Good morning Barry,
Attached are the updated files, there is more useful information in them.
Cheers,
Sophie
________________________________
From: Blondel, Sophie via Xolotl-psi-development
<[email protected]>
Sent: Monday, December 9, 2024 17:29
To: Barry Smith <[email protected]>
Cc: [email protected] <[email protected]>;
[email protected]
<[email protected]>
Subject: Re: [Xolotl-psi-development] [petsc-users] "-ts_exact_final_time
matchstep" leads to DIVERGED_STEP_REJECTED
Hi Barry,
I hope you are doing well.
Attached are the output. To give a little more context, this is a "new" way of
running the code where multiple instances are created and communicate together
every few time steps (like coupling the code with itself in memory). Here there
are 3 instances that each have a separate TS object, plus one "main" instance
that doesn't solve anything but compute rates to exchange between the other
instances.
Cheers,
Sophie
________________________________
From: Barry Smith <[email protected]>
Sent: Monday, December 9, 2024 15:12
To: Blondel, Sophie <[email protected]>
Cc: [email protected] <[email protected]>;
[email protected]
<[email protected]>
Subject: Re: [petsc-users] "-ts_exact_final_time matchstep" leads to
DIVERGED_STEP_REJECTED
On Dec 9, 2024, at 2:56 PM, Blondel, Sophie via petsc-users
<[email protected]> wrote:
Hi,
I am trying to understand a strange behavior I'm encountering: when running my
application with "-ts_exact_final_time stepover" everything goes well, but when
I switch to "matchstep" I get DIVERGED_STEP_REJECTED before the first time step
is finished.
This is in the very first time-step in TSSolve?
Please run with -ts_monitor and send all the output (best for a short time
interval and do it twice once with -ts_exact_final_time stepover and once with
exact.
Barry
I tried increasing the maximum number of rejections and it just takes longer to
diverge, and if I set the value to "unlimited" it is basically an infinite loop.
Is there a way to check why is the step rejected? Could the "matchstep" option
change tolerances somewhere that would cause that behavior?
Let me know if I should provide more information.
Best,
Sophie Blondel
[sophie-Precision-3580:86913] shmem: mmap: an error occurred while determining
whether or not
/tmp/ompi.sophie-Precision-3580.1000/jf.0/3920101376/shared_mem_cuda_pool.sophie-Precision-3580
could be created.
[sophie-Precision-3580:86913] create_and_attach: unable to create shared memory
BTL coordinating structure :: size 134217728
Starting Xolotl (3.0.1-39-fdde1002)
Tue Dec 10 11:02:51 2024
NetworkHandler: Loaded network of 2066 DOF with: Vacancy Basal Interstitial
MaterialHandler: The selected material is: AlphaZr with the following
processes: noSolve reaction sink
TemperatureHandler: Using the time profile defined in: temp.txt
Starting Xolotl (3.0.1-39-fdde1002)
Tue Dec 10 11:02:52 2024
NetworkHandler: Loaded network of 660 DOF with: Vacancy Basal Interstitial
MaterialHandler: The selected material is: AlphaZr with the following
processes: constant reaction sink
TemperatureHandler: Using the time profile defined in: temp.txt
Starting Xolotl (3.0.1-39-fdde1002)
Tue Dec 10 11:02:52 2024
NetworkHandler: Loaded network of 668 DOF with: Vacancy Basal Interstitial
MaterialHandler: The selected material is: AlphaZr with the following
processes: constant reaction sink
TemperatureHandler: Using the time profile defined in: temp.txt
Starting Xolotl (3.0.1-39-fdde1002)
Tue Dec 10 11:02:52 2024
NetworkHandler: Loaded network of 738 DOF with: Vacancy Basal Interstitial
MaterialHandler: The selected material is: AlphaZr with the following
processes: constant reaction sink
TemperatureHandler: Using the time profile defined in: temp.txt
MultiXolotl: Restart file written to: xolotlRestart.txt
SolverHandler: 0D simulation
SolverHandler: 0D simulation
SolverHandler: 0D simulation
0 TS dt 0. time 0.
0 TS dt 0. time 0.
0 TS dt 0. time 0.
0 TS dt 0. time 0.
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
0 TS dt 0. time 0.
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
0 TS dt 0. time 0.
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
TSAdapt basic step 0 stage rejected (SNES reason DIVERGED_FNORM_NAN)
t=0 + 0.000e+00 retrying with dt=0.000e+00
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 TSStep() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:3416
[0]PETSC ERROR: #2 TSSolve() at
/home/sophie/Code/petsc/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #3 solve() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:380
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: Invalid argument
[0]PETSC ERROR: You are destroying an option that has been used with
PetscOptionsPush() but does not have a corresponding PetscOptionsPop()
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 PetscOptionsDestroy() at
/home/sophie/Code/petsc/src/sys/objects/options.c:178
[0]PETSC ERROR: #2 finalize() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:484
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: Invalid argument
[0]PETSC ERROR: You are destroying an option that has been used with
PetscOptionsPush() but does not have a corresponding PetscOptionsPop()
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 PetscOptionsDestroy() at
/home/sophie/Code/petsc/src/sys/objects/options.c:178
[0]PETSC ERROR: #2 finalize() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:484
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: It appears a new error in the code was triggered after a
previous error, possibly because:
[0]PETSC ERROR: - The first error was not properly handled via (for example)
the use of
[0]PETSC ERROR: PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR: - The second error was triggered while handling the first
error.
