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
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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
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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
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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
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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
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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
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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
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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 ${MKLROOT}/lib/intel64/libmkl_blacs_openmpi_ilp64.a -Wl,--end-group -lgomp -lpthread -lm -ldl
Regards,
TO
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Re: installation error OpenMX ver 3.9 ( No.14 ) |
- Date: 2020/01/26 01:24
- Name: asad <bafekry.asad@gmail.com>
- Dear Taisuke.
Thanks for reply With your comments:
MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl CC = mpiicc -O3 -qopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include FC = mpiifort -O3 -qopenmp -I/usr/local/openmpi/include -I/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include LIB = -L${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
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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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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)
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
|