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Hi Matt, I configured the lib like this:</div>
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<span style="font-family: "Courier New", monospace;">$ ./configure --with-blaslapack-dir=/opt/intel/oneapi/mkl/2022.2.1 --with-debugging=0 --with-shared-libraries=0 --download-make</span><br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
and compiled. I still get some check segfault error. See below:</div>
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<span style="font-family: "Courier New", monospace;">$ make PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 PETSC_ARCH=arch-darwin-c-opt check</span>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Running check examples to verify correct installation</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Using PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 and PETSC_ARCH=arch-darwin-c-opt</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">*******************Error detected during compile or link!*******************</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">See https://petsc.org/release/faq/</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">/Users/mnv/Documents/Software/petsc-3.19.1/src/snes/tutorials ex19</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">*********************************************************************************</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -fPIC -wd1572
-Wno-unknown-pragmas -g -O3 -I/Users/mnv/Documents/Software/petsc-3.19.1/include -I/Users/mnv/Documents/Software/petsc-3.19.1/arch-darwin-c-opt/include -I/opt/X11/include -std=c99 ex19.c -L/Users/mnv/Documents/Software/petsc-3.19.1/arch-darwin-c-opt/lib
-Wl,-rpath,/opt/intel/oneapi/mkl/2022.2.1/lib -L/opt/intel/oneapi/mkl/2022.2.1/lib -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -L/opt/openmpi414_oneapi22u3/lib -Wl,-rpath,/opt/intel/oneapi/compiler/2022.2.1/mac/compiler/lib -L/opt/intel/oneapi/tbb/2021.7.1/lib
-L/opt/intel/oneapi/ippcp/2021.6.2/lib -L/opt/intel/oneapi/ipp/2021.6.2/lib -L/opt/intel/oneapi/dnnl/2022.2.1/cpu_iomp/lib -L/opt/intel/oneapi/dal/2021.7.1/lib -L/opt/intel/oneapi/compiler/2022.2.1/mac/compiler/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib
-Wl,-rpath,/opt/intel/oneapi/compiler/2022.2.1/mac/bin/intel64/../../compiler/lib -L/opt/intel/oneapi/compiler/2022.2.1/mac/bin/intel64/../../compiler/lib -Wl,-rpath,/Library/Developer/CommandLineTools/usr/lib/clang/14.0.3/lib/darwin -L/Library/Developer/CommandLineTools/usr/lib/clang/14.0.3/lib/darwin
-lpetsc -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lX11 -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen-rte -lopen-pal -limf -lm -lz -lifport -lifcoremt -lsvml -lipgo -lirc -lpthread -lclang_rt.osx -lmpi -lopen-rte -lopen-pal
-limf -lm -lz -lsvml -lirng -lc++ -lipgo -ldecimal -lirc -lclang_rt.osx -lmpi -lopen-rte -lopen-pal -limf -lm -lz -lsvml -lirng -lc++ -lipgo -ldecimal -lirc -lclang_rt.osx -o ex19</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler
(ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">In file included from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsys.h(44),</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscvec.h(9),</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscmat.h(7),</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscpc.h(7),</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscksp.h(7),</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsnes.h(7),</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> from ex19.c(68):</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">/Users/mnv/Documents/Software/petsc-3.19.1/include/petscsystypes.h(68): warning #2621: attribute "warn_unused_result" does not apply here</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> PETSC_ERROR_CODE_TYPEDEF enum PETSC_ERROR_CODE_NODISCARD {</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> ^</span></div>
<div><br class="ContentPasted0">
</div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">See https://petsc.org/release/faq/</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37807] *** Process received signal ***</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37807] Signal: Segmentation fault: 11 (11)</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37807] Signal code: Address not mapped (1)</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37807] Failing at address: 0x7f</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37807] *** End of error message ***</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Primary job terminated normally, but 1 process returned</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">a non-zero exit code. Per user-direction, the job has been aborted.</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">mpiexec noticed that process rank 0 with PID 0 on node excess exited on signal 11 (Segmentation fault: 11).</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">See https://petsc.org/release/faq/</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37831] *** Process received signal ***</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37831] Signal: Segmentation fault: 11 (11)</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37831] Signal code: Address not mapped (1)</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37831] Failing at address: 0x7f</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37831] *** End of error message ***</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37832] *** Process received signal ***</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37832] Signal: Segmentation fault: 11 (11)</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37832] Signal code: Address not mapped (1)</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37832] Failing at address: 0x7f</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">[excess:37832] *** End of error message ***</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Primary job terminated normally, but 1 process returned</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">a non-zero exit code. Per user-direction, the job has been aborted.