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CISteefel / CrunchTope

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Spack package recipe? #46

Open markyoder opened 4 days ago

markyoder commented 4 days ago

Hi. I am experimenting with writing a Spack package recipe for this code. Can you maybe help me better understand what are the actual dependencies? For example:

  1. LAPACK or other numerical libraries?
  2. MPI?
  3. ?

Thanks for any help you can provide!

smolins commented 4 days ago

PETSC and LAPACK. MPI is not necessary though it is convenient to build PETSC in parallel. If Alquimia uses it then it will need MPI. https://packages.spack.io/package.html?name=petsc, so maybe making it a requirement is best course of action. Sergi

On Thu, Nov 21, 2024 at 10:25 AM Mark R. Yoder, Ph.D. < @.***> wrote:

Hi. I am experimenting with writing a Spack package recipe for this code. Can you maybe help me better understand what are the actual dependencies? For example:

  1. LAPACK or other numerical libraries?
  2. MPI?
  3. ?

Thanks for any help you can provide!

— Reply to this email directly, view it on GitHub https://github.com/CISteefel/CrunchTope/issues/46, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADXOTGXXFUB4I22OI2KAN2T2BYQQHAVCNFSM6AAAAABSHUNEPSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGY4DANBUG42DCMA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

markyoder commented 4 days ago

Ok. Maybe I'll make '+alquimia' a variant. Otherwise, CrunchTope won't run in MPI mode, right?

This whole Spack package thing is unfamiliar territory to me, so who knows....

Thanks for the info!

CISteefel commented 4 days ago

CrunchClay (or now CrunchODiTi), a new variant, will run in MPI. So far, CrunchFlow/CrunchTope not.

It uses the PETSc solvers, but in serial mode (--mpiuni), so it does use sparse solvers (building on LAPACK), but just not (yet) in parallel.

--Carl

On Thu, Nov 21, 2024 at 11:08 AM Mark R. Yoder, Ph.D. < @.***> wrote:

Ok. Maybe I'll make '+alquimia' a variant. Otherwise, CrunchTope won't run in MPI mode, right?

This whole Spack package thing is unfamiliar territory to me, so who knows....

Thanks for the info!

— Reply to this email directly, view it on GitHub https://github.com/CISteefel/CrunchTope/issues/46#issuecomment-2492048057, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMXIFEM5DFBVE3V3EFNO37L2BYVRZAVCNFSM6AAAAABSHUNEPSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOJSGA2DQMBVG4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Carl I. Steefel Senior Scientist Energy Geosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720 USA @.** 510-502-3660 ++++++++++++++++++++++++++++++++++++ Crunch-Users Google Group* https://groups.google.com/a/lbl.gov/g/crunchusers

CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

markyoder commented 3 days ago

Almost there, I think... I think the Makefile for v2.10 is incomplete? My build seems to be stuck on a set of errors:

/scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:7641: undefined reference to `read_pumptimeseriesfile_'
/scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:7642: undefined reference to `read_pumplocationsfile_'
/scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:7645: undefined reference to `read_pump_timeseries2_'
/scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:8855: undefined reference to `read_watertablefile_'
/scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:8857: undefined reference to `read_watertable_timeseries_'
collect2: error: ld returned 1 exit status

The source files are there; it looks like they are just not listed in the Makefile. I did a successful build off the Main branch, but I was hoping to build this Spack package off of properly versioned instances.

CISteefel commented 3 days ago

Sorry about that, I think that Toshi did not update the Makefile with his new additions. I will ask him to do so today...

--Carl

On Fri, Nov 22, 2024 at 9:50 AM Mark R. Yoder, Ph.D. < @.***> wrote:

Almost there, I think... I think the Makefile for v2.10 is incomplete? My build seems to be stuck on a set of errors:

/scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:7641: undefined reference to read_pumptimeseriesfile_' /scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:7642: undefined reference toreadpumplocationsfile' /scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:7645: undefined reference to read_pump_timeseries2_' /scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:8855: undefined reference toreadwatertablefile' /scratch/users/myoder96/crunchflow/CT2/CrunchTope-2.10/StartTope.F90:8857: undefined reference to `read_watertabletimeseries' collect2: error: ld returned 1 exit status

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CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

markyoder commented 3 days ago

No worries; just a heads up! I can sort of fix it en-script, but it can be tricky without know ing some of the details -- like can I revert to *.F90, etc.

Most of this is pretty new to me, so you know! Anyway, thanks for the responses.

smolins commented 3 days ago

I think it is better not to fix this in the spack script. I will fix the github actions CI once Toshi updates the makefile so that these types of things don't happen.

