VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 21 2008 - 19:50:11 CDT

Hi Vlad, Axel,
  The Tachyon builds I incorporate into VMD normally do not use
the JPEG libraries. It's generally the case that if
you're taking the time to render something with a ray tracer rather
than with the Snapshot renderer, that you want the highest possible
image quality, free of block artifacts and so on. While you can
enable JPEG support in Tachyon and compile and link that into VMD,
it's not something I'd normally recommend people to use due to the
reduced image quality inherent in the use of JPEGs and other lossy
formats. The only real exception to this would be direct encoding
of JPEG frame sequences into an M-JPEG movie, but even in that case
the runtime to convert from a lossless format to an M-JPEG movie
is minor. Anyway, feel free to enable JPEG etc in Tachyon, but
you shouldn't feel that it's a necessity.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 21, 2008 at 07:45:50PM -0400, Axel Kohlmeyer wrote:
> On Tue, 22 Apr 2008, Cojocaru,Vlad wrote:
>
> VC> Dear Alex, Dear John, vmd users
>
> dear vlad,
>
> VC> I followed Alex's suggestion and modified the Make-arch file (for
> VC> the linux-64 architecture .. .I have 1 CPU Athlon 64 so I guess
> VC> that's the right option for compiling tachyon) as described below.
> VC> Tachyon compilation succeeds. However no success ... the compilation
> VC> of vmd fails with the same error. It's something about the linking
>
> because you need to change the flags there as well.
> the VMD build does not import the config from tachyon.
>
> the simplest way to handle this is to modify VMD's configure
> script by changing:
>
> $libtachyon_libs = "-ltachyon";
>
> into:
>
> $libtachyon_libs = "-ltachyon -ljpg -lpng -lz";
>
> and then rerun configure to get a new makefile.
>
> of course you can also simply change the makefile,
> but that will be overwritten every time you re-run configure.
>
> cheers,
> axel.
>
>
> VC> of the vmd executable to the tachyon library but now I am out of
> VC> ideas how I could fix this.
>
> VC>
> VC> I also attach a diff file between my modified configure and the original one.
> VC>
> VC> Best wishes
> VC> vlad
> VC>
> VC>
> VC> ---------------Modified Make-arch (in ./lib/tachyon/unix)-------------
> VC> # Linux on AMD64/EM64T, using gcc
> VC> linux-64:
> VC> $(MAKE) all \
> VC> "ARCH = linux-64" \
> VC> "CC = gcc" \
> VC> "CFLAGS = -m64 -Wall -O6 -fomit-frame-pointer -ffast-math -DLinux -DLP64 $(MISCFLAGS) $(USEJPEG) $(USEPNG)" \
> VC> "AR = ar" \
> VC> "ARFLAGS = r" \
> VC> "STRIP = strip" \
> VC> "RANLIB = ranlib" \
> VC> "LIBS = -L. -ltachyon $(MISCLIB) $(JPEGLIB) $(PNGLIB)"
> VC> "USEJPEG= -DUSEJPEG"
> VC> "JPEGINC= -I/usr/include"
> VC> "JPEGLIB= -L/usr/lib64 -ljpeg"
> VC> "USEPNG= -DUSEPNG"
> VC> "PNGINC= -I/usr/include"
> VC> "PNGLIB= -L/usr/lib64 -lpng -lz"
> VC>
> VC> ---------------VMD compilation error ---------------------------
> VC> ../lib/tachyon/compile/linux-64/libtachyon.a(jpeg.o): In function `writejpeg':
> VC> jpeg.c:(.text+0x3d): undefined reference to `jpeg_std_error'
> VC> jpeg.c:(.text+0x53): undefined reference to `jpeg_CreateCompress'
> VC> jpeg.c:(.text+0x5e): undefined reference to `jpeg_stdio_dest'
