AMBER Archive (2009)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Apr 07 2009 - 07:43:36 CDT

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_at_yahoo.com>
To: "AMBER Mailing List" <amber_at_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
xtprmtop_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_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/makefailed -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 c
ompletely 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_thr
eading_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>>>>>>> > _____________________________________
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