[Wien] WIEN2k_10.1 compilation problem (undefined reference to `__dlsym')
Maxim Rakitin
rms85 at physics.susu.ac.ru
Mon Oct 25 08:38:57 CEST 2010
The problem was connected with linker on the cluster. IT team has fixed it.
Best regards,
Maxim Rakitin
Postgraduate student
South Ural State University,
76 Lenin av., Chelyabinsk, Russia, 454080
Email: rms85 at physics.susu.ac.ru
Web: http://www.susu.ac.ru
23.10.2010 15:26, Maxim Rakitin ?????:
> Dear Prof. Blaha,
>
> Yes, I sourced all Intel files for mkl, ifort and icc variables. I
> added option -v to ifort comiler options, so I can see verbose output.
> Here is what the compiler says for lapw0 program compilation:
> =============================================================================
> ifort -o lapw0 cputim.o modules.o reallocate.o ainv.o am05_xscss.o
> b88.o blyp.o brj.o charg2.o charg3.o charge.o chfac.o chslv.o
> corgga.o corpbe_revtpss.o corpbe_tpss.o cub_xc_back.o corlsd.o
> dfxhpbe.o dfxrevtpss.o dfxtpss.o drho.o dylm.o efg.o energy.o epot1.o
> eramps.o errclr.o errflg.o ev92.o ev92ex.o exch.o exch17.o fftw_para.o
> fithi.o fxhpbe.o fx_revtpss.o fx_tpss.o gbass.o gcor.o gea.o geaex.o
> getff1.o getfft.o gpoint.o gpointm.o grans.o gtfnam.o hcth.o ifflim.o
> kcis.o lapw0.o latgen.o multfc.o multsu.o outerr.o pbea.o pbem.o
> pbe1.o pbe2.o pbesol.o poissn.o potfac.o pwxad4.o pwxad5.o qranf.o
> readstruct.o rean0.o rean1.o rean3.o rean4.o rhopw.o rotate.o rotdef.o
> rpbe.o setff0.o setff1.o setfft.o setff2.o seval.o sevald.o sevaldd.o
> sevali.o sevalin.o sicpbe.o sicpbe_revtpss.o sicpbe_tpss.o sogga.o
> sphbes.o spline.o srolyl.o stern.o sumfac.o suml.o th1.o th2.o vpw91.o
> vresp.o vs98.o vxc15.o vxc16.o vxc17.o vxc24.o vxc26.o vxclm2.o
> vxcpw2.o vxi35.o vxi35a.o wc05.o workf1.o xcener.o xcpot.o xcpot1.o
> xcpot3.o ykav.o ylm.o zfft3d.o W2kutils.o W2kinit.o -FR -w -mp1
> -prec-div -pad -ip -O3 -xP -L/opt/intel/mkl/10.0.3.020/lib/em64t
> -shared-intel -lguide -lpthread -L/opt/intel/mkl/10.0.3.020/lib/em64t
> -shared-intel -lmkl_em64t -lmkl_core -lmkl_sequential -liomp5
> -lmkl_lapack -lguide -v
> Version 10.1
> */opt/intel//fce/10.1.015/bin/fortcom* -mP1OPT_version=1010
> -mGLOB_source_language=GLOB_SOURCE_LANGUAGE_F90 -mGLOB_tune_for_fort
> -mGLOB_use_fort_dope_vector -mP2OPT_static_promotion
> -mP1OPT_print_version=FALSE -mP3OPT_use_mspp_call_convention
> -mCG_use_gas_got_workaround=F -mP2OPT_align_option_used=TRUE
> "-mGLOB_options_string=-o lapw0 -FR -w -mp1 -prec-div -pad -ip -O3 -xP
> -L/opt/intel/mkl/10.0.3.020/lib/em64t -shared-intel -lguide -lpthread
> -L/opt/intel/mkl/10.0.3.020/lib/em64t -shared-intel -lmkl_em64t
> -lmkl_core -lmkl_sequential -liomp5 -lmkl_lapack -lguide -v"
> -mGLOB_cxx_limited_range=FALSE -mP2OPT_eh_nirvana
