<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><br class=""></div> Karl,<div class=""><br class=""></div><div class=""> If a particular process is receiving values with MatSetValues() that belong to a different process it needs to allocate temporary space for those values. If there are many values destined for a different process this space can be arbitrarily large. The values are not pass to the final owning process until the MatAssemblyBegin/End calls.</div><div class=""><br class=""></div><div class=""> If you have not preallocated enough room the matrix actually makes a complete copy of itself with extra space for additional values, copies the values over and then deletes the old matrix this the memory use can double when the preallocation is not correct. </div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""> Barry</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 3, 2020, at 9:44 AM, Karl Lin <<a href="mailto:karl.linkui@gmail.com" class="">karl.linkui@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Yes, I did. The memory check for rss computes the memory footprint of column index using size of unsigned long long instead of int.</div><div class=""><br class=""></div><div class="">For Junchao, I wonder if keeping track of which loaded columns are owned by the current process and which loaded columns are not owned also needs some memory storage. Just a wild thought. <br class=""></div></div><br class=""><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Thu, Jul 2, 2020 at 11:40 PM Ernesto Prudencio <<a href="mailto:EPrudencio@slb.com" class="">EPrudencio@slb.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid">
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<div class="gmail-m_-112400587779626991WordSection1"><p class="MsoNormal">Karl,<u class=""><u class=""></u></u></p><u class=""><u class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class=""><p class="MsoNormal">Are you taking into account that every “integer” index might be 64 bits instead of 32 bits, depending on the PETSc configuration / compilation choices for PetscInt?<u class=""><u class=""></u></u></p><u class=""><u class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class=""><p class="MsoNormal">Ernesto.<u class=""><u class=""></u></u></p><u class=""><u class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class=""><p class="MsoNormal"><b class="">From:</b> petsc-users [mailto:<a href="mailto:petsc-users-bounces@mcs.anl.gov" target="_blank" class="">petsc-users-bounces@mcs.anl.gov</a>]
<b class="">On Behalf Of </b>Junchao Zhang<br class="">
<b class="">Sent:</b> Thursday, July 2, 2020 11:21 PM<br class="">
<b class="">To:</b> Karl Lin <<a href="mailto:karl.linkui@gmail.com" target="_blank" class="">karl.linkui@gmail.com</a>><br class="">
<b class="">Cc:</b> PETSc users list <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank" class="">petsc-users@mcs.anl.gov</a>><br class="">
<b class="">Subject:</b> [Ext] Re: [petsc-users] matcreate and assembly issue<u class=""><u class=""></u></u></p><u class=""><u class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
<div class=""><p class="MsoNormal">Is it because indices for the nonzeros also need memory?<br clear="all" class="">
<u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">--Junchao Zhang<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
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</u></u></div><u class=""><u class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></u></u></u></u></div><u class=""><u class=""><u class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">On Thu, Jul 2, 2020 at 10:04 PM Karl Lin <<a href="mailto:karl.linkui@gmail.com" target="_blank" class="">karl.linkui@gmail.com</a>> wrote:<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<blockquote style="border-width:medium medium medium 1pt;border-style:none none none solid;border-color:currentColor currentColor currentColor rgb(204,204,204);margin:5pt 0in 5pt 4.8pt;padding:0in 0in 0in 6pt" class="">
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<div class=""><p class="MsoNormal">Hi, Matthew<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">Thanks for the reply. However, I don't really get why additional malloc would double the memory footprint. If I know there is only 1GB matrix being loaded, there shouldn't be 2GB memory occupied even if Petsc needs to allocate more space.<u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">regards,<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal">Karl<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
</u></u></u></u></u></u></u></u></u></u></u></u></u></u></div><u class=""><u class=""><u class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
<div class="">
<div class=""><p class="MsoNormal">On Thu, Jul 2, 2020 at 8:10 PM Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>> wrote:<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
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<div class=""><p class="MsoNormal">On Thu, Jul 2, 2020 at 7:30 PM Karl Lin <<a href="mailto:karl.linkui@gmail.com" target="_blank" class="">karl.linkui@gmail.com</a>> wrote:<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
