<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Sun, Apr 24, 2016 at 9:31 PM, TAY wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div bgcolor="#FFFFFF" text="#000000"><span class="">
    <br>
    <div>On 25/4/2016 2:52 AM, Matthew Knepley
      wrote:<br>
    </div>
    <blockquote type="cite">
      <div dir="ltr">
        <div class="gmail_extra">
          <div class="gmail_quote">On Sun, Apr 24, 2016 at 10:12 AM,
            Wee-beng TAY <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
            wrote:<br>
            <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
              <div bgcolor="#FFFFFF" text="#000000">
                <p>Hi Matt,</p>
                <p>I have attached the page which explains what to
                  modify to use PETSc with the K computer.</p>
              </div>
            </blockquote>
            <div>These changes are now in
              knepley/feature-configure-kcomputer, so you</div>
            <div><br>
            </div>
            <div>  cd $PETSC_DIR</div>
            <div>  git fetch</div>
            <div>  git checkout knepley/feature-configure-kcomputer</div>
            <div>  <follow configure instructions from your email></div>
          </div>
        </div>
      </div>
    </blockquote>
    <br></span>
    Hi,<br>
    <br>
    I got the warning and error:<br>
    <br>
    " --LD_SHARED="" --LDDFLAGS="" --with-openmp=1
    --with-mpiexec=mpiexec --known-endian=big --with-shared-libraries=0
    --with-blas-lapack-lib="-SSL2" --with-scalapack-lib="-SCALAPACK"
    --prefix=/home/hp150306/t00196/lib/petsc-3.6.4_rel
    --with-fortran-interfaces=1 --download-hypre=1 --with-debugging=0
    --with-batch=1<br>
===============================================================================<br>
                 Configuring PETSc to compile on your system<br>
===============================================================================<br>
    ===============================================================================                                                                                                                                                                                                                                                                                                                                                                  
    *****WARNING: PETSC_DIR appears to be a Git clone - but git is not
    found in
    PATH********                                                                                                                                                                                                                                                                                                                                             
    ===============================================================================                                                                                                                                      
    TESTING: checkCCompiler from
    config.setCompilers(config/BuildSystem/config/setCompilers.py:553)                                                                                                                      
    Exception AttributeError: AttributeError("Popen3 instance has no
    attribute 'pid'",) in <bound method Popen3.__del__ of
    <popen2.Popen3 instance at 0x107bbf38>> ignored<br>
*******************************************************************************<br>
                        UNABLE to EXECUTE BINARIES for ./configure<br>
-------------------------------------------------------------------------------<br>
    [Errno 12] Cannot allocate memory<br>
*******************************************************************************<br></div></blockquote><div><br></div><div>For configure problems, you must send configure.log</div><div><br></div><div>  Thanks,</div><div><br></div><div>     Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
    <br>
    Any other solution?<br>
    <br>
    Thanks!<div><div class="h5"><br>
    <blockquote type="cite">
      <div dir="ltr">
        <div class="gmail_extra">
          <div class="gmail_quote">
            <div><br>
            </div>
            <div>  Thanks,</div>
            <div><br>
            </div>
            <div>    Matt</div>
            <div> </div>
            <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
              <div bgcolor="#FFFFFF" text="#000000">
                <p>Thanks<br>
                </p>
                <div>
                  <div>
                    <p><br>
                    </p>
                    <br>
                    <div>On 24/4/2016 10:52 PM, Matthew Knepley wrote:<br>
                    </div>
                    <blockquote type="cite">
                      <div dir="ltr">
                        <div class="gmail_extra">
                          <div class="gmail_quote">On Sun, Apr 24, 2016
