[Wien] NMR Integration crashes when using nmr_integ:localhost:4 in .machines Link error
Laurence Marks
laurence.marks at gmail.com
Fri Aug 29 15:18:25 CEST 2025
Find it elsewhere...
---
Emeritus Professor Laurence Marks (Laurie)
www.numis.northwestern.edu
https://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
On Fri, Aug 29, 2025, 08:12 Michael Fechtelkord via Wien <
wien at zeus.theochem.tuwien.ac.at> wrote:
> Thanks again Laurence!
>
>
> icc is already deprecated in my ifort package.
>
> Intel Server denies access to download the packages.
>
> - wget -c https://registrationcenter-download.intel.com/akdlm/irc_nas/17427/l_HPCKit_p_2021.1.0.2684_offline.sh
>
> Error 403 Forbidden
>
>
> Best regards,
>
> Michael
>
>
> Am 29.08.2025 um 14:54 schrieb Laurence Marks:
>
> 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 BochumUniversitätsstr. 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
>>
>
>
> --
> 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
>
> _______________________________________________
> Wien mailing listWien at zeus.theochem.tuwien.ac.athttp://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 BochumUniversitätsstr. 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
>
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