ExternalProject SUNDIALS 3.2.1 #1960

alexsavulescu · 2022-08-20T12:19:47Z

include work from cvode3 branch

closes #1328

Cvode version 3 test data must be visually compared to the legacy data for acceptable similarity.
Must use nrn-modeldb-ci to visually compare the differences.
test coverage substantially complete
merge rxd testdata and update submodule commit

* include work from cvode3 branch

nrnhines · 2023-05-05T07:28:24Z

@alkino Just to let you know, I have a fix for ctest -R netpar but need to extend to NRNMPI_DYNAMICLOAD.

alkino · 2023-05-05T08:22:49Z

@alkino Just to let you know, I have a fix for ctest -R netpar but need to extend to NRNMPI_DYNAMICLOAD.

NRNMPI_DYNAMICLOAD should be cleaned to be the same than in coreneuron (double implentation today): #2285, so feel free to rework everything

…cpp" This reverts commit e0b3ef1.

azure-pipelines · 2024-10-28T15:35:33Z

✔️ b398627 -> Azure artifacts URL

nrnhines · 2024-10-28T17:47:25Z

@pramodk Feel free to review as briefly as you wish. The most important remaining aspects are for me to check the three boxes in the beginning comment.

pramodk

Glad to see this is close to becoming a reality!

I didn’t have time to review the C++ changes, but I think @alkino can help with that.

I have just added two minor comments regarding the build parts.

pramodk · 2024-10-28T20:18:05Z

cmake/modules/FindSUNDIALS.cmake

+  GIT_REPOSITORY https://github.com/neuronsimulator/sundials.git
+  # GIT_TAG e2f29c34f324829302037a1492db480be8828084   6.2.0 -> CVodeMem no longer "visible" GIT_TAG
+  # c09e732080a214694b209032ec627c93fed45340  4
+  #GIT_TAG 811234254d37652954daff0ccdb7af9813736846 # 3.2.1
+  GIT_TAG 71b3daec18ce66a7c011be9501a31567aa5c09b6 # 3.2.1 hines/hoc_pow
+  # GIT_TAG 7ed895fd102226dbc52225e6b2c6e26ef1cafa0e  #2.7.0
+  # cmake-format: on


@nrnhines : is this LLNL/sundials@main...neuronsimulator:sundials:hines/hoc_pow only change that we need to have? Indeed it's look very trivial.

That is correct for Sundials version 3. We'll eventually see if changes need to be more substantial for later versions. There is some question about where to put the 10 nrn/src/nrniv/nvector_* files. They distinguish between (serial, thread, mpi) and (double, longdouble) and I don't think the changes are relevant to sundials as they have details that depend on how NEURON uses threads and mpi and NRN_ENABLE_MPI_DYNAMIC. At the moment, when
NRN_ENABLE_MPI_DYNAMIC=ON, then nm libnrniv.so | grep MPI shows nothing that points into libmpi. Instead, many things point into mpi specific interface libraries such as libnrnmpi_mpich.so and libnrnmpi_ompi.so . I think the worst case, ultimately, is that sundials gets built for each ```-DNRN_MPI_DYNAMIC="mpi;versions" and then all of sundials gets linked into each of the various libnrnmpi_.so

pramodk · 2024-10-28T20:23:33Z

cmake/modules/FindSUNDIALS.cmake

+  BUILD_BYPRODUCTS
+    <INSTALL_DIR>/lib/libsundials_ida.a <INSTALL_DIR>/lib/libsundials_cvode.a
+    <INSTALL_DIR>/lib/libsundials_nvecserial.a <INSTALL_DIR>/lib/libsundials_nvecpthreads.a
+    <INSTALL_DIR>/lib/libsundials_nvecparallel.a)


This was previously discussed with Alex, but still remember less-than-ideal experiences with ExternalProject_Add during 2016-17. I am still wondering if there might be better alternatives to using nested cmake configure steps. :)

I'll leave it to @alkino and @1uc to weigh in.

My experience with ExternalProject_Add for Sundials hasn't been too bad. At least any change to a build at the nrn level propagates to re-compile and build the sundials *.a files (that link into libnrniv.so). It could be better in terms of having a build tree as a subtree in the nrn build tree. (I often use mulitple nrn/build.../ with different cmake option choices and it would be nice if the latest nrn build did not cause the previous sundial build to be overwritten. I would also prefer to avoid git status not showing the untracked folder external/sundials At the moment the sundials repository seems to begin at nrn/external/sundials/src/sundials-external, the build takes place in nrn/external/sundials/src/sundials-external-build, and the install takes place in nrn/external/sundials/(include, lib). I suppose the way we have been handling InterViews and, more recently, fmt, might provide an alternative strategy.

I'm all in for ExternalProject_Add 🚀 given that we can do custom build/configure commands, it will be definitely useful for upgrading to newer sundials.

pramodk · 2024-10-28T20:25:47Z

src/nrniv/nvector_nrnparallel_ld.cpp

 #include "nvector_nrnparallel_ld.h"
-#include "sundialsmath.h"
-#include "sundialstypes.h"
+#define MPI_Comm int  // or perhaps get rid of them all


nitpick - just curious about this

I am seriously considering removing all references to MPI_Comm in nrn/src/nrniv nvector_parallel.* and nvector_nrnparallel_ld.* . These are basically copies of sundials files from version 2 and 3 but modified to allow
construction from within nrn/src/nrncvode/cvodeobj.cpp and also work without directly calling anything from within mpi.h. That is, they are valid for -DNRN_ENABLE_MPI_DYNAMIC= ON or OFF and don't involve any mpi.h structures (such as MPI_Comm) or functions. They only call things available from nrn/src/nrnmpi/nrnmpi.h. I left in the MPI_Comm tokens just as indicators of what might have to be changed in future movment toward Sundials version 7. At the moment, all of SUNDIALS used by neuron is inside libnrniv.so

nrnhines · 2024-10-29T11:42:07Z

@pramodk I was looking at the checkbox you added to the top commit
merge rxd testdata and update submodule commit
and was wondering what is meant. The nrn master already has

commit f8e94c53da9d59570e6922acef6715f85776ff2e
Author: adamjhn <adam.newton@yale.edu>
Date:   Thu Oct 24 14:59:12 2024 -0400

