AMBER Archive (2009)

Subject: Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Mon Apr 06 2009 - 23:25:36 CDT

Robert,
I have altered the MATH_LIBS param. the config.h with your given suggestion as below:
MATH_LIBS = -L$MKL_HOME/lib/64/ -Wl,--start-group $MKL_HOME/lib/64/libmkl_intel.a $MKL_HOME/lib/64/libmkl_sequential.a $MKL_HOME/lib/64/libmkl_core.a -Wl,--end-group -lpthread

But still errors occured as below:
ifort -c -auto -IPF_fma -ftz -ip -O3 erfcfun.f90
ifort -i-static -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o parallel.o pme_direct.o pme_recip.o pme_fft.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o cit.o dynamics.o bonds.o angles.o dihedrals.o runmd.o loadbal.o shake.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls..o nmr_lib.o get_cmdline.o master_setup.o alltasks_setup.o pme_setup.o ene_frc_splines.o nextprmtop_section.o -LKL_HOME/lib/64/ -Wl,--start-group KL_HOME/lib/64/libmkl_intel.a KL_HOME/lib/64/libmkl_sequential.a KL_HOME/lib/64/libmkl_core.a -Wl,--end-group -lpthread -lmpi
 -Wl,-rpath=/opt/intel/ipp/5.3/itanium/sharedlib:/opt/intel/mkl/10.0.010/lib/64:/opt/intel/fc/10.1.008/lib:/opt/intel/cc/10.1.008/lib:/opt/intel/fc/10.1.008/lib:/opt/intel/cc/10.1.008/lib:/usr/lib:/usr/local/lib
gb_ene.o: In function `gb_ene_mod_mp_gb_ene_':
gb_ene.f90:(.text+0x2152): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x22f2): undefined reference to `vdexp_'
gb_ene.f90:(.text+0x24e2): undefined reference to `vdinvsqrt_'
gb_ene.f90:(.text+0x2542): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x2672): undefined reference to `vdexp_'
gb_ene.f90:(.text+0x2692): undefined reference to `vdinvsqrt_'
gb_ene.f90:(.text+0x4e72): undefined reference to `vdinvsqrt_'
gb_ene.f90:(.text+0x5612): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x5632): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x5802): undefined reference to `vdln_'
gb_ene.o: In function `gb_ene_mod_mp_calc_born_radii_':
gb_ene.f90:(.text+0xe152): undefined reference to `vdinvsqrt_'
gb_ene.f90:(.text+0xefd2): undefined reference to `vdinv_'
gb_ene.f90:(.text+0xeff2): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x105d2): undefined reference to `vdln_'
gb_ene.f90:(.text+0x105f2): undefined reference to `vdln_'
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/pmemd/src'
make: *** [install] Error 2

Thanks for your assistance.

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

--- On Mon, 6/4/09, Robert Duke <rduke_at_email.unc.edu> wrote:

> From: Robert Duke <rduke_at_email.unc.edu>
> Subject: Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Monday, 6 April, 2009, 10:25 PM
> Okay, I don't have one of these machines handy, but
> there are two problems here, at least:
> 1) you specified the use of fftw, but you don't have it
> (or at least not the necessary info to find the libraries)
> 2) you specified MKL - not a problem in itself - but with
> MKL 10, the library layout has been completely whacked by
> our dear friends at intel, and we need to change the library
> linkage info.
>
> So first of all, fftw really does not help much, if at all,
> especially on more than one processor, so just configure for
> my public fft's:
>
> ./configure sgi_altix ifort mpi pubfft
>
> Secondly, we need to change the mkl linkage info (you could
> also just opt to not use mkl, and as long as you are not
> running generalized Born simulations, it won't matter
> much - you decide not to use mkl as part of the
> "configure" dialog):
>
> Anyway, best current guess for mkl linkage info, assuming
> you want MKL, is:
>
> MATH_LIBS = -L$MKL_HOME/lib/64/ -Wl,--start-group
> $MKL_HOME/lib/64/libmkl_intel.a
> $MKL_HOME/lib/64/libmkl_sequential.a
> $MKL_HOME/lib/64/libmkl_core.a -Wl,--end-group -lpthread
>
> (so you need to substitute in this line for the $MKL_HOME
> variable, and stick the result in config.h in place of the
> current definition of MATH_LIBS)
>
> I have no reason to believe that the 3 lines you added at
> the end of config.h are doing you any good.
>
> Regards - Bob Duke
>
> ----- Original Message ----- From: "Vijay Manickam
> Achari" <vjrajamany_at_yahoo.com>
> To: "Amber mailing List"
> <AMBER_at_ambermd.org>
> Sent: Monday, April 06, 2009 3:27 AM
> Subject: [AMBER] pmemd compilation/make failed
> -mkl_vml_service_threader_z_1i_c_1o
>
>
> Hi,
> I am configuring pmemd in SMP machine SGI Altix 4700
> itanium 128 cores (SLES 10.2 IA64 Intel compilers & MKL
> version 10.0.010) as below:
> /usr/local/amber9/src/pmemd # ./configure sgi_altix ifort
> mpi fftw
>
> But the compilation failed, as errors below:
>
> fft1d.f90:(.text+0x8c2): undefined reference to
> `dfftw_destroy_plan_'
> fft1d.o: In function `fft1d_mod_mp_fft1d_create_':
> fft1d.f90:(.text+0xbc2): undefined reference to
> `dfftw_plan_dft_1d_'
> fft1d.f90:(.text+0xbf2): undefined reference to
> `dfftw_plan_dft_1d_'
> /opt/intel/mkl/10.0.010/lib/64/libmkl_intel_thread.a(vml_threading_templates.o):
> In function `mkl_vml_service_threader_z_1i_c_1o':
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x92):
> 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_z_1i_c_1o_2325__par_loop0_2$0':
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x442):
> undefined reference to `__kmpc_ok_to_fork'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x472):
> undefined reference to `__kmpc_push_num_threads'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x4e2):
> undefined reference to `__kmpc_fork_call'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x502):
> undefined reference to `__kmpc_serialized_parallel'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x582):
> undefined reference to `__kmpc_end_serialized_parallel'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x6f2):
> undefined reference to `__kmpc_for_static_init_4'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x852):
> 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_z_1i_2o':
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x9c2):
> 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_z_1i_2o_2299__par_loop1_2$1':
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xd52):
> undefined reference to `__kmpc_ok_to_fork'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xd82):
> undefined reference to `__kmpc_push_num_threads'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xdf2):
> undefined reference to `__kmpc_fork_call'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xe12):
> undefined reference to `__kmpc_serialized_parallel'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xe92):
> undefined reference to `__kmpc_end_serialized_parallel'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xff2):
> undefined reference to `__kmpc_for_static_init_4'
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x1162):
> 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_z_2i_1o':
> _tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x1282):
> 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_z_2i_1o_2273__par_loop2_2$2':
>
> Attached is the config.h file for your review. Please
> assist me in this. Thanks.
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana_at_gmail.com
>
>
>
>
>
>
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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