[0]PETSC ERROR: Above is the traceback for the previous unhandled error,
below the traceback for the next error
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries are fatal, you should add
the appropriate error checking to the code
[0]PETSC ERROR: Invalid argument
[0]PETSC ERROR: You are destroying an option that has been used with
PetscOptionsPush() but does not have a corresponding PetscOptionsPop()
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program
crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-fieldsplit_0_pc_type value: sor source:
code
[0]PETSC ERROR: Option left: name:-fieldsplit_1_pc_type value: redundant
source: code
[0]PETSC ERROR: Option left: name:-pc_fieldsplit_detect_coupling (no value)
source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.4-378-g9ca9edede9e GIT
Date: 2024-08-01 13:52:28 +0000
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH on
sophie-Precision-3580 by sophie Tue Dec 10 11:02:51 2024
[0]PETSC ERROR: Configure options: PETSC_DIR=/home/sophie/Code/petsc
--prefix=/home/sophie/Code/petsc-install --with-cc=mpicc --with-cxx=mpicxx
--with-fc=0 --with-cuda=0 --with-openmp=0 --with-debugging=0
--with-shared-libraries --with-64-bit-indices --download-kokkos
--download-kokkos-kernels --download-boost --download-hdf5 --COPTFLAGS=-O3
--CXXOPTFLAGS=-O3
[0]PETSC ERROR: #1 PetscOptionsDestroy() at
/home/sophie/Code/petsc/src/sys/objects/options.c:178
[0]PETSC ERROR: #2 finalize() at
/home/sophie/Workspace/xolotl-alphaZr-source/xolotl/solver/src/PetscSolver.cpp:484
WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
There are 3 unused database options. They are:
Option left: name:-fieldsplit_0_pc_type value: sor source: code
Option left: name:-fieldsplit_1_pc_type value: redundant source: code
Option left: name:-pc_fieldsplit_detect_coupling (no value) source: code
[sophie-Precision-3580:87124] shmem: mmap: an error occurred while determining
whether or not
/tmp/ompi.sophie-Precision-3580.1000/jf.0/3451256832/shared_mem_cuda_pool.sophie-Precision-3580
could be created.
[sophie-Precision-3580:87124] create_and_attach: unable to create shared memory
BTL coordinating structure :: size 134217728
Starting Xolotl (3.0.1-39-fdde1002)
Tue Dec 10 11:06:30 2024
NetworkHandler: Loaded network of 2066 DOF with: Vacancy Basal Interstitial
MaterialHandler: The selected material is: AlphaZr with the following
processes: noSolve reaction sink
TemperatureHandler: Using the time profile defined in: temp.txt
Starting Xolotl (3.0.1-39-fdde1002)
Tue Dec 10 11:06:31 2024
NetworkHandler: Loaded network of 660 DOF with: Vacancy Basal Interstitial
MaterialHandler: The selected material is: AlphaZr with the following
processes: constant reaction sink
TemperatureHandler: Using the time profile defined in: temp.txt
Starting Xolotl (3.0.1-39-fdde1002)
Tue Dec 10 11:06:31 2024
NetworkHandler: Loaded network of 668 DOF with: Vacancy Basal Interstitial
MaterialHandler: The selected material is: AlphaZr with the following
processes: constant reaction sink
TemperatureHandler: Using the time profile defined in: temp.txt
Starting Xolotl (3.0.1-39-fdde1002)
