AMBER Archive (2004)

Subject: Re: AMBER: erreo in sander

From: David A. Case (
Date: Sat Mar 27 2004 - 03:13:20 CST

On Sat, Mar 27, 2004, Anshul Awasthi wrote:

> I am a very new user to amber and currently I am facing problem running
> minimization in sander. it says dbx not found. can anyone help me with this.
> MPI: Program /usr/people/bvs/amber7/exe/sander, Rank 0, Process 22712
> called MPI
> _Abort(<communicator>, 1)
> MPI: --------stack traceback-------
> PC: 0x5fe5080 MPI_SGI_stacktraceback in /usr/lib32/
> PC: 0x600e080 PMPI_Abort in /usr/lib32/
> PC: 0x603e018 pmpi_abort_ in /usr/lib32/
> PC: 0x1010649c mexit in /usr/people/bvs/amber7/exe/sander
> PC: 0x1008b834 compute_nfft in /usr/people/bvs/amber7/exe/sander
> PC: 0x10091d4c read_ewald in /usr/people/bvs/amber7/exe/sander
> PC: 0x1008e138 load_ewald_info in /usr/people/bvs/amber7/exe/sander
> PC: 0x10048d84 mdread1 in /usr/people/bvs/amber7/exe/sander
> PC: 0x10008c18 sander in /usr/people/bvs/amber7/exe/sander
> PC: 0xaed9d74 main in /usr/lib32/
> sh: dbx: not found
> MPI: -----stack traceback ends-----
> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
> MPI: aborting job

The traceback above indicates that the code got as far as "mexit()", which
means it was trying to quit, and failed. It looks like mexit() itself
was called from compute_nfft(), and that sander was unable to compute a good
fft size for your calculation.

You should post your input (mdin) file, which might have some clues, and
at least some information about what sort of calculation you are trying to
run. The specific problem above (a failure in mexit) seems related to MPI.
One suggestion is to do a "make clean" in the src directory, and to compile
a non-parallel version of sander. That should allow mexit() to succeed
in stopping the program, but will not solve the underlying problem in
compute_nfft(). Once everything is working in the non-parallel environment,
you can try again with a parallel run.

...hope this helps...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to