error with impi on centos7
Clicked A Few Times
7:37:18 AM PDT - Wed, Apr 15th 2015
Hi everyone:
I encountered an error in the compliation on centos7.
mpif90 -show
gfortran -I/home/zhanfei/intel//impi/5.0.1.035/intel64/include/gfortran/4.8.0 -I/home/zhanfei/intel//impi/5.0.1.035/intel64/include -L/home/zhanfei/intel//impi/5.0.1.035/intel64/lib/release -L/home/zhanfei/intel//impi/5.0.1.035/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /home/zhanfei/intel//impi/5.0.1.035/intel64/lib/release -Xlinker -rpath -Xlinker /home/zhanfei/intel//impi/5.0.1.035/intel64/lib -Xlinker -rpath -Xlinker /opt/intel/mpi-rt/5.0/intel64/lib/release -Xlinker -rpath -Xlinker /opt/intel/mpi-rt/5.0/intel64/lib -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread

my script is
export NWCHEM_TOP=/home/zhanfei/Nwchem-6.5.revision26243-src.2014-09-10
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/home/zhanfei/intel/impi/5.0.1.035/intel64
export MPI_LIB=/home/zhanfei/intel/impi/5.0.1.035/intel64/lib
export MPI_INCLUDE=/home/zhanfei/intel/impi/5.0.1.035/intel64/include
export LIBMPI="-lmpifort -lmpi -lmpigi -ldl -lrt -lpthread"
export FC=ifort

cd src
make clean
make nwchem_config
make FC=ifort >& install.log

the error message is below:

Non-optimizable loops:


LOOP BEGIN at tddft_grad_dvxc.f(409,7)
  remark #15532: loop was not vectorized: compile time constraints prevent loop optimization. Consider using -O3.
LOOP END
===============================================================
Converting tddft_grad_defaults.F -> tddft_grad_defaults.f
ifort -c -i8 -align -qopt-report-file=stderr -fimf-arch-consistency=true -O2 -g -fp-model source tddft_grad_defaults.f
===============================================================
tddft_grad_defaults.f(1055): error #5508: Declaration of routine 'TDDFT_GRAD_DEFAULTS' conflicts with a previous declaration
     subroutine tddft_grad_defaults(rtdb)
^
compilation aborted for tddft_grad_defaults.f (code 1)
make[2]: *** [/home/zhanfei/Nwchem-6.5.revision26243-src.2014-09-10/lib/LINUX64/libnwdft.a(tddft_grad_defaults.o)] Error 1
make[1]: *** [subdirs] Error 1
make: *** [libraries] Error 1

thanks in advanced
Sincerely

Forum Vet
12:01:24 PM PDT - Wed, Apr 15th 2015
What version of ifort are you using? In other words, please send the output of

ifort -V

Forum Vet
12:07:18 PM PDT - Wed, Apr 15th 2015
Please try the following

cd $NWCHEM_TOP/nwdft/lr_tddft_grad
rm *.mod *.f90 *.f
make FC=ifort


If this still does not work, please send the output of

ls -lrta $NWCHEM_TOP/nwdft/lr_tddft_grad

Clicked A Few Times
3:45:52 PM PDT - Wed, Apr 15th 2015
reply
Quote:Edoapra Apr 15th 7:07 pm
Please try the following

cd $NWCHEM_TOP/nwdft/lr_tddft_grad
rm *.mod *.f90 *.f
make FC=ifort


If this still does not work, please send the output of

ls -lrta $NWCHEM_TOP/nwdft/lr_tddft_grad

.
Thanks very much for your reply.
I use ifort15,
ifort -V
Intel(R) Fortran Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 15.0.0.090 Build 20140723
Copyright (C) 1985-2014 Intel Corporation. All rights reserved.

