SDSC: PKG - expanse/0.17.3/cpu/b - Missing NEURON (example application) #61
Comments
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Ready for testing; ncurses is a dependency. |
nwolter
changed the title
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Acceptance testing benchmark failing on finding some core *.hoc files. even though they are installed by Spack as part of the neuron package |
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If our benchmark is too old, we may consider using a newer (python-based) example as a test case. https://nrn.readthedocs.io/en/8.2.2/coreneuron/examples.html#examples |
mkandes
changed the title
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Reminder for @mahidhar to also retry the acceptance testing benchmark with the Spack-based Neuron deployed in production. |
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Hello All! Myself Pramod, one of the maintainers for NEURON and the corresponding Spack package. Looking into this along with @iomaganaris. 118 ./x86_64/special: Couldn't find: stdlib.hoc
38 ./x86_64/special: Couldn't find: nrngui.hoc
38 in parinit.hoc near line 2
38 {load_file("nrngui.hoc")}
^
118 in default.hoc near line 1These errors are a bit confusing because they indicate something fundamental is broken in the installation. Are you somehow setting the I cloned this spack from SDSC and installed the neuron package as: $ spack install neuron
$ spack spec -I neuron
Input spec
--------------------------------
- neuron
Concretized
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[+] neuron@8.0.0%gcc@11.4.0~caliper~coreneuron~cross-compile~interviews~ipo~legacy-unit+mpi+python~rx3d~tests build_type=RelWithDebInfo arch=linux-ubuntu22.04-skylake
- ^bison@3.8.2%gcc@11.4.0 arch=linux-ubuntu22.04-skylake
- ^cmake@3.22.1%gcc@11.4.0~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-ubuntu22.04-skylake
- ^flex@2.6.4%gcc@11.4.0+lex~nls patches=09c22e5c6fef327d3e48eb23f0d610dcd3a35ab9207f12e0f875701c677978d3 arch=linux-ubuntu22.04-skylake
[+] ^gettext@0.21%gcc@11.4.0+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-ubuntu22.04-skylake
[+] ^ncurses@6.3.20211021%gcc@11.4.0+symlinks+termlib abi=6 arch=linux-ubuntu22.04-skylake
[+] ^openmpi@4.1.3%gcc@11.4.0~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker~pmi+pmix+romio+rsh~singularity+static+vt+wrapper-rpath cuda_arch=none fabrics=none schedulers=none arch=linux-ubuntu22.04-skylake
[+] ^py-numpy@develop%gcc@11.4.0+blas+lapack patches=873745d7b547857fcfec9cae90b09c133b42a4f0c23b6c2d84cf37e2dd816604 arch=linux-ubuntu22.04-skylake
[+] ^python@3.10.12%gcc@11.4.0+bz2+ctypes+dbm~debug+libxml2+lzma+nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib patches=0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87,4c2457325f2b608b1b6a2c63087df8c26e07db3e3d493caf36a56f0ecf6fb768,f2fd060afc4b4618fe8104c4c5d771f36dc55b1db5a4623785a4ea707ec72fb4 arch=linux-ubuntu22.04-skylake
[+] ^readline@develop%gcc@11.4.0 arch=linux-ubuntu22.04-skylakethen load package and see if basic import is working: $ spack load neuron
$ which nrniv
/home/kumbhar/workarena/repos/external/spack_sdsc/opt/spack/linux-ubuntu22.04-skylake/gcc-11.4.0/neuron-8.0.0-p4oeyvzlbf36bofbazplqvong275feij/bin/nrniv
$ nrniv -python
NEURON -- VERSION 8.0.dev0 unknown branch (unknown commit id) Build Time: 2023-10-04-22:44:24
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2021
See http://neuron.yale.edu/neuron/credits
>>> from neuron import hlet's run internal tests of NEURON: >>> import neuron
>>> neuron.test()
testBytesize (neuron.tests.test_vector.VectorTestCase)
Test that Vector.__array_interface__ returns the proper bytesize (of a double) ... ok
testEndian (neuron.tests.test_vector.VectorTestCase)
Test that Vector.__array_interface__ returns the proper byteorder (endian) ... ok
testNumpyInteraction (neuron.tests.test_vector.VectorTestCase)
Testing numpy.array <=> hoc.Vector interaction ... ok
testPerformance (neuron.tests.test_vector.VectorTestCase)
Test performance of Vector<->list,array ...
