[Pw_forum] Error in thermo_pw.x run
Andrea Dal Corso
dalcorso at sissa.it
Thu Dec 10 14:18:32 CET 2015
These questions should be asked on the thermo_pw-forum mailing list.
There the question has been answered and the error has been corrected in
the cvs version:
Please see commit 21109 and make the same change in your source.
HTH,
Andrea
On Thu, 2015-12-10 at 17:11 +0530, Bramha Pandey wrote:
> Dear Barnali and Dear All Developers and Users,
> I am also getting the same error when running it on single machine with
> mpirun.
> Kindly anybody, help in this regards. I am trying to run example01 and
> errors are:::
>
> bpp at bpp:~/espresso-5.2.1/thermo_pw/examples/example01$ ./run_example
>
> /home/bpp/espresso-5.2.1/thermo_pw/examples/example01 : starting
>
> This example shows how to use thermo_pw.x to make a self-consistent
> calculation of Silicon.
>
> executables directory: /home/bpp/espresso-5.2.1/bin
> pseudo directory: /home/bpp/espresso-5.2.1/pseudo
> temporary directory: /home/bpp/espresso-5.2.1/tempdir
> checking that needed directories and files exist... done
>
> running thermo_pw.x as: mpirun -np 4
> /home/bpp/espresso-5.2.1/bin/thermo_pw.x -ni 2
>
> cleaning /home/bpp/espresso-5.2.1/tempdir... done
> running the scf calculation for Si...
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0 0xB736E133
> #1 0xB736E7D0
> #2 0xB76FC403
> 0xB73B4133
> #1 0xB73B47D0
> #2 0xB7742403
> #3 0x8057E2F in clean_ngeo_ at initialize_thermo_work.f90:338
> #4 0x8099B08 in thermo_readin_ at thermo_readin.f90:569
> #5 #3 0x804DF7B in thermo_pw at thermo_pw.f90:140
> 0x8057E2F in clean_ngeo_ at initialize_thermo_work.f90:338
> #4 0x8099B08 in thermo_readin_ at thermo_readin.f90:569
> #5 0x804DF7B in thermo_pw at thermo_pw.f90:140
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> 0xB73A4133
> #1 0xB73A47D0
> #2 0xB7732403
> #0 0xB7351133
> #1 0xB73517D0
> #2 0xB76DF403
> #3 0x8057E2F in clean_ngeo_ at initialize_thermo_work.f90:338
> #4 #3 0x8099B08 in thermo_readin_ at thermo_readin.f90:569
> #5 0x804DF7B in thermo_pw at thermo_pw.f90:140
> 0x8057E2F in clean_ngeo_ at initialize_thermo_work.f90:338
> #4 0x8099B08 in thermo_readin_ at thermo_readin.f90:569
> #5 0x804DF7B in thermo_pw at thermo_pw.f90:140
> Error condition encountered during test: exit status = 139
> Aborting
> You kind help will highly appreciated.
>
> --
> Regards
> Dr. Bramha P Pandey
> Asstt. Prof. ECE Deptt.
> GLA University, Mathura (U.P)
> India-281406.
>
> On Wed, Dec 9, 2015 at 6:20 PM, Barnali Bhattacharya <
> barnalidgbhatt at gmail.com> wrote:
>
> > Dear Sir/Madam,
> >
> > I am a user of Quantum espresso. I am interested in elastic constant and
> > install thermo_pw.0.3.0 in the quantum espresso (QE 5.2.1) root
> > directory. I have followed the flowing steps-
> >
> > cd espresso-5.2.1
> > ./configure --enable-openmp
> > cd thermo_pw
> > make join_qe
> > cd ../
> > make all
> >
> > Without showing any error thermo_pw.x has been built, but when I am trying
> > to run example(example13) , I get the following error-
> >
> > ............................................................................................................................
> > running thermo_pw.x as: mpirun -np 4
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x
> > -ni 2 -nk 1 -nd 1 -nb 1 -nt 1
> >
> > cleaning
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/tempdir... done
> > running the thermo mur_lc_elastic_constants calculation
> > to calculate the elastic constants of silicon at the
> > equilibrium lattice constant. The results are in si.elastic.out...
