AMBER Archive (2006)

Subject: Re: AMBER: seg fault during test.serial

From: David A. Case (
Date: Fri Sep 08 2006 - 20:19:16 CDT

On Fri, Sep 08, 2006, Lachele Foley (Lists) wrote:

> I compiled amber9 on an itanium machine (RHEL 3 build 4):
> 2.4.21-27.EL #1 SMP Wed Dec 1 21:54:21 EST 2004 ia64 ia64 ia64 GNU/Linux
> I downloaded the most recent bugfix.all and applied it. I also tried
> adding the flag "-cxxlib-icc" to the CPLUSPLUS line. The compile
> seems to go fine, but I get a seg fault during make test.serial. Here
> is the tail end of the output:
> cd crambin_qmmmnmr; ./Run.cnmr
> diffing with mdout.cnmr
> ==============================================================
> diffing with divcon.out
> ==============================================================
> cd qmmm2/crambin; ./Run.crambin_divcon
> getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0
> forrtl: severe (174): SIGSEGV, segmentation fault occurred

First: are you planning to use the divcon capability? If not, you can
probably wait as this problem is looked into. We are currently evaluating
some proposed fixes that look like optimization problems with some versions of
ifort (see the next item).

Second: what does "ifort -V" say? Sander is a fortran program, so the C/C++
flags are not relevant here.

Third: if you need divcon running on the ia64, you could try lowering the
optimization level by chaning the FOPTFLAGS variable in
amber9/src/dcqtp/mod/Makefile, and recompiling.

> The test just hangs there. I have to kill the process to get out of it.

This seems weird, since a segfault should end the job. Do you see this
behaviour if you run test by hand, or only when it is invoked by the Makefile?

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