module load inside rpmbuild inside docker

[Christoph Junghans]

Hi,

I wanted to bump the legion package to 19.04.0
(https://bugzilla.redhat.com/show_bug.cgi?id=1705033), however for
some reason all tests segfault with openmpi
(https://koji.fedoraproject.org/koji/taskinfo?taskID=34577005), so I
reported this upstream
(https://github.com/StanfordLegion/legion/issues/533) and included a
minimal dockerfile to reproduce this issue:

FROM fedora:rawhide
RUN dnf install -y spectool wget rpm-build dnf-plugins-core
RUN wget https://src.fedoraproject.org/fork/junghans/rpms/legion/raw/master/f/legi...
RUN spectool -g legion.spec
RUN dnf builddep -y legion.spec
RUN dnf install -y make
RUN rpmbuild -D"_sourcedir ${PWD}" -D"_srcrpmdir ${PWD}" -ba
legion.spec

This worked fine on Thursday(?) to reproduce the failing tests in
%check, but now rpmbuild fails at an earlier stage with:
+ module load mpi/mpich-x86_64
++ /usr/share/lmod/lmod/libexec/lmod sh load mpi/mpich-x86_64
Lmod has detected the following error: The following module(s) are unknown:
"mpi/mpich-x86_64"

If I jump into the container interactively (docker run -it ..
/bin/bash), "module load" as well as rpmbuild (and "module load"
inside) works.

If know this is a convoluted case, but any ideas how fix this?

Christoph


-- 
Christoph Junghans
Web: http://www.compphys.de

[Daniel Walsh]

On 5/3/19 6:00 PM, Christoph Junghans wrote:
>  Hi,
>
>  I wanted to bump the legion package to 19.04.0
>  (https://bugzilla.redhat.com/show_bug.cgi?id=1705033), however for
>  some reason all tests segfault with openmpi
>  (https://koji.fedoraproject.org/koji/taskinfo?taskID=34577005), so I
>  reported this upstream
>  (https://github.com/StanfordLegion/legion/issues/533) and included a
>  minimal dockerfile to reproduce this issue:
>
>  FROM fedora:rawhide
>  RUN dnf install -y spectool wget rpm-build dnf-plugins-core
>  RUN wget
> https://src.fedoraproject.org/fork/junghans/rpms/legion/raw/master/f/legi...
>  RUN spectool -g legion.spec
>  RUN dnf builddep -y legion.spec
>  RUN dnf install -y make
>  RUN rpmbuild -D"_sourcedir ${PWD}" -D"_srcrpmdir ${PWD}" -ba
> legion.spec
>
>  This worked fine on Thursday(?) to reproduce the failing tests in
>  %check, but now rpmbuild fails at an earlier stage with:
>  + module load mpi/mpich-x86_64
>  ++ /usr/share/lmod/lmod/libexec/lmod sh load mpi/mpich-x86_64
>  Lmod has detected the following error: The following module(s) are unknown:
>  "mpi/mpich-x86_64"
>
>  If I jump into the container interactively (docker run -it ..
>  /bin/bash), "module load" as well as rpmbuild (and "module load"
>  inside) works.
>
>  If know this is a convoluted case, but any ideas how fix this?
>
>  Christoph
>
>  
Are you running a privileged container in one case and not in the
other.  Normal running of containers should not allow you to load a
kernel module.


BTW Have you tried this with Podman?

[Neal Gompa]

On Sat, May 4, 2019 at 7:26 AM Daniel Walsh <dwalsh(a)redhat.com&gt; wrote:
>  On 5/3/19 6:00 PM, Christoph Junghans wrote:
>  > Hi,
>  >
>  > I wanted to bump the legion package to 19.04.0
>  > (https://bugzilla.redhat.com/show_bug.cgi?id=1705033), however for
>  > some reason all tests segfault with openmpi
>  > (https://koji.fedoraproject.org/koji/taskinfo?taskID=34577005), so I
>  > reported this upstream
>  > (https://github.com/StanfordLegion/legion/issues/533) and included a
>  > minimal dockerfile to reproduce this issue:
>  >
>  > FROM fedora:rawhide
>  > RUN dnf install -y spectool wget rpm-build dnf-plugins-core
>  > RUN wget
> https://src.fedoraproject.org/fork/junghans/rpms/legion/raw/master/f/legi...
>  > RUN spectool -g legion.spec
>  > RUN dnf builddep -y legion.spec
>  > RUN dnf install -y make
>  > RUN rpmbuild -D"_sourcedir ${PWD}" -D"_srcrpmdir ${PWD}" -ba
> legion.spec
>  >
>  > This worked fine on Thursday(?) to reproduce the failing tests in
>  > %check, but now rpmbuild fails at an earlier stage with:
>  > + module load mpi/mpich-x86_64
>  > ++ /usr/share/lmod/lmod/libexec/lmod sh load mpi/mpich-x86_64
>  > Lmod has detected the following error: The following module(s) are unknown:
>  > "mpi/mpich-x86_64"
>  >
>  > If I jump into the container interactively (docker run -it ..
>  > /bin/bash), "module load" as well as rpmbuild (and "module
> load"
>  > inside) works.
>  >
>  > If know this is a convoluted case, but any ideas how fix this?
>  >
>  > Christoph
>  >
>  >
>  Are you running a privileged container in one case and not in the
>  other.  Normal running of containers should not allow you to load a
>  kernel module.
>
>
>  BTW Have you tried this with Podman? 
I'm pretty sure these aren't kernel modules, but environment modules
for OpenMPI and such...



