Intel linker not found

[whatheway]

Trying to use intel basekit and when I try to untar a file on Rocky Linux 9 I get this error

tar -xzvf WRF-4.4.2.tar.gz

tar: Relink `/opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin/libimf.so' with `/lib64/libm.so.6' for IFUNC symbol `sinf'

Segmentation fault (core dumped)

If I try to symlink the files they recommend I get this error

ln -s /opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin/libimf.so /lib64/libm.so.6

ln: failed to create symbolic link '/lib64/libm.so.6': File exists

[whatheway]

I believe something is wrong with the setenv variable file for the oneapi tools.  It's not linking to the files properly

[SantoshY_Intel]

Hi,

Thanks for posting in the Intel communities.

We tried it on Rocky Linux 9.1 but were unable to reproduce your issue. It was working fine as expected.

I followed the below steps:

1. wget https://github.com/wrf-model/WRF/releases/download/v4.4.2/v4.4.2.tar.gz
2. tar -xzvf v4.4.2.tar.gz

Could you please let us know if the above-mentioned tar file is the same one you were using? If not, please provide the tar file so that we can try again.

Also, it doesn't seem to be an issue with Intel Base Toolkit, It seems to be an issue with your environment/OS. I have seen a couple of similar issues reported as bugs in past in RHEL & fedora forums.

So, could you please try on another machine & let us know if the issue persists?

Thanks & Regards,

Santosh

[whatheway]

@SantoshY_Intel 

I have tried other environments and it is only on RHEL distros like Centos9 and rocky linux 9

Here is a script that is run on rocky linux 9 that breaks and reproduces the errors.

please remove the .txt at the endd

[SantoshY_Intel · Accepted solution]

Hi,

Thanks for providing the reproducer script. I tried it on Rocky Linux 9.1, & I was able to reproduce your issue from my end as shown below:

tar: Relink `/opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin/libimf.so' with `/lib64/libm.so.6' for IFUNC symbol `sinf'
Intel_test.sh: line 229: 370466 Segmentation fault   (core dumped) tar -xvf Fortran_C_tests.tar -C $WRF_FOLDER/Tests/Environment
tar: Relink `/opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin/libimf.so' with `/lib64/libm.so.6' for IFUNC symbol `sinf'
Intel_test.sh: line 230: 370469 Segmentation fault   (core dumped) tar -xvf Fortran_C_NETCDF_MPI_tests.tar -C $WRF_FOLDER/Tests/Compatibility

I tried isolating the commands from the script, which is causing the issue from your script.

#! /bin/bash
 #################################### System Environment Tests ##############
 cd $WRF_FOLDER/Downloads
 wget -c -4 https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_NETCDF_MPI_tests.tar
 wget -c -4 https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_tests.tar
 tar -xvf Fortran_C_tests.tar -C $WRF_FOLDER/Tests/Environment
 tar -xvf Fortran_C_NETCDF_MPI_tests.tar -C $WRF_FOLDER/Tests/Compatibility
 export one="1"
 echo " "

I tried running this test separately, and it worked fine without any issues as shown below:

[sdp@001b21ea7043 ~]$ bash run
--2023-03-06 04:13:03--  https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_NETCDF_MPI_tests.tar
Resolving proxy-dmz.intel.com (proxy-dmz.intel.com)... 10.7.211.16
Connecting to proxy-dmz.intel.com (proxy-dmz.intel.com)|10.7.211.16|:912... connected.
Proxy request sent, awaiting response... 200 OK
Length: 9728 (9.5K) [application/x-tar]
Saving to: ‘Fortran_C_NETCDF_MPI_tests.tar’

Fortran_C_NETCDF_MPI_tests.tar  100%[====================================================>]   9.50K  --.-KB/s    in 0s

2023-03-06 04:13:04 (46.1 MB/s) - ‘Fortran_C_NETCDF_MPI_tests.tar’ saved [9728/9728]

--2023-03-06 04:13:04--  https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_tests.tar
Resolving proxy-dmz.intel.com (proxy-dmz.intel.com)... 10.7.211.16
Connecting to proxy-dmz.intel.com (proxy-dmz.intel.com)|10.7.211.16|:912... connected.
Proxy request sent, awaiting response... 200 OK
Length: 18944 (18K) [application/x-tar]
Saving to: ‘Fortran_C_tests.tar’

