AMBER Archive (2006)

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

From: frustrated modeller (
Date: Wed Jul 05 2006 - 19:29:52 CDT

In the time i have been trying to install amber8 i have made frequent
searches of the reflector for the error messages i was getting, and i was
also checking through the installation scripts etc and i have tried many
combinations, so many in fact i cant really keep track of what i have done
since i was trying to install amber8 for over 8 days solid. the version of
the intell icc compiler was from this file off the intel website
l_cc_p_9.1.038.tar.gz, the intel fortran compiler ifort was from this file
also from the intel website l_fc_p_9.1.032.tar.gz. I used the -p4 option
because someone who appeared to be using the same architecture was suggested
to do so by Ross Walker (march 22 2005), if -p4 is incorrect then please
tell me what is since i tryed -gnucompat without success. I thought i had
made clear the exact errors i got for each test. Most of them gave the same
error which was just a segmentations fault.
Here is an example:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
  Run.tip4p: Program error

I am not compiling amber8 as root since i do not have root access to the
machine i am installing it on, and the mkl libraries, icc, and ifort were
installed locally by myself in order that i could install amber8. For this
reason i cant do anything about the X libraries, but if that just means i
cant have xleap on this machine i can live with that cause i have access to
another machine that does have xleap working. I am more worried the tests
show that sander is not working and that is what i need most of all.



On 7/5/06, David A. Case <> wrote:
> 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.
> ....dac
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