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<div class="moz-cite-prefix">On 15-04-25 11:55 AM, Barry Smith
wrote:<br>
</div>
<blockquote
cite="mid:8E11BAE6-7DB2-43C6-AF40-21E6B2B49124@mcs.anl.gov"
type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">On Apr 25, 2015, at 1:51 PM, Danyang Su <a class="moz-txt-link-rfc2396E" href="mailto:danyang.su@gmail.com"><danyang.su@gmail.com></a> wrote:
On 15-04-25 11:32 AM, Barry Smith wrote:
</pre>
<blockquote type="cite">
<pre wrap=""> I told you this yesterday.
It is probably stopping here on a harmless underflow. You need to edit the PETSc code to not worry about underflow.
Edit the file /home/dsu/Soft/PETSc/petsc-3.5.2/src/sys/error/fp.c and locate
#elif defined PETSC_HAVE_XMMINTRIN_H
_MM_SET_EXCEPTION_MASK(_MM_MASK_INEXACT);
#else
change it to
#elif defined PETSC_HAVE_XMMINTRIN_H
_MM_SET_EXCEPTION_MASK(_MM_MASK_INEXACT | _MM_MASK_UNDERFLOW);
#else
Then run make gnumake in the PETSc directory to compile the new version. Now link and run the program again with -fp_trap and see where it gets stuck this time.
Did you do this?
Barry
</pre>
</blockquote>
<pre wrap="">Yes, I did change the code in fp.c and run 'make gnumake' in the PETSc directory. I just did a double check and ran make gnumake again and got the following information this time.
<a class="moz-txt-link-abbreviated" href="mailto:dsu@nwmop:~/Soft/PETSc/petsc-3.5.2$">dsu@nwmop:~/Soft/PETSc/petsc-3.5.2$</a> make gnumake
Building PETSc using GNU Make with 10 build threads
==========================================
make[1]: Entering directory `/home/dsu/Soft/PETSc/petsc-3.5.2'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/dsu/Soft/PETSc/petsc-3.5.2'
=========================================
Then I recompiled the codes, ran with -fp_trap and still got the following error
Backtrace for this error:
Note: The EXACT line numbers in the stack are not available,
[2]PETSC ERROR: INSTEAD the line number of the start of the function
[2]PETSC ERROR: is given.
[2]PETSC ERROR: [2] PetscDefaultFPTrap line 379 /home/dsu/Soft/PETSc/petsc-3.5.2/src/sys/error/fp.c
INSTEAD the line number of the start of the function
[3]PETSC ERROR: is given.
[3]PETSC ERROR: [3] PetscDefaultFPTrap line 379 /home/dsu/Soft/PETSc/petsc-3.5.2/src/sys/error/fp.c
[2]PETSC ERROR: User provided function() line 0 in Unknown file trapped floating point error
[3]PETSC ERROR: User provided function() line 0 in Unknown file trapped floating point error
</pre>
</blockquote>
<pre wrap="">
This is different then what you sent a few minutes ago where it crashed in hypre.