</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">mpiexec noticed that process rank 1 with PID 0 on node excess exited on signal 11 (Segmentation fault: 11).</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">See https://petsc.org/release/faq/</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">forrtl: severe (174): SIGSEGV, segmentation fault occurred</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Image PC Routine Line Source
</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">libifcoremt.dylib 000000010B7F7FE4 for__signal_handl Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">libsystem_platfor 00007FF8024C25ED _sigtramp Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">ex5f 00000001087AFA38 PetscGetArchType Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">ex5f 000000010887913B PetscErrorPrintfI Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">ex5f 000000010878D227 PetscInitialize_C Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">ex5f 000000010879D289 petscinitializef_ Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">ex5f 0000000108713C09 petscsys_mp_petsc Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">ex5f 0000000108710B5D MAIN__ Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">ex5f 0000000108710AEE main Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">dyld 00007FF80213B41F start Unknown Unknown</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Primary job terminated normally, but 1 process returned</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">a non-zero exit code. Per user-direction, the job has been aborted.</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">mpiexec detected that one or more processes exited with non-zero status, thus causing</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">the job to be terminated. The first process to do so was:</span></div>
<div><br class="ContentPasted0">
</div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> Process name: [[48108,1],0]</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;"> Exit code: 174</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">--------------------------------------------------------------------------</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Completed test examples</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">Error while running make check</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">make[1]: *** [check] Error 1</span></div>
<div class="ContentPasted0"><span style="font-family: "Courier New", monospace;">make: *** [check] Error 2</span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Vanella, Marcos (Fed) <marcos.vanella@nist.gov><br>
<b>Sent:</b> Monday, May 15, 2023 12:20 PM<br>
<b>To:</b> Matthew Knepley <knepley@gmail.com><br>
<b>Cc:</b> petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject:</b> Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers and OpenMPI</font>
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Thank you Matt I'll try this and let you know.</div>
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Marcos<br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Matthew Knepley <knepley@gmail.com><br>
<b>Sent:</b> Monday, May 15, 2023 12:08 PM<br>
<b>To:</b> Vanella, Marcos (Fed) <marcos.vanella@nist.gov><br>
<b>Cc:</b> petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject:</b> Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers and OpenMPI</font>
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<div dir="ltr">On Mon, May 15, 2023 at 11:19 AM Vanella, Marcos (Fed) via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>> wrote:<br>
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Hello, I'm trying to compile the PETSc library version 3.19.1 with OpenMPI 4.1.4 and the OneAPI 2022 Update 2 Intel Compiler suite on a Mac with OSX Ventura 13.3.1.</div>
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I can compile PETSc in debug mode with this configure and make lines. I can run the PETSC tests, which seem fine.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
When I compile the library in optimized mode, either using -O3 or O1, for example configuring with:</div>
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<div><br>
</div>
<div>I hate to yell "compiler bug" when this happens, but it sure seems like one. Can you just use</div>
<div><br>
</div>
<div> --with-debugging=0</div>
<div><br>
</div>
<div>without the custom COPTFLAGS, CXXOPTFLAGS, FOPTFLAGS? If that works, it is almost</div>
<div>certainly a compiler bug. If not, then we can go in the debugger and see what is failing.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
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<span style="font-family:"Courier New",monospace">$ ./configure --prefix=/opt/petsc-oneapi22u3 --with-blaslapack-dir=/opt/intel/oneapi/mkl/2022.2.1 COPTFLAGS='-m64 -O1 -g -diag-disable=10441' CXXOPTFLAGS='-m64 -O1 -g -diag-disable=10441' FOPTFLAGS='-m64 -O1
-g' LDFLAGS='-m64' --with-debugging=0 --with-shared-libraries=0 --download-make</span><br>
