AMBER Archive (2008)

Subject: Re: AMBER: compiling PMEMD with MKL10.0

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Feb 26 2008 - 05:00:32 CST

Hi Alessandro:
Could you please disclose the config file you used to compile pmend with intel
compilers? With version 9, Debian Linux amd64, and OpenMPI I was unsuccessful
(while sander compiled OK). Perhaps the problem is OpenMPI.

Thanks
francesco pietra

--- Alessandro Nascimento <al.s.nascimento_at_gmail.com> wrote:

> Hi amber users/developers/gurus,
>
> I tried recently to compile amber 9 using icc (10.1), ifort (10.1) and mkl(
> 10.0.1) and found the errors shown below.
> sander and other amber programs compile okay. However, PMEMD couldn't be
> compiled.
>
> It seems that mkl libraries are not being correctly used during compilation
> (the amber developers mailing list had something in this way)
> Wihtou MKL, I can compile PMEMD, but since it seems to improve the
> performance, it would be nice to have them compiled in.
> Any suggestion on how to fix it?
>
> thanks a lot
>
> (...)
> ifort -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
> -L/opt/intel/mkl/10.0.1.014/lib/em64t
> -lmkl_em64t -lpthread -limf -lsvml
> -Wl,-rpath=/opt/intel/cce/10.1.012/lib:/opt/intel/fce/10.1.012/lib
>
/opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_intel_thread.a(vml_threading_templates.o):
> In function `mkl_vml_service_threader_z_1i_c_1o':
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x5a):
> undefined reference to `__kmpc_global_thread_num'
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x131):
> undefined reference to `__kmpc_ok_to_fork'
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x156):
> undefined reference to `__kmpc_push_num_threads'
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x1b6):
> undefined reference to `__kmpc_fork_call'
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x1d4):
> undefined reference to `__kmpc_serialized_parallel'
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x251):
> undefined reference to `__kmpc_end_serialized_parallel'
>
> (...)
>
> /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_intel_thread.a(mkl_threading.o):
> In function `MKL_Get_Max_Threads':
> __tmp_mkl_threading.c:(.text+0x55): undefined reference to `omp_in_parallel'
> __tmp_mkl_threading.c:(.text+0x77): undefined reference to
> `omp_get_max_threads'
> /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_intel_thread.a(mkl_threading.o):
> In function `MKL_Domain_Get_Max_Threads':
> __tmp_mkl_threading.c:(.text+0x857): undefined reference to
> `omp_in_parallel'
> __tmp_mkl_threading.c:(.text+0x878): undefined reference to
> `omp_get_max_threads'
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory `/usr/local/amber9/src/pmemd/src'
> make: *** [all] Error 2
>
>
> My architecture:
>
> ~ $ uname -a
> Linux protoss 2.6.20-gentoo-r8 #24 SMP Thu Jun 21 11:23:54 GMT 2007 x86_64
> Intel(R) Core(TM)2 Quad CPU @ 2.40GHz GenuineIntel GNU/Linux
>
>
> --
> [ ]s
>
> --alessandro
>

     
____________________________________________________________________________________
Looking for last minute shopping deals?
Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping

      ____________________________________________________________________________________
Never miss a thing. Make Yahoo your home page.
http://www.yahoo.com/r/hs
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu