On Sun, Mar 4, 2012 at 05:43, Haren, S.W. van (Steven) <vanharen@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@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@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@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.