 Re: Error comes up when compiling openmx3.9 ( No.1 ) |
- Date: 2022/11/18 00:47
- Name: Cosmo
- Drea Developer:
Sorry for my offensive ask. When I installed openmx.3.9 on my linux server, the above error comes up. And there is no solution on this issue.
My makefile setting code is below:
========================================
FFTROOT=/data/xyxu-ICME/fftw
LBSROOT=/opt/intel/mkl
#MKLROOT = /opt/intel/mkl
openmp_flag = -fopenmp
fortran_lib = -lgfortran
CC = mpicc -O3 -openmp -I$(FFTROOT)/include -I$(LBSROOT)/include
FC = mpif90 -O3 -I$(LBSROOT)/include
LIB= -L$(FFTROOT)/lib -lfftw -L${LBSROOT}/lib/intel64 -mkl=parallel -lmkl_blacs_openmpi_lp64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lgfortran -lmpi
==========================================
And the error is:
============================================
mpif90 -O3 -I/opt/intel/mkl/include -I./elpa-2018.05.001 -c ./elpa-2018.05.001/elpa1_compute_real.F90
precision_macros.h(62): #warning: keyword redefined: PRECISION
./elpa-2018.05.001/elpa1_compute_real.F90(57): error #7013: This module file was not generated by any release of this compiler. [MPI]
use mpi
------^
./elpa-2018.05.001/elpa_reduce_add_vectors.F90(79): error #7013: This module file was not generated by any release of this compiler. [MPI]
use mpi
-------^
./elpa-2018.05.001/elpa_transpose_vectors.F90(160): error #6404: This name does not have a type, and must have an explicit type. [MPI_REAL8]
MPI_REAL8, &
-----------------------^
./elpa-2018.05.001/elpa_reduce_add_vectors.F90(157): error #6404: This name does not have a type, and must have an explicit type. [MPI_SUM]
MPI_SUM, ipt, comm_t, mpierr)
----------------------------------^
./elpa-2018.05.001/elpa1_solve_tridi_real_template.F90(282): error #6404: This name does not have a type, and must have an explicit type. [MPI_REAL8]
call mpi_send(d(noff+1), nmid, MPI_REAL8, n, 1, mpi_comm_cols, mpierr)
----------------------------------------------^
./elpa-2018.05.001/elpa1_solve_tridi_real_template.F90(289): error #6404: This name does not have a type, and must have an explicit type. [MPI_STATUS_IGNORE]
call mpi_recv(d(noff+1), nmid, MPI_REAL8, np_off, 1, mpi_comm_cols, MPI_STATUS_IGNORE, mpierr)
---------------------------------------------------------------------------------^
./elpa-2018.05.001/elpa1_solve_tridi_real_template.F90(536): error #6404: This name does not have a type, and must have an explicit type. [MPI_COMM_SELF]
matrixCols, mpi_comm_rows, mpi_comm_self, l_col(noff+1), p_col_i(noff+1), &
----------------------------------------------------------^
./elpa-2018.05.001/elpa1_solve_tridi_real_template.F90(282): error #6404: This name does not have a type, and must have an explicit type. [MPI_REAL8]
call mpi_send(d(noff+1), nmid, MPI_REAL8, n, 1, mpi_comm_cols, mpierr)
----------------------------------------------^
./elpa-2018.05.001/elpa1_solve_tridi_real_template.F90(289): error #6404: This name does not have a type, and must have an explicit type. [MPI_STATUS_IGNORE]
call mpi_recv(d(noff+1), nmid, MPI_REAL8, np_off, 1, mpi_comm_cols, MPI_STATUS_IGNORE, mpierr)
---------------------------------------------------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(853): error #6404: This name does not have a type, and must have an explicit type. [MPI_REAL8]
call mpi_send(q(l_rqs,lc1), l_rows, MPI_REAL8, pc2, mod(i,4096), mpi_comm_cols, mpierr)
----------------------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(858): error #6404: This name does not have a type, and must have an explicit type. [MPI_STATUS_IGNORE]
call mpi_recv(qtmp(1,nc), l_rows, MPI_REAL8, pc1, mod(i,4096), mpi_comm_cols, MPI_STATUS_IGNORE, mpierr)
