Xingping,
You should email to the amber-developer's list, not the amber mailing list ...
Ray
On Tue, Mar 27, 2012 at 6:00 PM, Xingping Liu <xingpinl.uci.edu> wrote:
> Hi all,
>
> I traced down the problem and found the difference is triggered by a
> 1.0e-10 important digit difference through linear algebra library
> subroutines between 32bit and 64bit machine. The difference would then
> jump to 1.0e-4 in the next iteration. And the sgesvd() can be more
> stable and would make the tests pass on 32bit machine.
>
> There is no specific reason for using dsvdc() instead of dgesvd().
> Maybe we should just set isvd to 2 to save the energy to look into the
> library subroutines.
>
> Best Regards!
> Xingping (From Dr. Ray Luo's lab)
>
>> Qin are seeing the same problem on a 32bit Linux, we are looking into it
> ...
>> Ray
>> On Fri, Mar 23, 2012 at 9:37 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>> Hi All,
>>> I've come across several issues related to PBSA under cygwin.
>>> AmberTools:
>>> Failure: pbsa_aug_c2 (Li.out, Cl.out, MG.out, Ca.out) Failure:
>>> sas2test (Rb.out.5, IM.out.5)
>>> All 6 errors have the same format:
>>> < The gmres dimension is 185
>>> > 10 - ssvdc() or sgesvd() failed in GrToPr!
>>> If I switch isvd from 1 to 2 in GrToPr.F90 (line 48) the errors go
> away, so unless there is some reason it shouldn't be set at 2 we can
> just put an ifdef for CYGWIN and make isvd = 2, otherwise default to 1
> (patch for GrToPr.F90 attached).
>>> Amber:
>>> 3 failures (sander_pbsa_tsr, sander_pbsa_ligand, 02_MMPBSA_Stability)
> All 3 exit with similar error messages:
>>> SA Bomb in sa_arc()3: Allocates aborted 0 0 5014
> 0 0
>>> I think this might be related to the fixed stack size in cygwin but
> since I can't easily change the stack size its tough to test. I'm
> looking into it but maybe the pbsa devs have an idea?
>>> Failure: sander_pbsa_frc (dbf_2/dadt/force.dat)
>>> 3c3
>>> < -0.961100E-01 -0.424215E+00 -0.888034E-01 ---
>>> > -0.961417E-01 -0.423961E+00 -0.894469E-01
>>> 40c40
>>> < -0.961100E-01 -0.424215E+00 -0.888034E-01 ---
>>> > -0.961417E-01 -0.423961E+00 -0.894469E-01
>>> Seems like round-off.
>>> Failure: sander_pbsa_frc (dbf_2/dgdc/force.dat)
>>> 16c16
>>> < 0.620819E-01 -0.187438E+01 0.140104E+01 ---
>>> > 0.754525E-01 -0.189257E+01 0.132932E+01
>>> 52c52
>>> < 0.620819E-01 -0.187438E+01 0.140104E+01 ---
>>> > 0.754525E-01 -0.189257E+01 0.132932E+01
>>> Some of these differences seem a little too big to be round-off; maybe
> the pbsa devs can comment on this.
>>> -Dan
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
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Received on Tue Mar 27 2012 - 19:30:03 PDT
