AMBER Archive (2006)

Subject: RE: AMBER: amber9 compilation error on SGI altix

From: Ross Walker (
Date: Sat Apr 22 2006 - 14:21:24 CDT

Dear Lihua,

> ifort -o nucgen nucgen.o ngfil.o ../lib/amopen.o ../lib/mexit.o
> ../lib/nxtsec.o -lscs
> icpc -c -o elsize.o
> /usr/include/c++/3.2.3/limits(1894): error: expected a ")"
> { return __glibcpp_long_double_signaling_NaN; }
> ^

I cut and pasted the following into google:

/usr/include/c++/3.2.3/limits(1894): error: icpc

And this is what I got:

>From the page:

Known issues:

There is currently an incompatibility between the Intel C++ compiler and the
g++ headers. This will result in C++ compilations yielding: ...

The workaround suggested on this page is to make icpc link against the icc
libraries instead of the gcc libraries. Something that I would think would
be sensible by default but who is to know Intel's mind...

Anyway, edit $AMBERHOME/src/config.h

and change



CPLUSPLUS = icpc -cxxlib-icc

Then try recompiling. Note if things still don't work you can edit
$AMBERHOME/src/etc/Makefile and remove the elsize$(SFX) entry from the list
of progs. elsize is a small standalone program that you only need for
finding a molecule's size when running igb>0 and alpb=1.

> For the origin platform, serial compilation was completed
> (with loads of
> warnings, though). However when tried the set of basic tests (make
> test.serial), we ran into the following errors:
> cd pbsa_trx; ./Run.trxox.min
> Segmentation fault (core dumped)
> ./Run.trxox.min: Program error

Unfortunately I don't have access to an SGI origin so can't help much here
but these sorts of problems often arrise from doing things like compiling in
64 bit but linking against 32 bit libraries etc. Check which libraries were
used to link against and whether the compiler was compiling in 32 bit or 64
bit mode. Note R5K chips were 32 bit but R10K were 64 bit so this sort of
thing can happen.

I would also check if some of the simpler programs work. E.g. try ambpdb and
see if this segfaults as well. If you can post details of the compiler
version, machine specs, the config.h file in $AMBERHOME/src and a few of the
warnings (particularly those that appear at link time the ld line) we may be
able to help some more.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to