> -mGLOB_diag_file=cputim.diag
> -mGLOB_as_output_backup_file_name=/tmp/ifortdzFyyeas_.s
> -mGLOB_machine_model=GLOB_MACHINE_MODEL_EFI2
> -mGLOB_fp_speculation=GLOB_FP_SPECULATION_FAST
> -mGLOB_precision_mask=0x0000001f -mGLOB_extended_instructions=0x28
> -mGLOB_advanced_optim=TRUE -mP2OPT_pad_local
> -mP2OPT_subs_out_of_bound=FALSE -mGLOB_ansi_alias
> -mIPOPT_ninl_user_level=2 -mIPOPT_args_in_regs=0
> -mPGOPTI_value_profile_use=T -mGLOB_opt_level=3 -mIPOPT_activate
> -mP2OPT_hlo_level=3 -mP2OPT_hlo -mPAROPT_par_report=1
> -mCG_emit_as_seg_grouping -mIPOPT_link -mIPOPT_ipo_activate
> -mIPOPT_ipo_mo_activate -mIPOPT_ipo_mo_nfiles=1
> -mIPOPT_source_files_list=/tmp/ifortG56wzplst
> -mIPOPT_short_data_info=/tmp/ifortfWfBj7sdata
> -mIPOPT_link_script_file=/tmp/ifortmztF3Oscript -mIPOPT_global_data
> "-mIPOPT_link_version=(GNU Binutils) 2.17.50.20070726-14 (SUSE Linux)"
> "-mIPOPT_cmdline_link="/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crt1.o"
> "/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crti.o"
> "/usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtbegin.o" "--eh-frame-hdr"
> "-dynamic-linker" "/lib64/ld-linux-x86-64.so.2" "-o" "lapw0"
> "/opt/intel//fce/10.1.015/lib/for_main.o" "cputim.o" "modules.o"
> "reallocate.o" "ainv.o" "am05_xscss.o" "b88.o" "blyp.o" "brj.o"
> "charg2.o" "charg3.o" "charge.o" "chfac.o" "chslv.o" "corgga.o"
> "corpbe_revtpss.o" "corpbe_tpss.o" "cub_xc_back.o" "corlsd.o"
> "dfxhpbe.o" "dfxrevtpss.o" "dfxtpss.o" "drho.o" "dylm.o" "efg.o"
> "energy.o" "epot1.o" "eramps.o" "errclr.o" "errflg.o" "ev92.o"
> "ev92ex.o" "exch.o" "exch17.o" "fftw_para.o" "fithi.o" "fxhpbe.o"
> "fx_revtpss.o" "fx_tpss.o" "gbass.o" "gcor.o" "gea.o" "geaex.o"
> "getff1.o" "getfft.o" "gpoint.o" "gpointm.o" "grans.o" "gtfnam.o"
> "hcth.o" "ifflim.o" "kcis.o" "lapw0.o" "latgen.o" "multfc.o"
> "multsu.o" "outerr.o" "pbea.o" "pbem.o" "pbe1.o" "pbe2.o" "pbesol.o"
> "poissn.o" "potfac.o" "pwxad4.o" "pwxad5.o" "qranf.o" "readstruct.o"
> "rean0.o" "rean1.o" "rean3.o" "rean4.o" "rhopw.o" "rotate.o"
> "rotdef.o" "rpbe.o" "setff0.o" "setff1.o" "setfft.o" "setff2.o"
> "seval.o" "sevald.o" "sevaldd.o" "sevali.o" "sevalin.o" "sicpbe.o"
> "sicpbe_revtpss.o" "sicpbe_tpss.o" "sogga.o" "sphbes.o" "spline.o"
> "srolyl.o" "stern.o" "sumfac.o" "suml.o" "th1.o" "th2.o" "vpw91.o"
> "vresp.o" "vs98.o" "vxc15.o" "vxc16.o" "vxc17.o" "vxc24.o" "vxc26.o"
> "vxclm2.o" "vxcpw2.o" "vxi35.o" "vxi35a.o" "wc05.o" "workf1.o"
> "xcener.o" "xcpot.o" "xcpot1.o" "xcpot3.o" "ykav.o" "ylm.o" "zfft3d.o"
> "W2kutils.o" "W2kinit.o" "-L/opt/intel/mkl/10.0.3.020/lib/em64t"
> "-lguide" "-lpthread" "-L/opt/intel/mkl/10.0.3.020/lib/em64t"
> "-lmkl_em64t" "-lmkl_core" "-lmkl_sequential" "-liomp5" "-lmkl_lapack"