Because there aren't the folder nwdft below $NWCHEM_TOP directly.I list the result about
$NWCHEM_TOP/src/nwdft/lr_tddft_grad.There aren't module files and f90 files.
ls -lrta $NWCHEM_TOP/src/nwdft/lr_tddft_grad
total 1644
-rw-r-----. 1 zhanfei zhanfei 3486 Sep 10 2014 tddft_grad_xy.F
-rw-r-----. 1 zhanfei zhanfei 987 Sep 10 2014 tddft_grad_util_print.F
-rw-r-----. 1 zhanfei zhanfei 357 Sep 10 2014 tddft_grad_util.fh

Clicked A Few Times
3:47:57 PM PDT - Wed, Apr 15th 2015
-rw-r-----. 1 zhanfei zhanfei 9346 Sep 10 2014 tddft_grad_trans_mo2ao.F
-rw-r-----. 1 zhanfei zhanfei 9323 Sep 10 2014 tddft_grad_trans_ao2mo.F
-rw-r-----. 1 zhanfei zhanfei 1974 Sep 10 2014 tddft_grad_tp.F
-rw-r-----. 1 zhanfei zhanfei 2394 Sep 10 2014 tddft_grad_store_gradient.F
-rw-r-----. 1 zhanfei zhanfei 8470 Sep 10 2014 tddft_grad_solve_save_x.F
-rw-r-----. 1 zhanfei zhanfei 5324 Sep 10 2014 tddft_grad_solve_product.F
-rw-r-----. 1 zhanfei zhanfei 4618 Sep 10 2014 tddft_grad_solve_precond.F
-rw-r-----. 1 zhanfei zhanfei 7690 Sep 10 2014 tddft_grad_solve_load_x.F
-rw-r-----. 1 zhanfei zhanfei 9268 Sep 10 2014 tddft_grad_solve.F
-rw-r-----. 1 zhanfei zhanfei 1687 Sep 10 2014 tddft_grad_solve_common.fh
-rw-r-----. 1 zhanfei zhanfei 1065 Sep 10 2014 tddft_grad_root_e.F
-rw-r-----. 1 zhanfei zhanfei 1970 Sep 10 2014 tddft_grad_r.F
-rw-r-----. 1 zhanfei zhanfei 9325 Sep 10 2014 tddft_grad_quadv0b.F
-rw-r-----. 1 zhanfei zhanfei 2432 Sep 10 2014 tddft_grad_print_result.F
-rw-r-----. 1 zhanfei zhanfei 2066 Sep 10 2014 tddft_grad_print_info.F
-rw-r-----. 1 zhanfei zhanfei 455 Sep 10 2014 tddft_grad_print_header.F
-rw-r-----. 1 zhanfei zhanfei 5209 Sep 10 2014 tddft_grad_print_array.F
-rw-r-----. 1 zhanfei zhanfei 1426 Sep 10 2014 tddft_grad_mo.F
-rw-r-----. 1 zhanfei zhanfei 5013 Sep 10 2014 tddft_grad_mat_to_vec.F
-rw-r-----. 1 zhanfei zhanfei 10211 Sep 10 2014 tddft_grad_make_2pdm.F
-rw-r-----. 1 zhanfei zhanfei 15336 Sep 10 2014 tddft_grad_load_xy.F
-rw-r-----. 1 zhanfei zhanfei 1427 Sep 10 2014 tddft_grad_load_mo.F
-rw-r-----. 1 zhanfei zhanfei 4960 Sep 10 2014 tddft_grad_irreg_acc.F
-rw-r-----. 1 zhanfei zhanfei 2094 Sep 10 2014 tddft_grad_ints.F
-rw-r-----. 1 zhanfei zhanfei 3565 Sep 10 2014 tddft_grad_init_func.F
-rw-r-----. 1 zhanfei zhanfei 16239 Sep 10 2014 tddft_grad_init.F
-rw-r-----. 1 zhanfei zhanfei 20156 Sep 10 2014 tddft_gradient.F
-rw-r-----. 1 zhanfei zhanfei 7480 Sep 10 2014 tddft_grad_gxc.F
-rw-r-----. 1 zhanfei zhanfei 19760 Sep 10 2014 tddft_grad_grad_2e.F
-rw-r-----. 1 zhanfei zhanfei 8126 Sep 10 2014 tddft_grad_grad_1e.F
-rw-r-----. 1 zhanfei zhanfei 1275 Sep 10 2014 tddft_grad_g.F
