NWChem 6.6 Mac LinAlg error

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Forum >> NWChem's corner >> Compiling NWChem

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Threads 2
Posts 7
8:28:48 AM PDT - Wed, Jul 6th 2016
I am having a similar problem installing nwchem to (http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1917/), but while their problem appeared to be fixed by switching from macports openmpi to homebrew openmpi and using make 64_to_32, that has not resolved my issue.

Specific error:
/var/folders/q6/q75j86w50jsdjb3743sld1h40000gn/T//cc8CU1Cx.s:22:suffix or operands invalid for `movq'
make[4]: *** [LinAlg/lapack+blas/gal_dcabs1.lo] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [build/.libs/libga.a] Error 1
make: *** [libraries] Error 1

Logs:
build/config.log, build/armci/config.log, and build/comex/config.log
https://www.dropbox.com/s/0pzm6i3eupenc01/config.log.zip?dl=0

I have tried compiling with macports and brew, with and without 64_to_32, and with gfortran 5.3 and 6.1. No successes yet.

How should I go about compiling NWChem?
Edited On 8:32:42 AM PDT - Wed, Jul 6th 2016 by Checksum

Forum Vet
Threads 9
Posts 1570
9:19:16 AM PDT - Wed, Jul 6th 2016
Since I have found only a portion of build/config.log in the zip file on dropbox, I am not quite sure if I can be of much help.
Anyhow, I believe your failure might be due to bit of the macports installation conflicting with the brew installation.
You might try to completely unset any env. variable that points to the macports locations (under /opt/local, most likely,
since I can see that your MPI settings seem to point to /opt/local/include/mpich-mp and blas to /opt/local/lib), and stick to brew for mpi and gfortran, instead
Anyhow, the most important thing is to see the actual gfortran command for compiling gal_dcabs1.f
Edited On 9:32:40 AM PDT - Wed, Jul 6th 2016 by Edoapra

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Threads 2
Posts 7
5:18:29 AM PDT - Thu, Jul 7th 2016
I think there was some kind of odd conflict in filestructure- I zipped a folder, and when unzipped I got a single file. This tar.gz should have all three of the config.log's.

https://www.dropbox.com/s/y4ukkht42gda5ah/build.tar.gz?dl=0

The gfortran command for compiling gal_dcabs1.f:
./util/util_nwchem_version.bash
Making libraries in tools
*** Building Parallel Tools ****
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in comex
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am
make[5]: Nothing to be done for `all-am'.
Making all in .
/bin/sh ./libtool  --tag=F77   --mode=compile gfortran   -fdefault-integer-8 -fno-aggressive-loop-optimizations  -c -o LinAlg/lapack+blas/gal_dcabs1.lo ../ga-5-4/LinAlg/lapack+blas/gal_dcabs1.f
libtool: compile:  gfortran -fdefault-integer-8 -fno-aggressive-loop-optimizations -c ../ga-5-4/LinAlg/lapack+blas/gal_dcabs1.f -o LinAlg/lapack+blas/gal_dcabs1.o
/var/folders/q6/q75j86w50jsdjb3743sld1h40000gn/T//cc8CU1Cx.s:21:suffix or operands invalid for `movq'


I uninstalled macports, un- and re-installed openmpi through brew, and tried again, with the same result.
Edited On 5:21:18 AM PDT - Thu, Jul 7th 2016 by Checksum

Forum Vet
Threads 9
Posts 1570
8:50:24 AM PDT - Thu, Jul 7th 2016
what gfortran are you using?
Could you please send me the output of the following commands
1) which gfortran
2) gfortran -v
3) gfortran -fdefault-integer-8 -fno-aggressive-loop-optimizations -c $NWCHEM_TOP/src/tools/ga-5-4/LinAlg/lapack+blas/gal_dcabs1.f
4) PATH=/usr/local/bin:/usr/bin:$PATH gfortran -v -fdefault-integer-8 -fno-aggressive-loop-optimizations -c $NWCHEM_TOP/src/tools/ga-5-4/LinAlg/lapack+blas/gal_dcabs1.f
Edited On 9:26:31 AM PDT - Thu, Jul 7th 2016 by Edoapra

Forum Vet
Threads 9
Posts 1570
8:54:19 AM PDT - Thu, Jul 7th 2016
Quote:Checksum Jul 7th 5:18 am

I uninstalled macports, un- and re-installed openmpi through brew, and tried again, with the same result.


