Oh yes, and Happy Holidays to everybody :)
On Sat, Dec 24, 2011 at 11:50 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> I have a few concerns about the sander/PBSA interface. When building in
> parallel, I hit this issue:
>
> mpif90 -c -O0 -ffree-form -I/opt/local/include -o pb_init.SANDER.o
> _pb_init.f
> _pb_init.f:394.11:
>
> common/mdi/nrp,nspm,ig, & !3
> 1
> Warning: Named COMMON block 'mdi' at (1) shall be of the same size
> _pb_init.f:426.11:
>
> common/mdr/t,dt,temp0,tautp,pres0,comp,taup,temp,tempi, & !9
> 1
> Warning: Named COMMON block 'mdr' at (1) shall be of the same size
> _pb_init.f:448.11:
>
> common/mds/
> restraintmask,bellymask,tgtfitmask,tgtrmsmask,noshakemask,crgmask,
> 1
> Warning: Named COMMON block 'mds' at (1) shall be of the same size
> cpp -traditional -P -DBINTRAJ -DMPI -DSANDER problem.f > _problem.f
> mpif90 -c -O3 -mtune=native -ffree-form -I/opt/local/include
> -I../../../src/sander \
> -o problem.SANDER.o _problem.f
> cpp -traditional -P -DBINTRAJ -DMPI decomp.f > _decomp.f
> mpif90 -c -O3 -mtune=native -ffree-form -I/opt/local/include -o decomp.o
> _decomp.f
> cpp -traditional -P -DBINTRAJ -DMPI pb_force.f > _pb_force.f
> mpif90 -c -O3 -mtune=native -ffree-form -I/opt/local/include -o
> pb_force.o _pb_force.f
> _pb_force.f:443.77:
>
> sa_init, sa_driver, sa_free,
> sa_free_mb, &
>
> 1
> Error: Symbol 'saslave_init' referenced at (1) not found in module
> 'solvent_accessibility'
> make[3]: *** [pb_force.o] Error 1
> make[2]: *** [libpbsa] Error 2
> make[1]: *** [parallel] Error 2
> make: *** [parallel] Error 2
>
>
> I'm a little concerned about a couple things here. First, this is the
> result of "make parallel" in AmberTools/src (which builds AmberTools in
> parallel first, then Amber). The compilation error went away after I ran a
> "make clean" in the pbsa directory, but I think the appropriate cleaning
> should probably be done automagically somehow (I don't think we should
> require a "make clean" between building AmberTools in parallel and Amber in
> parallel, should we?).
>
> Also, does the mismatch in common block size worry people? Should pbsa's
> md.h file and sander's md.h file be brought into line together?
>
> Thanks!
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Dec 24 2011 - 21:00:04 PST
