Add step to Cythonize parts of Distributed

[jakirkham]

Adds a step to the nightly benchmarks to Cythonize some modules in Distributed in-place. We go ahead and do this in the environment's site-packages as this environment exists for this benchmark work. So altering it this way shouldn't present an issue.

[jakirkham]

This already has some bits for Cython (though not everywhere). So went ahead and Cythonized it. Though if it causes issues for some reason, we can skip this as it is less critical atm.

[jakirkham]

We haven't made any changes here yet, but it seems like a good idea to queue this up so we are ready once we do.

[jakirkham]

Also please let me know if we want a cleanup step at the end. That should be easy to add.

[quasiben]

Seems to be working:

Cythonize Distributed
+ pushd /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/
/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages ~/GitRepos/dask-scheduler-performance/nightly-benchmark
+ cythonize -i distributed/protocol/serialize.py
Compiling /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.py because it changed.
[1/1] Cythonizing /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.py
running build_ext
building 'distributed.protocol.serialize' extension
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3/envs
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed
creating /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol
gcc -pthread -B /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/include/python3.8 -c /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.c -o /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.o
/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.c: In function ‘__pyx_pw_11distributed_8protocol_9serialize_25serialize’:
/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.c:6544:6: warning: ‘__pyx_v_dict_safe’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (__pyx_t_1) {
      ^
/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.c:5930:7: note: ‘__pyx_v_dict_safe’ was declared here
   int __pyx_v_dict_safe;
       ^~~~~~~~~~~~~~~~~
gcc -pthread -shared -B /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/compiler_compat -L/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib -Wl,-rpath=/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib -Wl,--no-as-needed -Wl,--sysroot=/ /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/tmp66f3_u_z/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.o -o /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.cpython-38-x86_64-linux-gnu.so
/gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /gpfs/fs1/bzaitlen/miniconda3/envs/20201130-nightly-0.17/lib/python3.8/site-packages/distributed/protocol/serialize.py
  tree = Parsing.p_module(s, pxd, full_module_name)
+ distributed/scheduler.py
/var/spool/slurm/d/job118884/slurm_script: line 26: distributed/scheduler.py: Permission denied
+ popd

[quasiben]

Thanks @jakirkham ! Merging in

[jakirkham]

Thanks Ben! 😄

This part seems interesting. What are the permissions on that file?

/var/spool/slurm/d/job118884/slurm_script: line 26: distributed/scheduler.py: Permission denied

Edit: NVM see the issue. Explained below ( #33 (review) ) with a fix in PR ( #34 ).

[jakirkham]

Oops forgot a \. Fixing with PR ( #34 ).