VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Aug 23 2012 - 07:24:39 CDT

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