(Here is the 2nd time I sent this message because it seems that the message is not in format)
Dear Prof.Case and Amber's developers,
I skipped the parallel installation for AmberTools 1.5 (as your suggestion) and then I installed Amber 11. I followed the steps,
% cd $AMBERHOME/AmberTools/src
% make clean
% ./configure -mpi intel
then remove the flags "-axSTPW" and "-ip" from file "config.h"
% cd $AMBERHOME
% ./AT15_Amber11.py
% cd $AMBERHOME/src
% make parallel
I encountered the error message as bellow. Could you please suggest me to solve the problem?
Thank you very much in advance.
-Xioling-
============
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Referenced in libFpbsa.a(amg1r5.o)
Referenced in libFpbsa.a(qs2i1d.o)
Referenced in libnetcdf.a(ncx.o)
IPO Error: unresolved : __svml_cos2
Referenced in libFpbsa.a(sa_driver.SANDER.o)
IPO Error: unresolved : __svml_sin2
Referenced in libFpbsa.a(sa_driver.SANDER.o)
IPO Error: unresolved : __svml_cosh2
Referenced in libFpbsa.a(pb_nlsolver.o)
IPO Error: unresolved : __svml_sinh2
Referenced in libFpbsa.a(pb_nlsolver.o)
/softwares/amber11/lib/libFpbsa.a(pb_force.SANDER.o)(.text+0x3d2f): In function `poisson_boltzmann_mp_gradu_.A':: undefined reference to `__intel_f2int'
/softwares/amber11/lib/libFpbsa.a(pb_force.SANDER.o)(.text+0x3d58): In function `poisson_boltzmann_mp_gradu_.A':: undefined reference to `__intel_f2int'
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/softwares/amber11/lib/libFpbsa.a(coed20.o)(.text+0xeed): In function `coec20_.A':: undefined reference to `__intel_f2int'
/softwares/amber11/lib/libFpbsa.a(coed20.o)(.text+0x4a79): In function `coed20_.A':: undefined reference to `__intel_f2int'
/softwares/amber11/lib/libFpbsa.a(coed20.o)(.text+0x4ede): more undefined references to `__intel_f2int' follow
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/softwares/amber11/src/sander'
make: *** [parallel] Error 2
=================
> >
> > However, for AmberTools, I can't compile as parallel.
>
> In addition to the comments Jason made, be sure that you have a need for
> a parallel build of AmberTools. This is a fairly specialized option:
>
> 1. the parallel version of ptraj requires a high-end computer with a parallel
> file system to give much benefit.
>
> 2. the parallel version of NAB can be quite useful, but be sure that you are
> planning to do large-scale NAB simulations. Even then, the openmp version of
> NAB might be better than the mpi version -- depends on your hardware
> configuration, but openmp is what I always use.
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Received on Thu Jun 16 2011 - 04:00:03 PDT