</div>
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<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
and using mpicc (icc), mpif90 (ifort) from Open MPI, the static lib compiles. Yet, I see right off the bat this segfault error in the first PETSc example:</div>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:"Courier New",monospace">$ make PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 PETSC_ARCH=arch-darwin-c-opt test</span>
<div><span style="font-family:"Courier New",monospace">/Users/mnv/Documents/Software/petsc-3.19.1/arch-darwin-c-opt/bin/make --no-print-directory -f /Users/mnv/Documents/Software/petsc-3.19.1/gmakefile.test PETSC_ARCH=arch-darwin-c-opt PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1
test</span></div>
<div><span style="font-family:"Courier New",monospace">/opt/intel/oneapi/intelpython/latest/bin/python3 /Users/mnv/Documents/Software/petsc-3.19.1/config/gmakegentest.py --petsc-dir=/Users/mnv/Documents/Software/petsc-3.19.1 --petsc-arch=arch-darwin-c-opt --testdir=./arch-darwin-c-opt/tests</span></div>
<div><span style="font-family:"Courier New",monospace">Using MAKEFLAGS: --no-print-directory -- PETSC_ARCH=arch-darwin-c-opt PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1</span></div>
<div><span style="font-family:"Courier New",monospace"> CC arch-darwin-c-opt/tests/sys/classes/draw/tests/ex1.o</span></div>
<div><span style="font-family:"Courier New",monospace">In file included from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsys.h(44),</span></div>
<div><span style="font-family:"Courier New",monospace"> from /Users/mnv/Documents/Software/petsc-3.19.1/src/sys/classes/draw/tests/ex1.c(4):</span></div>
<div><span style="font-family:"Courier New",monospace">/Users/mnv/Documents/Software/petsc-3.19.1/include/petscsystypes.h(68): warning #2621: attribute "warn_unused_result" does not apply here</span></div>
<div><span style="font-family:"Courier New",monospace"> PETSC_ERROR_CODE_TYPEDEF enum PETSC_ERROR_CODE_NODISCARD {</span></div>
<div><span style="font-family:"Courier New",monospace"> ^</span></div>
<div><br>
</div>
<div><span style="font-family:"Courier New",monospace"> CLINKER arch-darwin-c-opt/tests/sys/classes/draw/tests/ex1</span></div>
<div><span style="font-family:"Courier New",monospace"> TEST arch-darwin-c-opt/tests/counts/sys_classes_draw_tests-ex1_1.counts</span></div>
<div><span style="font-family:"Courier New",monospace">not ok sys_classes_draw_tests-ex1_1
<b># Error code: 139</b></span></div>
<div><b><span style="font-family:"Courier New",monospace"># [excess:98681] *** Process received signal ***</span></b></div>
<div><b><span style="font-family:"Courier New",monospace"># [excess:98681] Signal: Segmentation fault: 11 (11)</span></b></div>
<div><b><span style="font-family:"Courier New",monospace"># [excess:98681] Signal code: Address not mapped (1)</span></b></div>
<div><b><span style="font-family:"Courier New",monospace"># [excess:98681] Failing at address: 0x7f</span></b></div>
<div><b><span style="font-family:"Courier New",monospace"># [excess:98681] *** End of error message ***</span></b></div>
<div><span style="font-family:"Courier New",monospace"># --------------------------------------------------------------------------</span></div>
<div><span style="font-family:"Courier New",monospace"># Primary job terminated normally, but 1 process returned</span></div>
<div><span style="font-family:"Courier New",monospace"># a non-zero exit code. Per user-direction, the job has been aborted.</span></div>
<div><span style="font-family:"Courier New",monospace"># --------------------------------------------------------------------------</span></div>
<div><span style="font-family:"Courier New",monospace"># --------------------------------------------------------------------------</span></div>
<div><span style="font-family:"Courier New",monospace"># mpiexec noticed that process rank 0 with PID 0 on node excess exited on signal 11 (Segmentation fault: 11).</span></div>
<div><span style="font-family:"Courier New",monospace"># --------------------------------------------------------------------------</span></div>
<span style="font-family:"Courier New",monospace"> ok sys_classes_draw_tests-ex1_1 # SKIP Command failed so no diff</span></div>
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<span style="font-family:Calibri,Helvetica,sans-serif">I see the same segfault error in all PETSc examples.
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<span style="font-family:Calibri,Helvetica,sans-serif">Any help is mostly appreciated, I'm starting to work with PETSc. Our plan is to use the linear solver from PETSc for the Poisson equation on our numerical scheme and test this on a GPU cluster. So also,
any guideline on how to interface PETSc with a fortran code and personal experience is also most appreciated!</span></div>
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<span style="font-family:Calibri,Helvetica,sans-serif">Marcos<br>
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<span class="x_x_gmail_signature_prefix">-- </span><br>
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<div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
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<div><a href="http://www.cse.buffalo.edu/~knepley/" originalsrc="http://www.cse.buffalo.edu/~knepley/" shash="mg9pYDTBqDzx6OFf+jfaJnx0l/5/LUpiSMozOxqtSG/HgrN6t3f6Uhj05uZWofpfC64pEMOOSri4yr02sXYfPn16/mW0RS35qkGx5VdUSXbkusQXT27FgSDxq7QZkNvJBy1l143WWCskSBuZUehsPfd+dLrMQgkkr8+ULXavLz0=" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
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