[Wien] NMR Integration crashes when using nmr_integ:localhost:4 in .machines Link error

Fri Aug 29 14:54:13 CEST 2025

Use icc for fftw
Search for and download:
l_HPCKit_p_2021.1.0.2684.sh
l_BaseKit_p_2021.1.0.2659.sh

Fingers crossed the depositories are still available.

On Fri, Aug 29, 2025 at 7:34 AM Michael Fechtelkord via Wien <
wien at zeus.theochem.tuwien.ac.at> wrote:

> Thanks Laurence for your suggestions!
>
>
> 1) Using ifort / icc .. Compiling fftw3 with icx of the one-api package
> and "make check" gives the same relink error during mpirun .
>
> 2) Unfortunately I have only the latest and last ifort version
>
> 3) Does not change anything for the compilation of fftw3 because it is
> completely written in C and only linked to ifort in the WIEN2k compilation.
>
>
> Thanks again for your help!
>
>
> Best regards,
>
> Michael
>
>
> Am 29.08.2025 um 13:35 schrieb Laurence Marks:
>
> This link may help: https://github.com/spack/spack/issues/48296 . It
> appears to be an inconsistency between system libraries and ifort. Not easy
> to cure. (There might be other pages, search with ifort + Relink.)
>
> Three possibilities:
> 1. Compile fftw3 with ifort/icc. While ifort & gcc are supposed to be
> compatible, it could be that they are using different system libraries.
> 2. Regress to 2021.1.1 . I tested others and was not convinced they were
> better, in fact they could be buggy. You don't have to uninstall other
> versions, use a config file.
> 3. Add -mcmodel=medium to your ifort line. I had to after a recent OS
> update, although I cannot remember the exact reason why.
> ___
> Emeritus Professor Laurence Marks (Laurie)
> Department of Materials Science and Engineering, Northwestern University
> www.numis.northwestern.edu
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought" Albert Szent-Györgyi
>
> On Fri, Aug 29, 2025, 05:54 Michael Fechtelkord via Wien <
> wien at zeus.theochem.tuwien.ac.at> wrote:
>
>> Dear all,
>>
>>
>> I am back now to ifort 2021.13 because it crashes much less as the new
>> ifx compiler, also it produces omp errors using fftw3 during compilation.
>>
>> All worked fine since the last Open Suse Tumbleweed version using Kernel
>> 6.16.3-1 (Opensuse Tumbleweed 202250827). Parallel Jobs terminate when
>> using "mpirun" with the following error. The same error appears when I
>> have compiled fftw 3.10 with gcc 15.1 and run "make check" the check
>> routine crashes when using mpirun with the same error.
>>
>>
>> Does somebody  know what that relink error means and how to solve it? Is
>> it maybe the opensuse libm.so.6 library (glibc version 2.42.1) causing
>> the error, because the new version does not contain the symbol, libmpi
>> is reqeusting?
>>
>>
>>
>> Best  regards,
>>
>> Michael
>>
>> ---------------
>>
>>   EXECUTING:     mpirun -np 4 -machinefile .machine_nmrinteg
>> /usr/local/WIEN2k/nmr_mpi -case MgF2 -mode integ -green
>>
>> /usr/local/WIEN2k/nmr_mpi: Relink
>> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with `/lib64/libm.so.6'
>> for IFUNC symbol `modff'
>> /usr/local/WIEN2k/nmr_mpi: Relink
>> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with `/lib64/libm.so.6'
>> for IFUNC symbol `modff'
>> /usr/local/WIEN2k/nmr_mpi: Relink
>> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with `/lib64/libm.so.6'
>> for IFUNC symbol `modff'
>> /usr/local/WIEN2k/nmr_mpi: Relink
>> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with `/lib64/libm.so.6'
>> for IFUNC symbol `modff'
>>
>>
>> ===================================================================================
>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> =   RANK 0 PID 396989 RUNNING AT localhost
>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>
>> ===================================================================================
>>
>>
>> ===================================================================================
>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> =   RANK 1 PID 396990 RUNNING AT localhost
>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>
>> ===================================================================================
>>
>>
>> ===================================================================================
>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> =   RANK 2 PID 396991 RUNNING AT localhost
>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>
>> ===================================================================================
>>
>>
>> ===================================================================================
>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> =   RANK 3 PID 396992 RUNNING AT localhost
>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>
>> ===================================================================================
>>
>> stop
>>
>> /opt/fftw-3.3.10/mpi/.libs/mpi-bench: Relink
>> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with `/lib64/libm.so.6'
>> for IFUNC symbol `modff'
>>
>>
>> ===================================================================================
>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> =   RANK 0 PID 183831 RUNNING AT planck
>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>
>> ===================================================================================
>> FAILED mpirun -np 1 /opt/fftw-3.3.10/mpi/mpi-bench:
>>
>>
>> --
>> Dr. Michael Fechtelkord
>>
>> Institut für Geowissenschaften
>> Ruhr-Universität Bochum
>> Universitätsstr. 150
>> <https://www.google.com/maps/search/Universit%C3%A4tsstr.+150?entry=gmail&source=g>
>> D-44780 Bochum
>>
>> Phone: +49 (234) 32-24380
>> Fax:  +49 (234) 32-04380
>> Email:Michael.Fechtelkord at ruhr-uni-bochum.de
>> Web Page:
>> https://www.ruhr-uni-bochum.de/kristallographie/kc/mitarbeiter/fechtelkord/
>>
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the MAILING-LIST at:
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>
> --
> Dr. Michael Fechtelkord
>
> Institut für Geowissenschaften
> Ruhr-Universität Bochum
> Universitätsstr. 150
> D-44780 Bochum
>
> Phone: +49 (234) 32-24380
> Fax:  +49 (234) 32-04380
> Email: Michael.Fechtelkord at ruhr-uni-bochum.de
> Web Page: https://www.ruhr-uni-bochum.de/kristallographie/kc/mitarbeiter/fechtelkord/
>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>

-- 
Emeritus Professor Laurence Marks (Laurie)
Northwestern University
Webpage <http://www.numis.northwestern.edu> and Google Scholar link
<http://scholar.google.com/citations?user=zmHhI9gAAAAJ&hl=en>
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20250829/52c93bd8/attachment.htm>