Hi Carlos,
No problem.
I second (or third or 4th or ...) your request for someone
to thoroughly inspect the LES/PIMD/NEB code.
It smells fishy to me.
Scott
On Tue, 18 Sep 2007, Carlos Simmerling wrote:
> Hi Scott,
> I finally have time to get back to this.
> thanks for the info- I didn't mean to imply that
> you did something wrong, just pointing out (as you
> had already done I guess!) that the NEB test case
> didn't work and apparently had not been run in a long
> time. I didn't make the test case (or write the code)
> but in trying to use it I wanted to make sure everyone
> knows it does not work.
>
> the LES/PIMD/NEB stuff is convoluted and it's not clear
> which parts of the code are for which method, and
> I'm not sure who knows how any of it is working...
> some of the "LES" code is really for PIMD or NEB and
> there's not enough info in the code for me to know
> how to fix it (as you said).
>
> Perhaps Wei or whoever wrote this could please look
> at it and either add more comments or fix the code?
>
> thanks again
> Carlos
>
> On 9/6/07, Scott Brozell <sbrozell.scripps.edu> wrote:
> >
> > Hi,
> >
> > On Thu, 6 Sep 2007, Carlos Simmerling wrote:
> >
> > > Scott- I tracked this problem down to something you recently changed in
> > > sander.f
> > >
> > > ! SRB 07/2007 added pimd initialization for neb; this should be
> > > verified!
> > > if ( ipimd > 0 .or. ineb > 0 ) then
> > >
> > > this causes the same variables to be allocated in pimd_init and
> > neb_init.
> > >
> > > was there a reason for needing this, or should I revert it back?
> >
> > The reasons were given in the cvs logs:
> > RCS file: /thr/loyd/case/cvsroot/amber10/src/sander/sander.f,v
> > ----------------------------
> > revision 9.27
> > date: 2007/07/20 21:58:53; author: sbrozell; state: Exp; lines: +4 -1
> > Added pimd initialization for the case ipimd == 0 and ineb > 0.
> > Pimd initialization for neb is necessary because neb uses
> > several allocated pimd variables; pimd_vars:: nrg_all and
> > full_pimd_vars:: xall for example.
> > However, I have no idea whether I have done this correctly !
> > In addition, the role of neb in subroutine do_pme_recip looks
> > very suspicious.
> > There are currently no test cases with LES and neb.
> > Thus, pimd, neb, and les related code should be carefully inspected
> > by their developers !!!!!
> > ----------------------------
> > RCS file: /thr/loyd/case/cvsroot/amber10/src/sander/ew_force.f,v
> > revision 9.18
> > date: 2007/07/20 21:21:04; author: sbrozell; state: Exp; lines: +7 -5
> > Corrected the bug exercised by test/LES/Run.PME_LES.
> > This bug caused a seg fault because allocated variable
> > part_pimd_vars::pimd_mmchg was used without being defined.
> > I added the same guarding-if-statement used in another section
> > of subroutine do_pme_recip. That seems correct; however, do_pme_recip
> > should be carefully examined because the interplay between pimd, neb,
> > les, and variable mpoltype is not clear to me; in particular,
> > I wonder whether the last les ifdef code fragment should be inside
> > the mpoltype == 0 if-statement ????? Here is the fragment:
> > #ifdef LES
> > if( ipimd > 0 ) then
> > eer = eer_sum/ncopy
> > frc = frc + ftmp/ncopy
> > frcx_copy = frcx_copy/ncopy
> > end if
> > #endif
> > Regardless, the logic in do_pme_recip should be less convoluted or
> > at least clarified with comments.
> > In addition, the role of neb in do_pme_recip looks very suspicious.
> > There are currently no test cases with LES and neb.
> >
> >
> > And the mess was reported to amber-developers:
> > Date: Fri, 20 Jul 2007 15:18:46 -0700
> > From: Scott Brozell <sbrozell.scripps.edu>
> > Subject: amber-developers: PIMD, NEB, LES - request for code inspection
> > and tests
> >
> >
> > My commits were patches to get the code to compile and to not crash.
> > This was in context of the nightly testing.
> > In addition to my requests above for more tests of these features,
> > let us have some tests with small numbers of processors - 1 or 2 or maybe
> > 4.
> > The nightly tests are not running the neb tests because they
> > uses only 2 processors:
> > cd neb/neb_gb; ./Run.neb_classical
> > This test case requires a least 8 mpi threads.
> > The number of mpi threads must also be a multiple of 8 and not more than
> > 24.
> > Not running test, exiting.....
> > cd neb/neb_gb_large_system; ./Run.neb_ls_classical
> > This test case requires a least 32 mpi threads.
> > The number of mpi threads must also be a multiple of 32 and not more than
> > 128.
> > Not running test, exiting.....
> > export TESTsander=/tmp/amber10/exe/sander.LES.MPI; make
> > test.sander.PIMD.partial
> > make[1]: Entering directory `/tmp/amber10/test'
> > cd PIMD/part_pimd_water; ./Run.pimd
> > This test not set up for parallel
> > cannot run in parallel with #residues < #pes
> > cd PIMD/part_nmpimd_water; ./Run.nmpimd
> > This test not set up for parallel
> > cannot run in parallel with #residues < #pes
> >
> >
> > The ball is in the court of the PIMD, NEB, LES developers.
> >
> > Scott
> >
> >
> > > On 9/6/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> > > >
> > > > is the neb test case failing for anyone else with the current amber10
> > CVS
> > > > version?
> > > > The test case as well as my own runs are giving me
> > > >
> > > > ASSERTion 'ierr.eq.0' failed in pimd_init.f at line 240.
> > > >
> > > > I don't see anything obviously wrong with that code.
> > > >
> > > > just checking to see if anyone else is seeing this.
> > > > carlos
> > >
> >
> >
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling.gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
>
Received on Wed Sep 19 2007 - 06:07:42 PDT