Are you really sure that macports is gone? The file build/config.log still shows reference to /opt/local/include/mpich-mp,
the location of mpich (not openmpi) most likely out of macports, and not brew

Clicked A Few Times
Threads 2
Posts 7
12:52:31 PM PDT - Thu, Jul 7th 2016 
$ which gfortran
/usr/local/bin/gfortran
$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin15.0.0/5.3.0/lto-wrapper
Target: x86_64-apple-darwin15.0.0
Configured with: ../gcc-5.3.0/configure --enable-languages=fortran,c,c++
Thread model: posix
gcc version 5.3.0 (GCC) 
$ gfortran -fdefault-integer-8 -fno-aggressive-loop-optimizations -c $NWCHEM_TOP/src/tools/ga-5-4/LinAlg/lapack+blas/gal_dcabs1.f
<no output>


Macports is definitely gone- the /opt/local folder no longer exists. However, I guess there were some issues with leftover environment variables, or not remaking nwchem_config, or something.

With a cleaner reinstall of openmpi and openblast, I managed to get an nwchem install to proceed past the linalg issue, but I'm running into other issues:
Making libraries in ccca
gfortran  -c -cpp  -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations  -I. -I../basis -I/Users/owengray/nwchem-6.6//src/include -I/Users/owengray/nwchem-6.6//src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG   task_ccca.F
gfortran  -c -cpp  -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations  -I. -I../basis -I/Users/owengray/nwchem-6.6//src/include -I/Users/owengray/nwchem-6.6//src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG   ccca_utils.F
Got lock on /Users/owengray/nwchem-6.6//lib/MACX64/libccca.lock
ar r /Users/owengray/nwchem-6.6//lib/MACX64/libccca.a task_ccca.o ccca_utils.o
ranlib /Users/owengray/nwchem-6.6//lib/MACX64/libccca.a
/Applications/Xcode.app/Contents/Developer/usr/bin/make nwchem.o stubs.o
gfortran -cpp  -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations  -I.  -I/Users/owengray/nwchem-6.6//src/include -I/Users/owengray/nwchem-6.6//src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/Users/owengray/nwchem-6.6/'" -DNWCHEM_BRANCH="'6.6'"  -c -o nwchem.o nwchem.F
gfortran -cpp  -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations  -I.  -I/Users/owengray/nwchem-6.6//src/include -I/Users/owengray/nwchem-6.6//src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/Users/owengray/nwchem-6.6/'" -DNWCHEM_BRANCH="'6.6'"  -c -o stubs.o stubs.F
gfortran  -L/Users/owengray/nwchem-6.6//lib/MACX64 -L/Users/owengray/nwchem-6.6//src/tools/install/lib  -o /Users/owengray/nwchem-6.6//bin/MACX64/nwchem nwchem.o stubs.o -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -lnwclapack  -lnwcblas -lnwclapack  -lnwcblas   -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/1.10.2_1/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi   
Undefined symbols for architecture x86_64:
  "_ixamax_", referenced from:
      _pneb_w_dmax_ in libnwpwlib.a(Pneb.o)
  "_iyamax_", referenced from:
      _driver_sad_search_dir_ in libdriver.a(opt_drv.o)
      _sym_movecs_adapt_ in libnwcutil.a(sym_mo_adapt.o)
      _fd_make_vectors_ in libnwctask.a(task_num_grad.o)
      _tropt_pickstp_ in liboptim.a(tropt_drv.o)
      _dgefa_ in libvscf.a(vscf.o)
      _dneall_m_dmax_ in libnwpwlib.a(Dne.o)
      _mcscf_canonical_ in libmcscf.a(mcscf_aux.o)
      ...
  "_xaxpy_", referenced from:
      _pneb_w_axpy_ in libnwpwlib.a(Pneb.o)
      _silvestrelli_minimize_ in libpspw.a(silvestrelli_minimize.o)
      _silvestrelli_minimize_old_ in libpspw.a(silvestrelli_minimize_old.o)
      _cpsi_lmbda_ in libband.a(cpsi_lmbda.o)
      _sym_get_spin_op_ in libnwdft.a(sym_op_clsfy_so.o)
  "_xcopy_", referenced from:
      _c3db_cr_fft3b_ in libnwpwlib.a(C3dB-new.o)
      _c3db_rc_fft3f_ in libnwpwlib.a(C3dB-new.o)