                            at 4:14 AM, Wee-beng TAY <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank"></a><a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
                            wrote:<br>
                            <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
                              <div bgcolor="#FFFFFF" text="#000000">
                                <p>Hi,</p>
                                <p>I was recently given access to
                                  Japan's K computer. I'm trying to
                                  compile PETSc on their sys, which uses
                                  Fujitsu's compiler. There's a help
                                  file but it's in Japanese. I guess I
                                  need to change some options to make
                                  PETSc compile with Fujitsu's
                                  compiler. </p>
                              </div>
                            </blockquote>
                            <div>It looks like they want us to include
                              some different options for the build. If
                              you send what you want,</div>
                            <div>I will make a branch for you to try
                              out.</div>
                            <div><br>
                            </div>
                            <div>  Thanks,</div>
                            <div><br>
                            </div>
                            <div>     Matt <br>
                            </div>
                            <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
                              <div bgcolor="#FFFFFF" text="#000000">
                                <p>Part of the help is below. So how
                                  should I use the diff or some other
                                  command to do the correction? I tried
                                  to run:</p>
                                <p> diff -u
                                  petsc-3.6.4/config/BuildSystem/config/<a href="http://package.py.org" target="_blank">package.py.org</a>
                                  petsc-3.6.4/config/BuildSystem/config/package.py</p>
                                <p>but got the err:</p>
                                <p>diff:
                                  petsc-3.6.4/config/BuildSystem/config/<a href="http://package.py.org" target="_blank">package.py.org</a>:
                                  No such file or directory</p>
                                <p>Please advice. Thanks.<br>
                                </p>
                                <p><br>
                                </p>
                                <div><i><code>$ diff -u petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/</code></i><i><code>package</code></i><i><code>.<a href="http://py.org" target="_blank">py.org</a>
                                      petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/</code></i><i><code>package</code></i><i><code>.py</code></i></div>
                                <div><i><code>--- petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/</code></i><i><code>package</code></i><i><code>.<a href="http://py.org" target="_blank">py.org</a>       <span> </span></code></i><i><code>2015</code></i><i><code>-</code></i><i><code>12</code></i><i><code>-</code></i><i><code>04</code></i><i><span> </span></i><i><code>14</code></i><i><code>:</code></i><i><code>06</code></i><i><code>:</code></i><i><code>42.000000000</code></i><i><span> </span></i><i><code>+</code></i><i><code>0900</code></i></div>
                                <div><i><code>+++ petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/</code></i><i><code>package</code></i><i><code>.py   <span> </span></code></i><i><code>2016</code></i><i><code>-</code></i><i><code>01</code></i><i><code>-</code></i><i><code>22</code></i><i><span> </span></i><i><code>11</code></i><i><code>:</code></i><i><code>09</code></i><i><code>:</code></i><i><code>37.000000000</code></i><i><span> </span></i><i><code>+</code></i><i><code>0900</code></i></div>
                                <div><i><code>@@ -</code></i><i><code>174</code></i><i><code>,</code></i><i><code>7</code></i><i><span> </span></i><i><code>+</code></i><i><code>174</code></i><i><code>,</code></i><i><code>7</code></i><i><span> </span></i><i><code>@@</code></i></div>
                                <div><i><code>     </code></i><i><code>return</code></i><i><span> </span></i><i><code>''</code></i></div>
                                <div><i> </i></div>
                                <div><i><code>   </code></i><i><code>def
                                      getSharedFlag(self,cflags):</code></i></div>
                                <div><i><code>-   <span> </span></code></i><i><code>for</code></i><i><span> </span></i><i><code>flag

