AMBER Archive (2009)

Subject: Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Apr 08 2009 - 07:13:23 CDT

Okay, I gave you the latest update from Ross Walker on this stuff, but maybe
it was not checked out or maybe there is some other hole in the config
script I missed. I just confirmed that I still have access to a machine of
this type that has mkl 10+ on it, so I will check it out thoroughly and get
back to you. Sorry for the hassles on your end; feel free to complain to
intel about totally whacking their mkl library structure.
Regards - Bob
----- Original Message -----
From: "Vijay Manickam Achari" <vjrajamany_at_yahoo.com>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Wednesday, April 08, 2009 2:27 AM
Subject: Re: [AMBER]
pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o

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
xtprmtop_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/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 vjramana_at_gmail.com--- On Tue, 7/4/09, Robert Duke <rduke_at_email.unc.edu> wrote:> From: Robert Duke <rduke_at_email.unc.edu>> Subject: Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o> To: "AMBER Mailing List" <amber_at_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_at_email.unc.edu>> To: <vjrajamany_at_yahoo.com>; "AMBER Mailing>
List" <amber_at_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 $(MKL_HOME).> > Regards - Bob Duke> >> > ----- Original Message ----- From: "Vijay> Manickam Achari" <vjrajamany_at_yahoo.com>> > To: "AMBER Mailing List"> <amber_at_ambermd.org>> > Sent: Tuesday, April 07, 2009 12:25 AM> > Subject: Re: [AMBER] pmemd compilation/make> failed-mkl_vml_service_threader_z_1i_c_1o> >> >> >> > Robert,> > I have altered the MATH_LIBS param. the config.h with> your given suggestion as below:> > MATH_LIBS = -L$MKL_HOME/lib/64/ -Wl,--start-group> $MKL_HOME/lib/64/libmkl_intel.a> $MKL_HOME/lib/64/libmkl_sequential.a> $MKL_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> 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 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"> <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_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>> vjramana_at_gmail.com>>>>>>> >> _______________________________________________> >> AMBER mailing list> > AMBER_at_ambermd.org> >> http://lists.ambermd.org/mailman/listinfo/amber>> >>>>> _______________________________________________> AMBER> mailing list> AMBER_at_ambermd.org>>http://lists.ambermd.org/mailman/listinfo/amber_______________________________________________AMBER> mailing> listAMBER_at_ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber> >> > _______________________________________________> > AMBER mailing list> > AMBER_at_ambermd.org> > http://lists.ambermd.org/mailman/listinfo/amber> >>>> _______________________________________________> AMBER mailing list> AMBER_at_ambermd.org> http://lists.ambermd.org/mailman/listinfo/amber--------------------------------------------------------------------------------> _______________________________________________> AMBER mailing list> AMBER_at_ambermd.org> http://lists.ambermd.org/mailman/listinfo/amber>

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