Official Candidate Release of NWCHEM6.8 cannot be compiled on MAC

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Forum Regular
Threads 43
Posts 209
11:53:59 PM PDT - Thu, Nov 2nd 2017
Dear all
  The compilation of the candidate of NWCHEM6.8 on macOS Sierra 10.12.6 with gfortran6.3.0,
mpich 3.2_2 and Xcode 9.1 installed fails because of the following error
...
ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
make: *** [all] Error 1

Very Best Regards!
Edited On 4:25:52 PM PST - Sat, Dec 2nd 2017 by Xiongyan21

Gets Around
Threads 24
Posts 86
1:23:58 AM PDT - Fri, Nov 3rd 2017
Hello Xiongyan

I have found only 6.6 on http://www.nwchem-sw.org/index.php/Download.
Where do you get 6.8?

Best, Vladimir.


I'm sorry.
Here it is.
http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id2459

Point me to Changelog please.
Edited On 4:04:48 AM PDT - Fri, Nov 3rd 2017 by Vladimir

Forum Vet
Threads 9
Posts 1489
10:39:51 AM PDT - Fri, Nov 3rd 2017
Could you please run the simple test below to confirm that your gfortran installation is working?
rm  -f gfortrantest.f90 
cat >  gfortrantest.f90  <<EOF
      program main
      end
EOF
gfortran  gfortrantest.f90



Quote:Xiongyan21 Nov 2nd 10:53 pm
Dear all
The compilation of the candidate of NWCHEM6.8 on macOS Sierra 10.12.6
with gfortran6.3.0, mpich 3.2_2 and Xcode 9.1 installed fails
because of the following error
...
ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
make: *** [all] Error 1

Very Best Regards!

Forum Regular
Threads 43
Posts 209
7:49:53 PM PDT - Fri, Nov 3rd 2017
Dear Edoapra
The group of commands together gives

ld: library not found for -lSystem
collect2: error: ld returned 1 exit status,
although actually NWCHEM6.6, DALTON2016.2 and DIRAC16 have been successfully compiled on my MAC and they still can work.

 Very Best Regards!



 Thanks a lot!
Edited On 8:12:46 PM PDT - Fri, Nov 3rd 2017 by Xiongyan21

Forum Regular
Threads 43
Posts 209
11:25:15 PM PDT - Fri, Nov 3rd 2017
I downloaded the 1.04G gz form of NWCHEM6.8 and recompiled it, but still got the same mistake, also at the last stage