-rw-r-----. 1 zhanfei zhanfei 6095 Sep 10 2014 tddft_grad_get_dens.F
-rw-r-----. 1 zhanfei zhanfei 9440 Sep 10 2014 tddft_grad_fxc_l.F
-rw-r-----. 1 zhanfei zhanfei 1325 Sep 10 2014 tddft_grad_fix_exc.F
-rw-r-----. 1 zhanfei zhanfei 1593 Sep 10 2014 tddft_grad_finalize.F
-rw-r-----. 1 zhanfei zhanfei 3693 Sep 10 2014 tddft_grad_epsilon.F
-rw-r-----. 1 zhanfei zhanfei 1067 Sep 10 2014 tddft_grad_e.F
-rw-r-----. 1 zhanfei zhanfei 15081 Sep 10 2014 tddft_grad_dxcdmat.F
-rw-r-----. 1 zhanfei zhanfei 7329 Sep 10 2014 tddft_grad_dvxc.F
-rw-r-----. 1 zhanfei zhanfei 53100 Sep 10 2014 tddft_grad_dfxc.F
-rw-r-----. 1 zhanfei zhanfei 44324 Sep 10 2014 tddft_grad_compute_w.F
-rw-r-----. 1 zhanfei zhanfei 5480 Sep 10 2014 tddft_grad_compute_t.F
-rw-r-----. 1 zhanfei zhanfei 28136 Sep 10 2014 tddft_grad_compute_r.F
-rw-r-----. 1 zhanfei zhanfei 3079 Sep 10 2014 tddft_grad_compute_p.F
-rw-r-----. 1 zhanfei zhanfei 62646 Sep 10 2014 tddft_grad_compute_g.F
-rw-r-----. 1 zhanfei zhanfei 10405 Sep 10 2014 tddft_grad_compute_energy.F
-rw-r-----. 1 zhanfei zhanfei 861 Sep 10 2014 tddft_grad_compute_dao.F
-rw-r-----. 1 zhanfei zhanfei 1016 Sep 10 2014 tddft_grad_anti_symmetrize.F
-rw-r-----. 1 zhanfei zhanfei 2999 Apr 15 10:12 tddft_grad_input.F
-rw-r-----. 1 zhanfei zhanfei 1974 Apr 15 10:12 GNUmakefile
-rw-rw-r--. 1 zhanfei zhanfei 1886 Apr 15 10:14 tddft_grad_input.F.rej
-rw-rw-r--. 1 zhanfei zhanfei 4278 Apr 15 10:14 tddft_grad_defaults.F
-rw-rw-r--. 1 zhanfei zhanfei 408 Apr 15 10:14 GNUmakefile.rej
-rw-rw-r--. 1 zhanfei zhanfei 11066 Apr 15 10:18 dependencies
-rw-rw-r--. 1 zhanfei zhanfei 0 Apr 15 10:18 include_stamp
drwxr-x---. 17 zhanfei zhanfei 4096 Apr 15 10:25 ..
-rw-rw-r--. 1 zhanfei zhanfei 44816 Apr 15 10:27 tddft_gradient.o
-rw-rw-r--. 1 zhanfei zhanfei 39144 Apr 15 10:27 tddft_grad_init.o
-rw-rw-r--. 1 zhanfei zhanfei 12216 Apr 15 10:27 tddft_grad_input.o
-rw-rw-r--. 1 zhanfei zhanfei 7072 Apr 15 10:27 tddft_grad_finalize.o
-rw-rw-r--. 1 zhanfei zhanfei 9528 Apr 15 10:27 tddft_grad_print_info.o
-rw-rw-r--. 1 zhanfei zhanfei 4056 Apr 15 10:27 tddft_grad_print_header.o
-rw-rw-r--. 1 zhanfei zhanfei 10608 Apr 15 10:27 tddft_grad_ints.o
-rw-rw-r--. 1 zhanfei zhanfei 7568 Apr 15 10:27 tddft_grad_e.o
-rw-rw-r--. 1 zhanfei zhanfei 7592 Apr 15 10:27 tddft_grad_root_e.o
-rw-rw-r--. 1 zhanfei zhanfei 6680 Apr 15 10:27 tddft_grad_mo.o
-rw-rw-r--. 1 zhanfei zhanfei 11728 Apr 15 10:27 tddft_grad_xy.o
-rw-rw-r--. 1 zhanfei zhanfei 7400 Apr 15 10:27 tddft_grad_load_mo.o
-rw-rw-r--. 1 zhanfei zhanfei 8952 Apr 15 10:27 tddft_grad_tp.o