> > [cluster:05522] *** Process received signal ***
> > [cluster:05522] Signal: Segmentation fault (11)
> > [cluster:05522] Signal code: Address not mapped (1)
> > [cluster:05522] Failing at address: 0xffffffff
> > [cluster:05521] *** Process received signal ***
> > [cluster:05521] Signal: Segmentation fault (11)
> > [cluster:05521] Signal code: Address not mapped (1)
> > [cluster:05521] Failing at address: 0xffffffff
> > [cluster:05522] [ 0] /lib64/libpthread.so.0() [0x392240f500]
> > [cluster:05522] [ 1]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(clean_ngeo_+0x24)
> > [0x459fe4]
> > [cluster:05522] [ 2]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(thermo_readin_+0x296a)
> > [0x4aa88a]
> > [cluster:05522] [ 3]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(MAIN__+0x65)
> > [0x44f145]
> > [cluster:05522] [ 4]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(main+0x2a)
> > [0xb742aa]
> > [cluster:05522] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd)
> > [0x392181ecdd]
> > [cluster:05522] [ 6]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x()
> > [0x44f019]
> > [cluster:05522] *** End of error message ***
> > [cluster:05521] [ 0] /lib64/libpthread.so.0() [0x392240f500]
> > [cluster:05521] [ 1]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(clean_ngeo_+0x24)
> > [0x459fe4]
> > [cluster:05521] [ 2]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(thermo_readin_+0x296a)
> > [0x4aa88a]
> > [cluster:05521] [ 3]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(MAIN__+0x65)
> > [0x44f145]
> > [cluster:05521] [ 4]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(main+0x2a)
> > [0xb742aa]
> > [cluster:05521] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd)
> > [0x392181ecdd]
> > [cluster:05521] [ 6]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x()
> > [0x44f019]
> > [cluster:05521] *** End of error message ***
> > [cluster:05524] *** Process received signal ***
> > [cluster:05524] Signal: Segmentation fault (11)
> > [cluster:05524] Signal code: Address not mapped (1)
> > [cluster:05524] Failing at address: 0xffffffff
> > [cluster:05523] *** Process received signal ***
> > [cluster:05523] Signal: Segmentation fault (11)
> > [cluster:05523] Signal code: Address not mapped (1)
> > [cluster:05523] Failing at address: 0xffffffff
> > [cluster:05524] [ 0] /lib64/libpthread.so.0() [0x392240f500]
> > [cluster:05524] [ 1]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(clean_ngeo_+0x24)
> > [0x459fe4]
> > [cluster:05524] [ 2]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(thermo_readin_+0x296a)
> > [0x4aa88a]
> > [cluster:05524] [ 3]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(MAIN__+0x65)
> > [0x44f145]
> > [cluster:05524] [ 4]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(main+0x2a)
> > [0xb742aa]
> > [cluster:05524] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd)
> > [0x392181ecdd]
> > [cluster:05524] [ 6]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x()
> > [0x44f019]
> > [cluster:05524] *** End of error message ***
> > [cluster:05523] [ 0] /lib64/libpthread.so.0() [0x392240f500]
> > [cluster:05523] [ 1]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(clean_ngeo_+0x24)
> > [0x459fe4]
> > [cluster:05523] [ 2]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(thermo_readin_+0x296a)
> > [0x4aa88a]
> > [cluster:05523] [ 3]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(MAIN__+0x65)
> > [0x44f145]
> > [cluster:05523] [ 4]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(main+0x2a)
> > [0xb742aa]
> > [cluster:05523] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd)
> > [0x392181ecdd]
> > [cluster:05523] [ 6]
> > /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x()
> > [0x44f019]
> > [cluster:05523] *** End of error message ***
> >
> > mpirun noticed that process rank 0 with PID 5521 on node cluster.hpc.org
> > exited on signal 11 (Segmentation fault).
> >
> > Error condition encountered during test: exit status = 139
> > Aborting
> > [Utpal at cluster example13]$
> >
> > ............................................................................................................................................
> > I have checked that the libpthread.so.0 and libc.so.6 file are not in the
> > lib64 directory, it is in the lib directory. I have checked the Makefile
> > of thermo_pw/src and make.sys of espresso-5.2.1. But could not understand
> > where can I define this path?
> > Could anyone please help me to solve this problem? Any sort of help will
> > be thankfully acknowledged.
> >
> > Thanking you.
> >
> > Sincerely
> > Barnali Bhattacharya
> > Ph.D student, Department of physics,
> > Assam university
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
> _______________________________________________
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--
Andrea Dal Corso Tel. 0039-040-3787428
SISSA, Via Bonomea 265 Fax. 0039-040-3787249
I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it
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