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Author Topic: Problem with installing 3DNA on Mac OSX-Intel 10.4  (Read 6238 times)

Offline CWashburn

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Problem with installing 3DNA on Mac OSX-Intel 10.4
« on: June 26, 2012, 02:16:00 pm »
Hi,

I wasn't quite sure where to post this query, as it's related to installation on a Mac.

I ran through the setup, but when I tried to execute find_path -h i received the following error:

Bad CPU type in executable

I'm running Mac OSX version 10.4.11, with a 1.83 GHz Intel Core Duo.

I've tried using all three versions of 3DNA available, for both Intel based Macs and the other version provided, Yet I keep getting the same error. Is there a possible work around, or am I going to need to change hardware.

Thanks,

CWashburn
« Last Edit: June 26, 2012, 04:46:40 pm by xiangjun »

Offline xiangjun

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Re: Problem with installing 3DNA on Mac OSX-Intel 10.4
« Reply #1 on: June 26, 2012, 05:51:40 pm »
Hi CWashburn,

Thanks for your interest in using 3DNA. I believe your problem is not related to installing 3DNA on Mac OS X. Instead, it appears to be due to 3DNA binary incompatibility with your Mac OS X 10.4.11.

I compiled the Mac OS X version of the currently distributed 3DNA v2.1beta on 10.7.4 (Lion) and verified that the binary works on 10.6.x (Snow Leopard). However, that does not explain why you receive the same error message "Bad CPU type in executable" with previous versions of 3DNA (v2.0 and v1.5). Since you have an Intel Core Duo, the error is unlikely an Intel vs PPC architecture issue either.

Without a Mac OS X 10.4 machine at hand, it is difficult to figure out where the problem is or to recompile 3DNA specifically for your settings. However, we can do at least the followings:

  • Do you have access to a Mac with OS X 10.6 (Snow Leopard) or 10.7 (Lion)? Mac users are pretty quick in upgrading their OS, so presumably you could have a try on a newer OS X system and report back how it goes.
  • You can try the Linux or Windows version of 3DNA. For example, you could install VirtualBox on your Mac and then set up Linux on top of it.
  • I will see if I can find a Mac OS X 10.4 machine to test/compile 3DNA. Alternatively, you may well consider upgrade your hardware/software. In my understanding, Mac OS X 10.4 seems to be little used nowadays.

HTH,

Xiang-Jun

Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline xiangjun

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Re: Problem with installing 3DNA on Mac OSX-Intel 10.4
« Reply #2 on: June 26, 2012, 10:52:55 pm »
Quote
I'm running Mac OSX version 10.4.11, with a 1.83 GHz Intel Core Duo.
Following my previous reply, I've checked the various Mac OS X systems available from SBGrid Developer Support. So I recompiled 3DNA on "OS X 10.4 PowerPC", and "OS X 10.5 Intel". I believe one of the latest 3DNA 2.1beta (2012jun26) distribution, presumably PPC, at the download page should work on your system.

Please have a try and report back how it goes. Also, let me know the output (verbatim) of running "sw_vers" on your Mac OS X.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline CWashburn

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Re: Problem with installing 3DNA on Mac OSX-Intel 10.4
« Reply #3 on: June 27, 2012, 11:36:45 am »
Sadly, the recompiled version still didn't work, and I get the same error.

The output you requested is as follows:

ProductName:     Mac OS X
ProductVersion:  10.4.11
BuildVersion:       8S2167

I went ahead, and tried using the linux version of 3DNA using virtual box, and so far haven't encountered any errors, so I at least have the software up and running.

Thank you very much for the help,

CWashburn

Offline xiangjun

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Re: Problem with installing 3DNA on Mac OSX-Intel 10.4
« Reply #4 on: June 27, 2012, 05:41:28 pm »
Thanks for your feedback. I am glad that by VirtualBox + Linux, you now have 3DNA up and running. As always, if you have any 3DNA-related questions, please do not hesitate to post on the 3DNA Forum.

I will still keep an eye on the Mac OS X 10.4.11 Intel (x86) architecture. If I could have access to such a machine, I will compile a native 3DNA distribution for users like you -- I will post back here if I make any progress.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline xiangjun

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Re: Problem with installing 3DNA on Mac OSX-Intel 10.4
« Reply #5 on: July 02, 2012, 04:54:19 pm »
Following my previous response, I asked for help from SBGrid on compiling 3DNA for Mac OS X Intel 10.4. Ben Eisenbraun told me the OS is on longer supported by SBGrid, and suggested two alternatives (see his message below).

I tried to compile a 3DNA universal binary for Mac OS X 10.4 ppc and intel without luck. Compiling a 10.4/Intel compatible binary on the 10.5/Intel machine went through, so I have created a tarball for you to test. Please let us know if it works.

Xiang-Jun


Quote
Hi Xiang-Jun,

> I recently received a report from a 3DNA user that has "Mac OSX
> version 10.4.11, with a 1.83 GHz Intel Core Duo." Neither of the
> compiled versions of 3DNA with "sbgrid-dev-flex, OS X 10.5,
> x86/x86_64" or "sbgrid-dev-cotterpin, OS X 10.4, PowerPC" works for
> this architecture.

We no longer have a OS X Intel 10.4 machine. I have two ideas for you
though:

- cross-compile a 10.4/Intel binary on the 10.4/PPC machine. In the gcc
  manpage:

       -arch arch
           Compile for the specified target architecture arch.  The allowable
           values are i386, ppc and ppc64.  Multiple options work, and direct
           the compiler to produce ``universal'' binaries including object
           code for each architecture specified with -arch.  This option only
           works if assembler and libraries are available for each architec-
           ture specified.  (APPLE ONLY)

- compile a 10.4/Intel compatible binary on the 10.5/Intel machine using:

export MACOSX_DEPLOYMENT_TARGET=10.4
export LDFLAGS="-mmacosx-version-min=10.4 -Wl,-headerpad_max_install_names"

Those are probably enough. You might need to get into sysroot arguments to
gcc if you are using an OS X framework.

-ben

--
| Ben Eisenbraun
| SBGrid Consortium                          | http://sbgrid.org       |
| Harvard Medical School                     | http://hms.harvard.edu  |
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.