[Wien] NMR Integration crashes when using nmr_integ:localhost:4 in .machines Link error
Michael Fechtelkord
Michael.Fechtelkord at ruhr-uni-bochum.de
Mon Sep 1 15:26:09 CEST 2025
Hello Gavin,
thanks for your comprehensive report on this issue. I was using Open
Suse LEAP 15.6 before which uses an older kernel and also older
libraries. Tumbleweed uses the most recent developments and thus things
like this can happen. I have good experiences with Tumbleweed, cause it
supports the newest hardware. I am still using the latest ifort version
because it produces nearly no SIGSEV errors with WIEN2k compared to the
newest ifx version.
I think maybe the easiest is to switch mpi to mpiich (which updated
quite often) for WIEN2k and ELPA or use the workaround, I described.
Anyway, thanks for your advise again!
Best regards,
Michael
Am 01.09.2025 um 13:23 schrieb Gavin Abo:
> At [1], the current latest version of oneAPI is 2025.2. There it has
> under supported Linux distributions "SuSE LINUX Enterprise Server* 15
> SP4, SP5, SP6". Those look like they might be more aligned with the
> openSUSE Leap 15.x versions seen in the list at [2]. The openSUSE
> Tumbleweed looks like it's a rolling release that might always be
> ahead of what Intel is developing the oneAPI with. If that is the
> case, incompatibility risks are probably going to be higher using
> Tumbleweed than one of the distributions in Intel's oneAPI supported
> list.
>
> The error message has:
>
> `/lib64/libm.so.6' for IFUNC symbol `modff'
>
> The modff is a function in the libm library [3] that looks to be a
> part of the identified GLIBC. I see that you mentioned downgrading
> the GLIBC (which could need using an older OpenSUSE Leap version) is
> not a solution for you.
>
> A few other ideas below that you may or may not want to consider.
>
> Intel has a libimf Compiler Math Library [4] that seems to contain a
> modff function [5]. So, static linking to the libimf.a might be a
> possibility. There is a post about a RELINK error that might be of
> interest at [6].
>
> IFUNC in the above message is likely a GNU indirect function that
> resolves a function implementation picked by a resolver at runtime
> where glibc uses this to provide multiple implementations optimized
> for different architecture levels [7]. I don't recall what
> architecture was targeted for your compile, but say it was AVX and the
> new glibc has an issue with it. Maybe falling back to an architecture
> (see [8]) were optimization isn't as good if the processor your using
> also supports it, say SSE3, might be something to try.
>
> If the Intel MPI source code for libmpi.so.12 has to be compiled with
> the GLIBC 2.42 by Intel in a future release to fix the issue, an
> alternate solution might be to use a different Message Passing
> Interface (MPI) such as MPICH or OpenMPI [9].
>
> [1]
> https://www.intel.com/content/www/us/en/developer/articles/system-requirements/oneapi-base-toolkit/2025.html
> [2] https://en.wikipedia.org/wiki/OpenSUSE#Version_history
> [3] https://sourceware.org/newlib/libm.html#modf
> [4]
> https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/developer-guide-reference/2025-2/compiler-math-library.html
> [5]
> https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/developer-guide-reference/2025-2/nearest-integer-functions.html
> [6]
> https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/Trouble-linking-libimf-a-on-Linux/td-p/1342415
> [7] https://maskray.me/blog/2021-01-18-gnu-indirect-function
> [8]
> https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/developer-guide-reference/2025-2/arch.html
> [9] https://en.wikipedia.org/wiki/MPICH#MPICH_derivatives
>
> Kind Regards,
>
> Gavin
> WIEN2k user
>
> On 9/1/2025 1:30 AM, Michael Fechtelkord via Wien wrote:
>> Hello all,
>>
>>
>> thanks again for all your advise. I now used ifort 2021.1.1 and icc
>> 2021.4.0 for compilation (with flag -no-gcc) but the SIGSEV is still
>> there. As you can see it is a C-Library related communication error
>>
>> The new GLIBC 2.42 core library does not work together correctly with
>> Intels mpi (all versions, see error reports below). It will be
>> difficult to solve that problem, a downgrade of a Core library is not
>> recommendable, so I use as a work around the sequential integration
>> on one core. The integration step does not really take long and the
>> parallel calculation of the electron current is still working.
