig:autoimd-diagram' on page 3
> >>>>>>>>>undefined on
> >>>>>>>>>input lin
> >>>>>>>>>e 31.
> >>>>>>>>>
> >>>>>>>>>[3 <./autoimd-diagram.pdf>]
> >>>>>>>>>
> >>>>>>>>>LaTeX Warning: Reference `par:customize' on page 4 undefined on
> >>>>>>>>>input
> >>>>>>>>>line 58.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>LaTeX Warning: Reference `fig:autoimd-GUI' on page 4 undefined on
> >>>>>>>>>input line 78
> >>>>>>>>>.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 78--79
> >>>>>>>>>
> >>>>>>>>><autoimd-GUI.pdf, id=45, 431.6125pt x 298.11375pt> <use
> >>>>>>>>>autoimd-GUI.pdf>
> >>>>>>>>>
> >>>>>>>>>LaTeX Warning: Reference `fig:simsettings-GUI' on page 4
> >>>>>>>>>undefined on
> >>>>>>>>>input lin
> >>>>>>>>>e 85.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 85--86
> >>>>>>>>>
> >>>>>>>>><simsettings-GUI.pdf, id=46, 543.02875pt x 443.6575pt>
> >>>>>>>>><use simsettings-GUI.pdf>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 91--92
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 96--97
> >>>>>>>>>
> >>>>>>>>>[4 <./autoimd-GUI.pdf>]
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 100--101
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 104--105
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 106--107
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 111--112
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 115--116
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 118--119
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 125--126
> >>>>>>>>>
> >>>>>>>>>[5 <./simsettings-GUI.pdf>]
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 130--131
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 134--135
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 140--141
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 170--171
> >>>>>>>>>
> >>>>>>>>>[6]
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 194--195
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 207--208
> >>>>>>>>>
> >>>>>>>>>[7]
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 254--255
> >>>>>>>>>
> >>>>>>>>>) [8] (./ug.aux)
> >>>>>>>>>
> >>>>>>>>>Package rerunfilecheck Warning: File `ug.out' has changed.
> >>>>>>>>>(rerunfilecheck) Rerun to get outlines right
> >>>>>>>>>(rerunfilecheck) or use package `bookmark'.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>LaTeX Warning: There were undefined references.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>LaTeX Warning: Label(s) may have changed. Rerun to get
> >>>>>>>>>cross-references right.
> >>>>>>>>>
> >>>>>>>>>)
> >>>>>>>>>(see the transcript file for additional
> >>>>>>>>>information)</usr/share/texmf/fonts/typ
> >>>>>>>>>e1/public/amsfonts/cm/cmbx10.pfb></usr/share/texmf/fonts/type1/public/amsfonts/
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>cm/cmbx12.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmbx8.pfb></usr/
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>share/texmf/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texmf/fonts/ty
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>pe1/public/amsfonts/cm/cmr12.pfb></usr/share/texmf/fonts/type1/public/amsfonts/
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>cm/cmr17.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmr6.pfb></usr/sh
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>are/texmf/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texmf/fonts/type1
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>/public/amsfonts/cm/cmr8.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/c
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>msl8.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/shar
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>e/texmf/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texmf/fonts/type1
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>/public/amsfonts/cm/cmtt10.pfb>
> >>>>>>>>>Output written on ug.pdf (8 pages, 319257 bytes).
> >>>>>>>>>Transcript written on ug.log.
> >>>>>>>>>This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
> >>>>>>>>>restricted \write18 enabled.
