[petsc-users] HDF5 installation problems

Tue Mar 6 10:54:15 CST 2012

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: petsc-users-bounces at mcs.anl.gov 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.
>
>

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