                                      in [</code></i><i><code>'-PIC'</code></i><i><code>,<span> </span></code></i><i><code>'-fPIC'</code></i><i><code>,<span> </span></code></i><i><code>'-KPIC'</code></i><i><code>,<span> </span></code></i><i><code>'-qpic'</code></i><i><code>]:</code></i></div>
                                <div><i><code>+   <span> </span></code></i><i><code>for</code></i><i><span> </span></i><i><code>flag

                                      in [</code></i><i><code>'-KPIC'</code></i><i><code>,<span> </span></code></i><i><code>'-fPIC'</code></i><i><code>,<span> </span></code></i><i><code>'-PIC'</code></i><i><code>,<span> </span></code></i><i><code>'-qpic'</code></i><i><code>]:</code></i></div>
                                <div><i><code>       </code></i><i><code>if</code></i><i><span> </span></i><i><code>cflags.find(flag)

                                      >=</code></i><i><code>0</code></i><i><code>:<span> </span></code></i><i><code>return</code></i><i><span> </span></i><i><code>flag</code></i></div>
                                <div><i><code>     </code></i><i><code>return</code></i><i><span> </span></i><i><code>''</code></i></div>
                                <div><i><code> </code></i></div>
                                <div><i><code>$ diff -u petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/<a href="http://setCompilers.py.org" target="_blank">setCompilers.py.org</a>
                                      petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/setCompilers.py</code></i></div>
                                <div><i><code>--- petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/<a href="http://setCompilers.py.org" target="_blank">setCompilers.py.org</a>  <span> </span></code></i><i><code>2015</code></i><i><code>-</code></i><i><code>07</code></i><i><code>-</code></i><i><code>23</code></i><i><span> </span></i><i><code>00</code></i><i><code>:</code></i><i><code>22</code></i><i><code>:</code></i><i><code>46.000000000</code></i><i><span> </span></i><i><code>+</code></i><i><code>0900</code></i></div>
                                <div><i><code>+++ petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/setCompilers.py      <span> </span></code></i><i><code>2016</code></i><i><code>-</code></i><i><code>01</code></i><i><code>-</code></i><i><code>22</code></i><i><span> </span></i><i><code>11</code></i><i><code>:</code></i><i><code>10</code></i><i><code>:</code></i><i><code>05.000000000</code></i><i><span> </span></i><i><code>+</code></i><i><code>0900</code></i></div>
                                <div><i><code>@@ -</code></i><i><code>1017</code></i><i><code>,</code></i><i><code>7</code></i><i><span> </span></i><i><code>+</code></i><i><code>1017</code></i><i><code>,</code></i><i><code>7</code></i><i><span> </span></i><i><code>@@</code></i></div>
                                <div><i><code>       </code></i><i><code>self.pushLanguage(language)</code></i></div>
                                <div><i><code>       </code></i><i><code>#different

                                      compilers are sensitive to the
                                      order of testing these flags. So
                                      separete out GCC test.</code></i></div>
                                <div><i><code>       </code></i><i><code>if</code></i><i><span> </span></i><i><code>config.setCompilers.Configure.isGNU(self.getCompiler()):

                                      testFlags = [</code></i><i><code>'-fPIC'</code></i><i><code>]</code></i></div>
                                <div><i><code>-     <span> </span></code></i><i><code>else</code></i><i><code>:
                                      testFlags = [</code></i><i><code>'-PIC'</code></i><i><code>,<span> </span></code></i><i><code>'-fPIC'</code></i><i><code>,<span> </span></code></i><i><code>'-KPIC'</code></i><i><code>,</code></i><i><code>'-qpic'</code></i><i><code>]</code></i></div>
                                <div><i><code>+     <span> </span></code></i><i><code>else</code></i><i><code>:
                                      testFlags = [</code></i><i><code>'-KPIC'</code></i><i><code>,<span> </span></code></i><i><code>'-fPIC'</code></i><i><code>,<span> </span></code></i><i><code>'-PIC'</code></i><i><code>,</code></i><i><code>'-qpic'</code></i><i><code>]</code></i></div>
                                <div><i><code>       </code></i><i><code>for</code></i><i><span> </span></i><i><code>testFlag

                                      in testFlags:</code></i></div>
                                <div><i><code>         </code></i><i><code>try</code></i><i><code>:</code></i></div>
                                <div><i><code>           </code></i><i><code>self.logPrint(</code></i><i><code>'Trying

