[petsc-users] HDF5 installation problems

[Haren, S.W. van (Steven)]

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
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.