      _c3db_pfftby_ in libnwpwlib.a(C3dB_pfft.o)
      _c3db_pfftbz_ in libnwpwlib.a(C3dB_pfft.o)
      _c3db_pfftfz_ in libnwpwlib.a(C3dB_pfft.o)
      _c3db_pfftfy_ in libnwpwlib.a(C3dB_pfft.o)
      _c3db_cr_pfft3b_ in libnwpwlib.a(C3dB_pfft.o)
      ...
  "_xgemm_", referenced from:
      _zpatch_test_ in libnwcutil.a(util_patch_test.o)
      _cpsp_v_nonlocal_ in libband.a(cpsp.o)
      _cpsp_v_nonlocal_orb_ in libband.a(cpsp.o)
      _cram_ccm_izgemm_ in libnwpwlib.a(cram.o)
      _cram_ccm_sym_izgemm_ in libnwpwlib.a(cram.o)
      _cram_cmc_zgemm_ in libnwpwlib.a(cram.o)
      _dneall_www_multiply_ in libnwpwlib.a(Dne.o)
      ...
  "_xheev_", referenced from:
      _pneb_w_diag_ in libnwpwlib.a(Pneb.o)
      _pneb_wne_diag_ in libnwpwlib.a(Pneb.o)
      _vib_gendynamicmatrix_ in libvib.a(vib_phonon.o)
      _dft_scf_so_ in libnwdft.a(dft_scf_so.o)
  "_xscal_", referenced from:
      _cpsp_v_nonlocal_ in libband.a(cpsp.o)
      _cpsp_v_nonlocal_orb_ in libband.a(cpsp.o)
      _cpsp_f_vnonlocal_ in libband.a(cpsp.o)
      _cpsp_v_nonlocal_euv_2_ in libband.a(cpsp_stress.o)
      _cpsp_v_nonlocal_orb_2com_ in libband.a(cpsp_relativistic.o)
      _cpsp_v_spin_orbit_ in libband.a(cpsp_relativistic.o)
      _cpsp_v_spin_orbit_orb_ in libband.a(cpsp_relativistic.o)
      ...
  "_yasum_", referenced from:
      _tred2 in libpeigs.a(tred22.o)
      _inv_it3 in libpeigs.a(inv_it3.o)
  "_yaxpy_", referenced from:
      _geom_binvr_ in libnwcutil.a(geom_hnd.o)
      _mepgs_chk_ in liboptim.a(mepgs_drv.o)
      _gsopt_cart_pmat_ in liboptim.a(mepgs_drv.o)
      _gsopt_take_step_ in liboptim.a(mepgs_drv.o)
      _gsopt_pickstp_ in liboptim.a(mepgs_drv.o)
      _gsopt_compute_info_ in liboptim.a(mepgs_drv.o)
      _gsopt_initialize_ in liboptim.a(mepgs_drv.o)
      ...
  "_ycopy_", referenced from:
      _bas_rtdb_do_load_ in libnwcutil.a(basis.o)
      _geom_prt_dihedrals_ in libnwcutil.a(geom.o)
      _geom_calc_dihedral_ in libnwcutil.a(geom.o)
      _geom_vel_set_ in libnwcutil.a(geom.o)
      _geom_vel_get_ in libnwcutil.a(geom.o)
      _geom_lattice_set_ in libnwcutil.a(geom.o)
      _geom_amatrix_set_ in libnwcutil.a(geom.o)
      ...
  "_ydot_", referenced from:
      _out_of_plane_angle_ in libnwcutil.a(geom_hnd.o)
      _hnd_tftr_ in libnwcutil.a(geom_hnd.o)
      _geom_print_ in libnwcutil.a(geom.o)
      _geom_compute_values_ in libnwcutil.a(geom.o)
      _geom_rtdb_load_ in libnwcutil.a(geom.o)
      _geom_zmat_to_cart_ in libnwcutil.a(geom_input.o)
      _mepgs_hessian_update_ in liboptim.a(mepgs_drv.o)
      ...
  "_ygebak_", referenced from:
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
  "_ygebal_", referenced from:
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
  "_ygeev_", referenced from:
      _tce_eom_ydiagon_ in libtce.a(tce_eom_ydiagon.o)
  "_ygeevx_", referenced from:
      _util_dgeev_ in libnwcutil.a(util_dgeev.o)
  "_ygehrd_", referenced from:
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
  "_ygemm_", referenced from:
      _geom_binvr_ in libnwcutil.a(geom_hnd.o)
      _gsopt_project_hess_grad_ in liboptim.a(mepgs_drv.o)
      _gsopt_hss_init_ in liboptim.a(mepgs_drv.o)
      _gsopt_hess_cart_guess_ in liboptim.a(mepgs_drv.o)
      _mepgs_hss_init_ in liboptim.a(mepgs_drv.o)
      _mepgs_hess_cart_guess_ in liboptim.a(mepgs_drv.o)
      _driver_project_hess_grad_ in libdriver.a(opt_drv.o)
      ...
  "_ygemv_", referenced from:
      _geom_impose_constraints_ in libnwcutil.a(geom_input.o)
      _geom_update_cart_from_int_ in libnwcutil.a(geom_input.o)
      _mepgs_hessian_update_ in liboptim.a(mepgs_drv.o)
      _gsopt_hessian_update_ in liboptim.a(mepgs_drv.o)
      _gsopt_pickstp_ in liboptim.a(mepgs_drv.o)
      _gsopt_symmetrize_step_ in liboptim.a(mepgs_drv.o)
