Top Page > Browsing
Problem in installation openmx 3.9
Date: 2025/01/27 22:16
Name: EOM HUIYONG   <eomlife@korea.ac.kr>

Dear Openmx developers/user,

I am trying to install OpenMx 3.9 version on Ubuntu 22.04 with intel oneapi base toolkit and hpc toolkit 2021.3.0 version
(l_BaseKit_p_2021.3.0.3219_offline.sh, l_HPCKit_p_2021.3.0.3230_offline.sh)
There are some problems during installing OpenMx.


MKLROOT = /opt/intel/oneapi/mkl/2021.3.0/
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lifcore -lmkl_blacs_intelmpi_lp64
-liomp5 -lpthread -lm -ldl

After I wrote the script above on the makefile, I got some problems below.

hyong@hyong-960XFG:~/openmx3.9/source$ make all
mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I/opt/intel/oneapi/mkl/2021.3.0//include -I/opt/intel/oneapi/mkl/2021.3.0//include/fftw -I./elpa-2018.05.001 -c openmx.c
In file included from openmx.c(57):
/usr/include/stdio.h(189): error: attribute "__malloc__" does not take arguments
    __attribute_malloc__ __attr_dealloc_fclose __wur;
                        ^

In file included from openmx.c(57):
/usr/include/stdio.h(223): error: attribute "__malloc__" does not take arguments
    __THROW __attribute_malloc__ __wur __attr_dealloc_free;
                                        ^

In file included from openmx.c(57):
/usr/include/stdio.h(260): error: attribute "__malloc__" does not take arguments
    __attribute_malloc__ __attr_dealloc_fclose __wur;
                        ^

In file included from openmx.c(57):
/usr/include/stdio.h(294): error: attribute "__malloc__" does not take arguments
    __attribute_malloc__ __attr_dealloc_fclose __wur;
                        ^

In file included from openmx.c(57):
/usr/include/stdio.h(309): error: attribute "__malloc__" does not take arguments
    __THROW __attribute_malloc__ __attr_dealloc_fclose __wur;
                                ^

In file included from openmx.c(57):
/usr/include/stdio.h(315): error: attribute "__malloc__" does not take arguments
    __attribute_malloc__ __attr_dealloc_fclose __wur;
                        ^

In file included from openmx.c(57):
/usr/include/stdio.h(830): error: attribute "__malloc__" does not take arguments
    __attribute_malloc__ __attr_dealloc (pclose, 1) __wur;
                        ^

In file included from openmx.c(58):
/usr/include/stdlib.h(566): error: attribute "__malloc__" does not take arguments
      __attr_dealloc_free;
      ^

In file included from openmx.c(58):
/usr/include/stdlib.h(570): error: attribute "__malloc__" does not take arguments
      __THROW __attr_dealloc (reallocarray, 1);
              ^

compilation aborted for openmx.c (code 2)
make: *** [makefile:219: openmx.o] Error 2

I want to know what is the problem and what should I do.
I would greatly appreciate it if someone could suggest a solution to overcome this limitation or help me identify what I might be doing wrong.

Thank you in advance for your help!

Regards,
EOM HUIYONG

メンテ
Page: [1]

Re: Problem in installation openmx 3.9 ( No.1 )
Date: 2025/01/28 22:20
Name: Naoya Yamaguchi

Hi,

How about trying the latest version of oneAPI?
The same issue was reported in https://community.intel.com/t5/Intel-oneAPI-DPC-C-Compiler/Compilation-issues-with-ICPC-2021-4-and-C-14/td-p/1318571 .
The issue seemed to be solved in a newer version.

Regards,
Naoya Yamaguchi
メンテ
Re: Problem in installation openmx 3.9 ( No.2 )
Date: 2025/01/29 20:04
Name: SANTU BAIDYA

I have tried to install openmx3.9 on Ubuntu 22.04 LTS using intel oneapi 2025 latest version.

