[Wien] WIEN2k_10.1 compilation problem (undefined reference to `__dlsym')
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=0x001f -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
[Wien] WIEN2k_10.1 compilation problem (undefined reference to `__dlsym')
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 -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671
[Wien] WIEN2k_10.1 compilation problem (undefined reference to `__dlsym')
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=0x001f -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
[Wien] WIEN2k_10.1 compilation problem (undefined reference to `__dlsym')
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 -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20101022/1fd77330/attachment-0001.htm
