Hello,
I'm installing pnetcdf-1.12.3 using icx anf ifx in OneAPI 2023.1.0. However, when I configure it, I met the following error:
/bin/ld: cannot find -loopopt=1
icx: error: linker command failed with exit code 1 (use -v to see invocation)
configure:28388: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "PnetCDF"
| #define PACKAGE_TARNAME "pnetcdf"
| #define PACKAGE_VERSION "1.12.3"
| #define PACKAGE_STRING "PnetCDF 1.12.3"
| #define PACKAGE_BUGREPORT "parallel-netcdf@mcs.anl.gov"
| #define PACKAGE_URL "https://parallel-netcdf.github.io"
| #define PACKAGE "pnetcdf"
| #define VERSION "1.12.3"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define ENABLE_CXX 1
| #define ENABLE_FORTRAN 1
| /* end confdefs.h. */
| #define FC_DUMMY_MAIN _main
| #ifdef FC_DUMMY_MAIN
| #ifndef FC_DUMMY_MAIN_EQ_F77
| # ifdef __cplusplus
| extern "C"
| # endif
| int FC_DUMMY_MAIN() { return 1; }
| #endif
| #endif
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:28404: result: unknown
configure:28421: error: in `/opt/pnetcdf-1.12.3':
configure:28423: error: linking to Fortran libraries from C fails
Please see the attached `config.log' file for more details.
I have posted the question here https://community.intel.com/t5/Intel-Fortran-Compiler/pnetcdf-configure-error-using-icx-and-ifx/m-p/1489151#M166469 before. I have no idea why I cannot reply to that one, so I posted a new one here. But I updated to gcc 10.2.0, cmake 3.26.4 and autoconf 2.70 following your suggestions, and the error still happens.
Any help?
Thanks!
連結已複製
How did you set up the env vars to use the oneapi compilers? I cloned Pnetcdf and got the configure to work without issue. I did this
export MPICC="mpiicc -cc=icx"
export MPICXX="mpiicpc -cxx=icpx"
export MPIF77="mpiifort -fc=ifx"
export MPIF90="mpiifort -fc=ifx"
./configure --prefix=/cts/tools/library/pnetcdf-1.12.3you'll still need to specify the include and library paths for netcdf-c, of course, but this should get you past the configure step.
and I found I needed the autoreconf command shown here.
and of course
./configure --help
for all the options you may want to configure as well. Like the netcdf-c stuff.
ron
New error encountered while make.
@Lumos wrote:I got it!
Before running configure command to build PnetCDF, please run commands below first.
cd PnetCDF autoreconf -i
CC attr_getput.lo
attr_getput.c:219:1: error: expected identifier or '('
219 | <U+0001>
| ^
attr_getput.c:393:1: error: expected identifier or '('
393 | <U+0001>
| ^
attr_getput.c:427:1: error: expected identifier or '('
427 | <U+0001>
| ^
attr_getput.c:702:1: error: expected identifier or '('
702 | <U+0001>
| ^
4 errors generated.
make[3]: *** [Makefile:539: attr_getput.lo] Error 1
make[3]: Leaving directory '/LIBRARIES/intel2024/pnetcdf-1.12.3/src/dispatchers'
make[2]: *** [Makefile:455: all] Error 2
make[2]: Leaving directory '/LIBRARIES/intel2024/pnetcdf-1.12.3/src/dispatchers'
make[1]: *** [Makefile:482: all-recursive] Error 1
make[1]: Leaving directory '/LIBRARIES/intel2024/pnetcdf-1.12.3/src'
make: *** [Makefile:540: all-recursive] Error 1Any help would be greatly appreciated.
My flags:
export CC=mpiicx
export CXX=mpiicpx
export FC=mpiifx
export F90=mpiifx
export F77=mpiifx
export CFLAGS="-O2 -fPIC"
export FCFLAGS="-O2 -fPIC"
export CXXFLAGS="-O2 -fPIC"
export CPPFLAGS="-I/LIBRARIES/intel2024/hdf51.14.3/include -I/LIBRARIES/intel2024/szip2.1.1/include -I/LIBRARIES/intel2024/zlib1.3/include"
export LDFLAGS="-L/LIBRARIES/intel2024/hdf51.14.3/lib -lhdf5_hl -lhdf5 -lz -lm -L/LIBRARIES/intel2024/szip2.1.1/lib -L/LIBRARIES/intel2024/zlib1.3/lib"./configure --prefix=$DIR/pnetcdf1.12.3 --with-mpi=/Compiler/intel2024/oneapi/mpi/2021.11 --enable-subfiling --enable-shared --enable-large-file-test --enable-null-byte-header-padding --enable-burst-buffering --enable-profiling --enable-relax-coord-bound
I found a clue from this github issue: https://github.com/spack/spack/issues/37172
and it seems like the bison compiled by oneAPI will generate garbage output bytes in attr_getput.c
Use bison of gcc version will solve this issue.
Thank you very much for your reply. But I don't think I used bison. Here is the bison in the system.
$ which bison
/usr/bin/bison
$ bison -V
bison (GNU Bison) 3.0.4
Written by Robert Corbett and Richard Stallman.
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.What exactly should I do? Thank you very much!
