Greetings: I'm trying to get ifeffit and the horae packages running on an Intel-based Mac running OS 10.4.7. As someone else noted previously, the binary downloads don't work on Intel Macs. (As an aside to the person who asked about the console log, in my case the programs quit immediately after launching and no messages are generated in either console.log or system.log. I do have X11 installed; this behavior is the same with either X11 or Aquaterm chosen for output.) So I decided to compile from the source. Unfortunately, I ran into a problem when compiling horae-062a. Using the Makefile.PL for Mac OS (http://cars9.uchicago.edu/~ravel/misc/horae_on_mac/Makefile.PL ) seems to work fine, and after "make;make install" I get no errors and executables for Artemis et al. are produced. Unfortunately, attempting to run any of the executables produces an error similar to the following:
tchmac:/Applications/ifeffit/bin hufnagel$ ./artemis dyld: lazy symbol binding failed: Symbol not found: _iff_exec Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle Expected in: dynamic lookup
dyld: Symbol not found: _iff_exec Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle Expected in: dynamic lookup
Trace/BPT trap
A little digging around on the net suggested that this error comes from compiling with gcc-4.0 rather than gcc-3.3. Switching to that compiler, I can again run Makefile.PL successfully, but then when I run 'make' I get a new and exciting error:
[...much successful stuff deleted...] cp Zlib.pm ../../blib/lib/Compress/Zlib.pm AutoSplitting ../../blib/lib/Compress/Zlib.pm (../../blib/lib/auto/Compress/Zlib) /usr/bin/perl /System/Library/Perl/5.8.6/ExtUtils/xsubpp -typemap /System/Library/Perl/5.8.6/ExtUtils/typemap -typemap typemap Zlib.xs > Zlib.xsc && mv Zlib.xsc Zlib.c cc -c -I./zlib-src -g -pipe -fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -I/usr/local/include -O3 -DVERSION=\"1.41\" -DXS_VERSION=\"1.41\" "-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE" Zlib.c cc: installation problem, cannot exec `cc1': No such file or directory make[2]: *** [Zlib.o] Error 1 make[1]: *** [subdirs] Error 2 make: *** [subdirs] Error 2
and obviously no executables are produced. A little more digging on the web revealed that the cc1 stuff should be in the /usr/libexec/gcc tree. Unfortunately, while there is a subdirectory there for gcc-4.0 for Intel, the only files for gcc-3.3 are for PowerPC. That is, while there is a /usr/libexec/gcc/darwin/ppc/3.3/cc1, there is no corresponding subdirectory for Intel processors. The reason the compilation worked for gcc-4.0 is that there is, in fact, a /usr/libexec/gcc/i686-apple-darwin8/4.0.1/cc1. At this point, I am stuck. I can compile under gcc-4.0 but get executables which don't run, and I can't compile at all under gcc-3.3. I also ran into trouble compiling ifeffit, but I haven't exhausted my own abilities in chasing down those problems (yet). Any assistance/advice/condolences would be appreciated. Thanks, Todd Hufnagel -- Todd C. Hufnagel Professor Department of Materials Science and Engineering Johns Hopkins University 102 Maryland Hall 3400 North Charles Street Baltimore, MD 21218-2681 Voice: (410) 516-6277 Fax: (410) 516-5293 Email: hufnagel@jhu.edu http://www.jhu.edu/~matsci/people/faculty/hufnagel/hufnagel.html
On Friday 01 September 2006 14:49, Todd Hufnagel wrote:
A little digging around on the net suggested that this error comes from compiling with gcc-4.0 rather than gcc-3.3. Switching to that compiler, I can again run Makefile.PL successfully, but then when I
run 'make' I get a new and exciting error:
[...much successful stuff deleted...] cp Zlib.pm ../../blib/lib/Compress/Zlib.pm AutoSplitting ../../blib/lib/Compress/Zlib.pm (../../blib/lib/auto/Compress/Zlib) /usr/bin/perl /System/Library/Perl/5.8.6/ExtUtils/xsubpp -typemap /System/Library/Perl/5.8.6/ExtUtils/typemap -typemap typemap Zlib.xs > Zlib.xsc && mv Zlib.xsc Zlib.c cc -c -I./zlib-src -g -pipe -fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -I/usr/local/include -O3 -DVERSION=\"1.41\" -DXS_VERSION=\"1.41\" "-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE" Zlib.c cc: installation problem, cannot exec `cc1': No such file or directory make[2]: *** [Zlib.o] Error 1 make[1]: *** [subdirs] Error 2 make: *** [subdirs] Error 2
and obviously no executables are produced.