-- 
真実はいつも一つ！/ Always, there's only one truth!

[Christoph Junghans]

On Sat, May 4, 2019 at 5:30 AM Neal Gompa <ngompa13(a)gmail.com&gt; wrote:
>  On Sat, May 4, 2019 at 7:26 AM Daniel Walsh <dwalsh(a)redhat.com&gt; wrote:
>  >
>  > On 5/3/19 6:00 PM, Christoph Junghans wrote:
>  > > Hi,
>  > >
>  > > I wanted to bump the legion package to 19.04.0
>  > > (https://bugzilla.redhat.com/show_bug.cgi?id=1705033), however for
>  > > some reason all tests segfault with openmpi
>  > > (https://koji.fedoraproject.org/koji/taskinfo?taskID=34577005), so I
>  > > reported this upstream
>  > > (https://github.com/StanfordLegion/legion/issues/533) and included a
>  > > minimal dockerfile to reproduce this issue:
>  > >
>  > > FROM fedora:rawhide
>  > > RUN dnf install -y spectool wget rpm-build dnf-plugins-core
>  > > RUN wget
> https://src.fedoraproject.org/fork/junghans/rpms/legion/raw/master/f/legi...
>  > > RUN spectool -g legion.spec
>  > > RUN dnf builddep -y legion.spec
>  > > RUN dnf install -y make
>  > > RUN rpmbuild -D"_sourcedir ${PWD}" -D"_srcrpmdir ${PWD}"
> -ba legion.spec
>  > >
>  > > This worked fine on Thursday(?) to reproduce the failing tests in
>  > > %check, but now rpmbuild fails at an earlier stage with:
>  > > + module load mpi/mpich-x86_64
>  > > ++ /usr/share/lmod/lmod/libexec/lmod sh load mpi/mpich-x86_64
>  > > Lmod has detected the following error: The following module(s) are unknown:
>  > > "mpi/mpich-x86_64"
>  > >
>  > > If I jump into the container interactively (docker run -it ..
>  > > /bin/bash), "module load" as well as rpmbuild (and "module
> load"
>  > > inside) works.
>  > >
>  > > If know this is a convoluted case, but any ideas how fix this?
>  > >
>  > > Christoph
>  > >
>  > >
>  > Are you running a privileged container in one case and not in the
>  > other.  Normal running of containers should not allow you to load a
>  > kernel module.
>  >
>  >
>  > BTW Have you tried this with Podman?
>
>  I'm pretty sure these aren't kernel modules, but environment modules
>  for OpenMPI and such... 
Correct.

I am thinking there is something missing in the default environment in
the container, that gets loaded in the interactive mode.

Christoph
>  --
>  真実はいつも一つ！/ Always, there's only one truth!
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-- 
Christoph Junghans
Web: http://www.compphys.de

[Orion Poplawski]

On 5/3/19 4:00 PM, Christoph Junghans wrote:
>  Hi,
>  
>  I wanted to bump the legion package to 19.04.0
>  (https://bugzilla.redhat.com/show_bug.cgi?id=1705033), however for
>  some reason all tests segfault with openmpi
>  (https://koji.fedoraproject.org/koji/taskinfo?taskID=34577005), so I
>  reported this upstream
>  (https://github.com/StanfordLegion/legion/issues/533) and included a
>  minimal dockerfile to reproduce this issue:
>  
>  FROM fedora:rawhide
>  RUN dnf install -y spectool wget rpm-build dnf-plugins-core
>  RUN wget
> https://src.fedoraproject.org/fork/junghans/rpms/legion/raw/master/f/legi...
>  RUN spectool -g legion.spec
>  RUN dnf builddep -y legion.spec
>  RUN dnf install -y make
>  RUN rpmbuild -D"_sourcedir ${PWD}" -D"_srcrpmdir ${PWD}" -ba
> legion.spec
>  
>  This worked fine on Thursday(?) to reproduce the failing tests in
>  %check, but now rpmbuild fails at an earlier stage with:
>  + module load mpi/mpich-x86_64
>  ++ /usr/share/lmod/lmod/libexec/lmod sh load mpi/mpich-x86_64
>  Lmod has detected the following error: The following module(s) are unknown:
>  "mpi/mpich-x86_64"
>  
>  If I jump into the container interactively (docker run -it ..
>  /bin/bash), "module load" as well as rpmbuild (and "module load"
>  inside) works.
>  
>  If know this is a convoluted case, but any ideas how fix this?
>  
>  Christoph 
We depend on /etc/profile.d/00-modulepath.sh (from Lmod) to add 
/etc/modulefiles to MODULEPATH.  Perhaps this doesn't get sourced in 
during the sequence of docker RUN commands?




-- 
Orion Poplawski
Manager of NWRA Technical Systems          720-772-5637
NWRA, Boulder/CoRA Office             FAX: [phone]
3380 Mitchell Lane                       orion(a)nwra.com
Boulder, CO 80301                 https://www.nwra.com/