      _gsopt_project_hess_grad_ in liboptim.a(mepgs_drv.o)
      ...
  "_yger_", referenced from:
      _ecp_local2_ in libnwints.a(ecp_local2.o)
  "_ygesv_", referenced from:
      _get_charges_ in libdplot.a(get_charges.o)
      _ga_iter_lsolve_ in libnwcutil.a(ga_it_lsolve.o)
      _pspw_gen_apc_ in libpspw.a(pspw_APC.o)
      _pspw_potential_sic_oep_ in libpspw.a(pspw_sic.o)
      _xlm_y_rotation_matrix_ in libddscf.a(xlm_poles.o)
      _band_interpolate_eigs_ in libband.a(band_interpolate_structure.o)
      _mcscf_precond_ in libmcscf.a(mcscf_prcnd.o)
      ...
  "_ygesvd_", referenced from:
      _ga_svd_seq_ in libnwcutil.a(ga_it2.o)
      _cdft_newt_ in libnwdft.a(cdft_util.o)
  "_yhseqr_", referenced from:
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
  "_ylacpy_", referenced from:
      _dmatrix_dgemm3_ in libnwpwlib.a(DMatrix-mpi.o)
      _dmatrix_dgemm1_ in libnwpwlib.a(DMatrix-mpi.o)
      _dmatrix_dgemm2_ in libnwpwlib.a(DMatrix-mpi.o)
      _dmatrix_combo_dgemm2_ in libnwpwlib.a(DMatrix-mpi.o)
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
  "_ylagtf_", referenced from:
      _inv_it3 in libpeigs.a(inv_it3.o)
  "_ylagts_", referenced from:
      _inv_it3 in libpeigs.a(inv_it3.o)
  "_ylange_", referenced from:
      _ga_normf_ in libnwcutil.a(ga_normf.o)
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
  "_ylarnv_", referenced from:
      _clustrinv5_ in libpeigs.a(clustrxx5.o)
  "_ylascl_", referenced from:
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
  "_ylaset_", referenced from:
      _rimp2_v_e2_ in librimp2.a(rimp2_v_e2.o)
      _hf1prtoab_ in libnwints.a(hf1PRtoAB.o)
      _hf2prtoab_ in libnwints.a(hf2PRtoAB.o)
      _hf2qstocd_ in libnwints.a(hf2QStoCD.o)
      _xf3ci_step12a_ in librimp2.a(xf3ci_s12a.o)
      _xf3ci_step12b_ in librimp2.a(xf3ci_s12b.o)
      _eval_3ci_block_ in librimp2.a(eval_3ci.o)
      ...
  "_ynrm2_", referenced from:
      _selci_analci_ in libselci.a(davids.o)
      _tred2 in libpeigs.a(tred22.o)
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
      _inv_it3 in libpeigs.a(inv_it3.o)
      _mgs_3 in libpeigs.a(mgs5.o)
      _mgscs in libpeigs.a(mgscs.o)
  "_yorghr_", referenced from:
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
  "_yrot_", referenced from:
      _localizefb_ in libddscf.a(localize.o)
      _localizepm_ in libddscf.a(localize.o)
      _sdiag2_ in libnwints.a(big_service.o)
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
  "_yscal_", referenced from:
      _geom_binvr_ in libnwcutil.a(geom_hnd.o)
      _geom_lattice_set_ in libnwcutil.a(geom.o)
      _geom_amatrix_set_ in libnwcutil.a(geom.o)
      _bq_input_load_ in libbq.a(bq_input.o)
      _dplot_ in libdplot.a(dplot.o)
      _geom_3d_amatrix_ in libnwcutil.a(geom_3d.o)
      _geom_impose_constraints_ in libnwcutil.a(geom_input.o)
      ...
  "_yspsvx_", referenced from:
      _diis_bsolve_ in libnwdft.a(diis_bsolve.o)
      _diis_bsolve_so_ in libnwdft.a(diis_bsolve_so.o)
  "_ysterf_", referenced from:
      _pstebz10_ in libpeigs.a(pstebz10.o)
  "_yswap_", referenced from:
      _dgedi_ in libvscf.a(vscf.o)
  "_ysyev_", referenced from:
      _geom_binvr_ in libnwcutil.a(geom_hnd.o)
      _paw_cpmd_ in libpaw.a(paw_cpmd.o)
      _paw_sd_ in libpaw.a(paw_sd.o)
      _control_find_box_ in libnwpwlib.a(control.o)
      _dneall_m_diagonalize_ in libnwpwlib.a(Dne.o)
      _dneall_mne_diagonalize_ in libnwpwlib.a(Dne.o)
      _mcscf_naturalorb_ in libmcscf.a(mcscf_aux.o)
      ...
  "_ysygv_", referenced from:
      _detci_dvddiag_ in libmcscf.a(detci_diag.o)
      _pspw_rmmdiis_ in libpspw.a(pspw_rmmdiis.o)
  "_ytrevc_", referenced from:
      _tce_dgeev_ in libtce.a(tce_dgeev.o)
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [all] Error 1

