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Author Topic: 3DNA on SGI Altix  (Read 13775 times)

Offline dthomas

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3DNA on SGI Altix
« on: October 02, 2006, 10:00:59 pm »
Hi,

   I just tried to use the RedHat version of 3DNA on the Australia
National Facility computer (apac) http://nf.apac.edu.au/ without
much success. I was wondering if you could compile a version that
would work for me? The computer is an SGI Altix running SUSE 9.

 Thanks,

Don Thomas

Offline xiangjun

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« Reply #1 on: October 03, 2006, 08:56:00 pm »
Hi,

Thanks for your interest in using 3DNA. The issue you have seems to relate more to hardware architecture of SGI than to the Intel-based PC Linux. The Redhat binary of 3DNA runs Okay on all the Intel-based PC Linux system in my experience, including SUSE 9 which I have access to and have just verified.

A similar problem happens to the 3DNA Mac OS X binary which does not runs on the new Intel-based Mac OS X system.

What happens if you download the SGI version?

The current download of 3DNA is v1.5, released at the end of 2002, which is quite stable and robust. Over the years, however, there have been numerous improvements including minor bug fixes and newly added functionality etc. We are close to a new release v1.6 in the new future, and we will try to cover the mostly commonly used OSes.

BTW, how common is SGI running Linux?

Xiang-Jun

Offline dthomas

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SGI and Linux
« Reply #2 on: October 08, 2006, 11:25:54 am »
Hi,

 SGI no longer supports IRIX. All of the Altix machines and presumably all of their smaller machines run Linux.

Anyway, I will try the SGI build on the Altix machine.

Thanks,

Don

Offline dthomas

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3DNA on SGI Altix
« Reply #3 on: October 08, 2006, 10:40:12 pm »
Hi,

Well I tried the SGI version with no luck. I got the following error.

/home/571/dst571/X3DNA/bin/find_pair: Exec format error. Binary file not executable.

And before you ask the entire X3DNA/bin directory is 770 and it is in my path. I tried it from a script which I have been using for years and tried to run it directly with no luck.

I really think it needs to be recompiled on an SGI Altix to work.

If you don't have access to such a machine I am more than willing to compile the source for you.

Thanks,

Don

Offline xiangjun

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« Reply #4 on: October 09, 2006, 09:42:14 pm »
Hi,

Thanks for your feedback. I will check around to see if I can have access to SGI Altix Linux to get a compiled 3DNA version for you. We are closing for the new release of 3DNA v1.6. As noted in the FAQ, per Rutgers University policy, 3DNA is only distributed in binary form. Personally, I have access to PC Linux, Mac OS X, and Windows XP etc, which are the most common, but  certainly not complete. I will check with Dr. Olson to see if it would be feasible to allow for some users to help compile 3DNA.

Best regards,

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.