Anyways you need to use the -start_in_debugger business I sent in the previous email to see the exact place the problem occurs.</pre>
</blockquote>
Here is the information shown on gdb screen<br>
<br>
Program received signal SIGFPE, Arithmetic exception.<br>
0x00000000006c2bef in velocity_g (l_sufx=1, suffix=..., nmax=12,
njamxc=34, <br>
cinfradx=..., radial_coordx=.FALSE., _suffix=3)<br>
at ../../gas_advection/velocity_g.F90:1344<br>
1344 cinfrt = cinfrt_dg(i1) *
diff(ic,idim) !<font
color="#ff0000">diff is a very small value, e.g., 1.0d-316</font><br>
(gdb)<br>
<br>
After type cont on gdb screen, I got error information as below<br>
<br>
[1]PETSC ERROR: *** unknown floating point error occurred ***<br>
[1]PETSC ERROR: The specific exception can be determined by running
in a debugger. When the<br>
[1]PETSC ERROR: debugger traps the signal, the exception can be
found with fetestexcept(0x3d)<br>
[1]PETSC ERROR: where the result is a bitwise OR of the following
flags:<br>
[1]PETSC ERROR: FE_INVALID=0x1 FE_DIVBYZERO=0x4 FE_OVERFLOW=0x8
FE_UNDERFLOW=0x10 FE_INEXACT=0x20<br>
[1]PETSC ERROR: Try option -start_in_debugger<br>
[1]PETSC ERROR: likely location of problem given in stack below<br>
[1]PETSC ERROR: --------------------- Stack Frames
------------------------------------<br>
[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not
available,<br>
[1]PETSC ERROR: INSTEAD the line number of the start of the
function<br>
[1]PETSC ERROR: is given.<br>
[1]PETSC ERROR: [1] PetscDefaultFPTrap line 379
/home/dsu/Soft/PETSc/petsc-3.5.2/src/sys/error/fp.c<br>
[1]PETSC ERROR: User provided function() line 0 in Unknown file
trapped floating point error<br>
[0]PETSC ERROR: *** unknown floating point error occurred ***<br>
[0]PETSC ERROR: The specific exception can be determined by running
in a debugger. When the<br>
[0]PETSC ERROR: debugger traps the signal, the exception can be
found with fetestexcept(0x3d)<br>
[0]PETSC ERROR: where the result is a bitwise OR of the following
flags:<br>
[0]PETSC ERROR: FE_INVALID=0x1 FE_DIVBYZERO=0x4 FE_OVERFLOW=0x8
FE_UNDERFLOW=0x10 FE_INEXACT=0x20<br>
[0]PETSC ERROR: Try option -start_in_debugger<br>
[0]PETSC ERROR: likely location of problem given in stack below<br>
<br>
Thanks,<br>
<br>
Danyang<br>
<blockquote
cite="mid:8E11BAE6-7DB2-43C6-AF40-21E6B2B49124@mcs.anl.gov"
type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">Thanks,
Danyang
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">On Apr 25, 2015, at 1:05 AM, Danyang Su <a class="moz-txt-link-rfc2396E" href="mailto:danyang.su@gmail.com"><danyang.su@gmail.com></a> wrote:
Hi Barry and Satish,
How can I get rid of unknown floating point error when a very small value is multiplied.
e.g.,
cinfrt_dg(i1) and diff(ic,idim) are 1.0250235986806329E-008 8.6178408169776945E-317 respectively,
cinfrt = cinfrt_dg(i1) * diff(ic,idim)
I get the following error when run with "-fp_trap -start_in_debugger".
Backtrace for this error:
*** unknown floating point error occurred ***
[2]PETSC ERROR: The specific exception can be determined by running in a debugger. When the
[2]PETSC ERROR: debugger traps the signal, the exception can be found with fetestexcept(0x3d)
[2]PETSC ERROR: cinfrt_dg(i1),diff(ic,idim) 1.0250235986806329E-008 8.6178408169776945E-317
where the result is a bitwise OR of the following flags:
[2]PETSC ERROR: FE_INVALID=0x1 FE_DIVBYZERO=0x4 FE_OVERFLOW=0x8 FE_UNDERFLOW=0x10 FE_INEXACT=0x20
[2]PETSC ERROR: Try option -start_in_debugger
[2]PETSC ERROR: likely location of problem given in stack below
Thanks,
Danyang
On 15-04-24 01:54 PM, Danyang Su wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On 15-04-24 01:23 PM, Satish Balay wrote:
</pre>
<blockquote type="cite">
<pre wrap=""> c 4 1.0976214263087059E-067
I don't think this number can be stored in a real*4.
Satish
</pre>
</blockquote>
<pre wrap="">Thanks, Satish. It is caused by this number.