                                      '</code></i><i><code>+language+</code></i><i><code>'
                                      compiler flag '</code></i><i><code>+testFlag)</code></i></div>
                                <div><i><code>$ diff -u petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/packages/<a href="http://openmp.py.org" target="_blank">openmp.py.org</a>
                                      petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/packages/openmp.py</code></i></div>
                                <div><i><code>--- petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/packages/<a href="http://openmp.py.org" target="_blank">openmp.py.org</a>       <span> </span></code></i><i><code>2016</code></i><i><code>-</code></i><i><code>01</code></i><i><code>-</code></i><i><code>25</code></i><i><span> </span></i><i><code>15</code></i><i><code>:</code></i><i><code>42</code></i><i><code>:</code></i><i><code>23.000000000</code></i><i><code>+</code></i><i><code>0900</code></i></div>
                                <div><i><code>+++ petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/packages/openmp.py   <span> </span></code></i><i><code>2016</code></i><i><code>-</code></i><i><code>01</code></i><i><code>-</code></i><i><code>22</code></i><i><span> </span></i><i><code>17</code></i><i><code>:</code></i><i><code>13</code></i><i><code>:</code></i><i><code>52.000000000</code></i><i><span> </span></i><i><code>+</code></i><i><code>0900</code></i></div>
                                <div><i><code>@@ -</code></i><i><code>19</code></i><i><code>,</code></i><i><code>7</code></i><i><span> </span></i><i><code>+</code></i><i><code>19</code></i><i><code>,</code></i><i><code>8</code></i><i><span> </span></i><i><code>@@</code></i></div>
                                <div><i><code>     </code></i><i><code>self.found

                                      =<span> </span></code></i><i><code>0</code></i></div>
                                <div><i><code>     </code></i><i><code>self.setCompilers.pushLanguage(</code></i><i><code>'C'</code></i><i><code>)</code></i></div>
                                <div><i><code>     </code></i><i><code>#</code></i></div>
                                <div><i><code>-   <span> </span></code></i><i><code>for</code></i><i><span> </span></i><i><code>flag

                                      in [</code></i><i><code>"-fopenmp"</code></i><i><code>,
                                      # Gnu</code></i></div>
                                <div><i><code>+   <span> </span></code></i><i><code>for</code></i><i><span> </span></i><i><code>flag

                                      in [</code></i><i><code>"-Kopenmp"</code></i><i><code>,
                                      # Fujitsu</code></i></div>
                                <div><i><code>+                <span> </span></code></i><i><code>"-fopenmp"</code></i><i><code>,
                                      # Gnu</code></i></div>
                                <div><i><code>                  </code></i><i><code>"-qsmp=omp"</code></i><i><code>,#

                                      IBM XL C/C++</code></i></div>
                                <div><i><code>                  </code></i><i><code>"-h

                                      omp"</code></i><i><code>,   #
                                      Cray. Must come after XL because
                                      XL interprets<span> </span></code></i><i><code>this</code></i><i><span> </span></i><i><code>option

                                      as meaning</code></i><i><code>"-soname
                                      omp"</code></i></div>
                                <div><i><code>                  </code></i><i><code>"-mp"</code></i><i><code>,     

                                      # Portland Group</code></i></div>
                                <div><i> </i></div>
                                <div><i><code>$ diff -u ./petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/<a href="http://compilers.py.org" target="_blank">compilers.py.org</a>
                                      ./petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/compilers.py</code></i></div>
                                <div><i><code>--- ./petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/<a href="http://compilers.py.org" target="_blank">compilers.py.org</a>   <span> </span></code></i><i><code>2015</code></i><i><code>-</code></i><i><code>06</code></i><i><code>-</code></i><i><code>10</code></i><i><span> </span></i><i><code>06</code></i><i><code>:</code></i><i><code>24</code></i><i><code>:</code></i><i><code>49.000000000</code></i><i><span> </span></i><i><code>+</code></i><i><code>0900</code></i></div>
                                <div><i><code>+++ ./petsc-</code></i><i><code>3.6</code></i><i><code>.</code></i><i><code>3</code></i><i><code>/config/BuildSystem/config/compilers.py       <span> </span></code></i><i><code>2016</code></i><i><code>-</code></i><i><code>02</code></i><i><code>-</code></i><i><code>19</code></i><i><span> </span></i><i><code>11</code></i><i><code>:</code></i><i><code>56</code></i><i><code>:</code></i><i><code>12.000000000</code></i><i><span> </span></i><i><code>+</code></i><i><code>0900</code></i></div>
                                <div><i><code>@@ -</code></i><i><code>164</code></i><i><code>,</code></i><i><code>7</code></i><i><span> </span></i><i><code>+</code></i><i><code>164</code></i><i><code>,</code></i><i><code>7</code></i><i><span> </span></i><i><code>@@</code></i></div>
                                <div><i><code>   </code></i><i><code>def
                                      checkCLibraries(self):</code></i></div>
                                <div><i><code>     </code></i><i><code>''</code></i><i><code>'Determines

