From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Fri Aug 24 2012 - 07:15:31 CDT

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