Re: [petsc-users] Spack build and ptscotch
Hi Satish,
Many thanks for the interesting response. I'll see if I can figure out
something useful to do for our goals (a reliable spack package for our
simulator, which is dependent on bringing in
the exact right petsc build as dependency), but as you say, maintaining
these things and accounting for everything is a lot harder than it looks.
Time constraints from other projects
might limit how much more tinkering I can do, but we have a better idea of
the issues we face now.
Daniel
On Wed, Apr 24, 2024 at 4:25 PM Satish Balay wrote:
> This is the complexity with maintaining dependencies (and dependencies
> of dependencies), and different build systems
>
> - Its not easy to keep the "defaults" in both builds exactly the same.
> - And its not easy to expose all "variants" or keep the same variants in
> both builds.
> - And each pkg has its own issues that prevents some combinations to
> work or not [or tested combinations vs untested].
>
> This e-mail query has multiple things:
>
> - understand "why" the current impl of [spack, petsc] build tools are the
> way they are.
> - if they can be improved
> - and build use cases that you need working
> - [and subsequently your code working]
>
> Addressing them all is not easy - so lets stick with what you need to make
> progress.
>
> For one - we recommend using latest petsc version [i.e 3.21 - not 3.19] -
> any fixes we have will address the current release.
>
> > - spack: ptscotch will always be built without parmetis wrappers, can't
> turn on
>
> diff --git a/var/spack/repos/builtin/packages/petsc/package.py
> b/var/spack/repos/builtin/packages/petsc/package.py
> index b7b1d86b15..ae27ba4c4e 100644
> --- a/var/spack/repos/builtin/packages/petsc/package.py
> +++ b/var/spack/repos/builtin/packages/petsc/package.py
> @@ -268,9 +268,7 @@ def check_fortran_compiler(self):
> depends_on("metis@5:~int64", when="@3.8:+metis~int64")
> depends_on("metis@5:+int64", when="@3.8:+metis+int64")
>
> -# PTScotch: Currently disable Parmetis wrapper, this means
> -# nested disection won't be available thought PTScotch
> -depends_on("scotch+esmumps~metis+mpi", when="+ptscotch")
> +depends_on("scotch+esmumps+mpi", when="+ptscotch")
> depends_on("scotch+int64", when="+ptscotch+int64")
>
> depends_on("hdf5@:1.10+mpi", when="@:3.12+hdf5+mpi")
>
> Now you can try:
>
> spack install petsc~metis+ptscotch ^scotch+metis
> vs
> spack install petsc~metis+ptscotch ^scotch~metis [~metis is the default
> for scotch]
>
> Note the following comment in
> spack/var/spack/repos/builtin/packages/scotch/package.py
>
>
> # Vendored dependency of METIS/ParMETIS conflicts with standard
> # installations
> conflicts("metis", when="+metis")
> conflicts("parmetis", when="+metis")
> <
>
> > - classical: ptscotch will always be built with parmetis wrappers, can't
> seem to turn off
>
> Looks like spack uses cmake build of ptscotch. PETSc uses Makefile
> interface. It likely doesn't support turning off metis wrappers [without
> hacks].
>
> So you might either need to hack scotch build via petsc - or just install
> it separately - and use it with petsc.
>
> I see an effort to migrate scotch build in petsc to cmake
>
> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7242/__;!!G_uCfscf7eWS!axLWsOWdCnVQSjIurDkWvFmG4riOizNNPbVM78TQoVScHx7ERMUENiQ-VW2Lh5e83QHhKcA7-HO0nDJ_hTez8JffqQz8h1I$
>
> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7495/__;!!G_uCfscf7eWS!axLWsOWdCnVQSjIurDkWvFmG4riOizNNPbVM78TQoVScHx7ERMUENiQ-VW2Lh5e83QHhKcA7-HO0nDJ_hTez8JffgEb5IwI$
>
>
> Satish
>
> On Wed, 24 Apr 2024, Daniel Stone wrote:
>
> > Hi PETSc community,
> >
> > I've been looking at using Spack to build PETSc, in particular I need to
> > disable the default metis/parmetis dependencies and use PTScotch instead,
> > for our software.
