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Intel ifx compile error with gcc gxx gfortran installed in conda

SuperXCX
Beginner
‎03-13-2024 03:07 AM
600 Views

Dear experts:

My system is Linux version 5.10.16.3-microsoft-standard-WSL2 (oe-user@oe-host) (x86_64-msft-linux-gcc (GCC) 9.3.0, GNU ld (GNU Binutils) 2.34.0.20200220) #1 SMP Fri Apr 2 22:23:49 UTC 2021. Basically I have install whole Intel OneAPI and HPC toolkit, with ifx version as ifx (IFX) 2024.0.2 20231213.

First, I use ifx to complie a simple fortran.f90:

PROGRAM HELLO_WORLD
    WRITE (*,*) 'Hello, World!'
END PROGRAM HELLO_WORLD

with command

ifx fortran.f90 -o fortran -v

The compile is success and output message is

ifx version 2024.0.2
/home/sjtj/intel/oneapi/compiler/2024.0/bin/compiler/xfortcom    -triple x86_64-unknown-linux-gnu -emit-obj "-verify nomodule" -main-file-name fortran.f90 -mllvm --relocation-model=static "-options-string -o fortran -v " -mframe-pointer=none -omp_simd -target-cpu x86-64 -target-linker-version 2.38 -fveclib=SVML -mllvm -loopopt=1 -floopopt-pipeline=light -mllvm -disable-hir-generate-mkl-call -mllvm -paropt=11 -fintel-libirc-allowed -o /tmp/ifx1065350877UgB3Io/ifxC15m1v.o -D__INTEL_LLVM_COMPILER=20240002 -D__INTEL_LLVM_COMPILER_UPDATE=2 -D__unix__ -D__unix -D__linux__ -D__linux -D__gnu_linux__ -Dunix -Dlinux -D__ELF__ -D__x86_64 -D__x86_64__ -D__amd64 -D__amd64__ -D__INTEL_COMPILER_BUILD_DATE=20231213 -D__INTEL_COMPILER=20240002 -D__INTEL_COMPILER_UPDATE=2 -I. -I/home/sjtj/intel/oneapi/tbb/2021.11/env/../include -I/home/sjtj/intel/oneapi/mpi/2021.11/include -I/home/sjtj/intel/oneapi/mkl/2024.0/include -I/home/sjtj/intel/oneapi/ippcp/2021.9/include -I/home/sjtj/intel/oneapi/ipp/2021.10/include -I/home/sjtj/intel/oneapi/dpl/2022.3/include -I/home/sjtj/intel/oneapi/dpcpp-ct/2024.0/include -I/home/sjtj/intel/oneapi/dnnl/2024.0/include -I/home/sjtj/intel/oneapi/dev-utilities/2024.0/include -I/home/sjtj/intel/oneapi/dal/2024.0/include/dal -I/home/sjtj/intel/oneapi/compiler/2024.0/opt/oclfpga/include -I/home/sjtj/intel/oneapi/ccl/2021.11/include -I/home/sjtj/intel/oneapi/compiler/2024.0/opt/compiler/include -I/home/sjtj/intel/oneapi/compiler/2024.0/include -I/usr/local/include -I/home/sjtj/intel/oneapi/compiler/2024.0/lib/clang/17/include -I/usr/include -I/usr/include/x86_64-linux-gnu -omp_simd -O2 "-reentrancy threaded" "-unroll 2" -simd -offload_host fortran.f90
#include "..." search starts here:
#include <...> search starts here:
 .
 /home/sjtj/intel/oneapi/tbb/2021.11/env/../include
 /home/sjtj/intel/oneapi/mpi/2021.11/include
 /home/sjtj/intel/oneapi/mkl/2024.0/include
 /home/sjtj/intel/oneapi/ippcp/2021.9/include
 /home/sjtj/intel/oneapi/ipp/2021.10/include
 /home/sjtj/intel/oneapi/dpl/2022.3/include
 /home/sjtj/intel/oneapi/dpcpp-ct/2024.0/include
 /home/sjtj/intel/oneapi/dnnl/2024.0/include
 /home/sjtj/intel/oneapi/dev-utilities/2024.0/include
 /home/sjtj/intel/oneapi/dal/2024.0/include/dal
 /home/sjtj/intel/oneapi/compiler/2024.0/opt/oclfpga/include
 /home/sjtj/intel/oneapi/ccl/2021.11/include
 /home/sjtj/intel/oneapi/compiler/2024.0/opt/compiler/include
 /home/sjtj/intel/oneapi/compiler/2024.0/include
