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-
============... 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'.../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 `__inte
l_f2int'/softwares/amber11/lib/libFpbsa.a(coed20.o)(.text+0x4ede): more undefined references to `__intel_f2int' followmake[1]: *** [sander.MPI] Error 1make[1]: Leaving directory `/softwares/amber11/src/sander'make: *** [parallel] Error 2
=================
> Date: Wed, 15 Jun 2011 08:07:43 -0400
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] Parallel compilation of AmberTools1.5 failed
>
> On Wed, Jun 15, 2011, Xioling Chuang wrote:
> >
> > 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 Wed Jun 15 2011 - 22:30:03 PDT