> > I've had quite a bit of trouble with this - it seems like something in
> the
> > resulting build of our simulator ends up badly optimised and an mpi
> > bottleneck, when I build against
> > PETSc built with Spack.
> >
> > I've been trying to track this down, and noticed this in the PETSc Spack
> > build recipe:
> >
> > # PTScotch: Currently disable Parmetis wrapper, this means
> > # nested disection won't be available thought PTScotch
> > depends_on("scotch+esmumps~metis+mpi", when="+ptscotch")
> > depends_on("scotch+int64", when="+ptscotch+int64")
> >
> >
> > Sure enough - when I compare the build with Spack and a traditional build
> > with ./configure etc, I see that, in the traditional build, Scotch is
> > always built with the parmetis wrapper,
> > but not in the Scotch build. In fact, I'm not sure how to turn off the
> > parmetis wrapper option for scotch, in the case of a traditional build
> > (i.e. there doesn't seem to be a flag in the
> > configure script for it) - which would be a very useful test for me (I
> can
> > of course do similar experiments by
Re: [petsc-users] Spack build and ptscotch
This is the complexity with maintaining dependencies (and dependencies
of dependencies), and different build systems
- Its not easy to keep the "defaults" in both builds exactly the same.
- And its not easy to expose all "variants" or keep the same variants in both
builds.
- And each pkg has its own issues that prevents some combinations to
work or not [or tested combinations vs untested].
This e-mail query has multiple things:
- understand "why" the current impl of [spack, petsc] build tools are the way
they are.
- if they can be improved
- and build use cases that you need working
- [and subsequently your code working]
Addressing them all is not easy - so lets stick with what you need to make
progress.
For one - we recommend using latest petsc version [i.e 3.21 - not 3.19] - any
fixes we have will address the current release.
> - spack: ptscotch will always be built without parmetis wrappers, can't turn
> on
diff --git a/var/spack/repos/builtin/packages/petsc/package.py
b/var/spack/repos/builtin/packages/petsc/package.py
index b7b1d86b15..ae27ba4c4e 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -268,9 +268,7 @@ def check_fortran_compiler(self):
depends_on("metis@5:~int64", when="@3.8:+metis~int64")
depends_on("metis@5:+int64", when="@3.8:+metis+int64")
-# PTScotch: Currently disable Parmetis wrapper, this means
-# nested disection won't be available thought PTScotch
-depends_on("scotch+esmumps~metis+mpi", when="+ptscotch")
+depends_on("scotch+esmumps+mpi", when="+ptscotch")
depends_on("scotch+int64", when="+ptscotch+int64")
depends_on("hdf5@:1.10+mpi", when="@:3.12+hdf5+mpi")
Now you can try:
spack install petsc~metis+ptscotch ^scotch+metis
vs
spack install petsc~metis+ptscotch ^scotch~metis [~metis is the default for
scotch]
Note the following comment in
spack/var/spack/repos/builtin/packages/scotch/package.py
# Vendored dependency of METIS/ParMETIS conflicts with standard
# installations
conflicts("metis", when="+metis")
conflicts("parmetis", when="+metis")
<
> - classical: ptscotch will always be built with parmetis wrappers, can't seem
> to turn off
Looks like spack uses cmake build of ptscotch. PETSc uses Makefile interface.
It likely doesn't support turning off metis wrappers [without hacks].
So you might either need to hack scotch build via petsc - or just install it
separately - and use it with petsc.
I see an effort to migrate scotch build in petsc to cmake
https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7242/__;!!G_uCfscf7eWS!dL00pokNVI6oaNk_chaSyfI1zWFeTgYA9jbRW6n9YT73s51VwLBuXYc-MAJWEKXr8uBgEFrmhFQ_VJOSlvzW6OA$
https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7495/__;!!G_uCfscf7eWS!dL00pokNVI6oaNk_chaSyfI1zWFeTgYA9jbRW6n9YT73s51VwLBuXYc-MAJWEKXr8uBgEFrmhFQ_VJOS6OuSrPs$
Satish
On Wed, 24 Apr 2024, Daniel Stone wrote:
> Hi PETSc community,
>
> I've been looking at using Spack to build PETSc, in particular I need to
> disable the default metis/parmetis dependencies and use PTScotch instead,
> for our software.
