[mesa-users] compiling issues when calling mesa module in C++ program
Jean-Claude Passy
jcpassy at gmail.com
Wed Oct 28 13:04:27 EDT 2015
Hi Rob,
> > "_GOMP_critical_end", referenced from:
>
> You need to link openmp in
You were right. I had forgotten the flag -fopenmp
>
> > ___mtx_support_MOD_do_quad_band_multiply_xa in libmtx.a(mtx_support.o) (and other lines)
>
> Have you initialized the sdk before compiling?
Yes, it is initialized.
Thanks,
JC
> On Wed, Oct 28, 2015 at 5:21 AM, Jean-Claude Passy <jcpassy at gmail.com <mailto:jcpassy at gmail.com>> wrote:
> Hi everyone,
>
> I am trying to use the eos module in an external C++ program, and I have some linking issues. I would be glad if someone could help me to sort this out. Below is a description of what is happening:
>
> - module_eos.f is a module based on sample_eos.f
> - main_fortran.f is a simple program that calls this module. It was just a test to see whether I could use the module externally. When I build with ‘make fortran’, compilation is smooth and the executable works perfectly well.
> - main_cpp.C is also supposed to only call the module. At compilation, I get the warnings and errors at the bottom.
>
> So it looks like some links are missing (or have the wrong order), but it is not obvious to me how to fix this.
>
> I must add that I compile using MPI compilers (required by the external code) but I made sure that the MPi compilers were build using the SDK distribution. Also, I added some includes/libs/defines in the command line required by the external code (see Makefile).
>
> All the files can be found below. Happy to hear your suggestions.
>
> Thanks a lot,
>
>
> JC
>
>
>
>
>
>
>
> #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> [12:24:46] Obiwan:$ make
> …
> /Users/jcpassy/Work/Tools/openmpi-1.6.5/build/bin/mpic++ -DLINUX -DH5_USE_16_API -D__max_subgrids=100000 -D__max_baryons=30 -D__max_cpu_per_node=8 -D__memory_pool_size=100000 -DINITS64 -DLARGE_INTS -DCONFIG_PINT_8 -DIO_32 -DUSE_MPI -DCONFIG_PFLOAT_8 -DCONFIG_BFLOAT_8 -DUSE_HDF5_GROUPS -DTRANSFER -DNEW_GRID_IO -DFAST_SIB -DENZO_PERFORMANCE -DSAB -o bin/main_cpp.exe -g \
> -L/Users/jcpassy/Work/MESA/mesa_7503/lib -lstar -lionization -latm -lcolors -lmlt -lnse -lnet -leos -lkap -lrates -lneu -lchem -linterp_2d -linterp_1d -lnum -lf2crlibm -lcrlibm -lmtx -lconst -lutils -lmesaklu `mesasdk_lapack_link` `mesasdk_blas_link` `mesasdk_pgplot_link` `mesasdk_se_link` -L/Users/jcpassy/Work/yt-x86_64/lib -lhdf5 -L/Applications/mesasdk/lib -lgfortran -I/Users/jcpassy/Work/yt-x86_64/include -I/usr/include -I/Users/jcpassy/Work/Enzo/enzo-dev/src/enzo module_eos.o main_cpp.C
> …
> ld: warning: could not create compact unwind for ___eos_lib_MOD_eosdt_ideal_gas_get: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___eosde_eval_MOD_get_de_opal_scvh_for_x: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___eosdt_eval_MOD_get_helm_pc_results: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___eosdt_eval_MOD_get_opal_scvh_results: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___eosdt_eval_MOD_get_eosdt_results: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___eospt_eval_MOD_get_pt_opal_scvh_results: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___eosde_load_tables_MOD_load1_eosde_table: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___eosdt_load_tables_MOD_load1_eosdt_table: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___eospt_load_tables_MOD_load1_eospt_table: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___helm_MOD_helmeos2: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___mebdfi_stiff_MOD_stiff: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___mod_newton_MOD_do_newton: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for ___mod_rosenbrock_MOD_roscor: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _dgbtrf_: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _zgbtrf_: stack subq instruction is too different from dwarf stack size
> Undefined symbols for architecture x86_64:
> "_GOMP_critical_end", referenced from:
> ___eosde_load_tables_MOD_load_eosde_table in libeos.a(eosde_load_tables.o)
> ___eosdt_load_tables_MOD_load_eosdt_table in libeos.a(eosdt_load_tables.o)
> ___eospt_load_tables_MOD_load_eospt_table in libeos.a(eospt_load_tables.o)
> "_GOMP_critical_name_end", referenced from:
> ___eos_def_MOD_do_alloc_eos in libeos.a(eos_def.o)
> ___utils_lib_MOD_free_iounit in libutils.a(utils_lib.o)
> ___utils_lib_MOD_number_iounits_allocated in libutils.a(utils_lib.o)
> ___utils_lib_MOD_alloc_iounit in libutils.a(utils_lib.o)
> ___utils_dict_MOD_do_integer_dict_create_hash in libutils.a(utils_dict.o)
> ___utils_dict_MOD_do_integer_dict_define in libutils.a(utils_dict.o)
> ___utils_idict_MOD_do_integer_idict_create_hash in libutils.a(utils_idict.o)
> ...
