AMBER Archive (2009)

Subject: RE: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threade_z_1i_c_1o

From: Ross Walker (
Date: Wed Apr 08 2009 - 09:53:31 CDT

Done, sorry about this. I had it correct for everything else (em64t / opteron64 / ia32) I believe. I couldn't find an IA64 machine with anything later than MKL9.0 to test on unfortunately and this is largely where the problems lie. The degrees of freedom are now so huge :-(.

All the best

-----Original Message-----
From: [] On Behalf Of Robert Duke
Sent: Wednesday, April 08, 2009 6:36 AM
To: AMBER Mailing List
Subject: Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o

Okay, I figured it out. This is all basically due to a typo in the
configure script for amber 11 pmemd, which was never checked out. Oh, oops.
Vijay, you simply need to change the reference to libmkl_intel.a (there is
no such thing) to libmkl_intel_lp64.a. Ross, can you please fix this in the
checked-in amber11 source and wherever else this configure script might have
gotten propagated to. The change applies only to itanium 2, not the other
intel architectures, where we got this right. Vijay, sorry it took us so
long to figure out what is going on here. Too many machines, combined with
too many version-dependent linkage options for mkl.
Best Regards - Bob Duke

----- Original Message -----
From: "Vijay Manickam Achari" <>
To: "AMBER Mailing List" <>
Sent: Wednesday, April 08, 2009 2:27 AM
Subject: Re: [AMBER]

The same errors again.
Attached is the updated config.h script.

ifort -c -auto -IPF_fma -ftz -ip -O3 pmemd.f90
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
xtprmtop_section.o -L/opt/intel/mkl/10.0.010/lib/64/ -Wl,--start-group
/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/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: *** [all] Error 2ptmlxsmp:/usr/local/amber9/src/pmemd #Vijay Manickam Achari(Phd Student c/o Prof Rauzah Hashim)Chemistry Department,University of Malaya,Malaysia On Tue, 7/4/09, Robert Duke <> wrote:> From: Robert Duke <>> Subject: Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o> To: "AMBER Mailing List" <>> 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"> <>> To: <>; "AMBER Mailing>
List" <>> 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 $(MKL_HOME).> > Regards - Bob Duke> >> > ----- Original Message ----- From: "Vijay> Manickam Achari" <>> > To: "AMBER Mailing List"> <>> > Sent: Tuesday, April 07, 2009 12:25 AM> > Subject: Re: [AMBER] pmemd compilation/make> failed-mkl_vml_service_threader_z_1i_c_1o> >> >> >> > Robert,> > I have altered the MATH_LIBS param. the config.h with> your given suggestion as below:> > MATH_LIBS = -L$MKL_HOME/lib/64/ -Wl,--start-group> $MKL_HOME/lib/64/libmkl_intel.a> $MKL_HOME/lib/64/libmkl_sequential.a> $MKL_HOM
E/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/1
0.0.010/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 referen
ce 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> On Mon, 6/4/09, Robert Duke> <> wrote:> From: Robert Duke> <>> Subject: Re: [AMBER] pmemd> compilation/makefailed> -mkl_vml_service_threader_z_1i_c_1o> To: "AMBER> Mailing List" <>> 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 whack
ed 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 conf
ig.h are doing you any> good.>> Regards - Bob Duke>> ----- Original> Message ----- From: "Vijay Manickam> Achari"> <>> To: "Amber mailing> List"> <>> 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/t
reading_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_p
arallel'>_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,> Mala
ysia>>>>>>>>> >> _______________________________________________> >> AMBER mailing list> >> >>>> >>>>> _______________________________________________> AMBER> mailing list>>>> mailing> listAMBER_at_ambermd.org> >> > _______________________________________________> > AMBER mailing list> >> >> >>>> _______________________________________________> AMBER mailing list>>> _______________________________________________> AMBER mailing list>>>

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