--------------------------------------------------------------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(914): error #6404: This name does not have a type, and must have an explicit type. [MPI_REAL8]
call mpi_sendrecv(q(l_rqs,lc1), l_rows, MPI_REAL8, pc2, 1, &
------------------------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(916): error #6404: This name does not have a type, and must have an explicit type. [MPI_STATUS_IGNORE]
mpi_comm_cols, MPI_STATUS_IGNORE, mpierr)
-----------------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(955): error #6404: This name does not have a type, and must have an explicit type. [MPI_REAL8]
call mpi_allreduce(z, tmp, n, MPI_REAL8, MPI_SUM, mpi_comm_rows, mpierr)
----------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(955): error #6404: This name does not have a type, and must have an explicit type. [MPI_SUM]
call mpi_allreduce(z, tmp, n, MPI_REAL8, MPI_SUM, mpi_comm_rows, mpierr)
---------------------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(982): error #6404: This name does not have a type, and must have an explicit type. [MPI_STATUS_IGNORE]
mpi_comm_cols, MPI_STATUS_IGNORE, mpierr)
------------------------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(1007): error #6404: This name does not have a type, and must have an explicit type. [MPI_REAL8]
call mpi_allreduce(z, tmp, n, MPI_REAL8, MPI_PROD, mpi_comm_rows, mpierr)
----------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(1007): error #6404: This name does not have a type, and must have an explicit type. [MPI_PROD]
call mpi_allreduce(z, tmp, n, MPI_REAL8, MPI_PROD, mpi_comm_rows, mpierr)
---------------------------------------------------^
./elpa-2018.05.001/elpa1_merge_systems_real_template.F90(1034): error #6404: This name does not have a type, and must have an explicit type. [MPI_STATUS_IGNORE]
call mpi_recv(tmp, n, MPI_REAL8, np, 1111, mpi_comm_cols, MPI_STATUS_IGNORE, mpierr)
------------------------------------------------------------------------^
compilation aborted for ./elpa-2018.05.001/elpa1_compute_real.F90 (code 1)
=====================================================
What should I do to fix it up?
Best wish.
 |
| Re: Error comes up when compiling openmx3.9 ( No.2 ) |
- Date: 2022/11/18 02:31
- Name: Naoya Yamaguchi
- Hi,
Can you show output for the following commands?
$ mpicc -v
$ mpif90 -v
Regards,
Naoya Yamaguchi
|
| Re: Error comes up when compiling openmx3.9 ( No.3 ) |
- Date: 2022/11/18 09:10
- Name: Cosmo
- Dear Naoya Yamaguchi:
Here is the output when typing your commands:
===============================
$ mpicc -v
icc version 15.0.1 (gcc version 4.9.0 compatibility)
$ mpif90 -v
ifort version 15.0.1
===============================
How can I do?
|
| Re: Error comes up when compiling openmx3.9 ( No.4 ) |
- Date: 2022/11/18 12:38
- Name: Naoya Yamaguchi
- Dear Cosmo,
First, can you try the following?
$ make clean && make
Regards,
Naoya Yamaguchi
|
| Re: Error comes up when compiling openmx3.9 ( No.5 ) |
- Date: 2022/11/18 15:34
- Name: Cosmo
- Dear Naoya Yamaguchi,
I tried your commands already and it seems not working, same old errors.
Regards,
Cosmo
|
| Re: Error comes up when compiling openmx3.9 ( No.6 ) |
- Date: 2022/11/19 03:13
- Name: Naoya Yamaguchi
- Dear Cosmo,
The errors might be caused by the mismatch between the Intel compilers and MPI libraries.
>===============================
>$ mpicc -v
>icc version 15.0.1 (gcc version 4.9.0 compatibility)
>$ mpif90 -v
>ifort version 15.0.1
>===============================
Is the above all the parts of the output?
Regards,
Naoya Yamaguchi
|
| Re: Error comes up when compiling openmx3.9 ( No.7 ) |
- Date: 2022/12/11 19:34
- Name: Lin Tzu Ching <j859679340@gmail.com>
- Dear Naoya Yamaguchi,
I get similar error in the compiler openmx3.9 in the server , and I'm not the root user .