>>
>> I am sure that problem will arise soon for most who use mpirun and
>> have GLIBC 2.42 in their LINUX operating system.
>>
>> 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/2021.1.1//lib/release/libmpi.so.12' with
>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>> /usr/local/WIEN2k/nmr_mpi: Relink
>> `/opt/intel/oneapi/mpi/2021.1.1//lib/release/libmpi.so.12' with
>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>> /usr/local/WIEN2k/nmr_mpi: Relink
>> `/opt/intel/oneapi/mpi/2021.1.1//lib/release/libmpi.so.12' with
>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>> /usr/local/WIEN2k/nmr_mpi: Relink
>> `/opt/intel/oneapi/mpi/2021.1.1//lib/release/libmpi.so.12' with
>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>
>> ===================================================================================
>>
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = RANK 0 PID 391888 RUNNING AT localhost
>> = KILLED BY SIGNAL: 11 (Segmentation fault)
>> ===================================================================================
>>
>>
>> ===================================================================================
>>
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = RANK 1 PID 391889 RUNNING AT localhost
>> = KILLED BY SIGNAL: 11 (Segmentation fault)
>> ===================================================================================
>>
>>
>> ===================================================================================
>>
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = RANK 2 PID 391890 RUNNING AT localhost
>> = KILLED BY SIGNAL: 11 (Segmentation fault)
>> ===================================================================================
>>
>>
>> ===================================================================================
>>
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = RANK 3 PID 391891 RUNNING AT localhost
>> = KILLED BY SIGNAL: 11 (Segmentation fault)
>> ===================================================================================
>>
>>
>> stop
>>
>> /opt/fftw-3.3.10/mpi/.libs/mpi-bench: Relink
>> `/opt/intel/oneapi/mpi/2021.1.1//lib/release/libmpi.so.12' with
>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>
>> ===================================================================================
>>
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = RANK 0 PID 66889 RUNNING AT Marlowe
>> = KILLED BY SIGNAL: 11 (Segmentation fault)
>> ===================================================================================
>>
>> FAILED mpirun -np 1 /opt/fftw-3.3.10/mpi/mpi-bench:
>>
>>
>> Am 30.08.2025 um 10:15 schrieb Michael Fechtelkord via Wien:
>>> Hello Peter,
>>>
>>>
>>> lapw0 crashes with the same error:
>>>
>>> /usr/local/WIEN2k/lapw0_mpi: Relink
>>> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with
>>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>> /usr/local/WIEN2k/lapw0_mpi: Relink
>>> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with
>>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>> /usr/local/WIEN2k/lapw0_mpi: Relink
>>> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with
>>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>> /usr/local/WIEN2k/lapw0_mpi: Relink
>>> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with
>>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>> [1] Exitcode 255 mpirun -np 4 -machinefile
>>> .machine0 /usr/local/WIEN2k/lapw0_mpi lapw0.def >> .time00
>>>
>>> OMP_NUM_THREADS=1 does not change anything.
>>>
>>>
>>> I will try the 2021.1.0 version of oneapi soon and get back with the
>>> results soon.
>>>
>>>
>>> Best regards,
>>>
>>> Michael
>>>
>>>
>>> Am 29.08.2025 um 16:10 schrieb Peter Blaha:
>>>> Just for some more info:
>>>>
>>>> Does this crash also occur in an mpirun of lapw0 ?? (would point
>>>> to fftw)
>>>>
>>>> What is your OMP_NUM_THREADS variable ? Set it to one (also in
>>>> .bashrc).
>>>>
>>>>
>>>>
>>>> Am 29.08.2025 um 12:54 schrieb Michael Fechtelkord via Wien:
>>>>> 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:
>>>>>
>>>>>
>>>>
> _______________________________________________
> 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/
More information about the Wien
mailing list