...
all dim_grid_quadv0_gen(rtdb, g_vdim, 1, 1, .false., 0, 1)
                                    1
Warning: Rank mismatch in argument 'g_vdim' at (1) (scalar and rank-1)
gfortran -c -cpp -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations -I. -I../nwdft/include -I../ddscf -I../util -I../nwdft/grid -I../NWints/hondo -I/users/computation/nwchem6.8/src/include -I/users/computation/nwchem6.8/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DDBLEPREC_RYS dim_grid_quadv0a.F
gfortran -c -cpp -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations -I. -I../nwdft/include -I../ddscf -I../util -I../nwdft/grid -I../NWints/hondo -I/users/computation/nwchem6.8/src/include -I/users/computation/nwchem6.8/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DDBLEPREC_RYS dim_grid_quadv0b.F
gfortran -c -cpp -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations -I. -I../nwdft/include -I../ddscf -I../util -I../nwdft/grid -I../NWints/hondo -I/users/computation/nwchem6.8/src/include -I/users/computation/nwchem6.8/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DDBLEPREC_RYS dimqm_seeding.F
gfortran -c -cpp -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations -I. -I../nwdft/include -I../ddscf -I../util -I../nwdft/grid -I../NWints/hondo -I/users/computation/nwchem6.8/src/include -I/users/computation/nwchem6.8/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DDBLEPREC_RYS dimqm_rohf.F
gfortran -c -cpp -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations -I. -I../nwdft/include -I../ddscf -I../util -I../nwdft/grid -I../NWints/hondo -I/users/computation/nwchem6.8/src/include -I/users/computation/nwchem6.8/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DDBLEPREC_RYS dimqm_util.F
Got lock on /users/computation/nwchem6.8/lib/MACX64/libdimqm.lock
ar r /users/computation/nwchem6.8/lib/MACX64/libdimqm.a dimqm_input.o dimpar_input.o dimqm_prep.o dimqm_main.o dimqm_polarizability.o dimqm_f2d.o dimqm_iterative.o qmr_real.o qmr_complex.o matvecReal.o matvecComplex.o dimqm_EqmE.o t2.o pphilo.o dimqm_fldpot.o dimqm_EqmN.o dimqm_printAtomicDipoles.o dimqm_energy.o dimqm_printDipole.o dimqm_Dens2Dipoles.o dimqm_indDipoles.o dimqm_printAtoms.o dimqm_addop.o dimqm_lclfld.o dim_elfcon.o dim_1eelec.o dim_elfder.o dim_dervxyz.o dim_sxyz.o dimqm_screening.o seeded_qmr_real.o qmr_seed_real.o seeded_qmr_real_augment.o dimqm_tidy.o qmr_seed_complex.o seeded_qmr_complex.o dimqm_broadcast.o CubicSpline.o dim_fock_xc.o dim_getv.o dim_tabcd.o dim_eval_fnl.o dim_grid_quadv0.o dim_grid_quadv0a.o dim_grid_quadv0b.o dimqm_seeding.o dimqm_rohf.o dimqm_util.o
ar: creating archive /users/computation/nwchem6.8/lib/MACX64/libdimqm.a
ranlib /users/computation/nwchem6.8/lib/MACX64/libdimqm.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/computation/nwchem6.8/src/include -I/users/computation/nwchem6.8/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/computation/nwchem6.8'" -DNWCHEM_BRANCH="'6.8'" -c -o nwchem.o nwchem.F
gfortran -cpp -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations -I. -I/users/computation/nwchem6.8/src/include -I/users/computation/nwchem6.8/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/computation/nwchem6.8'" -DNWCHEM_BRANCH="'6.8'" -c -o stubs.o stubs.F
gfortran -L/users/computation/nwchem6.8/lib/MACX64 -L/users/computation/nwchem6.8/src/tools/install/lib -Wl,-flat_namespace -o /users/computation/nwchem6.8/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 -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -lnwclapack -lnwcblas /Library/Frameworks/Python.framework/versions/2.7/lib/python2.7/config/libpython2.7.a -lnwclapack -lnwcblas -L/usr/local/Cellar/mpich/3.2_2/lib -lmpifort -lmpi -lpmpi -lpthread -lpthread
ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
make: *** [all] Error 1
Edited On 11:27:14 PM PDT - Fri, Nov 3rd 2017 by Xiongyan21

Forum Vet
Threads 9
Posts 1489
11:29:11 PM PDT - Fri, Nov 3rd 2017
My suggestion is to execute the command
brew reinstall gcc

This is likely to fix your NWChem link problem. Se the following URL for details
https://github.com/Homebrew/legacy-homebrew/issues/45011


Quote:Xiongyan21 Nov 3rd 6:49 pm
Dear Edoapra
The group of commands together gives

ld: library not found for -lSystem
collect2: error: ld returned 1 exit status,
although actually NWCHEM6.6, DALTON2016.2 and DIRAC16 have been successfully compiled on my MAC and they still can work.

Very Best Regards!

Thanks a lot!

Forum Regular
Threads 43
Posts 209
11:51:46 PM PDT - Fri, Nov 3rd 2017
Dear Edoapra
 Thanks for your answer.

 I think I can resort to the patch of GCC for NWCHEM6.6 to overcome this problem,

because the reinstallation of GCC will result in the recompilations of other softwares,

which is not very beneficial when there are not any updates of them.

 I will do it later today. 

 Your suggestion will be followed if it is unsuccessful and there will be no patch to

remedy this when the formal one is released.



