VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 23 2012 - 09:41:42 CDT

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
> >>>>>>>
> >>>>>>>
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> >>>>>>>
> >>>>>>>
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> >>>>>>>
> >>>>>>>
> >>>>>>>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
>
> 

-- 
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