> VC> jpeg.c:(.text+0x7f): undefined reference to `jpeg_set_defaults'
> VC> jpeg.c:(.text+0x8e): undefined reference to `jpeg_set_quality'
> VC> jpeg.c:(.text+0x9b): undefined reference to `jpeg_start_compress'
> VC> jpeg.c:(.text+0xe5): undefined reference to `jpeg_write_scanlines'
> VC> jpeg.c:(.text+0xfa): undefined reference to `jpeg_finish_compress'
> VC> jpeg.c:(.text+0x102): undefined reference to `jpeg_destroy_compress'
> VC> ../lib/tachyon/compile/linux-64/libtachyon.a(jpeg.o): In function `readjpeg':
> VC> jpeg.c:(.text+0x16c): undefined reference to `jpeg_std_error'
> VC> jpeg.c:(.text+0x182): undefined reference to `jpeg_CreateDecompress'
> VC> jpeg.c:(.text+0x18d): undefined reference to `jpeg_stdio_src'
> VC> jpeg.c:(.text+0x19a): undefined reference to `jpeg_read_header'
> VC> jpeg.c:(.text+0x1a2): undefined reference to `jpeg_start_decompress'
> VC> jpeg.c:(.text+0x21e): undefined reference to `jpeg_read_scanlines'
> VC> jpeg.c:(.text+0x236): undefined reference to `jpeg_finish_decompress'
> VC> jpeg.c:(.text+0x23e): undefined reference to `jpeg_destroy_decompress'
> VC> ../lib/tachyon/compile/linux-64/libtachyon.a(pngfile.o): In function `writepng':
> VC> pngfile.c:(.text+0x2f): undefined reference to `png_create_write_struct'
> VC> pngfile.c:(.text+0x46): undefined reference to `png_create_info_struct'
> VC> pngfile.c:(.text+0x5c): undefined reference to `png_destroy_write_struct'
> VC> pngfile.c:(.text+0xb9): undefined reference to `png_init_io'
> VC> pngfile.c:(.text+0xfc): undefined reference to `png_set_IHDR'
> VC> pngfile.c:(.text+0x113): undefined reference to `png_set_gAMA'
> VC> pngfile.c:(.text+0x122): undefined reference to `png_malloc'
> VC> pngfile.c:(.text+0x16d): undefined reference to `png_set_text'
> VC> pngfile.c:(.text+0x17a): undefined reference to `png_malloc'
> VC> pngfile.c:(.text+0x1c1): undefined reference to `png_set_rows'
> VC> pngfile.c:(.text+0x1d4): undefined reference to `png_write_png'
> VC> pngfile.c:(.text+0x1e1): undefined reference to `png_free'
> VC> pngfile.c:(.text+0x1ee): undefined reference to `png_free'
> VC> pngfile.c:(.text+0x1fa): undefined reference to `png_destroy_write_struct'
> VC> pngfile.c:(.text+0x217): undefined reference to `png_destroy_write_struct'
> VC> ../lib/tachyon/compile/linux-64/libtachyon.a(pngfile.o): In function `readpng':
> VC> pngfile.c:(.text+0x252): undefined reference to `png_create_read_struct'
> VC> pngfile.c:(.text+0x264): undefined reference to `png_create_info_struct'
> VC> pngfile.c:(.text+0x27c): undefined reference to `png_destroy_read_struct'
> VC> pngfile.c:(.text+0x2d2): undefined reference to `png_init_io'
> VC> pngfile.c:(.text+0x2e8): undefined reference to `png_read_png'
> VC> pngfile.c:(.text+0x2f7): undefined reference to `png_get_image_width'
> VC> pngfile.c:(.text+0x30d): undefined reference to `png_get_image_height'
> VC> pngfile.c:(.text+0x323): undefined reference to `png_get_rows'
> VC> pngfile.c:(.text+0x416): undefined reference to `png_destroy_read_struct'
> VC> pngfile.c:(.text+0x438): undefined reference to `png_destroy_read_struct'
> VC> collect2: ld returned 1 exit status
> VC> make: *** [vmd_LINUXAMD64] Error 1
> VC>
> VC>
> VC>
> VC>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078