 /usr/local/include
 /home/sjtj/intel/oneapi/compiler/2024.0/lib/clang/17/include
 /usr/include
 /usr/include/x86_64-linux-gnu
End of search list.
ld    /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o --eh-frame-hdr --build-id -dynamic-linker /lib64/ld-linux-x86-64.so.2 -m elf_x86_64 -o fortran /home/sjtj/intel/oneapi/compiler/2024.0/lib/for_main.o -L/home/sjtj/intel/oneapi/tbb/2021.11/env/../lib/intel64/gcc4.8 -L/home/sjtj/intel/oneapi/mpi/2021.11/lib -L/home/sjtj/intel/oneapi/mkl/2024.0/lib/ -L/home/sjtj/intel/oneapi/ippcp/2021.9/lib/ -L/home/sjtj/intel/oneapi/ipp/2021.10/lib -L/home/sjtj/intel/oneapi/dpl/2022.3/lib -L/home/sjtj/intel/oneapi/dnnl/2024.0/lib -L/home/sjtj/intel/oneapi/dal/2024.0/lib -L/home/sjtj/intel/oneapi/compiler/2024.0/lib -L/home/sjtj/intel/oneapi/ccl/2021.11/lib/ -L/home/sjtj/intel/oneapi/compiler/2024.0/lib -L/home/sjtj/intel/oneapi/compiler/2024.0/lib -L/home/sjtj/intel/oneapi/compiler/2024.0/lib/clang/17/lib/x86_64-unknown-linux-gnu -L/home/sjtj/intel/oneapi/compiler/2024.0/lib -L/home/sjtj/intel/oneapi/tbb/2021.11/env/../lib/intel64/gcc4.8/../lib/ -L/home/sjtj/intel/oneapi/mpi/2021.11/lib/../lib/ -L/home/sjtj/intel/oneapi/mkl/2024.0/lib/../lib/ -L/home/sjtj/intel/oneapi/ippcp/2021.9/lib/../lib/ -L/home/sjtj/intel/oneapi/ipp/2021.10/lib/../lib/ -L/home/sjtj/intel/oneapi/dpl/2022.3/lib/../lib/ -L/home/sjtj/intel/oneapi/dnnl/2024.0/lib/../lib/ -L/home/sjtj/intel/oneapi/dal/2024.0/lib/../lib/ -L/home/sjtj/intel/oneapi/compiler/2024.0/lib/../lib/ -L/home/sjtj/intel/oneapi/ccl/2021.11/lib/../lib/ -L/usr/lib/gcc/x86_64-linux-gnu/11/ -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/ -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib64 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/ -L/lib/x86_64-linux-gnu/ -L/lib/../lib64 -L/lib/../lib/ -L/usr/lib/x86_64-linux-gnu/ -L/usr/lib/../lib64 -L/usr/lib/../lib/ -L/home/sjtj/intel/oneapi/tbb/2021.11/env/../lib/intel64/gcc4.8/ -L/home/sjtj/intel/oneapi/mpi/2021.11/lib/ -L/home/sjtj/intel/oneapi/mkl/2024.0/lib/ -L/home/sjtj/intel/oneapi/ippcp/2021.9/lib/ -L/home/sjtj/intel/oneapi/ipp/2021.10/lib/ -L/home/sjtj/intel/oneapi/dpl/2022.3/lib/ -L/home/sjtj/intel/oneapi/dnnl/2024.0/lib/ -L/home/sjtj/intel/oneapi/dal/2024.0/lib/ -L/home/sjtj/intel/oneapi/compiler/2024.0/lib/ -L/home/sjtj/intel/oneapi/ccl/2021.11/lib/ -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib /tmp/ifx1065350877UgB3Io/ifxC15m1v.o -Bdynamic -Bstatic -lifport -lifcoremt -Bdynamic -limf -Bstatic -lsvml -Bdynamic -lm -Bstatic -lipgo -lirc -Bdynamic -lpthread -Bstatic -lsvml -Bdynamic -lc -lgcc -lgcc_s -Bstatic -lirc_s -Bdynamic -ldl -lc /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o

Use ldd we see

linux-vdso.so.1 (0x00007fff5f761000)
libimf.so => /home/sjtj/intel/oneapi/compiler/2024.0/lib/libimf.so (0x00007f86e7303000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f86e7214000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f86e6feb000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f86e6fc9000)
libintlc.so.5 => /home/sjtj/intel/oneapi/compiler/2024.0/lib/libintlc.so.5 (0x00007f86e6f68000)
/lib64/ld-linux-x86-64.so.2 (0x00007f86e7723000)