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<blockquote style="border-width:medium medium medium 1pt;border-style:none none none solid;border-color:currentColor currentColor currentColor rgb(204,204,204);margin:5pt 0in 5pt 4.8pt;padding:0in 0in 0in 6pt" class="">
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<div class=""><p class="MsoNormal">Hi, Matt<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">Thanks for the tip last time. We just encountered another issue with large data sets. This time the behavior is the opposite from last time. The data is 13.5TB, the total number of matrix columns is 2.4 billion. Our program crashed during
matrix loading due to memory overflow in one node. As said before, we have a little memory check during loading the matrix to keep track of rss. The printout of rss in the log shows normal increase in many nodes, i.e., if we load in a portion of the matrix
that is 1GB, after MatSetValues for that portion, rss will increase roughly about 1GB. On the node that has memory overflow, the rss increased by 2GB after only 1GB of matrix is loaded through MatSetValues. We are very puzzled by this. What could make the
memory footprint twice as much as needed? Thanks in advance for any insight.<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
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<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">The only way I can imagine this happening is that you have not preallocated correctly, so that some values are causing additional mallocs.<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> Thanks,<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> Matt<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> <u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<blockquote style="border-width:medium medium medium 1pt;border-style:none none none solid;border-color:currentColor currentColor currentColor rgb(204,204,204);margin:5pt 0in 5pt 4.8pt;padding:0in 0in 0in 6pt" class="">
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<div class=""><p class="MsoNormal">Regards,<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal">Karl <u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
</u></u></u></u></u></u></div><u class=""><u class=""><u class="">
</u></u></u></div><u class=""><u class=""><u class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
<div class="">
<div class=""><p class="MsoNormal">On Thu, Jun 11, 2020 at 12:00 PM Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>> wrote:<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<blockquote style="border-width:medium medium medium 1pt;border-style:none none none solid;border-color:currentColor currentColor currentColor rgb(204,204,204);margin:5pt 0in 5pt 4.8pt;padding:0in 0in 0in 6pt" class="">
<div class="">
<div class=""><p class="MsoNormal">On Thu, Jun 11, 2020 at 12:52 PM Karl Lin <<a href="mailto:karl.linkui@gmail.com" target="_blank" class="">karl.linkui@gmail.com</a>> wrote:<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
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<blockquote style="border-width:medium medium medium 1pt;border-style:none none none solid;border-color:currentColor currentColor currentColor rgb(204,204,204);margin:5pt 0in 5pt 4.8pt;padding:0in 0in 0in 6pt" class="">
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<div class=""><p class="MsoNormal">Hi, Matthew<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">Thanks for the suggestion, just did another run and here are some detailed stack traces, maybe will provide some more insight:<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> *** Process received signal ***<br class="">
Signal: Aborted (6)<br class="">
Signal code: (-6)<br class="">
/lib64/libpthread.so.0(+0xf5f0)[0x2b56c46dc5f0]<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b56c5486337]<br class="">
[ 2] /lib64/libc.so.6(abort+0x148)[0x2b56c5487a28]<br class="">
[ 3] /libpetsc.so.3.10(PetscTraceBackErrorHandler+0xc4)[0x2b56c1e6a2d4]<br class="">
[ 4] /libpetsc.so.3.10(PetscError+0x1b5)[0x2b56c1e69f65]<br class="">
[ 5] /libpetsc.so.3.10(PetscCommBuildTwoSidedFReq+0x19f0)[0x2b56c1e03cf0]<br class="">
[ 6] /libpetsc.so.3.10(+0x77db17)[0x2b56c2425b17]<br class="">
[ 7] /libpetsc.so.3.10(+0x77a164)[0x2b56c2422164]<br class="">
[ 8] /libpetsc.so.3.10(MatAssemblyBegin_MPIAIJ+0x36)[0x2b56c23912b6]<br class="">
[ 9] /libpetsc.so.3.10(MatAssemblyBegin+0xca)[0x2b56c1feccda]<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">By reconfiguring, you mean recompiling petsc with that option, correct?<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
</u></u></u></u></u></u></u></u></u></u></u></u></u></u></div><u class=""><u class=""><u class="">
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</u></u></u></blockquote><u class=""><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">Reconfiguring.<u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal"> Thanks,<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> Matt<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> <u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">Thank you.<u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">Karl<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
</u></u></u></u></u></u></div><u class=""><u class=""><u class="">
</u></u></u></div><u class=""><u class=""><u class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