Executed "l = range(1000000)". Elapsed = 0.000011 s
Executed "v = h.Vector(l)". Elapsed = 0.052882 s
inplace:
Executed "v.from_python(l)". Elapsed = 0.050961 s
Executed "a = numpy.array(v)". Elapsed = 0.000553 s
inplace:
Executed "v.to_python(a)". Elapsed = 0.000387 s
Executed "v2 = h.Vector(a)". Elapsed = 0.001133 s
inplace:
Executed "v2.from_python(a)". Elapsed = 0.000376 s
Executed "l2 = list(v2)". Elapsed = 0.020353 s
inplace:
Executed "v.to_python(l2)". Elapsed = 0.004894 s
Executed "v2 = h.Vector(a[::-1])". Elapsed = 0.000923 s
Executed "a2 = numpy.array(v2)". Elapsed = 0.000488 s
ok
...
...
...
Ran 15 tests in 0.945s
FAILED (failures=1)there will be one failure related to rxd tests because we have Now, lets run a basic hello world test from https://raw.githubusercontent.com/neuronsimulator/nrn/master/src/parallel/test0.py $ wget https://raw.githubusercontent.com/neuronsimulator/nrn/master/src/parallel/test0.py
$ mpiexec -n 2 nrniv -python test0.py
Authorization required, but no authorization protocol specified
Authorization required, but no authorization protocol specified
NEURON -- VERSION 8.0.dev0 unknown branch (unknown commit id) Build Time: 2023-10-04-22:44:24
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2021
See http://neuron.yale.edu/neuron/credits
NEURON -- VERSION 8.0.dev0 unknown branch (unknown commit id) Build Time: 2023-10-04-22:44:24
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2021
See http://neuron.yale.edu/neuron/credits
numprocs=2
I am 0 of 2
I am 1 of 2All looks good! Now lets run the Model YuEtAl2012: $ git clone https://github.com/ModelDBRepository/144570.git
$ cd 144570/
$ nrnivmodl .
$ ./x86_64/special -mpi -c stop_time=10 -c is_split=1 parinit.hoc
Authorization required, but no authorization protocol specified
Authorization required, but no authorization protocol specified
Authorization required, but no authorization protocol specified
numprocs=1
NEURON -- VERSION 8.0.dev0 unknown branch (unknown commit id) Build Time: 2023-10-04-22:44:24
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2021
See http://neuron.yale.edu/neuron/credits
Additional mechanisms from files
"./ampanmda.mod" "./fi.mod" "./kamt.mod" "./kdrmt.mod" "./naxn.mod" "./ThreshDetect.mod"
cxgranule=177
cxspine=19
cxmitral=1234
cxsecden=502
cxmainmitral=232
cxfi=3
cxampa=4
cxtd=1
500 first and last mitral at 5 4995
10000 first and last granule at 0.25 4999.75
....In summary, I am not able to anything obviously wrong in the NEURON recipe or default version 8 that exists in your Spack. I am happy to in debugging this further as we would like to make sure the Spack package of NEURON works for everyone.
Maybe you can do 2 things:
Otherwise, I am happy to look at this together via a short Skype/zoom call. |
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@pramodk - Thanks so much for your time and effort here to help us sort out this issue. It sounds like maybe we're accidentally stepping on a standard Neuron environment variable. In our Spack deployment, we actually define a *HOME environment variable for EVERY explicitly installed software package that is accessible via our lmod environment. It look like we may need to undo this feature for neuron specifically somehow. Thanks again for the help. |
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that explains it then! 🎉
I would exclude that for NEURON. |
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Not sure about this one. Looks like we need ncurses
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