> "_GOMP_critical_name_start", referenced from:
> ___eos_def_MOD_do_alloc_eos in libeos.a(eos_def.o)
> ___utils_lib_MOD_free_iounit in libutils.a(utils_lib.o)
> ___utils_lib_MOD_number_iounits_allocated in libutils.a(utils_lib.o)
> ___utils_lib_MOD_alloc_iounit in libutils.a(utils_lib.o)
> ___utils_dict_MOD_do_integer_dict_create_hash in libutils.a(utils_dict.o)
> ___utils_dict_MOD_do_integer_dict_define in libutils.a(utils_dict.o)
> ___utils_idict_MOD_do_integer_idict_create_hash in libutils.a(utils_idict.o)
> ...
> "_GOMP_critical_start", referenced from:
> ___eosde_load_tables_MOD_load_eosde_table in libeos.a(eosde_load_tables.o)
> ___eosdt_load_tables_MOD_load_eosdt_table in libeos.a(eosdt_load_tables.o)
> ___eospt_load_tables_MOD_load_eospt_table in libeos.a(eospt_load_tables.o)
> "_GOMP_parallel", referenced from:
> ___bcyclic_MOD_cycle_solve in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_rhs in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_onestep in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_bcyclic_solve in libmtx.a(bcyclic.o)
> ___mtx_support_MOD_do_quad_block_multiply_xa in libmtx.a(mtx_support.o)
> ___mtx_support_MOD_do_block_multiply_xa in libmtx.a(mtx_support.o)
> ___mtx_support_MOD_do_lu_factored_block_dble_mv in libmtx.a(mtx_support.o)
> ...
> "_Sample_", referenced from:
> _main in main_cpp-0e7b04.o
> "___addtf3", referenced from:
> _qdgemv.4521 in libmtx.a(mtx_support.o)
> ___mtx_support_MOD_do_quad_band_multiply_xa in libmtx.a(mtx_support.o)
> ___mtx_support_MOD_do_quad_multiply_xa_plus_c in libmtx.a(mtx_support.o)
> ___mtx_support_MOD_do_quad_multiply_xa in libmtx.a(mtx_support.o)
> ___my_lapack95_quad_MOD_my_gemm_plus_mm in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_gemm_p1 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_gemv_p_mv in libmtx.a(my_lapack95_quad.o)
> ...
> "___divtf3", referenced from:
> ___my_lapack95_quad_MOD_my_getrs_dbg in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_5_by_5 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_4_by_4 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_5_by_1 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_4_by_1 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2_5_by_5 in libmtx.a(my_lapack95_quad.o)
> ...
> "___eqtf2", referenced from:
> ___mtx_support_MOD_do_quad_dense_to_col_sparse_0_based in libmtx.a(mtx_support.o)
> _qlamc4_ in libmtx.a(qlamch.o)
> _qlamc1_ in libmtx.a(qlamch.o)
> _klu_q_rgrowth in libmesaklu.a(klu_q_diagnostics.o)
> _klu_q_condest in libmesaklu.a(klu_q_diagnostics.o)
> _klu_q_rcond in libmesaklu.a(klu_q_diagnostics.o)
> _klu_q_factor in libmesaklu.a(klu_q_factor.o)
> ...
> "___extenddftf2", referenced from:
> ___utils_nan_MOD_do_fill_quad_with_nans in libutils.a(utils_nan.o)
> ___mtx_support_MOD_do_dense_to_col_sparse_0_based_qp in libmtx.a(mtx_support.o)
> "___fixtfsi", referenced from:
> _qlamc1_ in libmtx.a(qlamch.o)
> _klu_q_condest in libmesaklu.a(klu_q_diagnostics.o)
> "___floatsitf", referenced from:
> _qlamc5_ in libmtx.a(qlamch.o)
> _qlamc4_ in libmtx.a(qlamch.o)
> _qlamc1_ in libmtx.a(qlamch.o)
> _qlamc2_ in libmtx.a(qlamch.o)
> _qlamch_ in libmtx.a(qlamch.o)
> _klu_q_condest in libmesaklu.a(klu_q_diagnostics.o)
> "___getf2", referenced from:
> ___my_lapack95_quad_MOD_my_getf2_5_by_5 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2_4_by_4 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2 in libmtx.a(my_lapack95_quad.o)
> _qlamc5_ in libmtx.a(qlamch.o)
> _klu_q_condest in libmesaklu.a(klu_q_diagnostics.o)
> _klu_q_kernel in libmesaklu.a(klu_q_kernel.o)
> "___gttf2", referenced from:
> ___my_lapack95_quad_MOD_my_getf2_5_by_5 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2_4_by_4 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2 in libmtx.a(my_lapack95_quad.o)
> _qlamc2_ in libmtx.a(qlamch.o)
> _klu_q_rgrowth in libmesaklu.a(klu_q_diagnostics.o)
> _klu_q_condest in libmesaklu.a(klu_q_diagnostics.o)
> _klu_q_rcond in libmesaklu.a(klu_q_diagnostics.o)
> ...
