installation error OpenMX ver 3.9

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installation error OpenMX ver 3.9

Date: 2020/01/06 08:01
Name: Maedeh: Dear OpenMX developers,

I am getting this error while trying to install the new version (3.9) of OpenMX:

In file included from TRAN_DFT.c:25:
openmx_common.h:75: error: redefinition of typedef ‘Type_Orbs_Grid’
tran_prototypes.h:36: note: previous declaration of ‘Type_Orbs_Grid’ was here
make: *** [TRAN_DFT.o] Error 1

it looks like the error previously had mentioned in this link for the version 3.8:
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=1951

but I couldn't figure out how to solve it.

here are my Settings:

MKLROOT = /opt/intel/composerxe-2011.2.137/mkl/
CC = /opt/openmpi/bin/mpicc -O3 -fopenmp -I/opt/intel/composerxe-2011.2.137/mkl/include/fftw -I/opt/intel/mkl/lib/intel64/include
FC = /opt/openmpi/bin/mpif90 -O3 -fopenmp -I/opt/intel/mkl/lib/intel64/include
LIB = -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.4/lib -lgfortran -L/opt/openmpi/lib/lib -lmpi -libverbs -ldat -lrt -lnsl -lutil -lm -ldl -lm

any help will be appreciated.

Thanks

Best regards,
Maedeh

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Re: installation error OpenMX ver 3.9 ( No.1 )

Date: 2020/01/06 12:49
Name: Naoya Yamaguchi

Dear Maedeh,

I also encountered the same problem using gcc and solved it by following the solution shown in No.1 in the thread that you pointed out.

And for your information, I leave a setting in the case as follows:
CC = /usr/local/openmpi-4.0.2-gcc-9/bin/mpicc -O3 -fopenmp -ffast-math -I/opt/intel/mkl/include/fftw
FC = /usr/local/openmpi-4.0.2-gcc-9/bin/mpif90 -O3 -fopenmp -ffast-math
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -lmpi_mpifh

Regards,
Naoya Yamaguchi

Re: installation error OpenMX ver 3.9 ( No.2 )

Date: 2020/01/06 19:50
Name: Maedeh

Dear Naoya,

Thank You so much for your answer.

when I look at the "tran_prototypes.h" file the corresponding line is correct:

#ifndef ___Type_Orbs_Grid_definition___
typedef float Type_Orbs_Grid; /* type of Orbs_Grid */
#define ___Type_Orbs_Grid_definition___
#endif

and in "openmx_common.h" we have this line:

typedef float Type_Orbs_Grid; /* type of Orbs_Grid */
#define ___Type_Orbs_Grid_definition___
#define MPI_Type_Orbs_Grid MPI_FLOAT /* type of Orbs_Grid */

when I change it to the same lines as "tran_prototypes.h" file, I get this error:

Error: Syntax error in ALLOCATE statement at (1)
./elpa-2018.05.001/elpa1_solve_tridi_real_template.F90:226.65:
Included at ./elpa-2018.05.001/elpa1_compute_real.F90:106:

deallocate(limits,l_col,p_col,l_col_bc,p_col_bc, stat=istat, errmsg=error
1
Error: Syntax error in DEALLOCATE statement at (1)
Fatal Error: Error count reached limit of 25.
make: *** [elpa1_compute_real.o] Error 1

Best regards,
Maedeh

Re: installation error OpenMX ver 3.9 ( No.3 )

Date: 2020/01/06 21:30
Name: T. Ozaki

Hi,

Could you change in TRAN_DFT.c from the original:

#include "tran_variables.h"
#include "openmx_common.h"

to the following one?

#include "openmx_common.h"
#include "tran_variables.h"

The other parts should be the same as the original with the patch.

Regards,

TO

Re: installation error OpenMX ver 3.9 ( No.4 )

Date: 2020/01/07 10:22
Name: Naoya Yamaguchi

Dear Maedeh,

I also encountered the syntax error and solved it by using the latest version of gcc. I guess that the error comes from unavailableness of Fortran 2003 or 2008. You might solve it by changing options for FC as gfortran can accept the latest notation. But, I'm not sure because I tried it with gcc4 but the compilation is not successful.

Regards,
Naoya Yamaguchi

Re: installation error OpenMX ver 3.9 ( No.5 )

Date: 2020/01/07 19:13
Name: Maedeh

Dear professor Ozaki
I did the change, but the error is the same:

In file included from TRAN_DFT.c:24:
openmx_common.h:75: error: redefinition of typedef ‘Type_Orbs_Grid’
tran_prototypes.h:36: note: previous declaration of ‘Type_Orbs_Grid’ was here
make: *** [TRAN_DFT.o] Error 1

Best regards,
Maedeh

Re: installation error OpenMX ver 3.9 ( No.6 )

Date: 2020/01/07 19:27
Name: Maedeh

Dear Naoya,

Yes, The gcc version on the server which I am trying to install the OpenMX is 4.4.7. it can be the reason. Because I have already installed new OpenMX successfully on my system with gcc version 5.4.0.