Tue Dec 10 11:06:31 2024
NetworkHandler: Loaded network of 738 DOF with: Vacancy Basal Interstitial
MaterialHandler: The selected material is: AlphaZr with the following
processes: constant reaction sink
TemperatureHandler: Using the time profile defined in: temp.txt
MultiXolotl: Restart file written to: xolotlRestart.txt
SolverHandler: 0D simulation
SolverHandler: 0D simulation
SolverHandler: 0D simulation
0 TS dt 1e-12 time 0.
0 TS dt 1e-12 time 0.
0 TS dt 1e-12 time 0.
0 TS dt 1e-12 time 0.
TSAdapt basic arkimex 0:3 step 0 accepted t=0 + 1.000e-12
dt=1.010e-12 wlte=2.4e-35 wltea= -1 wlter= -1
1 TS dt 1.01e-12 time 1e-12
0 TS dt 1e-12 time 0.
TSAdapt basic arkimex 0:3 step 0 accepted t=0 + 1.000e-12
dt=1.010e-12 wlte=1.93e-32 wltea= -1 wlter= -1
1 TS dt 1.01e-12 time 1e-12
0 TS dt 1e-12 time 0.
TSAdapt basic arkimex 0:3 step 0 accepted t=0 + 1.000e-12
dt=1.010e-12 wlte=5.33e-32 wltea= -1 wlter= -1
1 TS dt 1.01e-12 time 1e-12
0 TS dt 1.01e-12 time 1e-12
TSAdapt basic arkimex 0:3 step 0 accepted t=1e-12 + 1.010e-12
dt=1.020e-12 wlte=3.62e-35 wltea= -1 wlter= -1
1 TS dt 1.0201e-12 time 2.01e-12
TSAdapt basic arkimex 0:3 step 1 accepted t=2.01e-12 + 1.020e-12
dt=1.020e-12 wlte=3.02e-35 wltea= -1 wlter= -1
2 TS dt 1.0201e-12 time 3.0301e-12
0 TS dt 1.01e-12 time 1e-12
TSAdapt basic arkimex 0:3 step 0 accepted t=1e-12 + 1.010e-12
dt=1.020e-12 wlte=3.73e-32 wltea= -1 wlter= -1
1 TS dt 1.0201e-12 time 2.01e-12
TSAdapt basic arkimex 0:3 step 1 accepted t=2.01e-12 + 1.020e-12
dt=1.020e-12 wlte=9.74e-33 wltea= -1 wlter= -1
2 TS dt 1.0201e-12 time 3.0301e-12
0 TS dt 1.01e-12 time 1e-12
TSAdapt basic arkimex 0:3 step 0 accepted t=1e-12 + 1.010e-12
dt=1.020e-12 wlte=3.57e-32 wltea= -1 wlter= -1
1 TS dt 1.0201e-12 time 2.01e-12
TSAdapt basic arkimex 0:3 step 1 accepted t=2.01e-12 + 1.020e-12
dt=1.020e-12 wlte=8.88e-33 wltea= -1 wlter= -1
2 TS dt 1.0201e-12 time 3.0301e-12
0 TS dt 1.0201e-12 time 3.0301e-12
0 TS dt 1.0201e-12 time 3.0301e-12
0 TS dt 1.0201e-12 time 3.0301e-12
0 TS dt 1.0201e-12 time 3.0301e-12
TSAdapt basic arkimex 0:3 step 0 accepted t=3.0301e-12 + 1.020e-12
dt=1.030e-12 wlte=8.37e-35 wltea= -1 wlter= -1
1 TS dt 1.0303e-12 time 4.0502e-12
TSAdapt basic arkimex 0:3 step 1 accepted t=4.0502e-12 + 1.030e-12
dt=1.041e-12 wlte=1.2e-34 wltea= -1 wlter= -1
2 TS dt 1.0406e-12 time 5.0805e-12
0 TS dt 1.0201e-12 time 3.0301e-12
TSAdapt basic arkimex 0:3 step 0 accepted t=3.0301e-12 + 1.020e-12
dt=1.030e-12 wlte=7.51e-32 wltea= -1 wlter= -1
1 TS dt 1.0303e-12 time 4.0502e-12
TSAdapt basic arkimex 0:3 step 1 accepted t=4.0502e-12 + 1.030e-12
dt=1.041e-12 wlte=7.46e-32 wltea= -1 wlter= -1
2 TS dt 1.0406e-12 time 5.0805e-12
0 TS dt 1.0201e-12 time 3.0301e-12
TSAdapt basic arkimex 0:3 step 0 accepted t=3.0301e-12 + 1.020e-12
dt=1.030e-12 wlte=7.09e-32 wltea= -1 wlter= -1
1 TS dt 1.0303e-12 time 4.0502e-12
TSAdapt basic arkimex 0:3 step 1 accepted t=4.0502e-12 + 1.030e-12
dt=1.041e-12 wlte=1.42e-31 wltea= -1 wlter= -1
2 TS dt 1.0406e-12 time 5.0805e-12
0 TS dt 1.0406e-12 time 5.0805e-12
TSAdapt basic arkimex 0:3 step 0 accepted t=5.0805e-12 + 1.041e-12
dt=1.051e-12 wlte=9.02e-35 wltea= -1 wlter= -1
1 TS dt 1.05101e-12 time 6.12111e-12
0 TS dt 1.0406e-12 time 5.0805e-12
TSAdapt basic arkimex 0:3 step 0 accepted t=5.0805e-12 + 1.041e-12
dt=1.051e-12 wlte=5.04e-33 wltea= -1 wlter= -1
1 TS dt 1.05101e-12 time 6.12111e-12
0 TS dt 1.0406e-12 time 5.0805e-12
TSAdapt basic arkimex 0:3 step 0 accepted t=5.0805e-12 + 1.041e-12
dt=1.051e-12 wlte=4.45e-33 wltea= -1 wlter= -1
1 TS dt 1.05101e-12 time 6.12111e-12