    Move reference data from test_rxd.py to test_rxd.json. (#3143)
    
    
    * Added a --save flag to regenerate the data.

and the sundials version that this PR uses is mentioned in nrn/cmake/modules/FindSUNDIALS.cmake

GIT_REPOSITORY https://github.com/neuronsimulator/sundials.git
GIT_TAG 71b3daec18ce66a7c011be9501a31567aa5c09b6 # 3.2.1 hines/hoc_pow

So it seems the checkbox should have an [x]

alexsavulescu · 2024-10-29T20:11:33Z

cmake/modules/FindSUNDIALS.cmake

+             -DBUILD_SHARED_LIBS=OFF
+             -DMPI_C_COMPILER=${MPI_C_COMPILER}
+             -DCMAKE_INSTALL_LIBDIR=${SUNDIALS_LIB_DIR}
+  BUILD_BYPRODUCTS


FYI: this is needed for Ninja

src/nrncvode/cvodeobj.cpp

azure-pipelines · 2024-10-31T01:26:00Z

✔️ 1c2308c -> Azure artifacts URL

azure-pipelines · 2024-11-02T15:30:58Z

✔️ 7286d43 -> Azure artifacts URL

sonarcloud · 2024-11-06T15:25:00Z

Quality Gate passed

Issues
169 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.8% Duplication on New Code

See analysis details on SonarCloud

bbpbuildbot · 2024-11-06T16:24:45Z

azure-pipelines · 2024-11-06T16:55:42Z

✔️ d38be72 -> Azure artifacts URL

alexsavulescu added 2 commits August 20, 2022 14:08

ExternalProject SUNDIALS 3.2.1

4581ab4

* include work from cvode3 branch

ninja needs BUILD_BYPRODUCTS in ExternalProject_Add

0a3692c

alexsavulescu mentioned this pull request Aug 20, 2022

Drop legacy SUNDIALS and go upstream #1328

Open

alexsavulescu changed the title ~~Slds~~ ExternalProject SUNDIALS 3.2.1 Aug 20, 2022

alexsavulescu marked this pull request as draft August 20, 2022 12:22

alkino added 2 commits December 11, 2022 20:58

Merge branch 'master' into slds

d38f489

Format

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alkino added 3 commits May 1, 2023 11:59

Merge remote-tracking branch 'origin/master'

daf0008

Format

857bd86

Fix name of SUNR functions

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alexsavulescu linked an issue May 3, 2023 that may be closed by this pull request

Drop legacy SUNDIALS and go upstream #1328

Open

nrnhines and others added 5 commits May 4, 2023 13:30

Fix segfault (missing IDASetUserData) and N_VSpace_... prototypes.

e613da1

Build sundials with the same type than nrn

f2c6b4d

Fully remove sundials

5c5ae92

Merge remote-tracking branch 'origin/master'

3341256

IDASetStopTime should not be called for interpolation.

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ctest -R netpar passes. MPI_Comm not available from cvodeobj.cpp

e0b3ef1

nrnhines added 2 commits May 5, 2023 12:46

Revert "ctest -R netpar passes. MPI_Comm not available from cvodeobj.…

5a11a3f

…cpp" This reverts commit e0b3ef1.

ctest -R netpar passes. Works with NRNMPI_DYNAMICLOAD.

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Problem translating long long foo for NRNMPI_DYNAMICLOAD

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update nrntest (cvode version 3 and no hhtable)

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Merge branch 'master' into slds

554b326

black format for test/.../*.py

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nrnhines marked this pull request as ready for review October 28, 2024 17:39

nrnhines requested a review from pramodk October 28, 2024 17:42

pramodk reviewed Oct 28, 2024

View reviewed changes

alexsavulescu commented Oct 29, 2024

View reviewed changes

src/nrncvode/cvodeobj.cpp Outdated Show resolved Hide resolved

nrnhines added 2 commits October 30, 2024 20:34

Changes after ctest coverage analysis.

68bc030

Merge branch 'master' into slds

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nrnhines added 7 commits November 1, 2024 13:54

Replace cvode.extra_scatter_gather with h.beforestep_callback

82c2f25

rxd tests use rxdtestdata hines/data-fix af269297

1204452

rxd/testdata when test/rxd/3d/test_multi_gridding_mix.py not skipped

11afb3b

Merge branch 'master' into hines/cv3

c084919

Replace cvode.extra_scatter_gather with h.beforestep_callback

f96ebe3

use rxdtestdata hines/cvode3 721ac55a

a5f2b48

Don't use cvode version specific filenames or keys for json data.

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nrnhines mentioned this pull request Nov 4, 2024

modeldb differences with cvode version 2 and 3 #3173

Open

nrnhines added 3 commits November 6, 2024 07:26

ecs_diffusion needs section to gather data.

a89f3e4

Merge branch 'master' into hines/rxd-data-fix

0467293

Merge branch 'hines/rxd-data-fix' into hines/cv3 and update testdata

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ExternalProject SUNDIALS 3.2.1 #1960

ExternalProject SUNDIALS 3.2.1 #1960

alexsavulescu commented Aug 20, 2022 •

edited by nrnhines

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ExternalProject SUNDIALS 3.2.1 #1960

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ExternalProject SUNDIALS 3.2.1 #1960

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