 Very Best regards?
Edited On 11:58:37 PM PDT - Fri, Nov 3rd 2017 by Xiongyan21

Forum Regular
Threads 43
Posts 209
6:25:11 AM PDT - Sat, Nov 4th 2017
The error is the same although the patch Gcc6_macs_optfix.patch for NWCHEM6.6 is applied.
Edited On 6:34:14 AM PDT - Sat, Nov 4th 2017 by Xiongyan21

Forum Regular
Threads 43
Posts 209
9:34:40 PM PST - Tue, Nov 14th 2017
The error is the same when the second release candidate of the 6.8 version of the NWChem suite of computational chemistry codes is compiled on the identical environment.
...
found for -lSystem
collect2: error: ld returned 1 exit status
make: *** [all] Error 1

Forum Regular
Threads 43
Posts 209
9:34:58 PM PST - Tue, Nov 14th 2017
The error is the same when the second release candidate of the 6.8 version of the NWChem suite of computational chemistry codes is compiled on the identical environment.
...
found for -lSystem
collect2: error: ld returned 1 exit status
make: *** [all] Error 1

Forum Vet
Threads 9
Posts 1489
10:36:32 AM PST - Wed, Nov 15th 2017
Sure
We cannot address broken compiler installations.
One ugly hack to fix might be the following
cd $NWCHEM_TOP/src
make BLASOPT="-L/usr/lib" link

Cheers
Quote:Xiongyan21 Nov 14th 8:34 pm
The error is the same when the second release candidate of the 6.8 version of the NWChem suite of computational chemistry codes is compiled on the identical environment.
...
found for -lSystem
collect2: error: ld returned 1 exit status
make: *** [all] Error 1
Edited On 10:47:12 AM PST - Wed, Nov 15th 2017 by Edoapra

Forum Regular
Threads 43
Posts 209
9:46:26 PM PST - Tue, Nov 21st 2017
Dear Edoapra 
 Now the error becomes
... 
"_ma_trace_", referenced from:

     _memory_input_ in libnwctask.a(memory_input.o)

 "_ma_verify_allocator_stuff_", referenced from:

     _gsopt_project_hess_grad_ in liboptim.a(mepgs_drv.o)

     _mepgs_proj_grad_ in liboptim.a(mepgs_drv.o)

     _driver_project_hess_grad_ in libdriver.a(opt_drv.o)

     _driver_hss_reinit_ in libdriver.a(opt_drv.o)

     _driver_hss_init_ in libdriver.a(opt_drv.o)

     _grad_force_ in libgradients.a(grad_force.o)

     _md_start_ in libnwmd.a(md_start.o)

     ...
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [all] Error 1

   What I should further do to remedy this?

 

   Thanks a lot !



   Very Best Regards!

Forum Regular
Threads 43
Posts 209
9:47:40 PM PST - Tue, Nov 21st 2017
Dear Edoapra 
Now the error becomes

...
"_ma_trace_", referenced from:

    _memory_input_ in libnwctask.a(memory_input.o)



"_ma_verify_allocator_stuff_", referenced from:



    _gsopt_project_hess_grad_ in liboptim.a(mepgs_drv.o)



    _mepgs_proj_grad_ in liboptim.a(mepgs_drv.o)



    _driver_project_hess_grad_ in libdriver.a(opt_drv.o)



    _driver_hss_reinit_ in libdriver.a(opt_drv.o)



    _driver_hss_init_ in libdriver.a(opt_drv.o)



    _grad_force_ in libgradients.a(grad_force.o)



    _md_start_ in libnwmd.a(md_start.o)



    ...

ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [all] Error 1

  What I should further do to remedy this?







  Thanks a lot !




  Very Best Regards!

Quote:Edoapra Nov 15th 9:36 am
Sure
We cannot address broken compiler installations.
One ugly hack to fix might be the following
cd $NWCHEM_TOP/src
make BLASOPT="-L/usr/lib" link

Cheers
Edited On 9:51:59 PM PST - Tue, Nov 21st 2017 by Xiongyan21


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