[AMBER-Developers] PBSA/sander worries

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 24 Dec 2011 23:50:27 -0500


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

common/mdi/nrp,nspm,ig, & !3
Warning: Named COMMON block 'mdi' at (1) shall be of the same size

common/mdr/t,dt,temp0,tautp,pres0,comp,taup,temp,tempi, & !9
Warning: Named COMMON block 'mdr' at (1) shall be of the same size

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
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

                                   sa_init, sa_driver, sa_free, sa_free_mb,

Error: Symbol 'saslave_init' referenced at (1) not found in module
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?


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Sat Dec 24 2011 - 21:00:03 PST
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