Xin Hu schrieb:
>
> 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.
Yes, this is what I would do.
Best regards
Holger
>
> 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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>
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Received on Tue Apr 12 2005 - 07:53:02 PDT