</pre>
<blockquote type="cite">
<pre wrap="">On Fri, 24 Apr 2015, Danyang Su wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On 15-04-24 11:12 AM, Barry Smith wrote:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">On Apr 24, 2015, at 1:05 PM, Danyang Su <a class="moz-txt-link-rfc2396E" href="mailto:danyang.su@gmail.com"><danyang.su@gmail.com></a> wrote:
Hi All,
One of my case crashes because of floating point exception when using 4
processors, as shown below. But if I run this case with 1 processor, it
works fine. I have tested the codes with around 100 cases up to 768
processors, all other cases work fine. I just wonder if this kind of error
is caused because of NaN in jacobi matrix, RHS or preconditioner?
</pre>
</blockquote>
<pre wrap=""> Yes, almost for sure it is one of these places.
First run the bad case with -fp_trap if all goes well you'll see the
function where the FPE is generated. Then run also with -start_in_debugger
and
type cont in all four debugger windows. When the FPE happens the debugger
should stop showing exactly where the FPE happens.
Barry
</pre>
</blockquote>
<pre wrap="">Hi Barry,
If run with -fp_trap -start_in_debugger, I got the following error
[0]PETSC ERROR: *** unknown floating point error occurred ***
[0]PETSC ERROR: The specific exception can be determined by running in a
debugger. When the
[0]PETSC ERROR: debugger traps the signal, the exception can be found with
fetestexcept(0x3d)
[0]PETSC ERROR: where the result is a bitwise OR of the following flags:
[0]PETSC ERROR: FE_INVALID=0x1 FE_DIVBYZERO=0x4 FE_OVERFLOW=0x8
FE_UNDERFLOW=0x10 FE_INEXACT=0x20
[0]PETSC ERROR: Try option -start_in_debugger
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: --------------------- Stack Frames
------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR: INSTEAD the line number of the start of the function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: [0] PetscDefaultFPTrap line 379
/home/dsu/Soft/PETSc/petsc-3.5.2/src/sys/error/fp.c
[0]PETSC ERROR: User provided function() line 0 in Unknown file trapped
floating point error
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x7F4FEAB1C7D7
#1 0x7F4FEAB1CDDE
#2 0x7F4FE9E1AD3F
#3 0x7F4FE9E1ACC9
#4 0x7F4FE9E1E0D7
#5 0x7F4FEB0B6DCB
#6 0x7F4FEB0B1825
#7 0x7F4FEB0B817F
#8 0x7F4FE9E1AD3F
#9 0x6972C8 in tprfrtlc_ at tprfrtlc.F90:2393 (discriminator 3)
#10 0x4C6C87 in gcreact_ at gcreact.F90:678
#11 0x707E19 in initicrt_ at initicrt.F90:589
#12 0x4F42D0 in initprob_ at initprob.F90:430
#13 0x5AAF72 in driver_pc at driver_pc.F90:438
I checked the code at tprfrtlc.F90:2393,
realbuffer_gb(1:nvars) = (/time,(c(ic),ic=1,nc-1), &
(cx(ix),ix=1,nxout)/)
All the values (time, c, cx) are reasonable, as shown below. The only
possibility is that realbuffer_gb is in declared as real*4 if using sing
precision output while time, c, cx are declared in real*8. I have a lot of
similar data conversion from real*8 to real*4 output, other code does not
return error.
time 0.0000000000000000
c 1 9.9999999999999995E-008
c 2 3.1555251077549618E-003
c 3 7.1657814842179362E-008
c 4 1.0976214263087059E-067
c 5 5.2879822292305797E-004
c 6 9.9999999999999964E-005
c 7 6.4055731968811337E-005
c 8 3.4607572892578404E-020
cx 1 3.4376650636008101E-005
cx 2 7.3989678854017763E-012
cx 3 9.5317170613607207E-012
cx 4 2.2344525794718353E-015
cx 5 3.0624685689695889E-008
cx 6 1.0046157902783967E-007
cx 7 1.5320169154914984E-004
cx 8 8.6930292776346176E-014
cx 9 3.5944267559348721E-005
cx 10 3.0072645866951157E-018
cx 11 2.3592486321095017E-013
Thanks,
Danyang
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">I can check all the entries of jacobi matrix to see if the value is valid,
but this seems not a good idea as it takes a long time to reach this
point. If I restart the simulation from a specified time (e.g., 7.685 in
this case), then the error does not occur.