My makefile setting code is below:
###############################################################################################
MKLROOT = /cluster/intel/compilers_and_libraries_2019.5.281/linux/mkl
FFTW = -I/cluster/intel/compilers_and_libraries_2019.5.281/linux/mkl/include/fftw
CC = mpicc -qopenmp -O3 -ip $(FFTW)
FC = mpifort -qopenmp -O3 -ip $(FFTW)
LIB= -L${MKLROOT}/lib/intel64 -mkl=parallel -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -lgfortran -lmpi -liomp5 -lpthread -lm -ldl -lifcore -lmpi_f77 -lmpi_f90 -lifcore
###############################################################################################
the compiler i
and this is output of may commands:
##################
$ mpicc -v
icc version 19.0.5.281 (gcc version 4.8.5 compatibility)
$ mpifort -v
ifort version 19.0.5.281
##################
the error is :
##########################
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90(67): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [ELPA2_COMPUTE_COMPLEX]
use elpa2_compute_complex
-------^
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90(468): error #6632: Keyword arguments are invalid without an explicit interface. [SUCCESS]
nrThreads, success=success, kernel=kernel)
------------------^
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90(468): error #6632: Keyword arguments are invalid without an explicit interface. [KERNEL]
nrThreads, success=success, kernel=kernel)
-----------------------------------^
compilation aborted for ./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90 (code 1)
make: *** [elpa_solve_evp_complex_2stage_double_impl.o] Error 1
##########################
could you help me?
Regards,
Lin Tzu Ching
|
| Re: Error comes up when compiling openmx3.9 ( No.8 ) |
- Date: 2022/12/11 21:17
- Name: Naoya Yamaguchi
- Dear Lin Tzu Ching,
I think that your error is a different one from the first report in this thread, and this kind of errors might be caused by a module file for the ELPA.
Can you try the following?
$ make clean && make
(Just in case, please don't use `make -j` now.)
Regards,
Naoya Yamaguchi
|
| Re: Error comes up when compiling openmx3.9 ( No.9 ) |
- Date: 2022/12/12 13:46
- Name: Lin Tzu Ching
- Dear Naoya Yamaguchi,
I got this error , when I run the command
$make clean && make:
###############
ld: can't find -lmpi_f77
ld: can't find -lmpi_f90
make: *** [openmx] Error 1
###############
if delete the -lmpi_f77 -lmpi_f90 in the LIB from the makefile ,means the makefile becomes:
###############
MKLROOT = /cluster/intel/compilers_and_libraries_2019.5.281/linux/mkl
FFTW = -I/cluster/intel/compilers_and_libraries_2019.5.281/linux/mkl/include/fftw
CC = mpicc -qopenmp -O3 -ip $(FFTW)
FC = mpifort -qopenmp -O3 -ip $(FFTW)
LIB= -L${MKLROOT}/lib/intel64 -mkl=parallel -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -lgfortran -lmpi -liomp5 -lpthread -lm -ldl
###############
the error becomes :
################
L2_compute_complex.F90:(.text+0xda2e): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0xdae0): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0xdb1c): undefined reference to for_errmsg
elpa2_compute_complex.F90:(.text+0xdba6): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0xdc57): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0xdc93): undefined reference to for_errmsg
elpa2_compute_complex.F90:(.text+0xdd1d): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0xddd0): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0xde0d): undefined reference to for_errmsg
elpa2_compute_complex.F90:(.text+0xde99): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0xdf4e): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0xe008): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0xe296): undefined reference to _f90_dope_vector_init
elpa2_compute_complex.F90:(.text+0xe2eb): undefined reference to _f90_dope_vector_init
elpa2_compute_complex.F90:(.text+0xe33d): undefined reference to _f90_dope_vector_init
elpa2_compute_complex.F90:(.text+0xe38a): undefined reference to _f90_dope_vector_init
elpa2_compute_complex.F90:(.text+0x10764): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0x107f4): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0x10884): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0x10915): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.F90:(.text+0x109a6): undefined reference to for_dealloc_allocatable
elpa2_compute_complex.o:elpa2_compute_complex.F90:(.text+0x10a37): undefollowing more undefined references to for_dealloc_allocatable
elpa2_compute_complex.o: for function elpa2_compute_complex_mp_tridiag_band_complex_double_:
........
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1933): undefined reference to for_dealloc_allocatable
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x19c4): undefined reference to for_dealloc_allocatable
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1a55): undefined reference to for_dealloc_allocatable
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1ae6): undefined reference to for_dealloc_allocatable
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1b68): undefined reference to for_concat
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1ba3): undefined reference to for_write_seq_lis
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1bcd): undefined reference to for_stop_core
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1beb): undefined reference to for_errmsg
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1cd4): undefined reference to for_check_mult_overflow64
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1d4b): undefined reference to for_alloc_allocatable
make: *** [openmx] Error 1
##############
I don't know what's happening.
Regards,
Lin Tzu Ching
|
| Re: Error comes up when compiling openmx3.9 ( No.10 ) |
- Date: 2022/12/12 15:02
- Name: Naoya Yamaguchi
- Dear Lin Tzu Ching,
Can you add `-lifcore` to `LIB?
