[WIP] Create Jenkinsfile

[tjesser-ucdavis-edu]

A Jenkinsfile describes the build sequence Jenkins uses without hiding the information in Jenkins settings.

Let me know if the Jenkins build should use autotools instead of cmake.

[tjesser-ucdavis-edu]

This PR depends on #9 as the buildenv container needs to install a Fortran compiler. I really should have caught that earlier.

[tjesser-ucdavis-edu]

I think this pull request is mostly complete, but I'm concerned about the output from the make test.

There appears to be a whole lot of this:

[cf965bf6687b:05381] Read -1, expected 1277952, errno = 1
[cf965bf6687b:05379] Read -1, expected 1277952, errno = 1
[cf965bf6687b:05382] Read -1, expected 1277952, errno = 1
[cf965bf6687b:05380] Read -1, expected 1277952, errno = 1
[cf965bf6687b:05382] Read -1, expected 3714048, errno = 1
[cf965bf6687b:05381] Read -1, expected 3833856, errno = 1
[cf965bf6687b:05380] Read -1, expected 3714048, errno = 1
[cf965bf6687b:05379] Read -1, expected 3833856, errno = 1
[cf965bf6687b:05381] Read -1, expected 5428224, errno = 1
[cf965bf6687b:05382] Read -1, expected 5603328, errno = 1
[cf965bf6687b:05380] Read -1, expected 5603328, errno = 1
[cf965bf6687b:05379] Read -1, expected 5428224, errno = 1
[cf965bf6687b:05381] Read -1, expected 1867776, errno = 1
[cf965bf6687b:05379] Read -1, expected 1867776, errno = 1
[cf965bf6687b:05380] Read -1, expected 1867776, errno = 1
[cf965bf6687b:05382] Read -1, expected 1867776, errno = 1
[cf965bf6687b:05380] Read -1, expected 1277952, errno = 1
[cf965bf6687b:05382] Read -1, expected 1277952, errno = 1
[cf965bf6687b:05381] Read -1, expected 1277952, errno = 1
[cf965bf6687b:05379] Read -1, expected 1277952, errno = 1
[cf965bf6687b:05379] Read -1, expected 3833856, errno = 1
[cf965bf6687b:05380] Read -1, expected 3714048, errno = 1
[cf965bf6687b:05381] Read -1, expected 3833856, errno = 1

@hirokemono Can you identify any cause for the large amount of errors?

[hirokemono]

Hi, Tyler, Is there any way to access the machine which Jenkins running? I don’t meet these errors in my environment, and This error message is not enough to figure out the problem. Thanks, Hiro.

…

2019/04/18 17:02、Tyler Esser ***@***.***>のメール: I think this pull request is mostly complete, but I'm concerned about the output from the make test. There appears to be a whole lot of this: [cf965bf6687b:05381] Read -1, expected 1277952, errno = 1 [cf965bf6687b:05379] Read -1, expected 1277952, errno = 1 [cf965bf6687b:05382] Read -1, expected 1277952, errno = 1 [cf965bf6687b:05380] Read -1, expected 1277952, errno = 1 [cf965bf6687b:05382] Read -1, expected 3714048, errno = 1 [cf965bf6687b:05381] Read -1, expected 3833856, errno = 1 [cf965bf6687b:05380] Read -1, expected 3714048, errno = 1 [cf965bf6687b:05379] Read -1, expected 3833856, errno = 1 [cf965bf6687b:05381] Read -1, expected 5428224, errno = 1 [cf965bf6687b:05382] Read -1, expected 5603328, errno = 1 [cf965bf6687b:05380] Read -1, expected 5603328, errno = 1 [cf965bf6687b:05379] Read -1, expected 5428224, errno = 1 [cf965bf6687b:05381] Read -1, expected 1867776, errno = 1 [cf965bf6687b:05379] Read -1, expected 1867776, errno = 1 [cf965bf6687b:05380] Read -1, expected 1867776, errno = 1 [cf965bf6687b:05382] Read -1, expected 1867776, errno = 1 [cf965bf6687b:05380] Read -1, expected 1277952, errno = 1 [cf965bf6687b:05382] Read -1, expected 1277952, errno = 1 [cf965bf6687b:05381] Read -1, expected 1277952, errno = 1 [cf965bf6687b:05379] Read -1, expected 1277952, errno = 1 [cf965bf6687b:05379] Read -1, expected 3833856, errno = 1 [cf965bf6687b:05380] Read -1, expected 3714048, errno = 1 [cf965bf6687b:05381] Read -1, expected 3833856, errno = 1 @hirokemono <https://github.com/hirokemono> Can you identify any cause for the large amount of errors? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABJC6BZMPVJU6LCCOEXQAX3PRED2FANCNFSM4HGVYODA>.