> I've had quite a bit of trouble with this - it seems like something in the
> resulting build of our simulator ends up badly optimised and an mpi
> bottleneck, when I build against
> PETSc built with Spack.
>
> I've been trying to track this down, and noticed this in the PETSc Spack
> build recipe:
>
> # PTScotch: Currently disable Parmetis wrapper, this means
> # nested disection won't be available thought PTScotch
> depends_on("scotch+esmumps~metis+mpi", when="+ptscotch")
> depends_on("scotch+int64", when="+ptscotch+int64")
>
>
> Sure enough - when I compare the build with Spack and a traditional build
> with ./configure etc, I see that, in the traditional build, Scotch is
> always built with the parmetis wrapper,
> but not in the Scotch build. In fact, I'm not sure how to turn off the
> parmetis wrapper option for scotch, in the case of a traditional build
> (i.e. there doesn't seem to be a flag in the
> configure script for it) - which would be a very useful test for me (I can
> of course do similar experiments by doing a classical build of petsc
> against ptscotch built separately without the
> wrappers, etc - will try that).
>
> Does anyone know why the parmetis wrapper is always disabled in the spack
> build options? Is there something about Spack that would prevent it from
> working? It's notable - but I might
> be missing it - that there's no warning that there's a difference in the
> way ptscotch is built between the spack and classical builds:
> - classical: ptscotch will always be built with parmetis wrappers, can't
> seem to turn off
> - spack: ptscotch will always be built without parmetis wrappers, can't
> turn on
>
> Any insight at all would be great, I'm new to Spack and am not super
> familiar with the logic that goes
[petsc-users] Spack build and ptscotch
Hi PETSc community,
I've been looking at using Spack to build PETSc, in particular I need to
disable the default metis/parmetis dependencies and use PTScotch instead,
for our software.
I've had quite a bit of trouble with this - it seems like something in the
resulting build of our simulator ends up badly optimised and an mpi
bottleneck, when I build against
PETSc built with Spack.
I've been trying to track this down, and noticed this in the PETSc Spack
build recipe:
# PTScotch: Currently disable Parmetis wrapper, this means
# nested disection won't be available thought PTScotch
depends_on("scotch+esmumps~metis+mpi", when="+ptscotch")
depends_on("scotch+int64", when="+ptscotch+int64")
Sure enough - when I compare the build with Spack and a traditional build
with ./configure etc, I see that, in the traditional build, Scotch is
always built with the parmetis wrapper,
but not in the Scotch build. In fact, I'm not sure how to turn off the
parmetis wrapper option for scotch, in the case of a traditional build
(i.e. there doesn't seem to be a flag in the
configure script for it) - which would be a very useful test for me (I can
of course do similar experiments by doing a classical build of petsc
against ptscotch built separately without the
wrappers, etc - will try that).
Does anyone know why the parmetis wrapper is always disabled in the spack
build options? Is there something about Spack that would prevent it from
working? It's notable - but I might
be missing it - that there's no warning that there's a difference in the
way ptscotch is built between the spack and classical builds:
- classical: ptscotch will always be built with parmetis wrappers, can't
seem to turn off
- spack: ptscotch will always be built without parmetis wrappers, can't
turn on
Any insight at all would be great, I'm new to Spack and am not super
familiar with the logic that goes into setting up builds for the system.
Here is the kind of command I give to Spack for PETSc builds, which may
well be less than ideal:
spack install petsc@3.19.1 ~metis +ptscotch ^hdf5 +fortran +hl
Separate tiny note: when building with hdf5, I have to ensure that the
fortran flag is set for it, as above. There's a fortran flag for the petsc
module, default true, and a fortran flag for the hdf5
module, default false. A naive user (i.e. me), will see the fortran flag
for the petsc module, and assume that all dependencies will correspondingly
be built with fortran capability - then see that
hdf5.mod is missing when trying to build their software against petsc. It's
the old "did you forget --with-hdf5-fortran-bindings?" issue, resurrected
for a new build system.
Thanks,
Daniel