> "-lguide" "-L/panfs/panasas/opt/intel/mkl/10.0.3.020/lib/em64t"
> "-L/panfs/panasas/opt/intel/mkl/10.0.3.020/lib/em64t"
> "-L/opt/intel//fce/10.1.015/lib"
> "-L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/"
> "-L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64"
> "-lifport" "-lifcore" "-limf" "-lsvml" "-lm" "-lipgo" "-lintlc" "-lc"
> "-lgcc_s" "-lgcc" "-lirc_s" "-ldl" "-lc"
> "/usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtend.o"
> "/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crtn.o""
> -mIPOPT_save_il0 -mIPOPT_il_in_obj -mIPOPT_ipo_activate_warn=FALSE
> -mIPOPT_obj_output_file_name=/tmp/ipo_ifortqevmli.o
> "-mGLOB_linker_version=(GNU Binutils) 2.17.50.20070726-14 (SUSE
> Linux)" -mP3OPT_asm_target=P3OPT_ASM_TARGET_GAS
> -mGLOB_obj_output_file=/tmp/ipo_ifortqevmli.o
> -mP1OPT_source_file_name=/tmp/ipo_ifortqevmli.f cputim.o modules.o
> reallocate.o ainv.o am05_xscss.o b88.o blyp.o brj.o charg2.o charg3.o
> charge.o chfac.o chslv.o corgga.o corpbe_revtpss.o corpbe_tpss.o
> cub_xc_back.o corlsd.o dfxhpbe.o dfxrevtpss.o dfxtpss.o drho.o dylm.o
> efg.o energy.o epot1.o eramps.o errclr.o errflg.o ev92.o ev92ex.o
> exch.o exch17.o fftw_para.o fithi.o fxhpbe.o fx_revtpss.o fx_tpss.o
> gbass.o gcor.o gea.o geaex.o getff1.o getfft.o gpoint.o gpointm.o
> grans.o gtfnam.o hcth.o ifflim.o kcis.o lapw0.o latgen.o multfc.o
> multsu.o outerr.o pbea.o pbem.o pbe1.o pbe2.o pbesol.o poissn.o
> potfac.o pwxad4.o pwxad5.o qranf.o readstruct.o rean0.o rean1.o
> rean3.o rean4.o rhopw.o rotate.o rotdef.o rpbe.o setff0.o setff1.o
> setfft.o setff2.o seval.o sevald.o sevaldd.o sevali.o sevalin.o
> sicpbe.o sicpbe_revtpss.o sicpbe_tpss.o sogga.o sphbes.o spline.o
> srolyl.o stern.o sumfac.o suml.o th1.o th2.o vpw91.o vresp.o vs98.o
> vxc15.o vxc16.o vxc17.o vxc24.o vxc26.o vxclm2.o vxcpw2.o vxi35.o
> vxi35a.o wc05.o workf1.o xcener.o xcpot.o xcpot1.o xcpot3.o ykav.o
> ylm.o zfft3d.o W2kutils.o W2kinit.o -mIPOPT_mo_unique_name=lapw0
> -mIPOPT_object_files=/tmp/ifortvgIp5Ztxt
> -mIPOPT_cmdline_link_new=/tmp/ifortYZdtPHtxt
> *ld* --eh-frame-hdr -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o
> lapw0 -L/opt/intel/mkl/10.0.3.020/lib/em64t
> -L/opt/intel/mkl/10.0.3.020/lib/em64t
> -L/panfs/panasas/opt/intel/mkl/10.0.3.020/lib/em64t
> -L/panfs/panasas/opt/intel/mkl/10.0.3.020/lib/em64t
> -L/opt/intel//fce/10.1.015/lib
> -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/
> -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64
> /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crt1.o
> /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crti.o
> /usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtbegin.o
> /opt/intel//fce/10.1.015/lib/for_main.o cputim.o modules.o
