Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux

From: David A. Case <>
Date: Wed, 5 Jul 2006 15:22:42 -0700

On Mon, Jul 03, 2006, frustrated modeller wrote:
> I have been trying to compile amber8 on a 64bit machine with Xeon
> processors. I have tried with both gcc and icc as the C compiler. I have
> got the most built with configure -p4 -static ifort. however it does not
> build Xleap.

Well, we are "frustrated" to get problem reports with so little real
information. The mailing list has lot of information on this situation.
Generally speaking, the most common problem is that 64-bit installations of X
may not have both 32 and 64-bit libraries. You can either install the 32-bit
libraries and make a 32-bit version of xleap, or you can apply the bugfixes,
and build a 64-bit version. But without some indication of error messages,
it's hard to be of much more help.

> When i go to the test directory and do make test most of the
> tests fail with a segmentation fault.

This is of course a serious problem, but it is a little hard to tell what the
best thing to do is. You could try removing the -p4 option (since you don't
have that architecture); you could report the output for "ifort -V" (so we
sould know what version of the compiler you have.) I must say that I have
never seen an installation that would correctly run the ubiquitin, pol_wat and
dna_pol tests, but fail for dhfr and pure_wat, since the former are just more
complex forms of the latter.

Be sure to look at discussion in the mailing list archives (try searching
for any compilation error messages). Amber 8 was released before 64-bit
processors were very common, and certain releases of the intel compilers
have had some bugs in them. But the combination of successes and failures
you report is quite unusual. So, just run one test at a time, look carefully
at the output (if any) and see if you can narrow down what is happening.


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Received on Sun Jul 09 2006 - 06:07:09 PDT
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