Then, I use conda to install gcc gxx gfortran with version

gcc (conda-forge gcc 13.2.0-5) 13.2.0
g++ (conda-forge gcc 13.2.0-5) 13.2.0
GNU Fortran (conda-forge gcc 13.2.0-5) 13.2.0

Still compile as above, it fails with the output message

ifx version 2024.0.2
/home/sjtj/intel/oneapi/compiler/2024.0/bin/compiler/xfortcom    -triple x86_64-unknown-linux-gnu -emit-obj "-verify nomodule" -main-file-name fortran.f90 -mllvm --relocation-model=static "-options-string -o fortran -v " -mframe-pointer=none -omp_simd -target-cpu x86-64 -target-linker-version 2.40 -fveclib=SVML -mllvm -loopopt=1 -floopopt-pipeline=light -mllvm -disable-hir-generate-mkl-call -mllvm -paropt=11 -fintel-libirc-allowed -o /tmp/ifx0677215345q5Oavv/ifxEgPvw8.o -D__INTEL_LLVM_COMPILER=20240002 -D__INTEL_LLVM_COMPILER_UPDATE=2 -D__unix__ -D__unix -D__linux__ -D__linux -D__gnu_linux__ -Dunix -Dlinux -D__ELF__ -D__x86_64 -D__x86_64__ -D__amd64 -D__amd64__ -D__INTEL_COMPILER_BUILD_DATE=20231213 -D__INTEL_COMPILER=20240002 -D__INTEL_COMPILER_UPDATE=2 -I. -I/home/sjtj/intel/oneapi/tbb/2021.11/env/../include -I/home/sjtj/intel/oneapi/mpi/2021.11/include -I/home/sjtj/intel/oneapi/mkl/2024.0/include -I/home/sjtj/intel/oneapi/ippcp/2021.9/include -I/home/sjtj/intel/oneapi/ipp/2021.10/include -I/home/sjtj/intel/oneapi/dpl/2022.3/include -I/home/sjtj/intel/oneapi/dpcpp-ct/2024.0/include -I/home/sjtj/intel/oneapi/dnnl/2024.0/include -I/home/sjtj/intel/oneapi/dev-utilities/2024.0/include -I/home/sjtj/intel/oneapi/dal/2024.0/include/dal -I/home/sjtj/intel/oneapi/compiler/2024.0/opt/oclfpga/include -I/home/sjtj/intel/oneapi/ccl/2021.11/include -I/home/sjtj/intel/oneapi/compiler/2024.0/opt/compiler/include -I/home/sjtj/intel/oneapi/compiler/2024.0/include -I/usr/local/include -I/home/sjtj/intel/oneapi/compiler/2024.0/lib/clang/17/include -I/usr/include -omp_simd -O2 "-reentrancy threaded" "-unroll 2" -simd -offload_host fortran.f90
#include "..." search starts here:
#include <...> search starts here:
 .
 /home/sjtj/intel/oneapi/tbb/2021.11/env/../include
 /home/sjtj/intel/oneapi/mpi/2021.11/include
 /home/sjtj/intel/oneapi/mkl/2024.0/include
 /home/sjtj/intel/oneapi/ippcp/2021.9/include
 /home/sjtj/intel/oneapi/ipp/2021.10/include
 /home/sjtj/intel/oneapi/dpl/2022.3/include
 /home/sjtj/intel/oneapi/dpcpp-ct/2024.0/include
 /home/sjtj/intel/oneapi/dnnl/2024.0/include
 /home/sjtj/intel/oneapi/dev-utilities/2024.0/include
 /home/sjtj/intel/oneapi/dal/2024.0/include/dal
 /home/sjtj/intel/oneapi/compiler/2024.0/opt/oclfpga/include
 /home/sjtj/intel/oneapi/ccl/2021.11/include
 /home/sjtj/intel/oneapi/compiler/2024.0/opt/compiler/include
 /home/sjtj/intel/oneapi/compiler/2024.0/include
 /usr/local/include
 /home/sjtj/intel/oneapi/compiler/2024.0/lib/clang/17/include
 /usr/include
End of search list.
/home/sjtj/miniconda3/envs/test/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/bin/ld    /home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib64/crt1.o /home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib64/crti.o /home/sjtj/miniconda3/envs/test/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/crtbeginS.o --eh-frame-hdr --build-id -dynamic-linker /lib64/ld-linux-x86-64.so.2 -m elf_x86_64 -o fortran /home/sjtj/intel/oneapi/compiler/2024.0/lib/for_main.o -L/home/sjtj/intel/oneapi/tbb/2021.11/env/../lib/intel64/gcc4.8 -L/home/sjtj/intel/oneapi/mpi/2021.11/lib -L/home/sjtj/intel/oneapi/mkl/2024.0/lib/ -L/home/sjtj/intel/oneapi/ippcp/2021.9/lib/ -L/home/sjtj/intel/oneapi/ipp/2021.10/lib -L/home/sjtj/intel/oneapi/dpl/2022.3/lib -L/home/sjtj/intel/oneapi/dnnl/2024.0/lib -L/home/sjtj/intel/oneapi/dal/2024.0/lib -L/home/sjtj/intel/oneapi/compiler/2024.0/lib -L/home/sjtj/intel/oneapi/ccl/2021.11/lib/ -L/home/sjtj/intel/oneapi/compiler/2024.0/lib -L/home/sjtj/intel/oneapi/compiler/2024.0/lib -L/home/sjtj/intel/oneapi/compiler/2024.0/lib/clang/17/lib/x86_64-unknown-linux-gnu -L/home/sjtj/intel/oneapi/compiler/2024.0/lib -L/home/sjtj/miniconda3/envs/test/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/ -L/home/sjtj/miniconda3/envs/test/bin/../lib/gcc/ -L/home/sjtj/intel/oneapi/tbb/2021.11/env/../lib/intel64/gcc4.8/../lib/ -L/home/sjtj/intel/oneapi/mpi/2021.11/lib/../lib/ -L/home/sjtj/intel/oneapi/mkl/2024.0/lib/../lib/ -L/home/sjtj/intel/oneapi/ippcp/2021.9/lib/../lib/ -L/home/sjtj/intel/oneapi/ipp/2021.10/lib/../lib/ -L/home/sjtj/intel/oneapi/dpl/2022.3/lib/../lib/ -L/home/sjtj/intel/oneapi/dnnl/2024.0/lib/../lib/ -L/home/sjtj/intel/oneapi/dal/2024.0/lib/../lib/ -L/home/sjtj/intel/oneapi/compiler/2024.0/lib/../lib/ -L/home/sjtj/intel/oneapi/ccl/2021.11/lib/../lib/ -L/home/sjtj/miniconda3/envs/test/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib/../lib/ -L/home/sjtj/miniconda3/envs/test/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../lib/ -L/home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib64 -L/home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib/ -L/home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib64 -L/home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/ -L/home/sjtj/intel/oneapi/tbb/2021.11/env/../lib/intel64/gcc4.8/ -L/home/sjtj/intel/oneapi/mpi/2021.11/lib/ -L/home/sjtj/intel/oneapi/mkl/2024.0/lib/ -L/home/sjtj/intel/oneapi/ippcp/2021.9/lib/ -L/home/sjtj/intel/oneapi/ipp/2021.10/lib/ -L/home/sjtj/intel/oneapi/dpl/2022.3/lib/ -L/home/sjtj/intel/oneapi/dnnl/2024.0/lib/ -L/home/sjtj/intel/oneapi/dal/2024.0/lib/ -L/home/sjtj/intel/oneapi/compiler/2024.0/lib/ -L/home/sjtj/intel/oneapi/ccl/2021.11/lib/ -L/home/sjtj/miniconda3/envs/test/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib/ -L/home/sjtj/miniconda3/envs/test/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../ -L/home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/lib64 -L/home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/lib/ -L/home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib64 -L/home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib /tmp/ifx0677215345q5Oavv/ifxEgPvw8.o -Bdynamic -Bstatic -lifport -lifcoremt -Bdynamic -limf -Bstatic -lsvml -Bdynamic -lm -Bstatic -lipgo -lirc -Bdynamic -lpthread -Bstatic -lsvml -Bdynamic -lc -lgcc -lgcc_s -Bstatic -lirc_s -Bdynamic -ldl -lc /home/sjtj/miniconda3/envs/test/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/crtendS.o /home/sjtj/miniconda3/envs/test/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib64/crtn.o
/home/sjtj/miniconda3/envs/test/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/sjtj/intel/oneapi/compiler/2024.0/lib/libintlc.so.5: undefined reference to `memcpy@GLIBC_2.14'

 The error seems to come from the changed linker ld. We wonder if it's the reason and the determination of the linker. If not, what's the reason and how to fix it.

If you know how to resolve it, I would appreciate it if you could advice me.

Thanks!

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Barbara_P_Intel
Employee
‎03-14-2024 01:50 PM
568 Views

Seems like a PATH variable changed with the GNU installation. Could the wrong ld be being used?

 

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