Best regards,
Maedeh

Re: installation error OpenMX ver 3.9 ( No.7 )

Date: 2020/01/07 19:35
Name: Naoya Yamaguchi

Dear Maedeh,

At least, you need to overcome the syntax error even though the redefinition error is solved, and to avoid the syntax error, you may need to prepare a set of new compilers.
And, the syntax error looks the next error that appears after solving the redefinition error in your environment.

PS

My post is too early, so please ignore the above, but for sharing information, I leave the above.

Regards,
Naoya Yamaguchi

Re: installation error OpenMX ver 3.9 ( No.8 )

Date: 2020/01/07 21:26
Name: T. Ozaki

Hi,

It would be good to hear that the problem can be solved with gcc 5.4.0.
For gcc 4.4.7, could you try again to change in TRAN_DFT.c from the original:

#include "tran_prototypes.h"
#include "tran_variables.h"
#include "openmx_common.h"

to the following one?

#include "openmx_common.h"
#include "tran_prototypes.h"
#include "tran_variables.h"

If you can solve the problem, please let us know.

Regards,

TO

Re: installation error OpenMX ver 3.9 ( No.9 )

Date: 2020/01/08 17:59
Name: Maedeh

Dear professor Ozaki

I did the change in TRAN_DFT.c and it still has the same error.

Best regards,
Maedeh

Re: installation error OpenMX ver 3.9 ( No.10 )

Date: 2020/01/21 00:19
Name: asad <bafekry.asad@gmail.com>

Dear OpenMX developers,

I am trying to use mpiifort,mpiicc, intelmpi and mkl to compile openmx3.9, but failed in the link step, this is my setting and error information.

My Settings:

MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpicc -O3 -fopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include
FC = mpif90 -O3 -fopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include
LIB = -L/usr/local/lib -lfftw3 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -L/usr/lib/gcc/x86_64-linux-gnu/5/lib -lgfortran -L/usr/local/openmpi/lib -lmpi_mpifh -lmpi_usempif08 -lmpi_usempi_ignore_tkr -L/usr/local/openmpi/lib -lmpi

Error information:

TRAN_Main_Analysis.o: undefined reference to symbol 'ompi_mpi_dblprec'
/usr/local/openmpi/lib/libmpi.so.1: error adding symbols: DSO missing from command line
makefile:202: recipe for target 'openmx' failed
make: *** [openmx] Error 1

Re: installation error OpenMX ver 3.9 ( No.11 )

Date: 2020/01/22 18:03
Name: T. Ozaki

Hi,

I wonder that adding the following OpenMP libraries to LIB may solve the problem:

-liomp5 -lpthread

Hope this works.

Regards,

TO

Re: installation error OpenMX ver 3.9 ( No.12 )

Date: 2020/01/23 22:02
Name: asad <bafekry.asad@gmail.com>

Thanks for reply dear Taisuke.
With adding the libraries to LIB:

MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpicc -O3 -fopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include
FC = mpif90 -O3 -fopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include
LIB = -L/usr/local/lib -lfftw3 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -L/usr/lib/gcc/x86_64-linux-gnu/5/lib -lgfortran -L/usr/local/openmpi/lib -lmpi_mpifh -lmpi_usempif08 -lmpi_usempi_ignore_tkr -L/usr/local/openmpi/lib -lmpi -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin -liomp5 -lpthread

i get that error again:

ld: TRAN_Main_Analysis.o: undefined reference to symbol 'ompi_mpi_dblprec'
/usr/local/openmpi/lib/libmpi.so.1: error adding symbols: DSO missing from command line
makefile:204: recipe for target 'openmx' failed
make: *** [openmx] Error 1

Re: installation error OpenMX ver 3.9 ( No.13 )

Date: 2020/01/25 16:55
Name: T. Ozaki

Hi,

You seem to use gcc comiler, MKL, and OpenMP.

