AMBER Archive (2009)

Subject: Re: [AMBER] amber9 installation problem in SMP IA64

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu Feb 12 2009 - 03:13:55 CST

When I compile pmemd, I get error as below too:

post this in malling group for pmemd installation in smp.thx.

/usr/local/amber9/src/pmemd # ./configure sgi_altix ifort lam fftw bintraj
then, edit the config.h to use hf77 instead of ifort
make install --> failed as below:
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x8032): undefined reference to `__kmpc_fork_call'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x8052): undefined reference to `__kmpc_serialized_parallel'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x80d2): undefined reference to `__kmpc_end_serialized_parallel'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x8232): undefined reference to `__kmpc_for_static_init_4'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x83a2): undefined reference to `__kmpc_for_static_fini'
/opt/intel/mkl/10.0.010//lib/64/libmkl_intel_thread.a(vml_threading_templates.o): In function `mkl_vml_service_threader_s_1i_1o':
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x84b2): undefined reference to `__kmpc_global_thread_num'
/opt/intel/mkl/10.0.010//lib/64/libmkl_intel_thread.a(vml_threading_templates.o): In function `L_mkl_vml_service_threader_s_1i_1o_1924__par_loop15_2$15':
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x8842): undefined reference to `__kmpc_ok_to_fork'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x8872): undefined reference to `__kmpc_push_num_threads'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x88d2): undefined reference to `__kmpc_fork_call'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x88f2): undefined reference to `__kmpc_serialized_parallel'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x8962): undefined reference to `__kmpc_end_serialized_parallel'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x8ab2): undefined reference to `__kmpc_for_static_init_4'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x8c12): undefined reference to `__kmpc_for_static_fini'
/opt/intel/mkl/10.0.010//lib/64/libmkl_intel_thread.a(vml_threading_templates.o): In function `mkl_vml_service_openmp_get_num_procs':
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x8cd2): undefined reference to `omp_get_num_procs'
/opt/intel/mkl/10.0.010//lib/64/libmkl_intel_thread.a(mkl_threading.o): In function `MKL_Get_Max_Threads':
__tmp_mkl_threading.c:(.text+0x1a2): undefined reference to `omp_get_max_threads_'
__tmp_mkl_threading.c:(.text+0x1d2): undefined reference to `omp_in_parallel_'
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/pmemd/src'
make: *** [install] Error 2
ptmlxsmp:/usr/local/amber9/src/pmemd #

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
 vjramana_at_gmail.com

--- On Wed, 11/2/09, David A. Case <case_at_biomaps.rutgers.edu> wrote:

> From: David A. Case <case_at_biomaps.rutgers.edu>
> Subject: Re: [AMBER] amber9 installation problem in SMP IA64
> To: vjrajamany_at_yahoo.com, "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Wednesday, 11 February, 2009, 9:07 PM
> On Wed, Feb 11, 2009, Vijay Manickam Achari wrote:
>
> > Thanks for the help. But when I run accordingly I get
> some errors too.
> > I have posted the error as below:
> >
> >
> > Installation of Amber9 (serial) is complete at Wed Feb
> 11 12:13:08 MYT 2009..
>
> This part looks good.
>
> >
> > /usr/local/amber9/src #
> > /usr/local/lam-7.0.6 # make distclean
> > /usr/local/lam-7.0.6 # ./configure
> --prefix=/usr/local/lam CC=icc FC=ifort CXX=icpc
> > /usr/local/lam-7.0.6 # make install
> > /usr/local/amber9/src # export
> MPI_HOME=/opt/mpich/ch-p4mpd
>
> I'm rather confused here. Why are you (apparently)
> configuring lam, and
> then setting MPI_HOME to mpich?
>
> > /opt/mpich/ch-p4mpd/lib/libmpich.a(farg.o): In
> function `mpir_iargc_':
> > (.text+0x22): undefined reference to
> `_gfortran_iargc'
>
> This certainly implies that your mpich setup used gfortran,
> but your
> sander installation is using ifort. You must use the same
> compiler to
> compile MPI as Amber.
>
> ....dac
>
>
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> AMBER_at_ambermd.org
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