[tjesser-ucdavis-edu]

If you can run Docker, you should be able to recreate the environment by running the same commands.

Enter the container:

docker run -it --rm geodynamics/calypso-buildenv-bionic /bin/bash

Inside the container:

git clone https://github.com/geodynamics/calypso
cd calypso
./configure --enable-fftw3 --with-blas --with-hdf5
make

[tjesser-ucdavis-edu]

I ran the container locally and got an OpenMPI error about running as root. Is there somewhere in the Makefile that we could add the --allow-run-as-root flag to mpirun?

Since most users probably shouldn't run be running mpirun as root, it'd be best to add the flag in the Jenkinsfile, instead of changing the Makefile directly.

[jedbrown]

You can export OMPI_ALLOW_RUN_AS_ROOT=1 from the Jenkinsfile if you really need to run as root. I think you'd be better off switching your container to non-root.

[tjesser-ucdavis-edu]

According to this PR open-mpi/ompi#5598, the envvar option is only available in OpenMPI 4.x. Ubuntu Bionic only has 2.1.1: https://packages.ubuntu.com/source/bionic/openmpi.

[jedbrown]

Oh, sad. FWIW, I generally use MPICH in containers for compatibility with Shifter/Singularity (not relevant here), and always use non-root containers on Jenkins.

[tjesser-ucdavis-edu]

I created a user in the container and ran the build, and interestingly, got the same Read -1 errors that Jenkins has. I wonder if Jenkins creates a user in the container.

Container commands:

useradd -m calypso_user
su - calypso_user
git clone https://github.com/geodynamics/calypso
cd calypso
./configure --enable-fftw3 --with-blas --with-hdf5
make

[hirokemono]

Hi, Tyler, These error message come from openMPI. I found a discussion about the same error for OpenMPI v.3 (and v.4 also) in docker container. Vader in a Docker Container · Issue #4948 · open-mpi/ompi <open-mpi/ompi#4948> Following the suggestion, I add a export command before make in Jenkinsfile as sh 'export OMPI_MCA_btl_vader_single_copy_mechanism=none; make' Now these errors are gone, but please update if you have more smarter way to describe the environmental valuables. Hiro.

…

2019/04/18 17:13、Hiroaki Matsui ***@***.***>のメール: Hi, Tyler, Is there any way to access the machine which Jenkins running? I don’t meet these errors in my environment, and This error message is not enough to figure out the problem. Thanks, Hiro. > 2019/04/18 17:02、Tyler Esser ***@***.*** ***@***.***>>のメール: > > I think this pull request is mostly complete, but I'm concerned about the output from the make test. > > There appears to be a whole lot of this: > > [cf965bf6687b:05381] Read -1, expected 1277952, errno = 1 > [cf965bf6687b:05379] Read -1, expected 1277952, errno = 1 > [cf965bf6687b:05382] Read -1, expected 1277952, errno = 1 > [cf965bf6687b:05380] Read -1, expected 1277952, errno = 1 > [cf965bf6687b:05382] Read -1, expected 3714048, errno = 1 > [cf965bf6687b:05381] Read -1, expected 3833856, errno = 1 > [cf965bf6687b:05380] Read -1, expected 3714048, errno = 1 > [cf965bf6687b:05379] Read -1, expected 3833856, errno = 1 > [cf965bf6687b:05381] Read -1, expected 5428224, errno = 1 > [cf965bf6687b:05382] Read -1, expected 5603328, errno = 1 > [cf965bf6687b:05380] Read -1, expected 5603328, errno = 1 > [cf965bf6687b:05379] Read -1, expected 5428224, errno = 1 > [cf965bf6687b:05381] Read -1, expected 1867776, errno = 1 > [cf965bf6687b:05379] Read -1, expected 1867776, errno = 1 > [cf965bf6687b:05380] Read -1, expected 1867776, errno = 1 > [cf965bf6687b:05382] Read -1, expected 1867776, errno = 1 > [cf965bf6687b:05380] Read -1, expected 1277952, errno = 1 > [cf965bf6687b:05382] Read -1, expected 1277952, errno = 1 > [cf965bf6687b:05381] Read -1, expected 1277952, errno = 1 > [cf965bf6687b:05379] Read -1, expected 1277952, errno = 1 > [cf965bf6687b:05379] Read -1, expected 3833856, errno = 1 > [cf965bf6687b:05380] Read -1, expected 3714048, errno = 1 > [cf965bf6687b:05381] Read -1, expected 3833856, errno = 1 > @hirokemono <https://github.com/hirokemono> Can you identify any cause for the large amount of errors? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABJC6BZMPVJU6LCCOEXQAX3PRED2FANCNFSM4HGVYODA>. >