AMBER Archive (2006)

Subject: AMBER:

From: Ross Walker (
Date: Sat Nov 04 2006 - 11:35:43 CST

Dear Lee,

Firstly did you apply the patch I sent several days ago to address hanging
when running in parallel? Did it work?

>I installed amber9 single version in intel itanium server called white box.
>After install, I runned testcase with make test.sander.QMMM.
>In crambin_md.out, I got strange messages as follow.

This is in serial yes?

>QMMM: Unable to achieve self consistency to the tolerances specified
>QMMM: No convergence in SCF after 1000 steps.
>QMMM: Job will continue with unconverged SCF. Warning energies
>QMMM: and forces for this step will not be accurate.
>QMMM: E = -0.2405E+06 DeltaE = 0.3389E-01 DeltaP = 0.2716E-01
>QMMM: Smallest DeltaE = 0.3947E-02 DeltaP = 0.5110E-01 Step = 74
>vlimit exceeded for step 12; vmax = 97.6111
>How can I overcom this warning?

Since this test case passes on other system I have tried I once again
suspect that this is a case of the compiler not doing what it is supposed
to. Can you please give me detailed specs of the machine so that I can try
to track this down.

For this I will need:

Operating system and version
Details of "cat /proc/cpuinfo"
Compiler version (use ifort -V if the intel compiler - I need the full
version number. E.g. 9.1.033)
Options passed to ./configure
A complete copy of crambin_md.out from the above test case.
The results of "echo $TESTsander" and "echo $DO_PARALLEL" in the same shell
in which you are running make test.sander.QMMM

Is this the only test case that fails? Can you do exactly the following...

cd $AMBERHOME/test/
make clean

Let all tests run to completion and then send me the file

Once I have these details I can try and reproduce the problem myself and see
if I can come up with yet another workaround...

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 |

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