Error determining PETSC version

[James B Tompkins]

Trying to do a fresh moose install on Ubuntu 14.04, and I'm having issues testing the install.  When running 'make -j8' I get various errors associated with petsc functions, and when attempting to run the tests I get "Error determining PETSC version."  I have tried using the Redistributable Package as well as the manual PETSC installation, but both return the same error at the testing stage.  Any help would be much appreciated. 

[Peterson, JW]

It sounds like libmesh got built without Petsc enabled. I'm not
exactly sure how that could have happened, but we'll know more if you
can send us your config.log file. It should be in
$MOOSE_DIR/libmesh/build/config.log, where $MOOSE_DIR is the location
of your github checkout of MOOSE.

--
John

[James B. Tompkins]

Sorry about that.  The file is attached.

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James B. Tompkins | Graduate Research Assistant

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Nuclear Science Center | Texas Engineering Experiment Station

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[Cody Permann]

John is correct, You can see from the config.log that libMesh is unable to find PETSc. There are a couple of things wrong here. It appears that you aren't using our environment or our "update_and_rebuild_libmesh.sh" script. Why are you overriding the values of CC and CXX? 

Make sure that you are sourcing the moose_profile so that the necessary libraries and compilers are setup correctly on your system. (See the Post Install step http://mooseframework.org/getting-started/ubuntu-1404/)

After starting a new terminal, run $MOOSE_DIR/scripts/update_and_rebuild_libmesh.sh and you should be good to go.

Let us know if you continue to run into problems.

Cody

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[Peterson, JW]

On Wed, Jan 7, 2015 at 9:17 AM, Cody Permann <codyp...@gmail.com> wrote:
> John is correct, You can see from the config.log that libMesh is unable to
> find PETSc. There are a couple of things wrong here. It appears that you
> aren't using our environment or our "update_and_rebuild_libmesh.sh" script.
> Why are you overriding the values of CC and CXX?

Right, the lines Cody is referring to in config.log are:

configure:29464: checking /include/petscversion.h usability
configure:29464: gcc -c conftest.c >&5
conftest.c:131:35: fatal error: /include/petscversion.h: No such file
or directory

This means that the environment variable $PETSC_DIR is not set. Which
leads to Cody's next point:

> Make sure that you are sourcing the moose_profile so that the necessary
> libraries and compilers are setup correctly on your system. (See the Post
> Install step http://mooseframework.org/getting-started/ubuntu-1404/)

Loading the proper moose-dev module is what sets $PETSC_DIR.

--
John

[James B. Tompkins]

I had added the source moose environment lines to my .bashrc file, closed all terminals then opened a new one and ran the /scripts/update_and_rebuild_libmesh.sh script after following the instructions provided for Ubuntu 14.04.  The following modules were loaded:

moose/.openmpi-1.8.1_gcc
moose/.openmpi_petsc-3.5.1-gcc
moose/.cppunit-gcc
moose-dev-gcc
moose-tools

When I received the PETSC version error, I decided to try the manual installation instructions (http://mooseframework.org/wiki/BasicManualInstallation/Linux/) and removed all moose directories (~projects/moose/ as well as /opts/moose/) created from the redistributable method.  Following the manual installation instructions, I again got the PETSC version error (I think this is how the CC and CXX values were overridden).  Before contacting the group, I removed manual install files and tried the Ubuntu 14.04 instructions again with the same results.

--
John

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[James B. Tompkins]

I did not have cmake the first time I tried to go through the Ubuntu 14.04 instructions (it is not mentioned in the Ubuntu instructions, but the manual installation instructions mention it is required to build petsc).  I only obtained cmake after going through the manual installation.  Could this be part of the problem?

[Derek Gaston]

To figure this out it will be best if you go back to the redistributable.  Too many variables in a manual setup.

Can you very meticulously go back through the Getting Started instructions here: http://mooseframework.org/getting-started/ubuntu-1404/

Then, when it doesn't work again can you do a:

env > enviro.txt

And email the enviro.txt file that gets created to us?

Sorry your having trouble - let's get it figured out!

