AMBER Archive (2006)

Subject: AMBER: amber9 compilation problems on EM64T xeon system

From: hayden (
Date: Thu Jul 06 2006 - 13:11:04 CDT

Dear Amber users

I am compiling amber9 on an EM64T architecture using a 64 bit ifort compiler
(fce_8.1.03x - whatever it is, it worked fine for amber8)

I can get compilation to happen and pass the run tests when I use the
following flags:

./configure -p4 -static ifort_x86_64

followed by "make serial"

However, when I leave out the "static" flag I get this error (following an
apparently error-free compilation):"
./../exe/sander: error while loading shared libraries:
cannot open shared object file: No such file or directory
  ./Run.dmp: Program error
make: *** [test.sander.BASIC] Error 1

This error happens for all or most of the tests. As I understand it the
keyword "static" prevents linking to shared libraries at compile time - does
this mean that the linking libraries have to be made available at run time?
The concept doesn't make much sense to me right now.

My question is therefore:

1. When should "static" be (or not be) used?
2. If I get round the compile-time problem using the "static" keyword, am I
likely to run into problems later on during run-time?
3. The shared object file that the error message refers to exists - why
can't it be seen? (I have set "LD_LIBRARY_PATH=/opt/intel_fce_80/lib" and does indeed reside there. I have also set symbolic links
from this library to the main library in /usr/lib - to no avail.)
4. The only way I can compile the parallel version (for lam mpi) without
catastrophic error messages is by omitting the "static keyword". However, I
then get the familiar "error while loading shared libraries:" error when attempting to run the executable. How can I get
both the serial and parallel versions to work?

(NB_1.: I compiled lam-mpi with the same compiler as I am using for amber9)
(NB_2: catastrophic errors as a result of "static" keyword are included in
the attachment).

Many thanks for any suggestions/explanations

Hayden Eastwood
Perdita Barran Research Group
Joseph Black Building
Edinburgh University
West Mains Road
Tel: 0131 650 4773
Research page:
"You have to be an academic to believe some things; no ordinary person would
be so stupid." -George Orwell

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