AMBER Archive (2005)

Subject: Re: AMBER: MM_PBSA error

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Mon Apr 11 2005 - 17:33:51 CDT


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

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----- Original Message ----- From: "Holger Gohlke" <gohlke_at_bioinformatik.uni-frankfurt.de> To: <amber_at_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 > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >

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