On Fri, Nov 22, 2024 at 10:06 AM Mark R. Yoder, Ph.D. < @.***> wrote:

No worries; just a heads up! I can sort of fix it en-script, but it can be tricky without know ing some of the details -- like can I revert to *.F90, etc.

Most of this is pretty new to me, so you know! Anyway, thanks for the responses.

— Reply to this email directly, view it on GitHub https://github.com/CISteefel/CrunchTope/issues/46#issuecomment-2494452334, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADXOTGRQJ7PK3EQOMPLXNR32B5XB7AVCNFSM6AAAAABSHUNEPSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOJUGQ2TEMZTGQ . You are receiving this because you commented.Message ID: @.***>

markyoder commented 3 days ago

Agreed. And to clarify, Master works, so the problem was probably noticed since the @2.10 tag. I'll also see if I can add a @develop or @master version into my recipe.

CISteefel commented 3 days ago

Well, I will have to speak to Toshi about this. He does not use Linux or Unix, he uses Windows (and the VFProject file is up to date)...

On Fri, Nov 22, 2024 at 10:10 AM Sergi Molins @.***> wrote:

I think it is better not to fix this in the spack script. I will fix the github actions CI once Toshi updates the makefile so that these types of things don't happen.

On Fri, Nov 22, 2024 at 10:06 AM Mark R. Yoder, Ph.D. < @.***> wrote:

No worries; just a heads up! I can sort of fix it en-script, but it can be tricky without know ing some of the details -- like can I revert to *.F90, etc.

Most of this is pretty new to me, so you know! Anyway, thanks for the responses.

— Reply to this email directly, view it on GitHub < https://github.com/CISteefel/CrunchTope/issues/46#issuecomment-2494452334>,

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CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

CISteefel commented 2 days ago

OK, I think the problem was mixing the old Makefile with the newer source.

If you download the latest, the Makefile residing in Source works with the current source code. I built it just now on my Mac with no problems...

--Carl

On Fri, Nov 22, 2024 at 10:18 AM Carl Steefel @.***> wrote:

Well, I will have to speak to Toshi about this. He does not use Linux or Unix, he uses Windows (and the VFProject file is up to date)...

On Fri, Nov 22, 2024 at 10:10 AM Sergi Molins @.***> wrote:

I think it is better not to fix this in the spack script. I will fix the github actions CI once Toshi updates the makefile so that these types of things don't happen.

On Fri, Nov 22, 2024 at 10:06 AM Mark R. Yoder, Ph.D. < @.***> wrote:

No worries; just a heads up! I can sort of fix it en-script, but it can be tricky without know ing some of the details -- like can I revert to *.F90, etc.

Most of this is pretty new to me, so you know! Anyway, thanks for the responses.

— Reply to this email directly, view it on GitHub < https://github.com/CISteefel/CrunchTope/issues/46#issuecomment-2494452334>,

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-- Carl I. Steefel Senior Scientist Energy Geosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720 USA @.** 510-502-3660 ++++++++++++++++++++++++++++++++++++ Crunch-Users Google Group* https://groups.google.com/a/lbl.gov/g/crunchusers

CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

-- Carl I. Steefel Senior Scientist Energy Geosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720 USA @.** 510-502-3660 ++++++++++++++++++++++++++++++++++++ Crunch-Users Google Group* https://groups.google.com/a/lbl.gov/g/crunchusers

CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

markyoder commented 2 days ago

Yes; the newest builds. I am trying to build the 2.10 tagged version. I would prefer for the Spack package to refer to numbered versions.

Generally, I would think that a tag/version should be self consistent. Would it be possible to correct the Makefile in the 2.10 tag?

Mark

Mark Yoder, PhD 805 451 8750 www.linkedin.com/in/Mark-R-Yoder-PhD http://www.linkedin.com/in/Mark-R-Yoder-PhD

"Difficulties are just things to overcome, after all." ~E. Shackleton

On Sat, Nov 23, 2024 at 4:42 PM CISteefel @.***> wrote:

OK, I think the problem was mixing the old Makefile with the newer source.

If you download the latest, the Makefile residing in Source works with the current source code. I built it just now on my Mac with no problems...

--Carl

On Fri, Nov 22, 2024 at 10:18 AM Carl Steefel @.***> wrote:

Well, I will have to speak to Toshi about this. He does not use Linux or Unix, he uses Windows (and the VFProject file is up to date)...