<div class="">
<div class=""><p class="MsoNormal">On Thu, Jun 11, 2020 at 10:56 AM Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>> wrote:<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<blockquote style="border-width:medium medium medium 1pt;border-style:none none none solid;border-color:currentColor currentColor currentColor rgb(204,204,204);margin:5pt 0in 5pt 4.8pt;padding:0in 0in 0in 6pt" class="">
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<div class=""><p class="MsoNormal">On Thu, Jun 11, 2020 at 11:51 AM Karl Lin <<a href="mailto:karl.linkui@gmail.com" target="_blank" class="">karl.linkui@gmail.com</a>> wrote:<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
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<blockquote style="border-width:medium medium medium 1pt;border-style:none none none solid;border-color:currentColor currentColor currentColor rgb(204,204,204);margin:5pt 0in 5pt 4.8pt;padding:0in 0in 0in 6pt" class="">
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<div class=""><p class="MsoNormal">Hi, there<u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">We have written a program using Petsc to solve large sparse matrix system. It has been working fine for a while. Recently we encountered a problem when the size of the sparse matrix is larger than 10TB. We used several hundred nodes and
2200 processes. The program always crashes during MatAssemblyBegin.Upon a closer look, there seems to be something unusual. We have a little memory check during loading the matrix to keep track of rss. The printout of rss in the log shows normal increase up
to rank 2160, i.e., if we load in a portion of matrix that is 1GB, after MatSetValues for that portion, rss will increase roughly about that number. From rank 2161 onwards, the rss in every rank doesn't increase after matrix loaded. Then comes MatAssemblyBegin,
the program crashed on rank 2160. <u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">Is there a upper limit on the number of processes Petsc can handle? or is there a upper limit in terms of the size of the matrix petsc can handle? Thank you very much for any info.<u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">It sounds like you overflowed int somewhere. We try and check for this, but catching every place is hard. Try reconfiguring with<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> --with-64-bit-indices<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> Thanks,<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> Matt<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"> <u class=""><u class=""></u></u></p><u class=""><u class="">
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<blockquote style="border-width:medium medium medium 1pt;border-style:none none none solid;border-color:currentColor currentColor currentColor rgb(204,204,204);margin:5pt 0in 5pt 4.8pt;padding:0in 0in 0in 6pt" class="">
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<div class=""><p class="MsoNormal">Regards,<u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
<div class=""><p class="MsoNormal">Karl <u class=""><u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class="">
</u></u></u></u></u></u></div><u class=""><u class=""><u class="">
</u></u></u></blockquote><u class=""><u class=""><u class="">
</u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></div><u class=""><u class=""><u class=""><p class="MsoNormal"><br clear="all" class="">
<u class=""><u class=""></u></u></p><u class=""><u class="">
<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
</u></u></div><u class=""><u class=""><p class="MsoNormal">-- <u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">
-- Norbert Wiener<u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal"><u class=""> <u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal"><a href="https://urldefense.com/v3/__http:/www.cse.buffalo.edu/*knepley/__;fg!!Kjv0uj3L4nM6H-I!1KBn92fUc-8pAvJy257WTFoHD80IUf6u5iIhyL_vrliEm3psAK4KAJFCdygnPA$" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><u class=""><u class=""></u></u></p><u class=""><u class="">
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</u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></u></div><u class=""><u class=""><u class=""><p class="MsoNormal"><br clear="all" class="">
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<div class=""><p class="MsoNormal">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">
-- Norbert Wiener<u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal"><a href="https://urldefense.com/v3/__http:/www.cse.buffalo.edu/*knepley/__;fg!!Kjv0uj3L4nM6H-I!1KBn92fUc-8pAvJy257WTFoHD80IUf6u5iIhyL_vrliEm3psAK4KAJFCdygnPA$" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><u class=""><u class=""></u></u></p><u class=""><u class="">
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<div class=""><p class="MsoNormal">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">
-- Norbert Wiener<u class=""><u class=""></u></u></p><u class=""><u class="">
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<span style="font-size: 10pt;" class="">Schlumberger-Private</span><u class=""><u class=""></u></u></div><u class=""><u class="">
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