the config.log files have last updated times long before the install failure, so they seem useless, so I've only uploaded the terminal output.
https://www.dropbox.com/s/dfs1wrb8jn8ixa9/nwchem_installog.rtf?dl=0
Edited On 12:57:00 PM PDT - Thu, Jul 7th 2016 by Checksum

Forum Vet
Threads 9
Posts 1570
9:16:47 AM PDT - Fri, Jul 8th 2016
1) add the env. variable USE_64TO32=y, e.g. (bash)


 export USE_64TO32=y
2) cd $NWCHEM_TOP/src/64to32blas
3) make
4) cd ..
5) make link

Clicked A Few Times
Threads 2
Posts 7
10:46:38 AM PDT - Fri, Jul 8th 2016
Error in make link:

gfortran -cpp  -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations  -I.  -I/Users/me/nwchem-6.6//src/include -I/Users/me/nwchem-6.6//src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/Users/me/nwchem-6.6/'" -DNWCHEM_BRANCH="'6.6'"  -c -o nwchem.o nwchem.F
gfortran -cpp  -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations  -I.  -I/Users/me/nwchem-6.6//src/include -I/Users/me/nwchem-6.6//src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/Users/me/nwchem-6.6/'" -DNWCHEM_BRANCH="'6.6'"  -c -o stubs.o stubs.F
gfortran  -L/Users/me/nwchem-6.6//lib/MACX64 -L/Users/me/nwchem-6.6//src/tools/install/lib  -o /Users/me/nwchem-6.6//bin/MACX64/nwchem nwchem.o stubs.o -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -lnwclapack  -lnwcblas -l64to32 -lnwclapack  -lnwcblas   -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/1.10.2_1/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi      -lpthread   
duplicate symbol _c3db_c_ptranspose_ijk_start_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_ptranspose2_jk_start_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_ptranspose1_jk_start_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c_balance_c_unbalance_start_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c_balance_c_balance_start_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_vector_isumall_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_isumall_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_vector_sumall_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_sumall_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_ptranspose_ijk_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_r_transpose_ijk_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_transpose_ijk_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_r_transpose_jk_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_transpose_jk_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_ptranspose2_jk_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_ptranspose1_jk_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_r_write_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_write_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_ptranspose_ijk_end_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_ptranspose2_jk_end_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_ptranspose1_jk_end_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c_balance_c_unbalance_end_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c_balance_c_balance_end_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_r_read_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
duplicate symbol _c3db_c_read_ in:
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-mpi.o)
    /Users/me/nwchem-6.6//lib/MACX64/libnwpwlib.a(C3dB-tcgmsg.o)
ld: 25 duplicate symbols for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [link] Error 1
Edited On 8:07:57 AM PDT - Thu, Jul 14th 2016 by Checksum