> "___letf2", referenced from:
> _qlamch_ in libmtx.a(qlamch.o)
> _klu_q_condest in libmesaklu.a(klu_q_diagnostics.o)
> _klu_q_kernel in libmesaklu.a(klu_q_kernel.o)
> "___lttf2", referenced from:
> ___my_lapack95_quad_MOD_my_getf2_5_by_5 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2_4_by_4 in libmtx.a(my_lapack95_quad.o)
> _qlamc5_ in libmtx.a(qlamch.o)
> _qlamc1_ in libmtx.a(qlamch.o)
> _qlamc2_ in libmtx.a(qlamch.o)
> _klu_q_rgrowth in libmesaklu.a(klu_q_diagnostics.o)
> _klu_q_condest in libmesaklu.a(klu_q_diagnostics.o)
> ...
> "___multf3", referenced from:
> _qdgemv.4521 in libmtx.a(mtx_support.o)
> ___mtx_support_MOD_do_quad_band_multiply_xa in libmtx.a(mtx_support.o)
> ___mtx_support_MOD_do_quad_multiply_xa_plus_c in libmtx.a(mtx_support.o)
> ___mtx_support_MOD_do_quad_multiply_xa in libmtx.a(mtx_support.o)
> ___my_lapack95_quad_MOD_my_getrs_dbg in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_5_by_5 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_4_by_4 in libmtx.a(my_lapack95_quad.o)
> ...
> "___netf2", referenced from:
> _qdgemv.4521 in libmtx.a(mtx_support.o)
> ___my_lapack95_quad_MOD_my_getrs_dbg in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2_5_by_5 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2_4_by_4 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_gemm_plus_mm in libmtx.a(my_lapack95_quad.o)
> ...
> "___subtf3", referenced from:
> ___my_lapack95_quad_MOD_my_getrs_dbg in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_5_by_5 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_4_by_4 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_5_by_1 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs_4_by_1 in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getrs in libmtx.a(my_lapack95_quad.o)
> ___my_lapack95_quad_MOD_my_getf2_5_by_5 in libmtx.a(my_lapack95_quad.o)
> ...
> "___trunctfdf2", referenced from:
> ___utils_isnan_MOD_check_for_bad_quad in libutils.a(utils_isnan_okay.o)
> "___unordtf2", referenced from:
> ___utils_isnan_MOD_check_for_bad_quad in libutils.a(utils_isnan_okay.o)
> "_omp_get_max_threads_", referenced from:
> ___utils_openmp_MOD_eval_omp_get_max_threads in libutils.a(utils_openmp.o)
> "_omp_get_num_threads", referenced from:
> ___bcyclic_MOD_cycle_solve._omp_fn.0 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_rhs._omp_fn.2 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_onestep._omp_fn.6 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_onestep._omp_fn.3 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_onestep._omp_fn.5 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_rhs._omp_fn.1 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_onestep._omp_fn.4 in libmtx.a(bcyclic.o)
> ...
> "_omp_get_thread_num", referenced from:
> ___bcyclic_MOD_cycle_solve._omp_fn.0 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_rhs._omp_fn.2 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_onestep._omp_fn.6 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_onestep._omp_fn.3 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_onestep._omp_fn.5 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_rhs._omp_fn.1 in libmtx.a(bcyclic.o)
> ___bcyclic_MOD_cycle_onestep._omp_fn.4 in libmtx.a(bcyclic.o)
> ...
> (maybe you meant: ___utils_openmp_MOD_eval_omp_get_thread_num, ___utils_lib_MOD_utils_omp_get_thread_num )
> "_omp_get_thread_num_", referenced from:
> ___utils_openmp_MOD_eval_omp_get_thread_num in libutils.a(utils_openmp.o)
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> make: *** [all] Error 1
>
>
> ------------------------------------------------------------------------------
>
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