On Fri, Nov 22, 2024 at 10:10 AM Sergi Molins @.***> wrote:

I think it is better not to fix this in the spack script. I will fix the github actions CI once Toshi updates the makefile so that these types of things don't happen.

On Fri, Nov 22, 2024 at 10:06 AM Mark R. Yoder, Ph.D. < @.***> wrote:

No worries; just a heads up! I can sort of fix it en-script, but it can be tricky without know ing some of the details -- like can I revert to *.F90, etc.

Most of this is pretty new to me, so you know! Anyway, thanks for the responses.

— Reply to this email directly, view it on GitHub <

https://github.com/CISteefel/CrunchTope/issues/46#issuecomment-2494452334>,

or unsubscribe <

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CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

-- Carl I. Steefel Senior Scientist Energy Geosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720 USA @.** 510-502-3660 ++++++++++++++++++++++++++++++++++++ Crunch-Users Google Group* https://groups.google.com/a/lbl.gov/g/crunchusers

CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

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CISteefel commented 2 days ago

Not sure there is any "correction" to be done. As far as I recall, the Makefile from that release worked with that source code. Anyway, easier to just use the newer one. We will release this soon...

--Carl

On Sat, Nov 23, 2024 at 4:52 PM Mark R. Yoder, Ph.D. < @.***> wrote:

Yes; the newest builds. I am trying to build the 2.10 tagged version. I would prefer for the Spack package to refer to numbered versions.

Generally, I would think that a tag/version should be self consistent. Would it be possible to correct the Makefile in the 2.10 tag?

Mark

Mark Yoder, PhD 805 451 8750 www.linkedin.com/in/Mark-R-Yoder-PhD http://www.linkedin.com/in/Mark-R-Yoder-PhD

"Difficulties are just things to overcome, after all." ~E. Shackleton

On Sat, Nov 23, 2024 at 4:42 PM CISteefel @.***> wrote:

OK, I think the problem was mixing the old Makefile with the newer source.

If you download the latest, the Makefile residing in Source works with the current source code. I built it just now on my Mac with no problems...

--Carl

On Fri, Nov 22, 2024 at 10:18 AM Carl Steefel @.***> wrote:

Well, I will have to speak to Toshi about this. He does not use Linux or Unix, he uses Windows (and the VFProject file is up to date)...

On Fri, Nov 22, 2024 at 10:10 AM Sergi Molins @.***> wrote:

I think it is better not to fix this in the spack script. I will fix the github actions CI once Toshi updates the makefile so that these types of things don't happen.

On Fri, Nov 22, 2024 at 10:06 AM Mark R. Yoder, Ph.D. < @.***> wrote:

No worries; just a heads up! I can sort of fix it en-script, but it can be tricky without know ing some of the details -- like can I revert to *.F90, etc.

Most of this is pretty new to me, so you know! Anyway, thanks for the responses.

— Reply to this email directly, view it on GitHub <

https://github.com/CISteefel/CrunchTope/issues/46#issuecomment-2494452334>,

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-- Carl I. Steefel Senior Scientist Energy Geosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720 USA @.** 510-502-3660 ++++++++++++++++++++++++++++++++++++ Crunch-Users Google Group* https://groups.google.com/a/lbl.gov/g/crunchusers

CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

-- Carl I. Steefel Senior Scientist Energy Geosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720 USA @.** 510-502-3660 ++++++++++++++++++++++++++++++++++++ Crunch-Users Google Group* https://groups.google.com/a/lbl.gov/g/crunchusers

CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

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CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

markyoder commented 1 day ago

Oh yeah, a version release of Master should do the trick.

I think you will find, however that the Makefile for 2.10 does not work. Spack downloads the .zip version of the source.

Anyway, new version would be great; I might write a patch for the earlier versions. Thanks!

Mark

Mark Yoder, PhD 805 451 8750 www.linkedin.com/in/Mark-R-Yoder-PhD http://www.linkedin.com/in/Mark-R-Yoder-PhD

"Difficulties are just things to overcome, after all." ~E. Shackleton

On Sat, Nov 23, 2024 at 8:19 PM CISteefel @.***> wrote:

Not sure there is any "correction" to be done. As far as I recall, the Makefile from that release worked with that source code. Anyway, easier to just use the newer one. We will release this soon...

--Carl

On Sat, Nov 23, 2024 at 4:52 PM Mark R. Yoder, Ph.D. < @.***> wrote:

Yes; the newest builds. I am trying to build the 2.10 tagged version. I would prefer for the Spack package to refer to numbered versions.

