Hi Brijit, I am a newbie to HPC. I guess that Dwarf error is because configure could not find scalapack and blacs libs. And I continued with make ignoring that warning.
Hi all, On our cluster we have intel-mkl library installed and i tried its path configure could not find it. I am appending ls command to intel-mkl directory and also configure options that i fired. Can anyone tell me how do I make use of those libraries to install Siesta-3.1 $ ls /export/apps/intel/Compiler/11.1/073/mkl/lib/em64t libmkl_avx.so libmkl_intel_sp2dp.so libmkl_blacs_ilp64.a libmkl_intel_thread.a libmkl_blacs_intelmpi_ilp64.a libmkl_intel_thread.so libmkl_blacs_intelmpi_ilp64.so libmkl_lapack95_ilp64.a libmkl_blacs_intelmpi_lp64.a libmkl_lapack95_lp64.a libmkl_blacs_intelmpi_lp64.so libmkl_lapack.so libmkl_blacs_lp64.a libmkl_mc3.so libmkl_blacs_openmpi_ilp64.a libmkl_mc.so libmkl_blacs_openmpi_lp64.a libmkl_p4n.so libmkl_blacs_sgimpt_ilp64.a libmkl_pgi_thread.a libmkl_blacs_sgimpt_lp64.a libmkl_pgi_thread.so libmkl_blas95_ilp64.a libmkl_scalapack_ilp64.a libmkl_blas95_lp64.a libmkl_scalapack_ilp64.so libmkl_cdft_core.a libmkl_scalapack_lp64.a libmkl_core.a libmkl_scalapack_lp64.so libmkl_core.so libmkl_sequential.a libmkl_def.so libmkl_sequential.so libmkl_gf_ilp64.a libmkl_solver_ilp64.a libmkl_gf_ilp64.so libmkl_solver_ilp64_sequential.a libmkl_gf_lp64.a libmkl_solver_lp64.a libmkl_gf_lp64.so libmkl_solver_lp64_sequential.a libmkl_gnu_thread.a libmkl_vml_avx.so libmkl_gnu_thread.so libmkl_vml_def.so libmkl_intel_ilp64.a libmkl_vml_mc2.so libmkl_intel_ilp64.so libmkl_vml_mc3.so libmkl_intel_lp64.a libmkl_vml_mc.so libmkl_intel_lp64.so libmkl_vml_p4n.so libmkl_intel_sp2dp.a * locale* (this is a directory) ../Src/configure --enable-mpi --with-blas=libmkl_blas95_ilp64.a --with-lapack=libmkl_lapack95_ilp64.a --with-blacs=libmkl_blacs_ilp64.a --with-scalapack=libmkl_scalapack_ilp64.a CC=gcc FC=gfortran --prefix=siesta-prefix-dir ** Path '/export/apps/intel/Compiler/11.1/073/mkl/lib/em64t' is included in LD_LIBRARY_PATH Thanks in advance, Dhirendra Vaidya, IIT Bombay On Sat, Jul 6, 2013 at 11:43 AM, Birjit Singh <[email protected]> wrote: > Hi Dhirendra, > Can you show the makefile. It seems to be non compatibility of your gcc > and mpi compiler. > > > > On Fri, Jul 5, 2013 at 9:27 PM, DHIRENDRA VAIDYA < > [email protected]> wrote: > >> Hi all, >> >> I am getting the following error when trying to install SIESTA-3.1 with >> gcc-4.8.1 and mpi-1.6.3 >> >> >> /usr/bin/ld: Dwarf Error: found dwarf version '4', this reader only >> handles version 2 information. >> cdiag.o: In function `cdiag_': >> cdiag.F:(.text+0x36a): undefined reference to `blacs_gridinfo_' >> cdiag.F:(.text+0x3bb): undefined reference to `descinit_' >> cdiag.F:(.text+0x8c5): undefined reference to `blacs_gridinfo_' >> cdiag.F:(.text+0x8e7): undefined reference to `indxg2p_' >> cdiag.F:(.text+0x910): undefined reference to `indxg2p_' >> cdiag.F:(.text+0x959): undefined reference to `numroc_' >> cdiag.F:(.text+0x97e): undefined reference to `numroc_' >> cdiag.F:(.text+0x9a5): undefined reference to `numroc_' >> cdiag.F:(.text+0x9c7): undefined reference to `numroc_' >> cdiag.F:(.text+0xa87): undefined reference to `blacs_gridinfo_' >> cdiag.F:(.text+0xaa9): undefined reference to `indxg2p_' >> cdiag.F:(.text+0xb14): undefined reference to `numroc_' >> cdiag.F:(.text+0xb42): undefined reference to `numroc_' >> cdiag.F:(.text+0xb9a): undefined reference to `descinit_' >> cdiag.F:(.text+0xe6d): undefined reference to `pzhegvx_' >> cdiag.F:(.text+0x1037): undefined reference to `pzgemr2d_' >> cdiag.F:(.text+0x10d4): undefined reference to `pzpotrf_' >> cdiag.F:(.text+0x11d7): undefined reference to `pzhengst_' >> cdiag.F:(.text+0x1368): undefined reference to `pzhemm_' >> cdiag.F:(.text+0x148c): undefined reference to `pzgemm_' >> cdiag.F:(.text+0x17a7): undefined reference to `pzgemm_' >> cdiag.F:(.text+0x1b7f): undefined reference to `pzgemr2d_' >> cdiag.F:(.text+0x1bf4): undefined reference to `pzgemr2d_' >> cdiag.F:(.text+0x1ca3): undefined reference to `pjlaenv_' >> cdiag.F:(.text+0x1ce7): undefined reference to `numroc_' >> cdiag.F:(.text+0x1d7b): undefined reference to `iceil_' >> cdiag.F:(.text+0x1fc7): undefined reference to `pzhegvx_' >> cdiag.F:(.text+0x23e2): undefined reference to `blacs_get_' >> cdiag.F:(.text+0x2409): undefined reference to `blacs_gridinit_' >> cdiag.F:(.text+0x2540): undefined reference to `pzpotrf_' >> cdiag.F:(.text+0x259a): undefined reference to `blacs_get_' >> cdiag.F:(.text+0x25b7): undefined reference to `blacs_gridinit_' >> cdiag.F:(.text+0x26e1): undefined reference to `pzheevd_' >> cdiag.F:(.text+0x27fc): undefined reference to `pztrsm_' >> cdiag.F:(.text+0x289f): undefined reference to `pzgemr2d_' >> cdiag.F:(.text+0x29a5): undefined reference to `pzhengst_' >> cdiag.F:(.text+0x2d7e): undefined reference to `pzheevx_' >> cdiag.F:(.text+0x3142): undefined reference to `pztrsm_' >> cdiag.F:(.text+0x3389): undefined reference to `pzheevx_' >> cdiag.F:(.text+0x35db): undefined reference to `pzheevd_' >> cdiag.F:(.text+0x369d): undefined reference to `pzhemm_' >> cdiag.F:(.text+0x3769): undefined reference to `pzgemm_' >> cdiag.F:(.text+0x3846): undefined reference to `pzgemm_' >> /usr/bin/ld: Dwarf Error: found dwarf version '4', this reader only >> handles version 2 information. >> rdiag.o: In function `rdiag_': >> rdiag.F:(.text+0x6ab): undefined reference to `blacs_gridinfo_' >> rdiag.F:(.text+0x6fa): undefined reference to `descinit_' >> rdiag.F:(.text+0x744): undefined reference to `numroc_' >> rdiag.F:(.text+0x76f): undefined reference to `numroc_' >> rdiag.F:(.text+0x7c5): undefined reference to `descinit_' >> rdiag.F:(.text+0x835): undefined reference to `blacs_gridinfo_' >> rdiag.F:(.text+0x881): undefined reference to `numroc_' >> rdiag.F:(.text+0x8a2): undefined reference to `numroc_' >> rdiag.F:(.text+0x8e8): undefined reference to `iceil_' >> rdiag.F:(.text+0x94c): undefined reference to `pjlaenv_' >> rdiag.F:(.text+0x995): undefined reference to `numroc_' >> rdiag.F:(.text+0xa1b): undefined reference to `blacs_gridinfo_' >> rdiag.F:(.text+0xa43): undefined reference to `numroc_' >> rdiag.F:(.text+0xa64): undefined reference to `numroc_' >> rdiag.F:(.text+0xab5): undefined reference to `indxg2p_' >> rdiag.F:(.text+0xadb): undefined reference to `indxg2p_' >> rdiag.F:(.text+0xaff): undefined reference to `numroc_' >> rdiag.F:(.text+0xb1f): undefined reference to `numroc_' >> rdiag.F:(.text+0xdb6): undefined reference to `pdsygvx_' >> rdiag.F:(.text+0xf67): undefined reference to `pdgemr2d_' >> rdiag.F:(.text+0x100e): undefined reference to `pdpotrf_' >> rdiag.F:(.text+0x1130): undefined reference to `pdsyngst_' >> rdiag.F:(.text+0x12c1): undefined reference to `pdsymm_' >> rdiag.F:(.text+0x13e5): undefined reference to `pdgemm_' >> rdiag.F:(.text+0x1697): undefined reference to `pdgemm_' >> rdiag.F:(.text+0x1a1c): undefined reference to `pdgemr2d_' >> rdiag.F:(.text+0x1a91): undefined reference to `pdgemr2d_' >> rdiag.F:(.text+0x1ca2): undefined reference to `pdsygvx_' >> rdiag.F:(.text+0x1fd2): undefined reference to `blacs_get_' >> rdiag.F:(.text+0x1ff9): undefined reference to `blacs_gridinit_' >> rdiag.F:(.text+0x21b8): undefined reference to `pdpotrf_' >> rdiag.F:(.text+0x21ea): undefined reference to `blacs_get_' >> rdiag.F:(.text+0x2207): undefined reference to `blacs_gridinit_' >> rdiag.F:(.text+0x22f5): undefined reference to `pdsyevd_' >> rdiag.F:(.text+0x2408): undefined reference to `pdtrsm_' >> rdiag.F:(.text+0x24ab): undefined reference to `pdgemr2d_' >> rdiag.F:(.text+0x2640): undefined reference to `pdsyngst_' >> rdiag.F:(.text+0x2b57): undefined reference to `pdsyevx_' >> rdiag.F:(.text+0x2d85): undefined reference to `pdtrsm_' >> rdiag.F:(.text+0x2f3b): undefined reference to `pdsyevx_' >> rdiag.F:(.text+0x30dc): undefined reference to `pdsyevd_' >> rdiag.F:(.text+0x319d): undefined reference to `pdsymm_' >> rdiag.F:(.text+0x3269): undefined reference to `pdgemm_' >> rdiag.F:(.text+0x3346): undefined reference to `pdgemm_' >> collect2: error: ld returned 1 exit status >> make: *** [siesta] Error 1 >> >> >> Any known fix for this. >> >> -- >> Warm Regards, >> Dhirendra Vaidya >> > > -- Warm Regards, Dhirendra Vaidya
