AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Feb 12 2009 - 08:54:49 CST

Hi Vijay,

Try adding -lpthread to the end of the library line.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Vijay Manickam Achari
> Sent: Thursday, February 12, 2009 1:14 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] amber9 installation problem in SMP IA64
>
> 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_templa
> tes.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_templa
> tes.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_templa
> tes.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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
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