[aspect-devel] aspect testing

E.M. Dragowsky dragowsky at case.edu
Mon Apr 30 13:04:27 PDT 2018 

Perhaps this will nonetheless be illuminating....

[mrd20 at comp163t solcx]$ gdb --args ./aspect solcx.prm
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-100.el7
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html
>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/mrd20/src/rider/aspect-1.5.0/aspect...done.
(gdb) run
Starting program:
/home/mrd20/src/rider/aspect-1.5.0/benchmark/solcx/./aspect solcx.prm
warning: Unable to open "librpm.so.3"
(/usr/local/base/8.0/lib/liblzma.so.5: version `XZ_5.1.2alpha' not found
(required by /usr/lib64/librpmio.so.3)), missing debuginfos notifications
will not be displayed
Missing separate debuginfo for /lib64/ld-linux-x86-64.so.2
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/a9/980cf253c79740e69f70dcb8fea7b8c2f641b5.debug
Missing separate debuginfo for /usr/lib64/libdl.so.2
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/ef/023e0c16991e8957337c90b0e51025fe27c897.debug
Missing separate debuginfo for /usr/lib64/librt.so.1
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/76/c4765826961c60be913f5549ebbc7bbe506899.debug
Missing separate debuginfo for /usr/lib64/libpthread.so.0
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/60/91139b61d901aa8425dbc16b7f51d455a416b4.debug
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/usr/lib64/libthread_db.so.1".
warning: File "/usr/local/gcc/6.3.0/lib64/libstdc++.so.6.0.22-gdb.py"
auto-loading has been declined by your `auto-load safe-path' set to
"$debugdir:$datadir/auto-load:/usr/bin/mono-gdb.py".
To enable execution of this file add
    add-auto-load-safe-path /usr/local/gcc/6.3.0/lib64/libstdc++.
so.6.0.22-gdb.py
line to your configuration file "/home/mrd20/.gdbinit".
To completely disable this security protection add
    set auto-load safe-path /
line to your configuration file "/home/mrd20/.gdbinit".
For more information about this security protection see the
"Auto-loading safe path" section in the GDB manual.  E.g., run from the
shell:
    info "(gdb)Auto-loading safe path"
Missing separate debuginfo for /usr/lib64/libm.so.6
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/6a/344a5ce77a247399aa2f22f92c698f574a7134.debug
Missing separate debuginfo for /usr/lib64/libc.so.6
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/ff/1d2de4cf353118960c5ea195ceb13699929c14.debug
Missing separate debuginfo for /usr/lib64/libmunge.so.2
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/46/f20738e09fba786a7456b579983aedd7aca2e5.debug
Missing separate debuginfo for /usr/lib64/libutil.so.1
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/b8/082f4480af5af680a0ad0ab4818cae1c077a0b.debug
Missing separate debuginfo for /usr/lib64/libhwloc.so.5
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/4a/3072d5354d22f00277ea1a80a7b654206a3f12.debug
Missing separate debuginfo for /usr/lib64/liblua-5.1.so
Try: yum --enablerepo='*debug*' install
/usr/lib/debug/.build-id/47/3f207910c926f2d177400f81a51cd5aae02173.debug
Detaching after fork from child process 17833.
[New Thread 0x7fffddc27700 (LWP 17838)]
[New Thread 0x7fffdd426700 (LWP 17839)]
-----------------------------------------------------------------------------
-- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion.
--     . version 1.5.0
--     . running in DEBUG mode
--     . running with 1 MPI process
--     . using Trilinos
-----------------------------------------------------------------------------

Loading shared library <./libsolcx.so>

Number of active cells: 256 (on 5 levels)
Number of degrees of freedom: 3,556 (2,178+289+1,089)

*** Timestep 0:  t=0 years
   Rebuilding Stokes preconditioner...
   Solving Stokes system... 30+4 iterations.
      Relative Stokes residual after nonlinear iteration 1: 1
   Solving Stokes system... 0+0 iterations.
      Relative Stokes residual after nonlinear iteration 2: 1.74731e-08

   Postprocessing:
     Errors u_L1, p_L1, u_L2, p_L2: 1.125998e-06, 2.994139e-03,
1.670011e-06, 9.778440e-03
     Writing graphical output:      output/solution/solution-00000

[New Thread 0x7fffdcaac700 (LWP 17840)]
Termination requested by criterion: end time


+---------------------------------------------+------------+------------+
| Total wallclock time elapsed since start    |      0.59s |            |
|                                             |            |            |
| Section                         | no. calls |  wall time | % of total |
+---------------------------------+-----------+------------+------------+
| Assemble Stokes system          |         2 |    0.0569s |       9.6% |
| Build Stokes preconditioner     |         1 |     0.045s |       7.6% |
| Solve Stokes system             |         2 |    0.0705s |        12% |
| Initialization                  |         1 |     0.106s |        18% |
| Postprocessing                  |         1 |     0.244s |        41% |
| Setup dof systems               |         1 |    0.0415s |         7% |
| Setup initial conditions        |         1 |   0.00778s |       1.3% |
+---------------------------------+-----------+------------+------------+

[Thread 0x7fffdcaac700 (LWP 17840) exited]
[Thread 0x7fffdd426700 (LWP 17839) exited]
[Thread 0x7fffddc27700 (LWP 17838) exited]
[Inferior 1 (process 17826) exited normally]


On Mon, Apr 30, 2018 at 4:03 PM, E.M. Dragowsky <dragowsky at case.edu> wrote:

> I am compiling to my user directory, and have set the install location to
> reflect that.
> Having said that, nothing is written to that location. The executable
> remains in the source/build directory (in-source build). The executable
> seems to be the only file built. I've not yet copied it to the "install
> location", as the testing does not seem to require the executable be
> anywhere other than the source/build directory.
>
> And the current situation with aspect-1.5.0 release as well as the latest
> development build is that these installs allow for building and running
> benchmark code. So the problem of aspect hanging has been overcome.
>
>
>
> On Mon, Apr 30, 2018 at 2:56 PM, Timo Heister <heister at clemson.edu> wrote:
>
>> > For example, does “./aspect tests/quick_mpi.prm” run the quick_mpi test
>> > without issue?
>>
>> This won't work, because this test needs a shared lib to be compiled.
>>
>> One other idea is the following: are you by any chance running on some
>> weird network file system that might not behave as expected? Is there
>> a different (local?) filesystem you can use?
>>
>> If not, you can try to find out why aspect is hanging by running it under
>> gdb:
>> gdb --args ./aspect some_prm.prm
>> then within gdb:
>> run
>> ctrl+c
>> backtrace
>>
>> and post the result.
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>>
>
>
>
> --
> E.M. Dragowsky, Ph.D.
> Research Computing -- UTech
> Case Western Reserve University
> (216) 368-0082
>



-- 
E.M. Dragowsky, Ph.D.
Research Computing -- UTech
Case Western Reserve University
(216) 368-0082
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