Robert,
The same errors again.
Attached is the updated config.h script.
ifort -c -auto -IPF_fma -ftz -ip -O3 pmemd.f90
/lib/cpp -traditional -P -DPUBFFT -DMPI -DSLOW_INDIRECTVEC -DMKL -DGB_IA64_ACCEL erfcfun.fpp erfcfun.f90
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 -L/opt/intel/mkl/10.0.010/lib/64/ -Wl,--start-group /opt/intel/mkl/10.0.010/lib/64/libmkl_intel.a /opt/intel/mkl/10.0.010/lib/64/libmkl_sequential.a /opt/intel/mkl/10.0.010/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: *** [all] 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.gmail.com
--- On Tue, 7/4/09, Robert Duke <rduke.email.unc.edu> wrote:
> From: Robert Duke <rduke.email.unc.edu>
> Subject: Re: [AMBER] pmemd compilation/makefailed-mkl_vml_service_threader_z_1i_c_1o
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Tuesday, 7 April, 2009, 8:55 PM
> Oops. Looking at the script again, you would actually want
> to set $MKL_HOME to /opt/intel/mkl/10.0.010 as the lib/64/
> part is already in the library names you list.
> Regards - Bob
> ----- Original Message ----- From: "Robert Duke"
> <rduke.email.unc.edu>
> To: <vjrajamany.yahoo.com>; "AMBER Mailing
> List" <amber.ambermd.org>
> Sent: Tuesday, April 07, 2009 8:43 AM
> Subject: Re: [AMBER] pmemd
> compilation/makefailed-mkl_vml_service_threader_z_1i_c_1o
>
>
> > Looks to me like you did not substitute the actual
> location of the math kernel libraries for $MKL_HOME in the
> config.h script. You must plug in this value. You could
> also place MKL_HOME = /opt/intel/mkl/10.0.010/lib/64 in a
> line above the line defining MATH_LIBS, and then change all
> references to $MKL_HOME to $(MKL_HOME).
> > Regards - Bob Duke
> >
> > ----- Original Message ----- From: "Vijay
> Manickam Achari" <vjrajamany.yahoo.com>
> > To: "AMBER Mailing List"
> <amber.ambermd.org>
> > Sent: Tuesday, April 07, 2009 12:25 AM
> > Subject: Re: [AMBER] pmemd compilation/make
> failed-mkl_vml_service_threader_z_1i_c_1o
> >
> >
> >
> > Robert,
> > I have altered the MATH_LIBS param. the config.h with
> your given suggestion as below:
> > MATH_LIBS = -L$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 prmtop_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/libgb_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 1make[1]:
> Leaving directory `/usr/local/amber9/src/pmemd/src'make:
> *** [install] Error 2Thanks for your assistance.Vijay
> Manickam Achari(Phd Student c/o Prof Rauzah Hashim)Chemistry
> Department,University of Malaya,Malaysia
> vjramana.gmail.com--- On Mon, 6/4/09, Robert Duke
> <rduke.email.unc.edu> wrote:> From: Robert Duke
> <rduke.email.unc.edu>> Subject: Re: [AMBER] pmemd
> compilation/makefailed
> -mkl_vml_service_threader_z_1i_c_1o> To: "AMBER
> Mailing List" <amber.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 co
> > mpletely 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.yahoo.com>> To: "Amber mailing
> List"> <AMBER.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_templ!
> > ates.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/vm!
> > l_thread
> > ing_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.gmail.com>>>>>>> >
> _______________________________________________> >
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Received on Wed Apr 08 2009 - 01:22:17 PDT