Forum Vet
Threads 9
Posts 1570
8:41:55 AM PDT - Mon, Jul 11th 2016
Unfortunately, you seem to have quite a few leftovers from previous compilations under different env. variables' settings.
If you still find one more, it might be better to restart from scratch
Please try the following

rm /Users/owengray/nwchem-6.6//lib/MACX64/libnwpwlib.a
cd $NWCHEM_TOP/src/nwpw
make
cd ..
make link

Clicked A Few Times
Threads 2
Posts 7
12:09:47 PM PDT - Wed, Jul 13th 2016
I managed to get 32-bit nwchem to compile without errors. It is somewhat disappointing that 64-bit nwchem seems to not be compatible with OSX, given that my computer has much more than 4GB of ram, and that I believe that certain nwchem calculations may involve large amounts of data that would ideally be stored in RAM, like the full excited state calculations I am doing.

However, mov2asc, compiled from the same terminal window as nwchem (and thus with the same environment variables) is giving:

dhcp-18-111-117-138:mov2asc me$ ./mov2asc 1 ~/Desktop/water_scf_test2.movecs ~/Desktop/ascout.asc
MA error: MA_init: invalid datatype: 7089068599809147893
Unable to initialize memory          1


A google indicates that this may be due to mov2asc being compiled as x86_64.

Some output asked for in another thread about this issue:
dhcp-18-111-117-138:mov2asc me$ echo $NWCHEM_TARGET
MACX64
dhcp-18-111-117-138:mov2asc me$ mpif90 -v
Using built-in specs.
COLLECT_GCC=/usr/local/bin/gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/6.1.0/libexec/gcc/x86_64-apple-darwin15.5.0/6.1.0/lto-wrapper
Target: x86_64-apple-darwin15.5.0
Configured with: ../configure --build=x86_64-apple-darwin15.5.0 --prefix=/usr/local/Cellar/gcc/6.1.0 --libdir=/usr/local/Cellar/gcc/6.1.0/lib/gcc/6 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-6 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew gcc 6.1.0' --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --enable-multilib
Thread model: posix
gcc version 6.1.0 (Homebrew gcc 6.1.0) 
dhcp-18-111-117-138:mov2asc me$ mpif90 -V
gfortran: error: unrecognized command line option '-V'
gfortran: fatal error: no input files
compilation terminated.
dhcp-18-111-117-138:mov2asc me$ mpif90 -show
/usr/local/bin/gfortran -I/usr/local/Cellar/open-mpi/1.10.2_1/include -Wl,-flat_namespace -Wl,-commons,use_dylibs -I/usr/local/Cellar/open-mpi/1.10.2_1/lib -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/1.10.2_1/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi


Also, what would cause mov2asc compiled on my mac to fail for .movecs files produced elsewhere? I do not see anything hardware- or OS-sensitive in the code for mov2asc unless a cray is used- could I overcome any such issues by editing the mov2asc files before recompiling? I ask this because mov2asc is apparently not compiling on that machine with default settings, and the admin is very busy.

The output of mpi90 -v on the machine that would be creating the movecs files I would like to convert locally is
$ mpif90 -v
Using built-in specs.
COLLECT_GCC=/cm/shared/apps/gcc/4.8.1/bin/gfortran
COLLECT_LTO_WRAPPER=/cm/shared/apps/gcc/4.8.1/libexec/gcc/x86_64-unknown-linux-gnu/4.8.1/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.8.1/configure --prefix=/cm/shared/apps/gcc/4.8.1 --enable-languages=c,c++,fortran --with-gmp-include=/usr/src/redhat/BUILD/gcc-4.8.1-obj/../gcc-4.8.1/our-gmp --with-gmp-lib=/usr/src/redhat/BUILD/gcc-4.8.1-obj/../gcc-4.8.1/our-gmp --with-mpc-include=/usr/src/redhat/BUILD/gcc-4.8.1-obj/../gcc-4.8.1/our-mpc/src --with-mpc-lib=/usr/src/redhat/BUILD/gcc-4.8.1-obj/../gcc-4.8.1/our-mpc/src/.libs --with-mpfr-include=/usr/src/redhat/BUILD/gcc-4.8.1-obj/../gcc-4.8.1/our-mpfr/src --with-mpfr-lib=/usr/src/redhat/BUILD/gcc-4.8.1-obj/../gcc-4.8.1/our-mpfr/src/.libs
Thread model: posix
gcc version 4.8.1 (GCC)
Edited On 8:08:52 AM PDT - Thu, Jul 14th 2016 by Checksum


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