> reallocate.o ainv.o am05_xscss.o b88.o blyp.o brj.o charg2.o charg3.o
> charge.o chfac.o chslv.o corgga.o corpbe_revtpss.o corpbe_tpss.o
> cub_xc_back.o corlsd.o dfxhpbe.o dfxrevtpss.o dfxtpss.o drho.o dylm.o
> efg.o energy.o epot1.o eramps.o errclr.o errflg.o ev92.o ev92ex.o
> exch.o exch17.o fftw_para.o fithi.o fxhpbe.o fx_revtpss.o fx_tpss.o
> gbass.o gcor.o gea.o geaex.o getff1.o getfft.o gpoint.o gpointm.o
> grans.o gtfnam.o hcth.o ifflim.o kcis.o lapw0.o latgen.o multfc.o
> multsu.o outerr.o pbea.o pbem.o pbe1.o pbe2.o pbesol.o poissn.o
> potfac.o pwxad4.o pwxad5.o qranf.o readstruct.o rean0.o rean1.o
> rean3.o rean4.o rhopw.o rotate.o rotdef.o rpbe.o setff0.o setff1.o
> setfft.o setff2.o seval.o sevald.o sevaldd.o sevali.o sevalin.o
> sicpbe.o sicpbe_revtpss.o sicpbe_tpss.o sogga.o sphbes.o spline.o
> srolyl.o stern.o sumfac.o suml.o th1.o th2.o vpw91.o vresp.o vs98.o
> vxc15.o vxc16.o vxc17.o vxc24.o vxc26.o vxclm2.o vxcpw2.o vxi35.o
> vxi35a.o wc05.o workf1.o xcener.o xcpot.o xcpot1.o xcpot3.o ykav.o
> ylm.o zfft3d.o W2kutils.o W2kinit.o -lguide -lpthread -lmkl_em64t
> -lmkl_core -lmkl_sequential -liomp5 -lmkl_lapack -lguide -lifport
> -lifcore -limf -lsvml -lm -lipgo -lintlc -lc -lgcc_s -lgcc -lirc_s
> -ldl -lc /usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtend.o
> /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crtn.o
> /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/libdl.a(dlsym.o):
> In function `dlsym':
> (.text+0x5): undefined reference to `__dlsym'
> rm /tmp/ifortYTJCRSlibgcc
>
> rm /tmp/ifortqK1kBAgnudirs
>
> rm /tmp/ifortvgIp5Ztxt
>
> rm /tmp/ifortYZdtPHtxt
>
> rm /tmp/ifortG56wzplst
>
> rm /tmp/ifortfWfBj7sdata
>
> rm /tmp/ifortmztF3Oscript
>
> rm /tmp/ipo_ifortqevmli.o
>
> rm /tmp/ifortcn9JNwgas
>
> rm /tmp/ifortdzFyyeas_.s
>
> rm /tmp/ifortNx4njWld_v
>
> rm /tmp/ifortEtmJ4Dldashv
>
> rm /tmp/ifortd2cHQlgnudirs
>
> rm /tmp/ifortotVAD3arg
> =============================================================================
>
> So as we can see, there are 2 main commands - fortcom and ld (paths
> with double slashes '//' seem to be work correctly). I tried to run
> them manually in $WIENROOT/SRC_lapw0 directory. The first one
> completed successfully, but the second command failed. Surprisingly,
> that when I removed *-ldl* flag (which finds libdl.so/a), lapw0 was
> generated without any problems. Although the exec was built, I don't
> know if it's correct or no. Is libdl library necessary for all WIEN2k
> executables? Or maybe linker cache isn't correct? Any ideas?
>
> Thanks,
> - Maxim
>
> 23.10.2010 12:35, Peter Blaha ?????:
>> > To fix it I sourced mklvarsem64t.sh, so the $INCLUDE variable became
>>
>> Did you also "source" the corresponding file for the ifort compiler ?