Derek

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James B. Tompkins | Graduate Research Assistant

Department of Nuclear Engineering | Texas A&M University
3133 TAMU | College Station, TX 77843

Nuclear Science Center | Texas Engineering Experiment Station

1095 Nuclear Science Road | College Station, TX 77843

ph: 979.845.7551 | mobile: 214.549.6174 | tomp...@tamu.edu | Zachary 60E

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James B. Tompkins | Graduate Research Assistant

Department of Nuclear Engineering | Texas A&M University
3133 TAMU | College Station, TX 77843

Nuclear Science Center | Texas Engineering Experiment Station

1095 Nuclear Science Road | College Station, TX 77843

ph: 979.845.7551 | mobile: 214.549.6174 | tomp...@tamu.edu | Zachary 60E

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[James B. Tompkins]

Attached is the file requested.

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[Miller, Jason M]

That environment looks fine to me.

Can you run through the update_and_rebuild_libmesh.sh script again and send the libmesh config log?

Thanks!

Jason Miller

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[James B. Tompkins]

Just finished running.

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[Miller, Jason M]

This is very odd to me, as your env looks fine, but your libmesh look contains nothing about any of that 'fine' environment :/

Can you verify, that before you run the update_and_rebuild_libmesh.sh script, that the following prints out something:

echo $PETSC_DIR

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[James B. Tompkins]

Yes, it returns the directory listed in the env (/opt/moose/petsc/openmpi_petsc-3.5.1/gcc-opt).

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[Miller, Jason M]

Is your default shell bash?

echo $0

And in which profile did you use to add the commands to source the /opt/moose/environments/moose_profile (.bash_profile, .profile, etc)

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[James B. Tompkins]

Yes, the default shell is bash.  I added the lines to the ~/.bashrc file in my home directory (/home/james/) by editing the file in Vi and saving after pasting the lines in the file.

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[Miller, Jason M]

Well... if the results of `env` are spot on (which they seem to be), and you attempt to build libmesh via that script, using the same terminal in which you just verified `env`, echo $PETSC_DIR and all that are returning the correct stuff... I am pretty much out of ideas. The only thing that would prevent the immediate environment from not being used when running a command, would be through the use of sudo or some such (which you should not be doing to build libMesh).

We can skip using the update_abd_rebuild_libmesh.sh script all together, just to see if indeed, configure is not picking up PETSC_DIR.

echo $PETSCH_DIR  # :) just for good measure!

mkdir /home/james/projects/moose/libmesh/testing

cd /home/james/projects/moose/libmesh/testing

../configure --with-methods="opt" \

             --prefix=/home/james/projects/moose/libmesh/testing-install \

             --enable-silent-rules \

             --enable-unique-id \

             --disable-warnings \

             --disable-cxx11 \

             --enable-openmp

lets see what the above does...?

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[James B. Tompkins]

Well, I think we have cornered the issue.  I was using sudo to run the script because without it, the script cannot write to /usr/bin/install. 

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[Cody Permann]

You only need "sudo" if you are installing to a location where you don't have permissions which we don't require. You certainly don't write to "/usr/bin/install", that's a program. You should be able to run the script without elevated permissions.

Cody

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[Derek Gaston]

What script can't write to /usr/bin/install?  None of our scripts try to do that.

You should install the redistributable package using sudo (like the instructions say)... but everything else is done just as your regular user in your home directory (just copy and paste the commands from here: http://mooseframework.org/getting-started/ )

Derek

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[James B. Tompkins]

Sorry, I'm a bit rusty with linux.  When I ran the script without sudo, the terminal reported that it didn't have permissions to /usr/bin/install and terminated the libmesh build. 

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[Cody Permann]

Not quite, you do have access to run "/usr/bin/install", but youl may not have permissions to write to the location it's attempting to write. I believe the only way that would happen is if you set your LIBMESH_DIR to a location where you don't have write permission. We do not require that you set LIBMESH_DIR at all.

Cody

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[James B. Tompkins]

It was the update_and_rebuild_libmesh.sh script that was having issues with permissions.  Let me check again after Jason's fix finishes running, but just before running it, I tried running the update libmesh script unelevated and it was still having permissions issues.

[Andrs, David]

ls -l /usr/bin/install ?

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[James B. Tompkins]

Alright, got it fixed.  Thanks for the help everyone!

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