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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.


メンテ
Page: [1]

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
メンテ
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?

メンテ
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
メンテ
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
メンテ
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


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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
メンテ
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
メンテ
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
メンテ
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
メンテ
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
メンテ
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).
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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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