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Compile Error! Date: 2014/12/14 21:30 Name: masoud To all, I try to install openmx3.7 and its patch. while i did as it was told to do in the installation process i recieve following error using makefile as CC = /opt/openmpi/bin/mpicc -Dnosse -fopenmp -Dnoomp -O3 -I/usr/local/include FC = /opt/openmpi/bin/mpif90 -Dnoomp -fopenmp -O3 -I/usr/local/include LIB =-L/export/home/sjalili/masoud/install/fftw-3.3.4/.libs -lfftw3 -L/export/home/sjalili/masoud/install/lapack-3.5.0 -llapack -lrefblas -L/opt/openmpi/lib -lmpi -lmpi_f90 -lmpi_f77 -lmpi_cxx -L/software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/compiler/lib/intel64 -lifcore -limf ______________________________________________________________________ truncation.o: In function `Set_RMI': truncation.c:(.text+0x5c1): undefined reference to `GOMP_parallel' truncation.o: In function `Estimate_Trn_System': truncation.c:(.text+0x633): undefined reference to `GOMP_parallel' truncation.o: In function `UCell_Box': truncation.c:(.text+0x8462): undefined reference to `GOMP_parallel' truncation.c:(.text+0x938f): undefined reference to `GOMP_parallel' truncation.c:(.text+0x9a47): undefined reference to `GOMP_parallel' truncation.o:truncation.c:(.text+0x9b65): more undefined references to `GOMP_parallel' follow elpa1.o: In function `__elpa1_MOD_solve_tridi_single': elpa1.f90:(.text+0x104): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0x116): undefined reference to `_gfortran_transfer_integer_write' elpa1.f90:(.text+0x12a): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0x157): undefined reference to `_gfortran_os_error' elpa1.o: In function `resort_ev.4096': elpa1.f90:(.text+0x971): undefined reference to `_gfortran_os_error' elpa1.o: In function `check_monotony.4072': elpa1.f90:(.text+0xd43): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0xd53): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0xd67): undefined reference to `_gfortran_transfer_integer_write' elpa1.f90:(.text+0xd7a): undefined reference to `_gfortran_transfer_real_write' elpa1.f90:(.text+0xd90): undefined reference to `_gfortran_transfer_real_write' elpa1.o: In function `__elpa1_MOD_merge_systems': elpa1.f90:(.text+0x52ba): undefined reference to `_gfortran_os_error' elpa1.o: In function `merge_recursive.5443': elpa1.f90:(.text+0x5ba3): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0x5bb5): undefined reference to `_gfortran_transfer_integer_write' elpa1.o: In function `__elpa1_MOD_invert_trm_complex': elpa1.f90:(.text+0x709b): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0x710e): undefined reference to `_gfortran_os_error' elpa1.o: In function `__elpa1_MOD_invert_trm_real': elpa1.f90:(.text+0x8173): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0x81ee): undefined reference to `_gfortran_os_error' elpa1.o: In function `__elpa1_MOD_solve_tridi': elpa1.f90:(.text+0x85ee): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0x864f): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0xa0df): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0xa0f5): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0xa10b): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0xa121): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0xa1b7): undefined reference to `_gfortran_os_error' elpa1.f90:(.text+0xa215): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0xa246): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0xa277): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0xa2a8): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0xa34d): undefined reference to `_gfortran_runtime_error_at' elpa1.o:elpa1.f90:(.text+0xa376): more undefined references to `_gfortran_runtime_error_at' follow elpa1.o: In function `__elpa1_MOD_mult_ah_b_complex': elpa1.f90:(.text+0xb548): undefined reference to `_gfortran_os_error' elpa1.o: In function `__elpa1_MOD_trans_ev_complex': elpa1.f90:(.text+0xc596): undefined reference to `_gfortran_os_error' elpa1.o: In function `__elpa1_MOD_mult_at_b_real': elpa1.f90:(.text+0xd7a2): undefined reference to `_gfortran_os_error' elpa1.o: In function `__elpa1_MOD_trans_ev_real': elpa1.f90:(.text+0xe748): undefined reference to `_gfortran_os_error' elpa1.o: In function `elpa_transpose_vectors_': elpa1.f90:(.text+0xed37): undefined reference to `_gfortran_os_error' elpa1.o: In function `__elpa1_MOD_cholesky_real': elpa1.f90:(.text+0x10274): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0x102f1): undefined reference to `_gfortran_os_error' elpa1.f90:(.text+0x1035c): undefined reference to `_gfortran_transfer_character_write' elpa1.o: In function `__elpa1_MOD_cholesky_complex': elpa1.f90:(.text+0x11a13): undefined reference to `_gfortran_transfer_character_write' elpa1.f90:(.text+0x11b23): undefined reference to `_gfortran_os_error' elpa1.f90:(.text+0x11b8e): undefined reference to `_gfortran_transfer_character_write' elpa1.o: In function `elpa_reduce_add_vectors_': elpa1.f90:(.text+0x12335): undefined reference to `_gfortran_os_error' elpa1.o: In function `__elpa1_MOD_tridiag_real': elpa1.f90:(.text+0x14e28): undefined reference to `_gfortran_runtime_error_at' elpa1.f90:(.text+0x14f73): undefined reference to `_gfortran_os_error' elpa1.o: In function `__elpa1_MOD_tridiag_complex': elpa1.f90:(.text+0x18248): undefined reference to `_gfortran_os_error' elpa1.f90:(.text+0x182ea): undefined reference to `_gfortran_runtime_error_at' solve_evp_real.o: In function `solve_evp_real_': solve_evp_real.f90:(.text+0x304): undefined reference to `_gfortran_transfer_character_write' solve_evp_real.f90:(.text+0x330): undefined reference to `_gfortran_transfer_real_write' solve_evp_real.f90:(.text+0x394): undefined reference to `_gfortran_transfer_character_write' solve_evp_real.f90:(.text+0x3c0): undefined reference to `_gfortran_transfer_real_write' solve_evp_real.f90:(.text+0x424): undefined reference to `_gfortran_transfer_character_write' solve_evp_real.f90:(.text+0x450): undefined reference to `_gfortran_transfer_real_write' solve_evp_real.f90:(.text+0x494): undefined reference to `_gfortran_os_error' solve_evp_complex.o: In function `solve_evp_complex_': solve_evp_complex.f90:(.text+0x495): undefined reference to `_gfortran_transfer_character_write' solve_evp_complex.f90:(.text+0x4c4): undefined reference to `_gfortran_transfer_real_write' solve_evp_complex.f90:(.text+0x543): undefined reference to `_gfortran_transfer_character_write' solve_evp_complex.f90:(.text+0x572): undefined reference to `_gfortran_transfer_real_write' solve_evp_complex.f90:(.text+0x5f1): undefined reference to `_gfortran_transfer_character_write' solve_evp_complex.f90:(.text+0x620): undefined reference to `_gfortran_transfer_real_write' solve_evp_complex.f90:(.text+0x672): undefined reference to `_gfortran_os_error' /export/home/sjalili/masoud/install/lapack-3.5.0/liblapack.a(dlarnv.o): In function `dlarnv_': dlarnv.f:(.text+0x3bb): undefined reference to `__svml_log2' dlarnv.f:(.text+0x3d6): undefined reference to `__svml_cos2' dlarnv.f:(.text+0x498): undefined reference to `__svml_log2' dlarnv.f:(.text+0x4aa): undefined reference to `__svml_cos2' dlarnv.f:(.text+0x549): undefined reference to `__svml_log2' dlarnv.f:(.text+0x564): undefined reference to `__svml_cos2' /export/home/sjalili/masoud/install/lapack-3.5.0/liblapack.a(dlacn2.o): In function `dlacn2_': dlacn2.f:(.text+0x4f3): undefined reference to `__svml_round2' dlacn2.f:(.text+0x55f): undefined reference to `__svml_round2' dlacn2.f:(.text+0x5b6): undefined reference to `__svml_round2' dlacn2.f:(.text+0x684): undefined reference to `__svml_round2' dlacn2.f:(.text+0x6e9): undefined reference to `__svml_round2' /export/home/sjalili/masoud/install/lapack-3.5.0/liblapack.a(dlacn2.o):dlacn2.f:(.text+0x732): more undefined references to `__svml_round2' follow collect2: error: ld returned 1 exit status makefile:207: recipe for target 'openmx' failed make: *** [openmx] Error 1 ______________________________________________________ by defining -lgfortran in the system CC = /opt/openmpi/bin/mpicc -Dnosse -fopenmp -Dnoomp -O3 -I/usr/local/include FC = /opt/openmpi/bin/mpif90 -Dnoomp -fopenmp -O3 -I/usr/local/include LIB =-L/export/home/sjalili/masoud/install/fftw-3.3.4/.libs -lfftw3 -L/export/home/sjalili/masoud/install/lapack-3.5.0 -llapack -lrefblas -L/opt/openmpi/lib -lmpi -lmpi_f90 -lmpi_f77 -lmpi_cxx -L/software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/compiler/lib/intel64 -lifcore -limf -L/usr/local/bin -lgfortran then i recived follwing warning and errors _______________________________________________________ /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.9.1/../../../../x86_64-unknown-linux-gnu/bin/ld: warning: libgfortran.so.1, needed by /opt/openmpi/lib/libmpi_f90.so, may conflict with libgfortran.so.3 truncation.o: In function `Set_RMI': truncation.c:(.text+0x5c1): undefined reference to `GOMP_parallel' truncation.o: In function `Estimate_Trn_System': truncation.c:(.text+0x633): undefined reference to `GOMP_parallel' truncation.o: In function `UCell_Box': truncation.c:(.text+0x8462): undefined reference to `GOMP_parallel' truncation.c:(.text+0x938f): undefined reference to `GOMP_parallel' truncation.c:(.text+0x9a47): undefined reference to `GOMP_parallel' truncation.o:truncation.c:(.text+0x9b65): more undefined references to `GOMP_parallel' follow /export/home/sjalili/masoud/install/lapack-3.5.0/liblapack.a(dlarnv.o): In function `dlarnv_': dlarnv.f:(.text+0x3bb): undefined reference to `__svml_log2' dlarnv.f:(.text+0x3d6): undefined reference to `__svml_cos2' dlarnv.f:(.text+0x498): undefined reference to `__svml_log2' dlarnv.f:(.text+0x4aa): undefined reference to `__svml_cos2' dlarnv.f:(.text+0x549): undefined reference to `__svml_log2' dlarnv.f:(.text+0x564): undefined reference to `__svml_cos2' /export/home/sjalili/masoud/install/lapack-3.5.0/liblapack.a(dlacn2.o): In function `dlacn2_': dlacn2.f:(.text+0x4f3): undefined reference to `__svml_round2' dlacn2.f:(.text+0x55f): undefined reference to `__svml_round2' dlacn2.f:(.text+0x5b6): undefined reference to `__svml_round2' dlacn2.f:(.text+0x684): undefined reference to `__svml_round2' dlacn2.f:(.text+0x6e9): undefined reference to `__svml_round2' /export/home/sjalili/masoud/install/lapack-3.5.0/liblapack.a(dlacn2.o):dlacn2.f:(.text+0x732): more undefined references to `__svml_round2' follow collect2: error: ld returned 1 exit status makefile:206: recipe for target 'openmx' failed make: *** [openmx] Error 1 ___________________________________________________________ Does anyone have any idea what should i do? Excuse me but I am new in this envirement and package.

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Re: Compile Error! ( No.1 ) Date: 2014/12/15 14:53 Name: T.V.T. Duy  <duytvt@issp.u-tokyo.ac.jp> Hi, Please try using the following settings and tell us the results. CC = /opt/openmpi/bin/mpicc -fopenmp -O3 -I/usr/local/include -I/export/home/sjalili/masoud/install/fftw-3.3.4/include FC = /opt/openmpi/bin/mpif90 -O3 -I/usr/local/include LIB =-L/export/home/sjalili/masoud/install/fftw-3.3.4/.libs -lfftw3 -L/opt/openmpi/lib -lmpi -lmpi_f90 -lmpi_f77 -lmpi_cxx -L/software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/compiler/lib/intel64 -lifcore -limf -L/software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lgfortran Best regards, T.V.T. Duy Re: Compile Error! ( No.2 ) Date: 2014/12/15 22:30 Name: masoud Hi Thanks for your time, I did, it made following warning and errors ________________________________________________________________________ /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.9.1/../../../../x86_64-unknown-linux-gnu/bin/ld: warning: libgfortran.so.1, needed by /opt/openmpi/lib/libmpi_f90.so, may conflict with libgfortran.so.3 truncation.o: In function `Set_RMI': truncation.c:(.text+0x5c1): undefined reference to `GOMP_parallel' truncation.o: In function `Estimate_Trn_System': truncation.c:(.text+0x633): undefined reference to `GOMP_parallel' truncation.o: In function `UCell_Box': truncation.c:(.text+0x8462): undefined reference to `GOMP_parallel' truncation.c:(.text+0x938f): undefined reference to `GOMP_parallel' truncation.c:(.text+0x9a47): undefined reference to `GOMP_parallel' truncation.o:truncation.c:(.text+0x9b65): more undefined references to `GOMP_parallel' follow /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_add' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_4' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_master' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_fini' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_flush' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8u' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_fork_call' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_push_num_threads' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ordered' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_barrier' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx8_add' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_global_thread_num' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_4' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_critical' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_serialized_parallel' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_reduce_nowait' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_max' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_master' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_single' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `ompc_set_nested' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed8_add' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx4_add' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ok_to_fork' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_single' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce_nowait' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_serialized_parallel' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_add' /software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_max' collect2: error: ld returned 1 exit status makefile:207: recipe for target 'openmx' failed make: *** [openmx] Error 1 ____________________________________________________________________ any suggestion? Re: Compile Error! ( No.3 ) Date: 2014/12/16 10:29 Name: T.V.T. Duy  <duytvt@issp.u-tokyo.ac.jp> Dear Masoud, Thanks a lot for your efforts. Could you please modify LIB as below and try again? LIB =-L/export/home/sjalili/masoud/install/fftw-3.3.4/.libs -lfftw3 -L/opt/openmpi/lib -lmpi -lmpi_f90 -lmpi_f77 -lmpi_cxx -L/software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/compiler/lib/intel64 -lifcore -limf -L/software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lgfortran Also, I have noticed that you are using GCC version 4.9.1, which fails to link with the Intel OpenMP runtime library (libiomp5), or causes run-time crash, unless your Intel Composer is updated with the update #4 releases. Please try and let's figure out some workaround. Best regards, T.V.T. Duy Re: Compile Error! ( No.4 ) Date: 2014/12/16 14:24 Name: masoud Hi, thanks for the tip, compile made following errors and warning _______________________________________ /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.9.1/../../../../x86_64-unknown-linux-gnu/bin/ld: warning: libgfortran.so.1, needed by /opt/openmpi/lib/libmpi_f90.so, not found (try using -rpath or -rpath-link) truncation.o: In function `Set_RMI': truncation.c:(.text+0x5c1): undefined reference to `GOMP_parallel' truncation.o: In function `Estimate_Trn_System': truncation.c:(.text+0x633): undefined reference to `GOMP_parallel' truncation.o: In function `UCell_Box': truncation.c:(.text+0x8462): undefined reference to `GOMP_parallel' truncation.c:(.text+0x938f): undefined reference to `GOMP_parallel' truncation.c:(.text+0x9a47): undefined reference to `GOMP_parallel' truncation.o:truncation.c:(.text+0x9b65): more undefined references to `GOMP_parallel' follow collect2: error: ld returned 1 exit status makefile:205: recipe for target 'openmx' failed make: * [openmx] Error 1 ______________________________________________________ by consulting with a friend i use mpich2 instead of openmpi, the code compiled but when i run the example following error made ./openmx: error while loading shared libraries: libgfortran.so.3: wrong ELF class: ELFCLASS32 any idea how i can solve it? thanks in advanced Masoud Re: Compile Error! ( No.5 ) Date: 2014/12/17 10:12 Name: T.V.T. Duy  <duytvt@issp.u-tokyo.ac.jp> Hi, The run-time crash is caused by your GCC version 4.9, which could not be linked to your Intel Composer, as there is a conflict between the two in handling the OpenMP code. Could you please try with the following settings? CC = /opt/openmpi/bin/mpicc -Dnoomp -O3 -I/usr/local/include -I/export/home/sjalili/masoud/install/fftw-3.3.4/include FC = /opt/openmpi/bin/mpif90 -O3 -I/usr/local/include LIB =-L/export/home/sjalili/masoud/install/fftw-3.3.4/.libs -lfftw3 -L/opt/openmpi/lib -lmpi -lmpi_f90 -lmpi_f77 -lmpi_cxx -L/software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/compiler/lib/intel64 -lifcore -limf -L/software/intel/parallel_studio_xe_2013/composer_xe_2013_sp1.3.174/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lgfortran T.V.T. Duy Re: Compile Error! ( No.6 ) Date: 2014/12/17 14:49 Name: masoud Hi Thanks for the response i check the new makefile, it make errors on mkl i add -liomp5 -lmkl_intel_thread it... no error only warning _______________________ /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.9.1/../../../../x86_64-unknown-linux-gnu/bin/ld: warning: libgfortran.so.1, needed by /opt/openmpi/lib/libmpi_f90.so, not found (try using -rpath or -rpath-link) _____________________________________________________________ and on the run it said same: ../source/openmx: error while loading shared libraries: libgfortran.so.3: wrong ELF class: ELFCLASS32 ../source/openmx: error while loading shared libraries: libgfortran.so.3: wrong ELF class: ELFCLASS32 what is wrong with my system that it makes such error? how can i solve it?how can i use -rpath or -rpath-link that mentioned in the compile warning? thank you for your time and helps Masoud Re: Compile Error! ( No.7 ) Date: 2014/12/22 14:09 Name: T.V.T. Duy  <duytvt@issp.u-tokyo.ac.jp> Dear Masoud, I am sorry for my late response. The problem is caused by a conflict in the OpenMP interfaces between the GCC version 4.9 and Intel Composer library. I suggest you to use the ACML library instead. Could you please try installing ACML and compiling OpenMX with it? http://developer.amd.com/tools-and-sdks/cpu-development/amd-core-math-library-acml/ Best regards, T.V.T. Duy Re: Compile Error! ( No.8 ) Date: 2015/01/04 17:03 Name: masoud Hi Sorry for late response. thanks for your time and consideration I use ACML but still same problem. Same warning /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.9.1/../../../../x86_64-unknown-linux-gnu/bin/ld: warning: libgfortran.so.1, needed by /opt/openmpi/lib/libmpi_f90.so, not found (try using -rpath or -rpath-link) in the compling process and then the error in the RUN. ../source/openmx: error while loading shared libraries: libgfortran.so.3: wrong ELF class: ELFCLASS32 ../source/openmx: error while loading shared libraries: libgfortran.so.3: wrong ELF class: ELFCLASS32 not known what to do... the administrator of the cluster can not solve it too. any idea? thanks yours masoud Re: Compile Error! ( No.9 ) Date: 2015/01/06 22:43 Name: masoud Here is my ldd openmx it seems that the problem is related to not finding link with libgoftrean.so.3 linux-vdso.so.1 => (0x00007fffe55a7000) libifcore.so.5 => /usr/local/lib/libifcore.so.5 (0x00002abd6fb9a000) libimf.so => /usr/local/lib/libimf.so (0x00002abd6feda000) libmkl_intel_lp64.so => /usr/local/lib/libmkl_intel_lp64.so (0x00002abd7039e000) libmkl_core.so => /usr/local/lib/libmkl_core.so (0x00002abd70ab1000) libiomp5.so => /usr/local/lib/libiomp5.so (0x00002abd71d11000) libmkl_intel_thread.so => /usr/local/lib/libmkl_intel_thread.so (0x00002abd7202d000) libgfortran.so.3 => not found libm.so.6 => /lib64/libm.so.6 (0x0000003ed1600000) librt.so.1 => /lib64/librt.so.1 (0x0000003ed2600000) libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003ed1e00000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003edf400000) libc.so.6 => /lib64/libc.so.6 (0x0000003ed1200000) libdl.so.2 => /lib64/libdl.so.2 (0x0000003ed1a00000) libintlc.so.5 => /usr/local/lib/libintlc.so.5 (0x00002abd73096000) /lib64/ld-linux-x86-64.so.2 (0x0000003ed0e00000) any idea how i can solve it. i check with acml same problem. yorus masoud Re: Compile Error! ( No.10 ) Date: 2015/01/08 16:08 Name: Masoud Hi Finally we found the problem that was the missing link between lib64 and 32.. any how we add it and it run now. However, we got a new problem during the processing i run mpirun -np 2 openmx Methane2.dat > test.std& and after a run we got Assertion failed in file ch3u_buffer.c at line 77: FALSE memcpy argument memory ranges overlap, dst_=0x18678560 src_=0x18678560 len_=64 internal ABORT - process 0 Assertion failed in file ch3u_buffer.c at line 77: FALSE memcpy argument memory ranges overlap, dst_=0x19a9c960 src_=0x19a9c960 len_=72 internal ABORT - process 1 anyone have any idea what should we do now? yours Masoud Re: Compile Error! ( No.11 ) Date: 2015/01/08 20:26 Name: Artem Pulkin  <artem.pulkin@epfl.ch> First of all, you should be able to run now in serial mode. Secondly, I suggest you to google your errors prior to asking for someone to solve it. It has been discussed a number of times at OpenMX forum. For example, here: http://www.openmx-square.org/forum/patio.cgi?mode=view&no=1419 In short, you should use another mpi library (it seems like you are using mpich2). Re: Compile Error! ( No.12 ) Date: 2015/02/19 00:05 Name: Masoud Only to help other users with same problem. Even with Mpich2 the problem exist. However, by linking the gfortran 32 and 64 to the openmpi you may achieve stable calculation. masoud

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