Fortran_C_tests.tar             100%[====================================================>]  18.50K  --.-KB/s    in 0.03s

2023-03-06 04:13:04 (568 KB/s) - ‘Fortran_C_tests.tar’ saved [18944/18944]

./._kelly_reqs.txt
kelly_reqs.txt
./._TEST_1_fortran_only_fixed.f
TEST_1_fortran_only_fixed.f
./._TEST_2_fortran_only_free.f90
TEST_2_fortran_only_free.f90
./._TEST_3_c_only.c
TEST_3_c_only.c
./._TEST_4_fortran+c_c.c
TEST_4_fortran+c_c.c
./._TEST_4_fortran+c_f.f90
TEST_4_fortran+c_f.f90
TEST_csh.csh
TEST_perl.pl
TEST_sh.sh
./._01_fortran+c+netcdf_c.c
01_fortran+c+netcdf_c.c
./._01_fortran+c+netcdf_f.f
01_fortran+c+netcdf_f.f
./._02_fortran+c+netcdf+mpi_c.c
02_fortran+c+netcdf+mpi_c.c
./._02_fortran+c+netcdf+mpi_f.f
02_fortran+c+netcdf+mpi_f.f

So it seems to be an issue within the script.

Also, I tried commenting the lines of code which build and install the HDF5 in the script you gave &then ran the script. It worked fine as expected. So, it might be an issue with the HDF5 installation which is causing the relink issue.

Please try to exclude the installation of HDF5 in your script & let us know if you could get the expected results.

Thanks & Regards,

Santosh

[whatheway]

HDF5 is required for the installation of the program I am using.

Can you think of another solution

[whatheway]

@SantoshY_Intel 

HDF5 is required for the installation of the program I am using.

Can you think of another solution

[SantoshY_Intel]

Hi,

We are working on your issue and we will get back to you soon.

Thanks & Regards,

Santosh

[whatheway]

Thank you for continuing to work on this.

[SantoshY_Intel]

Hi,

According to the Intel® oneAPI Base Toolkit System Requirements, Rocky Linux supports all components except Intel® oneAPI DPC++/C++ Compiler.

So, we recommend you use the ICX compiler with a supported target operating system.

Since you already confirmed that the issue is observed only on Rocky Linux & Centos machines, which are unsupported target OS, could you please confirm if we can close this issue?

Thanks & Regards,

Santosh

[whatheway]

Thank you. Go ahead and close

[rumekintun]

using icx .. :

library szip:

webpage: https://support.hdfgroup.org/doc_resource/SZIP/

libtool: link: icx -shared -fPIC -DPIC .libs/rice.o .libs/sz_api.o .libs/encoding.o -lm -O2 -Wl,-soname -Wl,libsz.so.2 -o .libs/libsz.so.2.0.0
libtool: link: (cd ".libs" && rm -f "libsz.so.2" && ln -s "libsz.so.2.0.0" "libsz.so.2")
libtool: link: (cd ".libs" && rm -f "libsz.so" && ln -s "libsz.so.2.0.0" "libsz.so")
libtool: link: ar cru .libs/libsz.a rice.o sz_api.o encoding.o
ar: Relink `/opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin/libimf.so' with `/lib64/libm.so.6' for IFUNC symbol `sinf'
../libtool: line 1720: 1174608 Segmentation fault (core dumped) ar cru .libs/libsz.a rice.o sz_api.o encoding.o

make[2]: *** [Makefile:419: libsz.la] Error 139
make[2]: Leaving directory '/home/rodrigo/WRF/SRC/szip-2.1.1/src'
make[1]: *** [Makefile:334: all] Error 2
make[1]: Leaving directory '/home/rodrigo/WRF/SRC/szip-2.1.1/src'
make: *** [Makefile:381: all-recursive] Error 1

the same like  @whatheway whatheway

I'm trying to compile WRF..  but i need compile before:

szip

hdf5

netcdf4

there is a big community running WRF model

I'm working on "CentOS Stream release 8"

CC=icx

FC=ifx

CXX=icpx

[SantoshY_Intel]

Hi,

Thanks for accepting our solution. If you need any additional information, please post a new question as this thread will no longer be monitored by Intel.

Thanks & Regards,

Santosh