[gpaw-users] general comment on memory leaks.

[abhishek khetan]

Attached are the files. The cif file is actually a gpaw converged output
that i extracted using ase and then changed one atom in it. It is quite
huge in size though.

Maybe such errors are related to my installation, although I cannot find it
in any way.

Thanks and Best,


On Thu, Jan 14, 2016 at 5:47 PM, Ask Hjorth Larsen <asklarsen at gmail.com>
wrote:

> Please attach both input script and text output.
>
> Best regards
> Ask
>
> 2016-01-14 17:38 GMT+01:00 abhishek khetan <askhetan at gmail.com>:
> > Dear gpaw developers,
> >
> > i have found that in general for large systems (> 150 atoms) or systems
> with
> > memory intensive methods like the GW, there are always segfault errors
> of a
> > similar kind. I have a scalapack compiled working version of gpaw-0.12
> which
> > passes all tests in the suite. For a system, small in size, the various
> > methods in gpaw run properly but for bigger systems of the desired sizes
> of
> > the same kind, gpaw fails with the exact same kind of error.
> >
> > gpaw-python:18622 terminated with signal 11 at PC=3d8d6acba8
> > SP=7ffe9b9d47b0.  Backtrace:
> >
> > I have posted about this in the context of GW method on the gpaw forums a
> > couple of dozen times before, but i haven't seen anyone else report
> similar
> > errors. Now I am encountering the same unsolved errors in even simple
> > relaxation problems where the unit cell happens to be quite large. For
> > slightly smaller cases where the systems do converge, i see that the
> memory
> > reuirements are actually very modest (1-2) gigs per core for 60 cores.
> >
> > Any ideas/ methods/ procedures that i can resolve this error as a user ?
> Am
> > I allowed to make a ticket on this or request for a ticket on this on the
> > TRAC ?
> >
> > Thanks and Best,
> >
> > askhetan
> >
> > _______________________________________________
> > gpaw-users mailing list
> > gpaw-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>



-- 
|| radhe radhe ||

abhishek
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An MPI process has executed an operation involving a call to the
"fork()" system call to create a child process.  Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your MPI job may hang, crash, or produce silent
data corruption.  The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.  

The process that invoked fork was:

  Local host:          linuxitvc17.rz.RWTH-Aachen.DE (PID 17579)
  MPI_COMM_WORLD rank: 1

If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------

gpaw-python:17643 terminated with signal 11 at PC=35bccacba8 SP=7ffccc34fd10.  Backtrace:
/lib64/libc.so.6(__libc_fork+0x138)[0x35bccacba8]
/lib64/libc.so.6(_IO_proc_open+0x137)[0x35bcc685f7]
/lib64/libc.so.6(popen+0x69)[0x35bcc688e9]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python[0x6816da]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5a33)[0
x644943]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5ee0)[0
x644df0]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5ee0)[0
x644df0]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCode+0x32)[0x6465
72]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyRun_FileExFlags+0xb0)[0x66
6020]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyRun_SimpleFileExFlags+0xef
)[0x6661ff]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(Py_Main+0xc74)[0x67ad14]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(main+0x65)[0x421581]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x35bcc1ed5d]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python[0x420f29]

gpaw-python:17654 terminated with signal 11 at PC=35bccacba8 SP=7ffc9e36c3c0.  Backtrace:
/lib64/libc.so.6(__libc_fork+0x138)[0x35bccacba8]
/lib64/libc.so.6(_IO_proc_open+0x137)[0x35bcc685f7]
/lib64/libc.so.6(popen+0x69)[0x35bcc688e9]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python[0x6816da]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5a33)[0
x644943]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5ee0)[0
x644df0]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5ee0)[0
x644df0]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalFrameEx+0x5b8a)[0
x644a9a]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCodeEx+0x88e)[0x6
4645e]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyEval_EvalCode+0x32)[0x6465
72]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyRun_FileExFlags+0xb0)[0x66
6020]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(PyRun_SimpleFileExFlags+0xef
)[0x6661ff]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(Py_Main+0xc74)[0x67ad14]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python(main+0x65)[0x421581]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x35bcc1ed5d]
/home/ak498084/Utility/GPAW/gpaw_devel/gpaw-0.12/build/bin.linux-x86_64-2.7/gpaw-python[0x420f29]
[linuxitvc17.rz.RWTH-Aachen.DE:17576] 83 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-
fork
[linuxitvc17.rz.RWTH-Aachen.DE:17576] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error mess
ages
/home/ak498084/.lsbatch/1452789113.25619746: line 138: 17183 Killed                  /opt/lsf/9.1/linux2.6-glibc2.3-
x86_64/etc/envclean.pl /opt/lsf/9.1/linux2.6-glibc2.3-x86_64/etc/qcommonjobstarter.sh "$LSB_JOBFILENAME.shell"
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