Re: AMBER: MM_PBSA error

From: Xin Hu <hux.mail.rockefeller.edu>
Date: Mon, 11 Apr 2005 18:33:51 -0400

Hi Holger,
Thank you very much for your help. I looked over out sander program and
there is only one parallel executable of "sander" (when I compiled the
parallel version, it replaced the 'serial' version of sander). (Actually
this version is both working for single and multiple processors.)

 As you suggested, should I go ahead to re-compile a "serial" amber again
and get a "single-CPU sander" (named sander_serial)? so I can specify in the
mm_pbsa.in file: SANDER /usr/local/amber8/exe/sander_serial". I will try to
re-compile and let you know the result.

Thanks,

Xin

---
----- Original Message ----- 
From: "Holger Gohlke" <gohlke.bioinformatik.uni-frankfurt.de>
To: <amber.scripps.edu>
Sent: Monday, April 11, 2005 4:49 PM
Subject: Re: AMBER: MM_PBSA error
> Hi,
>
> I think the problem is that the sander version that is called by mm_pbsa
> is the parallel version, which requires to set "mpirun" or the like in
> front of the sander call. You should be able to circumvent this by
> adding a line "SANDER <path_to_a_one_processor_version_of_sander>" to
> the end of the mm_pbsa.in file (in the section .PROGRAMS).
>
> Best regards
>
> Holger
>
>
>
> Xin Hu schrieb:
>
> Dear Amber user
>
> I have a problem with the MM_PBSA calculation. I followed the examples
> in /src/mm_pbsa/example/02_MMPBSA_Stability to run the calculation on
> entropy energies,
>
> it showed an error:
>
> =>> Calculating energy / entropy contributions
>    Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1
>        Calc MM/GB/SAS
>
>  Unit    6 Error on OPEN: sander_com.1.out
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_14716:  p4_error: : 1
>        /usr/local/amber8/exe/sander -O -i sander_com.in -o
> sander_com.1.out -c ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1 -p
> ../ras_raf_II_wt.prmtop not successful
>
> I was aware that if I ingore the path specified in the command, or I add
> the full  path (the working directory) to the output files, it works
> properly.
>
> So I tried to modify the script in src/mm_pbsa, the script
> "mm_pbsa_util.pm" or "mm_pbsa_calceneent.pm", attemping to delete the
> path associated with command "sander", or adding
>
> path to the output file, however, neither way is working with errors
> showing "compilation failed" "strict subs" etc.
>
> I wonder if anyone has caught the same problem and I appreciate for
> help. The Amber8 is runnung on a linux cluster with MPI on parallel.
>
> Thanks,
>
> Xin
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Received on Mon Apr 11 2005 - 23:53:00 PDT