I'll start with my standard disclaimer that I don't own a Mac and don't have any personal experience trying to do what you are doing. You failure comes while trying to build the Compress::Zlib module, which is one of the things in the 0CPAN subdirectory of the tarball. One place to go searching for information about getting that built is the CPAN testers site. Here's the link to the testers page for that Module. There are several entries for building 2.41 under Darwin. http://testers.cpan.org/show/Compress-Zlib.html I don't use very many features of C::Z in horae, so you can also try building earlier or later versions. Other versions should be drop-in replacements for the version that comes in the tarball. Fortunately Compress::Zlib is a part of the Phalanx project: http://qa.perl.org/phalanx/100/ Scroll down on that page and you'll find more information about that module, including links to the testers, bugs, and annotated CPAN pages. All potentially useful. Another possibility is to remove C::L from the horae tarball and use some other method of installing that module. That would be an attractive option if C::L is available using fink. Anpther possibility is that the perl installation that Apple distributes already has C::L installed. You can test that by doing this at the command line: perl -e 'use Compress::Zlib' If it spits back a cryptic error message, then you need to install C::L. If it responds with nothing, then C::L is already installed. If that happens, delete the C::L directory from the horae tarball and try building again. HTH, B P.S. This module is a requirement for Artemis. It is needed to build Artemis project files. If you never use Artemis, you can live without having C::L installed on your computer. In that case, delete it from the tarball and build without it. Artemis will be broken, but Athena and Hephaestus should work fine. -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/
Hi I have been the one who made the binary installers for the power pc version of horae. I have yet to build the intel version as I don't have access at work to an intel based mac (I did try a little on my wife's new imac, but ran into the same problem you did). I will be getting a new Mac Pro machine shortly and would like to give it a try there. The problem with gcc3 and ggc4 is something I am aware about too. One thing I had started to try using was g95 and/or gfortran, the gcc 4 fortran compilers (g95 standard fortran). The automatic build sequence is broken for these, hence on the powerpc, I took the easy way out and compiled the binary installer with gcc3 (which I also have). I also hope to buy another compiler for the new mac as well (perhaps Intel?). I would be interested in helping and would be most grateful to be kept up to date as making a binary installer would help out a lot of other users as well. Paul Fons
The Intel Fortran compiler will compile ifeffit on Mactel machines. I have not tried horae. Jeff On Sep 2, 2006, at 12:24 AM, Paul Fons wrote:
Hi I have been the one who made the binary installers for the power pc version of horae. I have yet to build the intel version as I don't have access at work to an intel based mac (I did try a little on my wife's new imac, but ran into the same problem you did). I will be getting a new Mac Pro machine shortly and would like to give it a try there. The problem with gcc3 and ggc4 is something I am aware about too. One thing I had started to try using was g95 and/or gfortran, the gcc 4 fortran compilers (g95 standard fortran). The automatic build sequence is broken for these, hence on the powerpc, I took the easy way out and compiled the binary installer with gcc3 (which I also have). I also hope to buy another compiler for the new mac as well (perhaps Intel?). I would be interested in helping and would be most grateful to be kept up to date as making a binary installer would help out a lot of other users as well.
Paul Fons _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (4)
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Bruce Ravel -
Jeff Terry -
Paul Fons -
Todd Hufnagel