> >>>>>>>>>entering extended mode
> >>>>>>>>>(./ug.tex
> >>>>>>>>>LaTeX2e <2009/09/24>
> >>>>>>>>>Babel <v3.8l> and hyphenation patterns for english, dumylang,
> >>>>>>>>>nohyphenation, ge
> >>>>>>>>>rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek,
> >>>>>>>>>ibycus, arabi
> >>>>>>>>>c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian,
> >>>>>>>>>czech, danis
> >>>>>>>>>h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic,
> >>>>>>>>>farsi, finnis
> >>>>>>>>>h, french, galician, german, ngerman, swissgerman, monogreek,
> >>>>>>>>>greek,
> >>>>>>>>>hungarian,
> >>>>>>>>>icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam,
> >>>>>>>>>marathi, or
> >>>>>>>>>iya, panjabi, tamil, telugu, indonesian, interlingua, irish,
> >>>>>>>>>italian,
> >>>>>>>>>kurmanji,
> >>>>>>>>>lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal,
> >>>>>>>>>nynorsk, pol
> >>>>>>>>>ish, portuguese, romanian, russian, sanskrit, serbian, serbianc,
> >>>>>>>>>slovak, sloven
> >>>>>>>>>ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian,
> >>>>>>>>>welsh, loaded
> >>>>>>>>>.
> >>>>>>>>>(/usr/share/texmf/tex/latex/base/article.cls
> >>>>>>>>>Document Class: article 2007/10/19 v1.4h Standard LaTeX document
> >>>>>>>>>class
> >>>>>>>>>(/usr/share/texmf/tex/latex/base/size10.clo))
> >>>>>>>>>(/usr/share/texmf/tex/latex/graphics/graphicx.sty
> >>>>>>>>>(/usr/share/texmf/tex/latex/graphics/keyval.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/graphics/graphics.sty
> >>>>>>>>>(/usr/share/texmf/tex/latex/graphics/trig.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/latexconfig/graphics.cfg)
> >>>>>>>>>(/usr/share/texmf/tex/latex/pdftex-def/pdftex.def
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/infwarerr.sty)
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty))))
> >>>>>>>>>(/usr/lib/texmf/tex/latex/html/html.sty
> >>>>>>>>>(/usr/share/texmf/tex/latex/hyperref/hyperref.sty
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/hobsub-hyperref.sty
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/hobsub-generic.sty))
> >>>>>>>>>(/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
> >>>>>>>>>(/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg)
> >>>>>>>>>(/usr/share/texmf/tex/latex/url/url.sty))
> >>>>>>>>>
> >>>>>>>>>Package hyperref Message: Driver (autodetected): hpdftex.
> >>>>>>>>>
> >>>>>>>>>(/usr/share/texmf/tex/latex/hyperref/hpdftex.def
> >>>>>>>>>(/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.sty)))
> >>>>>>>>>(./ug_macros.tex)
> >>>>>>>>>(./ug.aux) (/usr/share/texmf/tex/context/base/supp-pdf.mkii
> >>>>>>>>>[Loading MPS to PDF converter (version 2006.09.02).]
> >>>>>>>>>) (/usr/share/texmf/tex/latex/oberdiek/epstopdf-base.sty
> >>>>>>>>>(/usr/share/texmf/tex/latex/oberdiek/grfext.sty)
> >>>>>>>>>(/usr/share/texmf/tex/latex/latexconfig/epstopdf-sys.cfg))
> >>>>>>>>>(/usr/share/texmf/tex/latex/hyperref/nameref.sty
> >>>>>>>>>(/usr/share/texmf/tex/generic/oberdiek/gettitlestring.sty))
> >>>>>>>>>(./ug.out)
> >>>>>>>>>(./ug.out) (./ug_title.tex)
> >>>>>>>>>[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.ma
> >>>>>>>>>p}] (./ug.toc) [2] (./ug_text.tex
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 10--11
> >>>>>>>>>
> >>>>>>>>>(/usr/share/texmf/tex/latex/base/omscmr.fd)
> >>>>>>>>><autoimd-diagram.pdf, id=55, 301.125pt x 288.07625pt>
> >>>>>>>>><use autoimd-diagram.pdf> [3 <./autoimd-diagram.pdf>]
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 78--79
> >>>>>>>>>
> >>>>>>>>><autoimd-GUI.pdf, id=82, 431.6125pt x 298.11375pt> <use
> >>>>>>>>>autoimd-GUI.pdf>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 85--86
> >>>>>>>>>
> >>>>>>>>><simsettings-GUI.pdf, id=84, 543.02875pt x 443.6575pt>
> >>>>>>>>><use simsettings-GUI.pdf>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 91--92
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 96--97
> >>>>>>>>>
> >>>>>>>>>[4 <./autoimd-GUI.pdf>]
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 100--101
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 104--105
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 106--107
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 111--112
