[QE-users] "Segmentation fault" error in versions 7.2 and 7.1 of QE
Paolo Giannozzi
paolo.giannozzi at uniud.it
Sun May 21 22:58:03 CEST 2023
0. Don't mess up with versions, use the latest.
1. Once you have set LAPACK_EXTERNAL or whatever is needed, "make" will
compile blas and lapack
2. Compiling with debug is often the first thing to do, not the latest
3. All failing tests have something in common: try to figure out what
Paolo
On 21/05/2023 09:43, Niccolò Damian wrote:
>
> Dear Professor Giannozzi and dear Experts,
> Thank You for Your kind reply.
> I tried what you suggested at point 1. and tried then "make run-tests"
> in the directory "test-suite", but I still got the "Segmentation fault"
> error messages as before and again 157 tests out 234 passed (I'm working
> for the time being with the 7.1 version since I made "veryclean" for the
> 7.2 version).
>
> As for point 2., in the path "$(TOPDIR)/external/lapack/" I have neither
> libblas.a nor liblapack.a (in the 7.1 version I have only two files
> .yml: .appveyor.yml and .travis.yml; in the 7.2 version I have instead
> the directories and files showed in this snapshot
> https://drive.google.com/file/d/1W1o0iC67fUTLtQiEo3AZINpPcKStDeOe/view?usp=share_link <https://drive.google.com/file/d/1W1o0iC67fUTLtQiEo3AZINpPcKStDeOe/view?usp=share_link> ) and I did not modified such directory for both versions. What should I do?
> As for blas I'm using the newest version of libblas3 (3.9.0-1build1),
> while for lapack I'm using the newest version of liblapack-dev
> (3.9.0-1build1): is the problem (as I guess) related to them?
> Are they not suitable? Should I autoremove and reinstall other versions
> or types?
>
> I will proceed as You kindly suggested in point 3. once this problem has
> been solved.
>
>
> A side question: since now I'm trying to find from where the error
> arises with these two versions in my PC, can I work at the same time
> with both the two versions 7.1 and 7.2 configured and "made all" in two
> different directories (at the same level) or should I (as I am doing
> now) work with only one configured and "made all" (with the other one
> "made veryclean") at a time?
>
> Thank You again in advance.
>
> Best regards,
> Niccolò Damian
> Physics Master student at University of Padua
>
> Il giorno sab 20 mag 2023 alle ore 21:56 Paolo Giannozzi
> <paolo.giannozzi at uniud.it <mailto:paolo.giannozzi at uniud.it>> ha scritto:
>
> 0. I use since several years the Windows Subsystem for Linux as my main
> develop platform, so it works, no doubts.
>
> 1. Please verify whether this explains your problem:
> https://gitlab.com/QEF/q-e/-/wikis/Support/Segfault-with-gfortran-and-WSL <https://gitlab.com/QEF/q-e/-/wikis/Support/Segfault-with-gfortran-and-WSL>
>
> 2. "configure" no longer recognizes options "--with-internal-blas" and
> "--with-internal-lapack". If you want to try whether the problem arises
> from pre-(badly-)compiled blas and lapack, edit make.inc as follows:
> BLAS_LIBS = $(TOPDIR)/external/lapack/libblas.a
> LAPACK = liblapack
> LAPACK_LIBS = $(TOPDIR)/external/lapack/liblapack.a
>
> 3. You may also try "./configure --enable-debug". It should at least
> say
> something more about the place where the code crashes.
>
> Paolo
>
>
> On 20/05/2023 13:23, Niccolò Damian wrote:
> >
> > You don't often get email from niccolo.damian at studenti.unipd.it
> <mailto:niccolo.damian at studenti.unipd.it>. Learn
> > why this is important
> <https://aka.ms/LearnAboutSenderIdentification
> <https://aka.ms/LearnAboutSenderIdentification>>
> >
> >
> > Dear Experts,
> > In the previous days I have tried to install Quantum espresso
> version
> > 7.2 in Ubuntu 20.04.6 LTS app in my Windows PC (I have Windows 10)
> > through Windows Subsystem for Linux.
> > There I have the version 9.4.0 of gfortran.
> >
> > I have followed the instructions and, when I tried to check
> whether the
> > installation was successful or not (no error messages were printed
> > before), only two thirds of the tests passed, and those that
> failed were
> > regarding (more than half of) the "pw" directories. The errors
> where all
> > of the following form:
> >
> >
> /home/nick/Quantum_espresso/qe-7.2/test-suite/..//test-suite/run-pw.sh:
> > line 52: 4169 Segmentation fault (core dumped) ${PARA_PREFIX}
> > ${ESPRESSO_ROOT}/bin/pw.x ${PARA_SUFFIX} -input $1 > $2 2> $3
> > pw_dipole - 2dcutoff.in
> <http://2dcutoff.in/>
> > <http://2dcutoff.in/
> <http://2dcutoff.in/>>: **FAILED**.
> > Different sets of data extracted from benchmark and test.
> > Data only in benchmark: n1, ef1, p1, band, f1, e1.
> >
> > In the attachment you can find the run-pw.sh file, which to me
> doesn't
> > have any problem at line 52.
> > I followed then what suggested in the User Guide, recompiling with
> >
> > ./configure --with-internal-blas --with-internal-lapack
> >
> > but the result didn't change.
> > I then did "make veryclean" and tried to compile and install in
> another
> > directory (parallel to the previous one) the version 7.1, using the
> > ./configure with the two options above, succeeding in the end
> even if I
> > don't know if those options worked, since there was the message
> > "configure: WARNING: unrecognized options: --with-internal-blas,
> > --with-internal-lapack".
> > Anyway again, when running the tests the result was the same above.
> > I tried also to run single examples but the message on terminal
> was (for
> > both versions):
> >
> > Program received signal SIGSEGV: Segmentation fault - invalid memory
> > reference.
> >
> > Backtrace for this error:
> > #0 0x7f6c32090d21 in ???
> > #1 0x7f6c3208fef5 in ???
> > #2 0x7f6c31ce308f in ???
> > #3 0x7fffdae329fc in ???
> > Segmentation fault (core dumped)
> >
> > that is also what I get in the output files of the tests (except
> for the
> > last line). The output files of the examples instead did not clarify
> > what the problem is, since they stopped with no useful information.
> >
> > I have already checked what advised here
> >
> https://gitlab.com/QEF/q-e/-/wikis/Support/Problem-downloading-pseudopotential-files <https://gitlab.com/QEF/q-e/-/wikis/Support/Problem-downloading-pseudopotential-files> <https://gitlab.com/QEF/q-e/-/wikis/Support/Problem-downloading-pseudopotential-files <https://gitlab.com/QEF/q-e/-/wikis/Support/Problem-downloading-pseudopotential-files>>
> > and the URLs are correct.
> > I have also tried to look for a solution on the internet, but I
> did not
> > manage to solve the problem.
> >
> > I kindly ask for Your help, since I do not know what to do anymore.
> >
> > Thank You in advance,
> > Niccolò Damian
> > Physics Master student at University of Padua
> >
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> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
>
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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