-rw-rw-r--. 1 zhanfei zhanfei 12144 Apr 15 10:27 tddft_grad_compute_t.o
-rw-rw-r--. 1 zhanfei zhanfei 6664 Apr 15 10:27 tddft_grad_r.o
-rw-rw-r--. 1 zhanfei zhanfei 35504 Apr 15 10:27 tddft_grad_load_xy.o
-rw-rw-r--. 1 zhanfei zhanfei 22136 Apr 15 10:27 tddft_grad_trans_mo2ao.o
-rw-rw-r--. 1 zhanfei zhanfei 49192 Apr 15 10:27 tddft_grad_compute_r.o
-rw-rw-r--. 1 zhanfei zhanfei 22176 Apr 15 10:27 tddft_grad_trans_ao2mo.o
-rw-rw-r--. 1 zhanfei zhanfei 6608 Apr 15 10:27 tddft_grad_mat_to_vec.o
-rw-rw-r--. 1 zhanfei zhanfei 10632 Apr 15 10:27 tddft_grad_epsilon.o
-rw-rw-r--. 1 zhanfei zhanfei 17640 Apr 15 10:27 tddft_grad_solve.o
-rw-rw-r--. 1 zhanfei zhanfei 16680 Apr 15 10:27 tddft_grad_solve_product.o
-rw-rw-r--. 1 zhanfei zhanfei 8216 Apr 15 10:27 tddft_grad_solve_precond.o
-rw-rw-r--. 1 zhanfei zhanfei 8544 Apr 15 10:27 tddft_grad_compute_p.o
-rw-rw-r--. 1 zhanfei zhanfei 5768 Apr 15 10:27 tddft_grad_g.o
-rw-rw-r--. 1 zhanfei zhanfei 4504 Apr 15 10:27 tddft_grad_compute_dao.o
-rw-rw-r--. 1 zhanfei zhanfei 12384 Apr 15 10:27 tddft_grad_get_dens.o
-rw-rw-r--. 1 zhanfei zhanfei 103664 Apr 15 10:27 tddft_grad_compute_w.o
-rw-rw-r--. 1 zhanfei zhanfei 138848 Apr 15 10:27 tddft_grad_compute_g.o
-rw-rw-r--. 1 zhanfei zhanfei 15264 Apr 15 10:27 tddft_grad_grad_1e.o
-rw-rw-r--. 1 zhanfei zhanfei 25424 Apr 15 10:27 tddft_grad_grad_2e.o
-rw-rw-r--. 1 zhanfei zhanfei 10712 Apr 15 10:27 tddft_grad_print_result.o
-rw-rw-r--. 1 zhanfei zhanfei 17840 Apr 15 10:27 tddft_grad_print_array.o
-rw-rw-r--. 1 zhanfei zhanfei 33736 Apr 15 10:27 tddft_grad_make_2pdm.o
-rw-rw-r--. 1 zhanfei zhanfei 22848 Apr 15 10:27 tddft_grad_compute_energy.o
-rw-rw-r--. 1 zhanfei zhanfei 5640 Apr 15 10:27 tddft_grad_anti_symmetrize.o
-rw-rw-r--. 1 zhanfei zhanfei 10024 Apr 15 10:27 tddft_grad_irreg_acc.o
-rw-rw-r--. 1 zhanfei zhanfei 15232 Apr 15 10:27 tddft_grad_gxc.o
-rw-rw-r--. 1 zhanfei zhanfei 3808 Apr 15 10:27 tddft_grad_fix_exc.o
-rw-rw-r--. 1 zhanfei zhanfei 8168 Apr 15 10:27 tddft_grad_store_gradient.o
-rw-rw-r--. 1 zhanfei zhanfei 13184 Apr 15 10:27 tddft_grad_fxc_l.o
-rw-rw-r--. 1 zhanfei zhanfei 3544 Apr 15 10:27 tddft_grad_util_print.o
-rw-rw-r--. 1 zhanfei zhanfei 20280 Apr 15 10:27 tddft_grad_solve_load_x.o
-rw-rw-r--. 1 zhanfei zhanfei 21328 Apr 15 10:27 tddft_grad_solve_save_x.o
-rw-rw-r--. 1 zhanfei zhanfei 19296 Apr 15 10:27 tddft_grad_dxcdmat.o
-rw-rw-r--. 1 zhanfei zhanfei 19704 Apr 15 10:27 tddft_grad_quadv0b.o
-rw-rw-r--. 1 zhanfei zhanfei 13872 Apr 15 10:27 tddft_grad_dvxc.o
-rw-rw-r--. 1 zhanfei zhanfei 43672 Apr 15 10:27 tddft_grad_dfxc.o
drwxr-x---. 2 zhanfei zhanfei 4096 Apr 15 18:38 .