Generally, I would think that a tag/version should be self consistent. Would it be possible to correct the Makefile in the 2.10 tag?

Mark

Mark Yoder, PhD 805 451 8750 www.linkedin.com/in/Mark-R-Yoder-PhD http://www.linkedin.com/in/Mark-R-Yoder-PhD

"Difficulties are just things to overcome, after all." ~E. Shackleton

On Sat, Nov 23, 2024 at 4:42 PM CISteefel @.***> wrote:

OK, I think the problem was mixing the old Makefile with the newer source.

If you download the latest, the Makefile residing in Source works with the current source code. I built it just now on my Mac with no problems...

--Carl

On Fri, Nov 22, 2024 at 10:18 AM Carl Steefel @.***> wrote:

Well, I will have to speak to Toshi about this. He does not use Linux or Unix, he uses Windows (and the VFProject file is up to date)...

On Fri, Nov 22, 2024 at 10:10 AM Sergi Molins @.***> wrote:

I think it is better not to fix this in the spack script. I will fix the github actions CI once Toshi updates the makefile so that these types of things don't happen.

On Fri, Nov 22, 2024 at 10:06 AM Mark R. Yoder, Ph.D. < @.***> wrote:

No worries; just a heads up! I can sort of fix it en-script, but it can be tricky without know ing some of the details -- like can I revert to *.F90, etc.

Most of this is pretty new to me, so you know! Anyway, thanks for the responses.

— Reply to this email directly, view it on GitHub <

https://github.com/CISteefel/CrunchTope/issues/46#issuecomment-2494452334>,

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-- Carl I. Steefel Senior Scientist Energy Geosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720 USA @.** 510-502-3660 ++++++++++++++++++++++++++++++++++++ Crunch-Users Google Group* https://groups.google.com/a/lbl.gov/g/crunchusers

CrunchTope Source https://github.com/CISteefel/CrunchTope

CrunchTope Release v2.10 (February 7, 2023) https://github.com/CISteefel/CrunchTope/releases/tag/v2.10 https://github.com/CISteefel/CrunchTope/releases/tag/v2.10

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CrunchTope Source https://github.com/CISteefel/CrunchTope

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CISteefel commented 20 hours ago

OK, you were right Mark, there was a problem with the Makefile. A couple of Toshi's source files did not make it in there.

I think I fixed it now. In v2.10, I could not delete the earlier source code files, but you would use:

CrunchTope-2.10.tar.gz

I will make a CrunchTope-v3.00 soon, just waiting for Toshi to add some instructions on his new Exercises...

--Carl

On Sun, Nov 24, 2024 at 1:18 PM Mark R. Yoder, Ph.D. < @.***> wrote:

Oh yeah, a version release of Master should do the trick.

I think you will find, however that the Makefile for 2.10 does not work. Spack downloads the .zip version of the source.

Anyway, new version would be great; I might write a patch for the earlier versions. Thanks!

Mark

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On Sat, Nov 23, 2024 at 8:19 PM CISteefel @.***> wrote:

Not sure there is any "correction" to be done. As far as I recall, the Makefile from that release worked with that source code. Anyway, easier to just use the newer one. We will release this soon...

--Carl

On Sat, Nov 23, 2024 at 4:52 PM Mark R. Yoder, Ph.D. < @.***> wrote:

Yes; the newest builds. I am trying to build the 2.10 tagged version. I would prefer for the Spack package to refer to numbered versions.

Generally, I would think that a tag/version should be self consistent. Would it be possible to correct the Makefile in the 2.10 tag?

Mark

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On Sat, Nov 23, 2024 at 4:42 PM CISteefel @.***> wrote:

OK, I think the problem was mixing the old Makefile with the newer source.

If you download the latest, the Makefile residing in Source works with the current source code. I built it just now on my Mac with no problems...

--Carl

On Fri, Nov 22, 2024 at 10:18 AM Carl Steefel @.***> wrote:

Well, I will have to speak to Toshi about this. He does not use Linux or Unix, he uses Windows (and the VFProject file is up to date)...

On Fri, Nov 22, 2024 at 10:10 AM Sergi Molins @.***> wrote:

I think it is better not to fix this in the spack script. I will fix the github actions CI once Toshi updates the makefile so that these types of things don't happen.

On Fri, Nov 22, 2024 at 10:06 AM Mark R. Yoder, Ph.D. < @.***> wrote:

No worries; just a heads up! I can sort of fix it en-script, but it can be tricky without know ing some of the details -- like can I revert to *.F90, etc.

Most of this is pretty new to me, so you know! Anyway, thanks for the responses.

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