My makefile has the following


MKLROOT = /opt/intel/oneapi/mkl/2025.0/
CC = mpiicx -O3 -xHOST  -qopenmp -I${MKLROOT}/include -I/opt/intel/oneapi/mkl/2025.0/include/fftw/
FC = mpiifx -O3 -xHOST  -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lifcore -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl


But I am getting error
mpiicx -O3 -xHOST  -qopenmp -I/opt/intel/oneapi/mkl/2025.0//include -I/opt/intel/oneapi/mkl/2025.0/include/fftw/ -I./elpa-2018.05.001 -c XC_PBE.c
mpiicx -O3 -xHOST  -qopenmp -I/opt/intel/oneapi/mkl/2025.0//include -I/opt/intel/oneapi/mkl/2025.0/include/fftw/ -I./elpa-2018.05.001 -c XC_EX.c
mpiicx -O3 -xHOST  -qopenmp -I/opt/intel/oneapi/mkl/2025.0//include -I/opt/intel/oneapi/mkl/2025.0/include/fftw/ -I./elpa-2018.05.001 -c DFT.c
DFT.c:1960:7: error: call to undeclared library function 'strstr' with type 'char *(const char *, const char *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
1960 |  if (strstr(nanchar,"nan")!=NULL || strstr(nanchar,"NaN")!=NULL
      |      ^
DFT.c:1960:7: note: include the header <string.h> or explicitly provide a declaration for 'strstr'
DFT.c:2522:15: error: call to undeclared function 'numroc_'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2522 |    na_rows = numroc_(&n, &nblk, &my_prow, &ZERO, &np_rows);
      |              ^
DFT.c:2525:16: error: call to undeclared function 'Csys2blacs_handle'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2525 |    bhandle2 = Csys2blacs_handle(MPI_CommWD2[myworld2]);
      |                ^
DFT.c:2527:5: error: call to undeclared function 'Cblacs_gridinit'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2527 |    Cblacs_gridinit(&ictxt2, "Row", np_rows, np_cols);
      |    ^
DFT.c:2536:5: error: call to undeclared function 'descinit_'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2536 |    descinit_(descS, &n, &n, &nblk, &nblk, &ZERO, &ZERO, &ictxt2, &na_rows, &info);
      |    ^
DFT.c:2694:5: error: call to undeclared function 'Cfree_blacs_system_handle'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2694 |    Cfree_blacs_system_handle(bhandle2);
      |    ^
DFT.c:2695:5: error: call to undeclared function 'Cblacs_gridexit'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2695 |    Cblacs_gridexit(ictxt2);
      |    ^
DFT.c:2905:15: error: call to undeclared function 'numroc_'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2905 |    na_rows = numroc_(&n, &nblk, &my_prow, &ZERO, &np_rows);
      |              ^
DFT.c:2908:16: error: call to undeclared function 'Csys2blacs_handle'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2908 |    bhandle2 = Csys2blacs_handle(MPI_CommWD2[myworld2]);
      |                ^
DFT.c:2910:5: error: call to undeclared function 'Cblacs_gridinit'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2910 |    Cblacs_gridinit(&ictxt2, "Row", np_rows, np_cols);
      |    ^
DFT.c:2926:5: error: call to undeclared function 'descinit_'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
2926 |    descinit_(descS, &n, &n, &nblk, &nblk, &ZERO, &ZERO, &ictxt2, &na_rows, &info);
      |    ^
DFT.c:3121:5: error: call to undeclared function 'Cfree_blacs_system_handle'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
3121 |    Cfree_blacs_system_handle(bhandle2);
      |    ^
DFT.c:3122:5: error: call to undeclared function 'Cblacs_gridexit'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
3122 |    Cblacs_gridexit(ictxt2);
      |    ^
DFT.c:3298:15: error: call to undeclared function 'numroc_'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
3298 |    na_rows = numroc_(&n, &nblk, &my_prow, &ZERO, &np_rows);
      |              ^
DFT.c:3301:16: error: call to undeclared function 'Csys2blacs_handle'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
3301 |    bhandle1 = Csys2blacs_handle(MPI_CommWD1[myworld1]);
      |                ^
DFT.c:3304:5: error: call to undeclared function 'Cblacs_gridinit'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
3304 |    Cblacs_gridinit(&ictxt1, "Row", np_rows, np_cols);
      |    ^
DFT.c:3312:5: error: call to undeclared function 'descinit_'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
3312 |    descinit_(descS, &n,  &n,  &nblk,  &nblk,  &ZERO, &ZERO, &ictxt1, &na_rows,  &info);
      |    ^
DFT.c:3357:5: error: call to undeclared function 'Cfree_blacs_system_handle'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
3357 |    Cfree_blacs_system_handle(bhandle1);
      |    ^
DFT.c:3358:5: error: call to undeclared function 'Cblacs_gridexit'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
3358 |    Cblacs_gridexit(ictxt1);
      |    ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [makefile:298: DFT.o] Error 1

Please help me with this installation.
Thank you.
メンテ

Page: [1]

Thread Title (must) Move the thread to the top
Your Name (must)
E-Mail (must)
URL
Password (used in modification of the submitted text)
Comment (must)

   Save Cookie