AMBER Archive (2006)

Subject: RE: AMBER: amber9 compilation problems on EM64T xeon system

From: Yong Duan (duan_at_ucdavis.edu)
Date: Thu Jul 06 2006 - 14:38:05 CDT

I am using Intel ifort 9.0 to compile AMBER 9 and everything seems ok. But
I've never tried Intel 8.x compilers for x86_64. Can you try "file
libcxaguard.so.5" to find out its file type?

FYI, my config.h was generated by

./configure -static -opteron -mpich ifort_x86_64 (for parallel version on
opteron w/ mpich).

Also, the "-static" can be omitted without any problem.

Hope this helps.

yong

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of hayden
> Sent: Thursday, July 06, 2006 11:11 AM
> To: amber_at_scripps.edu
> Subject: AMBER: amber9 compilation problems on EM64T xeon system
>
>
>
> 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:
> libcxaguard.so.5:
> 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
> libcxaguard.so.5 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:
> libcxaguard.so.5" 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
> _________________________________________
> Hayden Eastwood
> Perdita Barran Research Group
> Joseph Black Building
> Edinburgh University
> West Mains Road
> EH9 3JJ
>
> Tel: 0131 650 4773
> e-mail: s0237717_at_sms.ed.ac.uk
> Research page:http://homepages.ed.ac.uk/pbarran/PBRG/
> "You have to be an academic to believe some things; no
> ordinary person would
> be so stupid." -George Orwell
>

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