Regards,
Naoya Yamaguchi
|
| Re: Error comes up when compiling openmx3.9 ( No.11 ) |
- Date: 2022/12/12 15:27
- Name: Lin Tzu Ching
- Dear Naoya Yamaguchi,
The error is :
#######################
L1.o: for function elpa_transpose_vectors_..0:
elpa1.f90:(.text+0x4704): undefined reference to mpi_comm_rank_
elpa1.f90:(.text+0x4719): undefined reference to mpi_comm_size_
elpa1.f90:(.text+0x4730): undefined reference to mpi_comm_rank_
elpa1.f90:(.text+0x4747): undefined reference to mpi_comm_size_
elpa1.f90:(.text+0x4b15): undefined reference to mpi_bcast_
elpa1.o: for function elpa1_mp_trans_ev_real_:
elpa1.f90:(.text+0x5002): undefined reference to mpi_comm_rank_
elpa1.f90:(.text+0x5021): undefined reference to mpi_comm_size_
elpa1.f90:(.text+0x5040): undefined reference to mpi_comm_rank_
elpa1.f90:(.text+0x505f): undefined reference to mpi_comm_size_
elpa1.f90:(.text+0x5de6): undefined reference to mpi_bcast_
elpa1.f90:(.text+0x62bf): undefined reference to mpi_allreduce_
elpa1.f90:(.text+0x66e5): undefined reference to mpi_allreduce_
elpa1.o: for function elpa1_mp_mult_at_b_real_:
elpa1.f90:(.text+0x71df): undefined reference to mpi_comm_rank_
elpa1.f90:(.text+0x71fe): undefined reference to mpi_comm_size_
elpa1.f90:(.text+0x721d): undefined reference to mpi_comm_rank_
elpa1.f90:(.text+0x723c): undefined reference to mpi_comm_size_
elpa1.f90:(.text+0x7e56): undefined reference to mpi_bcast_
elpa1.f90:(.text+0x8a47): undefined reference to mpi_reduce_
elpa1.o: for function elpa1_mp_tridiag_complex_:
elpa1.f90:(.text+0x9438): undefined reference to mpi_comm_rank_
....
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x182b): undefined reference to for_errmsg
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x18a2): undefined reference to for_dealloc_allocatable
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1933): undefined reference to for_dealloc_allocatable
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x19c4): undefined reference to for_dealloc_allocatable
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1a55): undefined reference to for_dealloc_allocatable
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1ae6): undefined reference to for_dealloc_allocatable
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1b68): undefined reference to for_concat
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1ba3): undefined reference to for_write_seq_lis
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1bcd): undefined reference to for_stop_core
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1beb): undefined reference to for_errmsg
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1cd4): undefined reference to for_check_mult_overflow64
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1d4b): undefined reference to for_alloc_allocatable
make: *** [openmx] Error 1
##################################
Regards,
Lin Tzu Ching
|
| Re: Error comes up when compiling openmx3.9 ( No.12 ) |
- Date: 2022/12/12 20:32
- Name: Naoya Yamaguchi
- Dear Lin Tzu Ching,
Which MPI did you use?
If you cannot find it by yourself, installing the Intel oneAPI is a more simple way.
Regards,
Naoya Yamaguchi
|
| Re: Error comes up when compiling openmx3.9 ( No.13 ) |
- Date: 2022/12/12 20:51
- Name: Lin Tzu Ching
- Dear Naoya Yamaguchi,
I change the makefile as below and it's work:
#################
#MKLROOT = /opt/intel/mkl
CC = mpicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpif90 -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -mkl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lifcoremt -liomp5 -lpthread -lm -ldl
##################
Even though I don't know what happened, it would be great if you could explain it to me.
Thank you for your time and consideration. I appreciate your help with this matter.
Regards,
Lin Tzu Ching
|
| Re: Error comes up when compiling openmx3.9 ( No.14 ) |
- Date: 2022/12/12 20:59
- Name: Xinliang Huang <xilhuang@foxmail.com>
- Hi,
I followed the following tutorial to install successfully. You can try it as a reference.
https://mp.weixin.qq.com/s?src=11×tamp=1670846154&ver=4222&signature=TZ22MxKYmSrpdhP8ylY*w0wHei-tUjt4*kGqnIsc6IeJ7-ofw6b7ulA-cNsNwr-0Pi2TL15jS6eEhsBAhXZ6S2Dr9UNFBYtj2pp9CVsdrxux9BCZOXuMWfQFC8MqNoFT&new=1
Regards,
Xinliang Huang
|
|
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Error comes up when compiling openmx3.9