[Pw_forum] Error in thermo_pw.x run
Bramha Pandey
pandey.bramha at gmail.com
Thu Dec 10 14:22:45 CET 2015
Thanks alot Dear Andrea Sir for your prompt response.
And sorry for wrong forum posting...
Will see ..
--
Regards
Dr. Bramha P Pandey
Asstt. Prof. ECE Deptt.
GLA University, Mathura (U.P)
India-281406.
On Thu, Dec 10, 2015 at 6:48 PM, Andrea Dal Corso <dalcorso at sissa.it> wrote:
> 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
> > >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> 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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>
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