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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
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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
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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
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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
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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
メンテ
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
メンテ
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
メンテ
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
メンテ
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
メンテ
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
メンテ
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
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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
メンテ
Re: installation error OpenMX ver 3.9 ( No.13 )
Date: 2020/01/28 23:41
Name: T. Ozaki

Hi,

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

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
メンテ
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
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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
メンテ
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
メンテ
Re: installation error OpenMX ver 3.9 ( No.17 )
Date: 2020/01/28 12:41
Name: Mitsuaki Kawamura  <mkawamura@issp.u-tokyo.ac.jp>

Dear Asad

How about to change all "_ilp64" to "_lp64"?

Best regards,
Mitsuaki Kawamura(ISSP)
メンテ
Re: installation error OpenMX ver 3.9 ( No.18 )
Date: 2020/01/28 18:49
Name: asad  <bafekry.asad@gmail.com>

Dear Mitsuaki.
with your comments, i get this error again
.
.
.
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_lp64.a(mkl_blacs_memory.o): In function `mkl_blacs_malloc':
mkl_blacs_memory.c:(.text+0x8d): undefined reference to `mkl_serv_iface_malloc'
mkl_blacs_memory.c:(.text+0xec): undefined reference to `mkl_serv_iface_free'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_blacs_intelmpi_lp64.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_lp64.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_lp64.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/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:181: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.19 )
Date: 2020/01/28 19:06
Name: mitsuaki kawamura  <mkawamura@issp.u-tokyo.ac.jp>

Dear Asad

Did you execute
$ make clean
before
$ make
?

Bert regards
Mitsuaki Kawamura
メンテ
Re: installation error OpenMX ver 3.9 ( No.20 )
Date: 2020/01/28 21:43
Name: asad  <bafekry.asad@gmail.com>

Dear Mitsuaki.
Yes i did
メンテ
Re: installation error OpenMX ver 3.9 ( No.21 )
Date: 2020/01/29 01:24
Name: Naoya Yamaguchi

Dear Asad,

Could you try the following parallelly if you can use Intel compilers, Intel MPI, and Intel MKL?
If not, please tell it to us through this forum.

CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.22 )
Date: 2020/01/29 01:29
Name: T. Ozaki

Hi Asad,

If my guess, that you are using gcc comiler, MKL, and OpenMPI, is correct,
I am wondering why you did not follow the suggestion by
Intel Math Kernel Library Link Line Advisor:
https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor

Why did you link both libmkl_blas95_ilp64.a and libmkl_blacs_intelmpi_ilp64.a,
and also link both libmkl_lapack95_ilp64.a and libmkl_scalapack_ilp64.a?

Regards,

TO
メンテ
Re: installation error OpenMX ver 3.9 ( No.23 )
Date: 2020/01/29 04:20
Name: asad  <bafekry.asad@gmail.com>

Hi Naoya. Thanks your comments. Based on your suggestion, i see this error:

/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/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/libpthread.a(ptw-read.o): In function `__read_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/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/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:184: recipe for target 'openmx' failed
make: *** [openmx] Error 1
#######################################################33
Hi Taisuke. Thanks your comment. Based on your suggestion ("Why did you link both libmkl_blas95_ilp64.a and libmkl_blacs_intelmpi_ilp64.a,
and also link both libmkl_lapack95_ilp64.a and libmkl_scalapack_ilp64.a")

i see this error:

mkl_get_mpi_wrappers.c:(.text+0x4b): undefined reference to `MKLMPI_Get_wrappers'
/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-read.o): In function `__read_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-read.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
makefile:182: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.24 )
Date: 2020/01/29 09:45
Name: Naoya Yamaguchi

Dear Asad,

Have you tried my setting without any modification including changes of paths?
My suggestion is different from that from Prof. Ozaki and Dr. Kawamura, and I guess that you mixed or included tags.
If so, just copying and pasting my setting without any changes, please try it again.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.25 )
Date: 2020/01/29 11:22
Name: Mitsuaki Kawamura  <mkawamura@issp.u-tokyo.ac.jp>

Dear Asad

Could you also try this ?

CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -mkl=parallel
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp -mkl=parallel
LIB= -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lifcore -lm -ldl

Best regards,
Mitsuaki Kawamura
メンテ
Re: installation error OpenMX ver 3.9 ( No.26 )
Date: 2020/01/29 15:21
Name: asad  <bafekry.asad@gmail.com>

Hi Naoya.
I tested your command lines exactley.
This is error:

/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/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/libpthread.a(ptw-read.o): In function `__read_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/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/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:184: recipe for target 'openmx' failed
make: *** [openmx] Error 1

######################################################333
Hi Mitsuaki.
based on your coomend,
this is error:
.
.
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/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:187: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.27 )
Date: 2020/01/29 15:42
Name: Naoya Yamaguchi

Dear Asad,

Could you paste the whole part of your makefile by pasting the output of cat command?

e.g. $ cat makefile

And, Please also paste the output of the env command.

e.g. $ env

I want to know why the errors about libpthread.a appear.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.28 )
Date: 2020/01/29 18:27
Name: asad  <bafekry.asad@gmail.com>

Hi Naoya.
Thanks your reply.

MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64_lin -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore

#################error lines:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/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-read.o): In function `__read_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:184: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.29 )
Date: 2020/01/29 18:44
Name: Naoya Yamaguchi

Dear Asad,

I think that you changed "intel64" in my setting into "intel64_lin" and it causes some of the errors.

Can you try it again after modifying "intel64_lin" into "intel64"?

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.30 )
Date: 2020/01/29 19:07
Name: asad  <bafekry.asad@gmail.com>

Naoya,
with this:
MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore

i see again:

/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/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/libpthread.a(ptw-read.o): In function `__read_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/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/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:184: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.32 )
Date: 2020/01/29 19:45
Name: Naoya Yamaguchi

Dear Asad,

I paste a list of the files included in a directory "compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/" as below:

ls ***/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/
libmkl_ao_worker.so libmkl_blacs_openmpi_ilp64.so libmkl_cdft_core.so libmkl_intel_ilp64.a libmkl_pgi_thread.a libmkl_vml_avx512_mic.so
libmkl_avx2.so libmkl_blacs_openmpi_lp64.a libmkl_core.a libmkl_intel_ilp64.so libmkl_pgi_thread.so libmkl_vml_avx512.so
libmkl_avx512_mic.so libmkl_blacs_openmpi_lp64.so libmkl_core.so libmkl_intel_lp64.a libmkl_rt.so libmkl_vml_avx.so
libmkl_avx512.so libmkl_blacs_sgimpt_ilp64.a libmkl_def.so libmkl_intel_lp64.so libmkl_scalapack_ilp64.a libmkl_vml_cmpt.so
libmkl_avx.so libmkl_blacs_sgimpt_ilp64.so libmkl_gf_ilp64.a libmkl_intel_thread.a libmkl_scalapack_ilp64.so libmkl_vml_def.so
libmkl_blacs_intelmpi_ilp64.a libmkl_blacs_sgimpt_lp64.a libmkl_gf_ilp64.so libmkl_intel_thread.so libmkl_scalapack_lp64.a libmkl_vml_mc2.so
libmkl_blacs_intelmpi_ilp64.so libmkl_blacs_sgimpt_lp64.so libmkl_gf_lp64.a libmkl_lapack95_ilp64.a libmkl_scalapack_lp64.so libmkl_vml_mc3.so
libmkl_blacs_intelmpi_lp64.a libmkl_blas95_ilp64.a libmkl_gf_lp64.so libmkl_lapack95_lp64.a libmkl_sequential.a libmkl_vml_mc.so
libmkl_blacs_intelmpi_lp64.so libmkl_blas95_lp64.a libmkl_gnu_thread.a libmkl_mc3.so libmkl_sequential.so locale
libmkl_blacs_openmpi_ilp64.a libmkl_cdft_core.a libmkl_gnu_thread.so libmkl_mc.so libmkl_vml_avx2.so

And, I think that libpthread.a should not exist there.
Please copy, paste and try the following:
MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore -Wl,--exclude-libs,libpthread.a

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.33 )
Date: 2020/01/29 21:10
Name: asad  <bafekry.asad@gmail.com>

Again error with last command lines

/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/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/libpthread.a(ptw-read.o): In function `__read_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/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/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:183: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.34 )
Date: 2020/01/29 21:21
Name: Naoya Yamaguchi

Dear Asad,

How about the following?
MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore -Wl,--exclude-libs,ALL

And can you paste the output of env command?

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.35 )
Date: 2020/01/29 21:40
Name: asad  <bafekry.asad@gmail.com>

Naoya, i see this:

.
.
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/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/libpthread.a(ptw-read.o): In function `__read_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/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/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
ld: openmx: hidden symbol `PMPI_Info_set' in /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libmpi.a(info_set.o) is referenced by DSO
ld: final link failed: Bad value
makefile:184: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.36 )
Date: 2020/01/29 22:01
Name: Naoya Yamaguchi

Dear Asad,

Could you show us the output of env command if you can?

Regards,
Naoya Yamaguchi
メンテ

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