petsc: :info:configure Fortran could not successfully link C++ objects

[jmstephensjr@…]

Attempting to upgrade from petsc @3.3-p0_0. Upgrade preceded by selfupdate and clean --all petsc. Software stack as follows: macports version 2.1.2, Xcode version 3.2.6, and Mac OS X version 10.6.8.

By the way, libyaml @0.1.4_1 installed just fine. (I think this is a new dependency.)

[mmoll@…]

Did you install openmpi (or mpich) with one of the gcc4x variants? You need a working version of openmpif90. If that's not it, please attach configure.log from the petsc build directory (/opt/local/var/macports/build/.../configure.log).

[jmstephensjr@…]

Attaching configure.log, found in /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_petsc/petsc/work/petsc-3.3-p2.

[jmstephensjr@…]

Replying to mmoll@…:

Did you install openmpi (or mpich) with one of the gcc4x variants? You need a working version of openmpif90. If that's not it, please attach configure.log from the petsc build directory (/opt/local/var/macports/build/.../configure.log).

I have installed/active the port openmpi @1.5.5_0+gcc45.

[mmoll@…]

Does the attached patch of the petsc Portfile fix the problem?

[jmstephensjr@…]

Replying to mmoll@…:

Does the attached patch of the petsc Portfile fix the problem?

I want to make sure I am on the same page before I clobber anything. Here are the steps:

1. Copy Portfile.diff to /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/math/petsc

2. execute /usr/bin/patch Portfile < Portfile.diff

Thanks.

[mmoll@…]

Yes, please give that a try and let me know if it works. If you already have petsc installed, you need to deactivate it first ("sudo port deactivate petsc") before upgrading to the new version.

[jmstephensjr@…]

OK, I uninstalled slepc and deactivated petsc. I still have petsc @3.3-p0_0 installed, but not active. I ran the steps, and the upgrade failed. I have attached new logs.

If you would like, I can completely uninstall petsc, run clean --all petsc, and start with a fresh install. After it fails (how do you download only?), I will run the patch to the portfile, and try to reinstall, and give you an update.

Note: as we are heading into Monday, I want to make clear that this is not urgent on my end... and of course, thanks for all your help.

[jmstephensjr@…]

file after patch, located in /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/math/petsc

[mmoll@…]

Ah, I think you need to install hdf5-18 with one of the gcc4X variants. Petsc is looking for libhdf5_fortran.

[jmstephensjr@…]

New error...

Incomplete LAPACK install? Perhaps lapack package is installed - but lapack-dev/lapack-devel is required.

Here is what I did. I already had hdf5-18 @1.8.9_0 installed on account of octave. I ran uninstall and clean --all on hdf5-18 @1.8.9_0 and installed the gcc45 variant (which is the variant used in openmpi, atlas, etc). I then ran uninstall and clean --all on petsc and did a fresh install. I got the new error.

Logs to follow.

[jmstephensjr@…]

after rebuild of hdf5-18 with +gcc45

[jmstephensjr@…]

after rebuild of hdf5-18 with +gcc45

[jmstephensjr@…]

list of ports installed

[mmoll@…]

I think this time it's failing because its atlas detection is broken. Can you check if things work if you temporarily deactivate atlas? If so, then the next thing is create atlas & accelerate variants and get petsc to use the right one.

[jmstephensjr@…]

Success.

Firstly, I deactivated atlas @3.10.0_0+gcc45, which required that I also deactivate qrupdate @1.1.2_1+atlas+gcc45 and octave @3.2.4_8+atlas+gcc45.

Secondly, I ran clean --all on petsc and did a fresh install. It failed.

Thirdly, I applied Portfile.diff and tried again to install. This time it worked. I now have petsc @3.3-p2_1+openmpi (active).

I will attached logs for your reference.

What now? Does this mean that petsc is looking in the wrong place for LAPACK or is atlas writing the files in the wrong place? Should I open a ticket on atlas?

Can I reactivate the deactivated ports?

[jmstephensjr@…]

Um...

RE the attaching of logs for your reference... it seems that both /opt/local/var/macports/logs and /opt/local/var/macports/build are empty. I realize now that at the conclusion of the successful install the port gets cleaned and work files are removed.

Let me know if there are (other) files you would like me to send along.

[jmstephensjr@…]

Replying to jmstephensjr@…:

What now? Does this mean that petsc is looking in the wrong place for LAPACK or is atlas writing the files in the wrong place? Should I open a ticket on atlas?

I went back and read your last comment again. I realize that you already answered the question. I will wait for an atlas and accelerate variant.

[mmoll@…]

In the meantime you can re-activate your deactivated ports.

[mmoll@…]

Should be fixed in r100485.