Forum Vet
4:05:21 PM PDT - Wed, Apr 15th 2015
Zhanfei
After looking at the files, I can see that
you have applied the patch Tddft_grad.patch, but something went wrong in the patching operation
(presence of tddft_grad_input.F.rej).
A possible fix would be to take the patch out

Anyhow, could you please send me the output of the command

grep -i tddft_grad_defaults $NWCHEM_TOP/nwdft/lr_tddft_grad/*F*

Clicked A Few Times
6:35:39 PM PDT - Wed, Apr 15th 2015
Quote:Edoapra Apr 15th 11:05 pm
Zhanfei
After looking at the files, I can see that
you have applied the patch Tddft_grad.patch, but something went wrong in the patching operation
(presence of tddft_grad_input.F.rej).
A possible fix would be to take the patch out

Anyhow, could you please send me the output of the command

grep -i tddft_grad_defaults $NWCHEM_TOP/nwdft/lr_tddft_grad/*F*


Thanks very much for your reply
I have taken the patch out and the error has changed.
[zhanfei@localhost src]$ grep -i tddft_grad_defaults $NWCHEM_TOP/nwdft/lr_tddft_grad/*F*
grep: /nwdft/lr_tddft_grad/*F*: No such file or directory
Now the error is:
/home/zhanfei/Nwchem-6.5.revision26243-src.2014-09-10/src/tools/build/comex/../../ga-5-3/comex/src-mpi/groups.c:145: undefined reference to `ompi_mpi_group_null'
/home/zhanfei/Nwchem-6.5.revision26243-src.2014-09-10/src/tools/build/comex/../../ga-5-3/comex/src-mpi/groups.c:152: undefined reference to `ompi_mpi_comm_null'
/home/zhanfei/Nwchem-6.5/src/tools/install/lib/libarmci.a(lt1-groups.o): In function `comex_create_group_and_igroup':
/home/zhanfei/Nwchem-6.5.revision26243-src.2014-09-10/src/tools/build/comex/../../ga-5-3/comex/src-mpi/groups.c:67: undefined reference to `ompi_mpi_comm_null'
/home/zhanfei/Nwchem-6.5.revision26243-src.2014-09-10/src/tools/build/comex/../../ga-5-3/comex/src-mpi/groups.c:68: undefined reference to `ompi_mpi_group_null'
/home/zhanfei/Nwchem-6.5/src/tools/install/lib/libarmci.a(lt1-groups.o): In function `comex_group_create':
/home/zhanfei/Nwchem-6.5.revision26243-src.2014-09-10/src/tools/build/comex/../../ga-5-3/comex/src-mpi/groups.c:226: undefined reference to `ompi_mpi_comm_self'
make: *** [all] Error 1

Forum Vet
10:49:44 AM PDT - Thu, Apr 16th 2015
Zhanfei
Your earlier posting shows a clear problem concerning MPI
1) mpif90 -show indicates gfortran as Fortran compiler an Intel MPI as MPI
2) Your compilations snippets show that a) the tools were compiled with OpenMPI and b) that you used ifort as a Fortran compiler

Please stick to a single Fortran compiler and to a single MPI implementation.


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