<div dir="ltr">I'll leave it running for a few hours and see what happens.<div><br></div><div>In the meantime, is it possible to tell PETSc to compile a specific .c file using gcc-4.9? Something along the lines of this:</div>
<div><br></div><div><div>ALL:</div><div><br></div><div>include ${PETSC_DIR}/conf/variables</div><div>include ${PETSC_DIR}/conf/rules</div><div>include ${PETSC_DIR}/conf/test</div><div><br></div><div>main: main.o</div><div>
<span class="" style="white-space:pre"> </span>gcc-4.9 -${CLINKER} -fopenmp -o main main.o ${PETSC_LIB}</div><div><span class="" style="white-space:pre"> </span>${RM} -f main.o</div></div><div><br></div><div>The main reason I want to compile with gcc-4.9 is because I need to use openmp for a simple parallel for loop. With the gcc compiler I have now (clang), there's no support for openmp. I can get gcc-4.9 to work outside of PETSc, but am not sure how to get it to work here if I want to do it for a single example, or if that's even possible.</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 24, 2014 at 10:03 PM, Barry Smith <span dir="ltr"><<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Leave it to run for several hours it could be that gcc-4.9 is just taking a very long time on mpich.<br>
<span class="HOEnZb"><font color="#888888"><br>
Barry<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On Apr 24, 2014, at 8:35 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com">knepley@gmail.com</a>> wrote:<br>
<br>
> On Thu, Apr 24, 2014 at 9:27 PM, Justin Dong <<a href="mailto:jsd1@rice.edu">jsd1@rice.edu</a>> wrote:<br>
> Hi all,<br>
><br>
> I'm trying to configure PETSc on Mac OS X with gcc-4.9. Currently, it's configured with gcc that comes with Xcode, but I want to use gcc-4.9 that I installed myself. I try:<br>
><br>
><br>
> ./configure --with-cc=gcc-4.9 --with-fc=gfortran --download-f-blas-lapack --download-mpich<br>
><br>
><br>
><br>
> But while configuring MPICH it gets stuck indefinitely. I've included the output below after I terminate the process. I don't have this issue if I just configure with cc=gcc. Any ideas what the problem is here?<br>
><br>
> From the stack trace, its just taking a long time. If it overruns the timeout, it should just die. You can try<br>
> running using -useThreads=0 if you suspect the timeout is not working.<br>
><br>
> Matt<br>
><br>
> ^CTraceback (most recent call last):<br>
><br>
> File "./configure", line 10, in <module><br>
><br>
> execfile(os.path.join(os.path.dirname(__file__), 'config', 'configure.py'))<br>
><br>
> File "./config/configure.py", line 372, in <module><br>
><br>
> petsc_configure([])<br>
><br>
> File "./config/configure.py", line 287, in petsc_configure<br>
><br>
> framework.configure(out = sys.stdout)<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/framework.py", line 933, in configure<br>
><br>
> child.configure()<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py", line 558, in configure<br>
><br>
> self.executeTest(self.configureLibrary)<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/base.py", line 115, in executeTest<br>
><br>
> ret = apply(test, args,kargs)<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/packages/MPI.py", line 748, in configureLibrary<br>
><br>
> config.package.Package.configureLibrary(self)<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py", line 486, in configureLibrary<br>
><br>
> for location, directory, lib, incl in self.generateGuesses():<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py", line 232, in generateGuesses<br>
><br>
> d = self.checkDownload(1)<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/packages/MPI.py", line 351, in checkDownload<br>
><br>
> return config.package.Package.checkDownload(self, requireDownload)<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py", line 340, in checkDownload<br>
><br>
> return self.getInstallDir()<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py", line 187, in getInstallDir<br>
><br>
> return os.path.abspath(self.Install())<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/packages/MPI.py", line 366, in Install<br>
><br>
> return self.InstallMPICH()<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/packages/MPI.py", line 544, in InstallMPICH<br>
><br>
> output,err,ret = config.base.Configure.executeShellCommand('cd '+mpichDir+' && ./configure '+args, timeout=2000, log = self.framework.log)<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/script.py", line 254, in executeShellCommand<br>
><br>
> (output, error, status) = runInShell(command, log, cwd)<br>
><br>
> File "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/script.py", line 243, in runInShell<br>
><br>
> thread.join(timeout)<br>
><br>
> File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 958, in join<br>
><br>
> self.__block.wait(delay)<br>
><br>
> File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 358, in wait<br>
><br>
> _sleep(delay)<br>
><br>
><br>
> KeyboardInterrupt<br>
><br>
><br>
><br>
><br>
><br>
> Sincerely,<br>
><br>
> Justin<br>
><br>
><br>
><br>
><br>
> --<br>
> 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<br>
<br>
</div></div></blockquote></div><br></div>