AMBER Archive (2006)

Subject: Re: AMBER: Amber9 test error on SGI Altix

From: Ray Luo (
Date: Tue May 09 2006 - 07:57:57 CDT

Please patch the latest Amber9 bugfixes and try again. wrote:

>Dear Amber Users,
> Compilation went peacefully(both serial and parallel 64 bit
>compilation) on SGI Altix using intel fortran compiler
>9.0.031. I am not able to figure out the error while
>running test.serial.
>%%%%%%%%%%%%%% test.serial error %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>cd dmp; ./Run.dmp
>diffing with mdout.dmp
>possible FAILURE: check mdout.dmp.dif
>cd adenine; ./Run.adenine
>diffing with mdout.adenine
>possible FAILURE: check mdout.adenine.dif
>cd cytosine; ./Run.cytosine
> ./Run.cytosine: Program error
>make: *** [test.sander.BASIC] Error 1
>On openning cytosine.out I got the following error
>vlimit exceeded for step 3; vmax = 217.6443
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 1 1 1 2
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>test.parallel error is totally different
>cd cytosine; ./Run.cytosine
>MPI: On host altix, Program /altix_home/scratch/amber9/exe/sander.MPI,
>Rank 0, Process 27101 called MPI_Abort(<communicator>, 1)
>MPI: --------stack traceback-------
>Assertion failed: addrSize == 4 src/st/file/parsesymsdwarf2.C 2246
>This is an unexpected condition and may indicate the presence of a defect.
>If you wish to report this, please include the stack trace that follows.
>Do not know how to unwind a stack on this machine!!
>The "where" command has failed because there is no running program.
>MPI: Linux Application Debugger for 32-bit applications, Version 7.0,
>Build 20021021
>MPI: Reading symbolic information ...
>MPI: -----stack traceback ends-----
>MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
>MPI: aborting job
> ./Run.cytosine: Program error
>make[1]: *** [test.sander.BASIC] Error 1
>make[1]: Leaving directory `/altix_home/scratch/amber9/test'
>make: *** [test.sander.BASIC.MPI] Error 2
>Thanks in advance
>The AMBER Mail Reflector
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Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
Home page:

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