Molcas Forum

David

Member

Registered: 2017-05-16

Posts: 84

Compiling Openmolcas together with Gromacs

Dear OpenMolcas developers, I had a problem when I installed openmolcas interfaces with gromacs program. I turned on gromacs option (-D GROMACS=ON) during the configuration step, however, it reports error as below. As a comparison, I turned off gromacs option (-D GROMACS=ON) during the configuration, and the installation procedure can terminate normally. Thanks a lot and any relevant imformation will be appreciated!

7696 [ 76%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/natorb_rasscf.f.o
7697 [ 76%] Building Fortran object CMakeFiles/gugaci.dir/src/gugaci/complete_ext_loop.f.o
7698 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_pds_lp64_pds_sym_pos_fwd_ker_par_nrhs_real'
7699 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_spblas_lp64_scsr1ntluc__mmout_par'
7700 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_sparse_s_dense_l_sv64x64_i4'
7701 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_sparse_c_dense_u_sv64x64_i8'
7702 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_spblas_ccsr0ctunf__mmout_par'
7703 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_sparse_z_bsr0ng_n_mv_ker_i4'
7704 [ 76%] Building Fortran object CMakeFiles/scf.dir/src/scf/occsets.f.o
7705 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_spblas_lp64_ccsr1nsluc__mmout_par'
7706 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_spblas_lp64_zcsr1nd_uc__mmout_seq'
7707 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_blas_xidamax'
7708 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_cpds_lp64_sp_cpds_slv_bwd_single_real'
7709 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_pds_pds_unsym_fwd_ker_t_seq_nrhs_real'
7710 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_lapack_cgbredr'
7711 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_pds_lp64_sp_pds_her_pos_fwd_ker_seq_nrhs_cmplx'
7712 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_cpds_sp_cpds_fct_right_real'
7713 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_spblas_ccsr0nhuuf__mmout_par'
7714 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_sparse_s_sv_bwd_ker1_high_opt_i4'
7715 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_pds_sp_pds_sym_indef_diag_fwd_ker_seq_cmplx'
7716 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_sparse_s_csc_mv_def_ker_i8'
7717 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_pds_pds_her_indef_diag_ker_loop_nrhs_cmplx'
7718 /opt/longrun/anaconda3/lib/libmkl_intel_lp64.so: undefined reference to `mkl_pds_lp64_pardiso_export_s'
7719 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_pds_lp64_sp_pds_unsym_ker_loop_nrhs_cmplx'
7720 /opt/longrun/anaconda3/lib/libmkl_intel_lp64.so: undefined reference to `mkl_pds_lp64_pardiso_export_c'
7721 /opt/longrun/anaconda3/lib/libmkl_intel_thread.so: undefined reference to `mkl_pds_lp64_pds_fct_right_single_cmplx'
7722 [ 76%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/neworb_rasscf.f.o
7723 make[2]: *** [bin/guessorb.exe] Error 1
7724 make[1]: *** [CMakeFiles/guessorb.exe.dir/all] Error 2
7725 make[1]: *** Waiting for unfinished jobs....
7726 [ 76%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/opnfls_rasscf.f.o
7727 [ 76%] Built target guga
7728 [ 76%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/ortho.f.o
7729 [ 76%] Building Fortran object CMakeFiles/scf.dir/src/scf/aufbau.f.o
7730 [ 76%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/ortho1.f.o
7731 [ 76%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/mkmaw_cp2.f.o
7732 [ 76%] Building Fortran object CMakeFiles/gugaci.dir/src/gugaci/davdiag.f.o
7733 [ 76%] Building Fortran object CMakeFiles/scf.dir/src/scf/c_adjust.f.o
7734 [ 76%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/mkpref_rpt2.f.o
7735 [ 76%] Building Fortran object CMakeFiles/scf.dir/src/scf/chklumo.f.o
7736 [ 76%] Building Fortran object CMakeFiles/scf.dir/src/scf/chkort.f.o
7737 [ 76%] Building Fortran object CMakeFiles/gugaci.dir/src/gugaci/dbl_upwalk.f.o
7738 [ 76%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/mkrhs.f.o
7739 [ 76%] Building Fortran object CMakeFiles/cpf.dir/src/cpf/vsadd.f.o
7740 [ 76%] Building Fortran object CMakeFiles/cpf.dir/src/cpf/vsmsb.f.o
7741 [ 76%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/ortho2.f.o
7742 [ 77%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/outctl.f.o
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7766 [ 77%] Building Fortran object CMakeFiles/scf.dir/src/scf/dgrd.f.o
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7769 [ 77%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/proc_inp.f.o
7770 [ 77%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/prttim.f.o
7771 [ 77%] Building Fortran object CMakeFiles/gugaci.dir/src/gugaci/dblploop1_g.f.o
7772 [ 77%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/mktg3.f.o
7773 [ 77%] Building Fortran object CMakeFiles/scf.dir/src/scf/diis_x.f.o
7774 [ 77%] Building Fortran object CMakeFiles/gugaci.dir/src/gugaci/dblploop2.f.o
7775 [ 77%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/mkwwop.f.o
7776 [ 77%] Building Fortran object CMakeFiles/scf.dir/src/scf/dmat.f.o
7777 [ 77%] Building Fortran object CMakeFiles/gugaci.dir/src/gugaci/dblploop3.f.o
7778 [ 77%] Building Fortran object CMakeFiles/scf.dir/src/scf/done_scf.f.o
7779 [ 77%] Building Fortran object CMakeFiles/scf.dir/src/scf/dumpcmo.f.o
7780 [ 77%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/mltctl.f.o
7781 [ 77%] Building Fortran object CMakeFiles/scf.dir/src/scf/dumpeor.f.o
7782 [ 77%] Building Fortran object CMakeFiles/scf.dir/src/scf/egrad.f.o
7783 [ 77%] Building Fortran object CMakeFiles/scf.dir/src/scf/eneclc.f.o
7784 [ 77%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/putrlx.f.o
7785 [ 77%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/mltdxp.f.o
7786 [ 77%] Building Fortran object CMakeFiles/rasscf.dir/src/rasscf/qcmaquis_rdinp.f.o
7787 [ 77%] Building Fortran object CMakeFiles/scf.dir/src/scf/errv.f.o
7788 [ 77%] Building Fortran object CMakeFiles/gugaci.dir/src/gugaci/dblploop4.f.o
7789 [ 77%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/mltmv.f.o
7790 [ 77%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/mltr1.f.o
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7831 [ 78%] Building Fortran object CMakeFiles/scf.dir/src/scf/memalo.f.o
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8003 make: *** [all] Error 2

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: Compiling Openmolcas together with Gromacs

What you show is some MKL linking problems. Maybe Gromacs was compiled with different (incompatible) options. Run "make -j 1" to have a sorted (not shuffled) output.

David

Member

Registered: 2017-05-16

Posts: 84

Re: Compiling Openmolcas together with Gromacs

Dear Ignacio, thank you for your reply! I have tried compiling openmolcas again with its default linear algebra library and the installation procedure is done without any problem. By the way, as the manual mentioned in QM/MM calculation with gromacs, do I need any extra file in addition to "topol.tpr" file?

Last edited by David (2020-01-05 08:53:18)