RE: AMBER: Segmentation fault

From: Ross Walker <>
Date: Tue, 14 Oct 2008 07:53:08 -0700

This is going to be pretty hard to debug since RedHat 9.0 is a pretty
ancient operating system. I don't know if the Intel compilers even support
it anymore. Do you get any output files in the LES directory at all? Is this
the only test case that fails here? You can temporarily comment it out of
the Makefile $AMBERHOME/test/Makefile line 182 and then try running the test
suite again. If this is the only test case that fails then assuming you
don't want to run LES calculations you are fine. It is the addles code here
that is segfaulting and not the sander code.


You could also try building addles without optimization and see if that
helps. Do the following.


1) cd $AMBERHOME/src/

2) make clean

3) edit config_amber.h edit the FOPTFLAGS lines and remove the -ip -O3 and
-axWP entries and change it to -O0.

4) cd addless

5) make install


Check that this replaces addles in $AMBERHOME/exe/addles by looking at the
file timestamp. Then try running the LES test case again and see if it works
this time.


All the best



From: [] On Behalf Of
Sent: Monday, October 13, 2008 11:53 PM
To: amber
Subject: AMBER: Segmentation fault


hello all,

i have installedl the amber10 on the redhat 9.0 system.

when i did the test and i got the error.

the error following:


[root.john LES]# ./Run.PME_LES
  Amber 8 ADDLES and SANDER.LES test:
Segmentation fault
  ./Run.PME_LES: Program error

can someone give me some suggestion?





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Received on Wed Oct 15 2008 - 05:10:47 PDT
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