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 115--116
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 118--119
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 125--126
> >>>>>>>>>
> >>>>>>>>>[5 <./simsettings-GUI.pdf>]
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 130--131
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 134--135
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 140--141
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 170--171
> >>>>>>>>>
> >>>>>>>>>[6]
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 194--195
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 207--208
> >>>>>>>>>
> >>>>>>>>>[7]
> >>>>>>>>>Underfull \hbox (badness 10000) in paragraph at lines 254--255
> >>>>>>>>>
> >>>>>>>>>) [8] (./ug.aux) )
> >>>>>>>>>(see the transcript file for additional
> >>>>>>>>>information)</usr/share/texmf/fonts/typ
> >>>>>>>>>e1/public/amsfonts/cm/cmbx10.pfb></usr/share/texmf/fonts/type1/public/amsfonts/
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>cm/cmbx12.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmbx8.pfb></usr/
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>share/texmf/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texmf/fonts/ty
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>pe1/public/amsfonts/cm/cmr12.pfb></usr/share/texmf/fonts/type1/public/amsfonts/
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>cm/cmr17.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmr6.pfb></usr/sh
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>are/texmf/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texmf/fonts/type1
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>/public/amsfonts/cm/cmr8.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/c
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>msl8.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/shar
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>e/texmf/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texmf/fonts/type1
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>/public/amsfonts/cm/cmtt10.pfb>
> >>>>>>>>>Output written on ug.pdf (8 pages, 322174 bytes).
> >>>>>>>>>Transcript written on ug.log.
> >>>>>>>>>Copying autoimd 1.7 files to
> >>>>>>>>>/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/autoimd1.7
> >>>>>>>>>
> >>>>>>>>>Copying autoionize 1.3 files to
> >>>>>>>>>/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/autoionize1.3
> >>>>>>>>>
> >>>>>>>>>Copying bendix 1.0 files to
> >>>>>>>>>/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/bendix1.0
> >>>>>>>>>cp: cannot stat `doc/GUI-tips.gif': No such file or directory
> >>>>>>>>>cp: cannot stat `doc/Monsieur_Bendix_smaller_still.gif': No such
> >>>>>>>>>file
> >>>>>>>>>or directory
> >>>>>>>>>make[1]: *** [distrib] Error 1
> >>>>>>>>>make: *** [distrib] Error 1
> >>>>>>>>>
> >>>>>>>>--
> >>>>>>>>Dr. Vlad Cojocaru
> >>>>>>>>Max Planck Institute for Molecular Biomedicine
> >>>>>>>>Department of Cell and Developmental Biology
> >>>>>>>>Röntgenstrasse 20, 48149 Münster, Germany
> >>>>>>>>Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >>>>>>>>Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >>>>>>>>http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
> >>>>>>>>
> >>>>>>>>
> >>>>>>--
> >>>>>>Dr. Vlad Cojocaru
> >>>>>>Max Planck Institute for Molecular Biomedicine
> >>>>>>Department of Cell and Developmental Biology
> >>>>>>Röntgenstrasse 20, 48149 Münster, Germany
> >>>>>>Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >>>>>>Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >>>>>>http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
> >>>>>>
> >>>>>>
> >>--
> >>Dr. Vlad Cojocaru
> >>Max Planck Institute for Molecular Biomedicine
> >>Department of Cell and Developmental Biology
> >>Röntgenstrasse 20, 48149 Münster, Germany
> >>Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >>Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >>http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
> >>
> >>
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>
> 

-- 
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