                                      the libraries needed to link with
                                      C'</code></i><i><code>''</code></i></div>
                                <div><i><code>     </code></i><i><code>oldFlags

                                      = self.setCompilers.LDFLAGS</code></i></div>
                                <div><i><code>-   
                                      self.setCompilers.LDFLAGS +=<span> </span></code></i><i><code>'
                                      -v'</code></i></div>
                                <div><i><code>+   
                                      self.setCompilers.LDFLAGS +=<span> </span></code></i><i><code>'
                                      -###'</code></i></div>
                                <div><i><code>     </code></i><i><code>self.pushLanguage(</code></i><i><code>'C'</code></i><i><code>)</code></i></div>
                                <div><i><code>     </code></i><i><code>(output,

                                      returnCode) = self.outputLink(</code></i><i><code>''</code></i><i><code>,<span> </span></code></i><i><code>''</code></i><i><code>)</code></i></div>
                                <div><i><code>     </code></i><i><code>self.setCompilers.LDFLAGS

                                      = oldFlags</code></i></div>
                                <div><i><code>@@ -</code></i><i><code>413</code></i><i><code>,</code></i><i><code>7</code></i><i><span> </span></i><i><code>+</code></i><i><code>413</code></i><i><code>,</code></i><i><code>7</code></i><i><span> </span></i><i><code>@@</code></i></div>
                                <div><i><code>   </code></i><i><code>def
                                      checkCxxLibraries(self):</code></i></div>
                                <div><i><code>     </code></i><i><code>''</code></i><i><code>'Determines

                                      the libraries needed to link with
                                      C++'</code></i><i><code>''</code></i></div>
                                <div><i><code>     </code></i><i><code>oldFlags

                                      = self.setCompilers.LDFLAGS</code></i></div>
                                <div><i><code>-   
                                      self.setCompilers.LDFLAGS +=<span> </span></code></i><i><code>'
                                      -v'</code></i></div>
                                <div><i><code>+   
                                      self.setCompilers.LDFLAGS +=<span> </span></code></i><i><code>'
                                      -###'</code></i></div>
                                <div><i><code>     </code></i><i><code>self.pushLanguage(</code></i><i><code>'Cxx'</code></i><i><code>)</code></i></div>
                                <div><i><code>     </code></i><i><code>(output,

                                      returnCode) = self.outputLink(</code></i><i><code>''</code></i><i><code>,<span> </span></code></i><i><code>''</code></i><i><code>)</code></i></div>
                                <div><i><code>     </code></i><i><code>self.setCompilers.LDFLAGS

                                      = oldFlags</code></i></div>
                                <p><br>
                                </p>
                                <p><br>
                                </p>
                                <p><br>
                                </p>
                                <p><br>
                                </p>
                                <p><br>
                                </p>
                              </div>
                            </blockquote>
                          </div>
                          <br>
                          <br clear="all">
                          <div><br>
                          </div>
                          -- <br>
                          <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>
                        </div>
                      </div>
                    </blockquote>
                    <br>
                  </div>
                </div>
              </div>
            </blockquote>
          </div>
          <br>
          <br clear="all">
          <div><br>
          </div>
          -- <br>
          <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>
        </div>
      </div>
    </blockquote>
    <br>
  </div></div></div>

</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">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>
</div></div>