>>
>> Am 22.10.2010 11:39, schrieb Maxim Rakitin:
>>> Dear WIEN2k experts,
>>>
>>> I tried to compile WIEN2k_10.1 on the cluster of my university (SuSE
>>> linux, Xeon 53XX processors), but I got an error during the process:
>>>
>>>
>>> usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/libdl.a(dlsym.o):
>>> In function `dlsym':
>>> (.text+0x5): undefined reference to `__dlsym'
>>>
>>> Here is a part of the compilation log of lapw0 (serial version):
>>>
>>> icc -c W2kutils.c
>>> ifort -FR -w -mp1 -prec-div -pad -ip -DINTEL_VML -O3 -xP -c
>>> W2kinit.F
>>> ifort -o lapw0 cputim.o modules.o reallocate.o ainv.o am05_xscss.o
>>> b88.o blyp.o brj.o charg2.o charg3.o charge.o chfac.o chslv.o
>>> corgga.o corpbe_revtpss.o corpbe_tpss.o cub_xc_back.o corlsd.o
>>> dfxhpbe.o dfxrevtpss.o dfxtpss.o drho.o dylm.o efg.o energy.o
>>> epot1.o eramps.o errclr.o errflg.o ev92.o ev92ex.o exch.o exch17.o
>>> fftw_para.o fithi.o fxhpbe.o fx_revtpss.o fx_tpss.o gbass.o gcor.o
>>> gea.o geaex.o getff1.o getfft.o gpoint.o gpointm.o grans.o
>>> gtfnam.o
>>> hcth.o ifflim.o kcis.o lapw0.o latgen.o multfc.o multsu.o outerr.o
>>> pbea.o pbem.o pbe1.o pbe2.o pbesol.o poissn.o potfac.o pwxad4.o
>>> pwxad5.o qranf.o readstruct.o rean0.o rean1.o rean3.o rean4.o
>>> rhopw.o rotate.o rotdef.o rpbe.o setff0.o setff1.o setfft.o
>>> setff2.o
>>> seval.o sevald.o sevaldd.o sevali.o sevalin.o sicpbe.o
>>> sicpbe_revtpss.o sicpbe_tpss.o sogga.o sphbes.o spline.o srolyl.o
>>> stern.o sumfac.o suml.o th1.o th2.o vpw91.o vresp.o vs98.o vxc15.o
>>> vxc16.o vxc17.o vxc24.o vxc26.o vxclm2.o vxcpw2.o vxi35.o vxi35a.o
>>> wc05.o workf1.o xcener.o xcpot.o xcpot1.o xcpot3.o ykav.o ylm.o
>>> zfft3d.o W2kutils.o W2kinit.o -FR -w -mp1 -prec-div -pad -ip
>>> -DINTEL_VML -O3 -xP -L/opt/intel/mkl/10.0.3.020/lib/em64t -lguide
>>> -lpthread -L/opt/intel/mkl/10.0.3.020/lib/em64t -lmkl_em64t
>>> -lmkl_core -lmkl_sequential -liomp5 -lmkl_lapack -lguide -lpthread
>>>
>>> It seems to me that the problem is connected with new routines W2k*,
>>> because when I compile the package without $INCLUDE wariable, I got the
>>> following error:
>>>
>>> fortcom: Error: W2kinit.F, line 28: Cannot open include file
>>> 'mkl_vml.fi'
>>> include 'mkl_vml.fi'
>>> ---------------^
>>>
>>> To fix it I sourced mklvarsem64t.sh, so the $INCLUDE variable became
>>> available. But this produced the error in the beginning of this mail. I
>>> tried different combinations of input parameters (FOPT, FPOPT, etc),
>>> but
>>> this didn't help. FYI, in the previous versions of WIEN2k I haven't met
>>> such kind of problems.
>>>
>>> Could anyboby please help me to find where the problem came from? I
>>> really appreciate any help and advice. If you need additional
>>> information on my compilation options or cluster details, please let me
>>> know.
>>>
>>> Thanks a lot.
>>>
>>> --
>>> Best regards,
>>> Maxim Rakitin
>>> Postgraduate student
>>> South Ural State University,
>>> 76 Lenin av., Chelyabinsk, Russia, 454080
>>> Email:rms85 at physics.susu.ac.ru
>>> Web:http://www.susu.ac.ru
>>>
>>>
>>>
>>> _______________________________________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>
>
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