For such a case, Intel Math Kernel Library Link Line Advisor:
https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor

recommends the following setting:

${MKLROOT}/lib/intel64/libmkl_scalapack_ilp64.a -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_blacs_openmpi_ilp64.a -Wl,--end-group -lgomp -lpthread -lm -ldl

Regards,

TO

Re: installation error OpenMX ver 3.9 ( No.14 )

Date: 2020/01/26 01:24
Name: asad <bafekry.asad@gmail.com>

Dear Taisuke.
Thanks for reply
With your comments:

MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpiicc -O3 -qopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include
FC = mpiifort -O3 -qopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include
LIB = -L${MKLROOT}/lib/intel64_lin/libmkl_blas95_ilp64.a -L${MKLROOT}/lib/intel64_lin/libifcore.a -L${MKLROOT}/lib/intel64_lin/libmkl_lapack95_ilp64.a -lmkl_blacs_intelmpi_ilp64 -liomp5 -lpthread -lm -ldl

i give this error:

elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1b8a): undefined reference to `for_alloc_allocatable'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(ptw-fsync.o): In function `__fsync_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(ptw-write.o): In function `__write_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(ptw-close.o): In function `__close_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(ptw-close.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `mkl_serv_iface_deallocate'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `MKL_free'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `MKL_malloc'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `mkl_serv_iface_malloc'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `mkl_serv_print'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `MKL_calloc'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `mkl_serv_iface_allocate'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `mkl_serv_vsprintf_s'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `mkl_serv_get_mpi_wrappers'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.so: undefined reference to `mkl_serv_iface_free'
makefile:210: recipe for target 'openmx' failed
make: *** [openmx] Error 1

Re: installation error OpenMX ver 3.9 ( No.15 )

Date: 2020/01/26 09:50
Name: T. Ozaki

Hi,

Please take a look at

http://www.openmx-square.org/forum/patio.cgi?mode=view&no=1501
page 11 in http://www.openmx-square.org/tech_notes/OpenMX-Compile.pdf
https://software.intel.com/en-us/forums/intel-math-kernel-library/topic/540372

Regards,

TO

Re: installation error OpenMX ver 3.9 ( No.16 )

Date: 2020/01/26 21:13
Name: asad <bafekry.asad@gmail.com>

Hi Taisuke.
Thanks for reply
With change the Flag lines based on your suggestion:

CC = mpiicc -O3 -qopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include
FC = mpiifort -O3 -qopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include
#LIB = -L${MKLROOT}/lib/intel64_lin/libmkl_blas95_ilp64.a -L${MKLROOT}/lib/intel64_lin/libmkl_scalapack_lp64.a -L${MKLROOT}/lib/intel64_lin/libifcore.a -L${MKLROOT}/lib/intel64_lin/libmkl_lapack95_ilp64.a -lmkl_blacs_intelmpi_ilp64 -lmkl_scalapack_lp64 -liomp5 -lpthread -lm -ldl
LIB = -L$(MKLROOT)/lib/intel64_lin/libmkl_blas95_ilp64.a $(MKLROOT)/lib/intel64_lin/libmkl_lapack95_ilp64.a $(MKLROOT)/lib/intel64_lin/libmkl_scalapack_ilp64.a -Wl,--start-group $(MKLROOT)/lib/intel64_lin/libmkl_intel_ilp64.a $(MKLROOT)/lib/intel64_lin/libmkl_core.a $(MKLROOT)/lib/intel64_lin/libmkl_intel_thread.a -Wl,--end-group $(MKLROOT)/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.a $(MKLROOT)/lib/intel64_lin/libpthread.a -lm -L/usr/local/openmpi/lib/libmpi_mpifh.so -L/usr/local/openmpi/lib/libmpi_usempif08.so -L$(MKLROOT)/lib/intel64_lin/libifcore.a -L$(MKLROOT)/lib/intel64_lin/libiomp5.a

I get this error again:

elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1a6c): undefined reference to `for_stop_core'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1a8c): undefined reference to `for_errmsg'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1b4b): undefined reference to `for_check_mult_overflow64'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1b8a): undefined reference to `for_alloc_allocatable'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.a(mklmpi-impl.o): In function `MKLMPI_Type_create_struct':
mklmpi-impl.c:(.text+0x419e): undefined reference to `MKL_calloc'
mklmpi-impl.c:(.text+0x41b0): undefined reference to `MKL_calloc'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.a(mklmpi-impl.o): In function `MKLMPI_Waitall':
mklmpi-impl.c:(.text+0x4a67): undefined reference to `MKL_calloc'
mklmpi-impl.c:(.text+0x4c7b): undefined reference to `MKL_calloc'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.a(mklmpi-impl.o): In function `MKLMPI_Waitany':
mklmpi-impl.c:(.text+0x50f5): undefined reference to `MKL_calloc'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_ilp64.a(mkl_blacs_memory.o): In function `mkl_blacs_malloc':
mkl_blacs_memory.c:(.text+0x8b): undefined reference to `mkl_serv_iface_malloc'
mkl_blacs_memory.c:(.text+0xeb): undefined reference to `mkl_serv_iface_free'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(ptw-fsync.o): In function `__fsync_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(ptw-write.o): In function `__write_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(ptw-close.o): In function `__close_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(ptw-close.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
makefile:213: recipe for target 'openmx' failed
make: *** [openmx] Error 1

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