Dear Jed, Thanks for your help.
After some more investigation it turned out that hdf5 was testing its parallel abilities with 6 processes during the testing if (if I installed it via PETSC configure). After this I installed hdf5 manually and then configured Petsc using: ./configure --with-shared-libraries --with-hdf5-lib=/home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6/hdf5/lib/libhdf5.so --with-hdf5 --with-hdf5-include=/home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6/hdf5/include/ Now it works like a charm! Thanks again for your help. Kind regards, Steven -----Original Message----- From: [email protected] on behalf of Jed Brown Sent: Sun 3/4/2012 3:15 PM To: PETSc users list Subject: Re: [petsc-users] HDF5 installation problems On Sun, Mar 4, 2012 at 05:43, Haren, S.W. van (Steven) <vanharen at nrg.eu>wrote: > Dear Jed, > > Thanks for your reply. > > These are the last lines from the configure.log: > > sh: cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && > make clean && make && make install > Executing: cd > /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make > clean && make && make install > Runaway process exceeded time limit of 2500s > Possibilities: 1. System clock was changed or the machine was suspended, causing incorrect timeout. (As an aside, the Python docs are horrible. They act like time is one thing, so I have to read the source code to find out that threading.Thread.join() implements a timeout using time(2) which is neither monotone nor continuous.) 2. The compilation actually takes a long time on this machine, perhaps because it doesn't get much time to run due to other jobs. You could try increasing the timeout or running make manually from externalpackages/hdf5-1.8.6/. 3. The hdf5 build process is getting stuck somewhere, I suggest trying to complete the install manually from externalpackages/hdf5-1.8.6/. If you can't get it working, send configure.log and HDF5 attempted build logs to petsc-maint at mcs.anl.gov. > sh: > > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > > ------------------------------------------------------------------------------- > Error running make on HDF5: Could not execute "cd > /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make > clean && make && make install": > Runaway process exceeded time limit of 2500s > > ******************************************************************************* > File "./config/configure.py", line 283, in petsc_configure > framework.configure(out = sys.stdout) > File > "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/framework.py", > line 925, in configure > child.configure() > File > "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", > line 506, in configure > self.executeTest(self.configureLibrary) > File > "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/base.py", > line 115, in executeTest > ret = apply(test, args,kargs) > File > "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/packages/hdf5.py", > line 63, in configureLibrary > config.package.Package.configureLibrary(self) > File > "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", > line 433, in configureLibrary > for location, directory, lib, incl in self.generateGuesses(): > File > "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", > line 228, in generateGuesses > d = self.checkDownload(1) > File > "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", > line 313, in checkDownload > return self.getInstallDir() > File > "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", > line 183, in getInstallDir > return os.path.abspath(self.Install()) > File > "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/packages/hdf5.py", > line 56, in Install > raise RuntimeError('Error running make on HDF5: '+str(e)) > > Using the top command I cannot really identify a process that uses all the > memory. The memory use increases untill completely full. But the maximum > percentage used by any process does not go above 10 percent. Even when the > compilation is stopped the memory is not freed. I don't really understand > this. Could you give me a few pointers based on the configure.log output? > > Hoe should I attach a debugger? Any good links were I can read how to do > that? > > Thanks in advance. > > Kind regards, > > Steven > > > -----Original Message----- > From: petsc-users-bounces at mcs.anl.gov on behalf of Jed Brown > Sent: Wed 2/29/2012 10:43 PM > To: PETSc users list > Subject: Re: [petsc-users] HDF5 installation problems > > On Wed, Feb 29, 2012 at 15:35, Haren, S.W. van (Steven) <vanharen at nrg.eu > >wrote: > > > Dear all, > > > > I try to configure Petsc to use HDF5. > > > > During the HDF5 compilation stage the memory use increases untill the > > computer basically stalls and almost all memory is used. After 2500s the > > compilation is stopped because of a runaway process. > > > > Check configure.log and/or attach a debugger to find out where it got > stuck. At least use "top" to find out which process is taking all the time > and memory. > > -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 5689 bytes Desc: not available URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120306/722d9c8f/attachment.bin>