Would you please give me any suggestion on debugging this case?
Thanks and Regards,
Danyang
timestep: 2730 time: 7.665E+00 years delt: 1.000E-02 years iter: 1
timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
timestep: 2731 time: 7.675E+00 years delt: 1.000E-02 years iter: 1
timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
timestep: 2732 time: 7.685E+00 years delt: 1.000E-02 years iter: 1
timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
timestep: 2733 time: 7.695E+00 years delt: 1.000E-02 years iter: 1
timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
timestep: 2734 time: 7.705E+00 years delt: 1.000E-02 years iter: 1
timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
Reduce time step for reactive transport
timestep: 2734 time: 7.700E+00 years delt: 5.000E-03 years iter: 1
timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
Reduce time step for reactive transport
timestep: 2734 time: 7.697E+00 years delt: 2.500E-03 years iter: 1
timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: Floating point exception
[2]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[2]PETSC ERROR: Floating point exception
[2]PETSC ERROR: Vec entry at local location 0 is not-a-number or infinite
at end of function: Parameter number 3
[2]PETSC ERROR: See <a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
for trouble shooting.
[2]PETSC ERROR: Petsc Release Version 3.5.2, Sep, 08, 2014
[2]PETSC ERROR: [1]PETSC ERROR: Vec entry at local location 0 is
not-a-number or infinite at end of function: Parameter number 3
[1]PETSC ERROR: See <a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
for trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.5.2, Sep, 08, 2014
[1]PETSC ERROR: ../min3p_thcm_petsc_dbg on a linux-gnu-dbg named nwmop by
dsu Thu Apr 23 15:38:52 2015
[1]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu-dbg --with-cc=gcc
--with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich
--download-mumps --download-hypre --download-superlu_dist --download-metis
--download-parmetis --download-scalapack
[1]PETSC ERROR: #1 VecValidValues() line 34 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/vec/vec/interface/rvector.c
../min3p_thcm_petsc_dbg on a linux-gnu-dbg named nwmop by dsu Thu Apr 23
15:38:52 2015
[2]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu-dbg --with-cc=gcc
--with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich
--download-mumps --download-hypre --download-superlu_dist --download-metis
--download-parmetis --download-scalapack
[2]PETSC ERROR: #1 VecValidValues() line 34 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/vec/vec/interface/rvector.c
[2]PETSC ERROR: [1]PETSC ERROR: #2 PCApply() line 442 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/pc/interface/precon.c
[1]PETSC ERROR: #2 PCApply() line 442 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/pc/interface/precon.c
[2]PETSC ERROR: #3 KSP_PCApply() line 230 in
/home/dsu/Soft/PETSc/petsc-3.5.2/include/petsc-private/kspimpl.h
#3 KSP_PCApply() line 230 in
/home/dsu/Soft/PETSc/petsc-3.5.2/include/petsc-private/kspimpl.h
[1]PETSC ERROR: #4 KSPInitialResidual() line 63 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/interface/itres.c
[2]PETSC ERROR: #4 KSPInitialResidual() line 63 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/interface/itres.c
[1]PETSC ERROR: #5 KSPSolve_GMRES() line 234 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/impls/gmres/gmres.c
[2]PETSC ERROR: #5 KSPSolve_GMRES() line 234 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/impls/gmres/gmres.c
[2]PETSC ERROR: #6 KSPSolve() line 459 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/interface/itfunc.c
[1]PETSC ERROR: #6 KSPSolve() line 459 in
/home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/interface/itfunc.c
^C[mpiexec@nwmop] Sending Ctrl-C to processes as requested
[mpiexec@nwmop] Press Ctrl-C again to force abort
</pre>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<pre wrap="">
</pre>
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