VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Aug 23 2012 - 03:00:56 CDT

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