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WIP: Attempts to adjust for Singularity #195

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WIP: Attempts to adjust for Singularity #195

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acf0ee4
WIP: Attempts to adjust for Singularity
jakirkham Apr 5, 2018
d5ff254
WIP: Use node local scratch space
jakirkham Apr 5, 2018
0900315
WIP: Set empirically determined Adaptive values
jakirkham Apr 5, 2018
b22954a
WIP: Rename image to match `singularity pull`
jakirkham May 9, 2018
069a444
Merge 'nanshe-org/master' into 'jakirkham/adj_for_singularity'
jakirkham Mar 6, 2019
2c8957c
Update configuration for cluster workers
jakirkham Mar 6, 2019
4598365
Specify normal queue for dictionary learning
jakirkham Mar 6, 2019
62c3ee6
Use 32 cores for dictionary learning
jakirkham Mar 6, 2019
9c01cfb
Update dictionary learning arguments
jakirkham Mar 6, 2019
b702b54
Merge 'nanshe-org/master' into 'jakirkham/adj_for_singularity'
jakirkham Mar 18, 2019
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34 changes: 30 additions & 4 deletions nanshe_ipython.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -86,12 +86,27 @@
"from psutil import cpu_count\n",
"\n",
"cluster_kwargs = {\n",
" \"ip\": \"\"\n",
" \"preexec_commands\": (\n",
" \"singularity exec --bind /scratch --bind /misc ~/nanshe_workflow.simg \\\\\",\n",
" ),\n",
" \"ip\": \"\",\n",
" \"threads_per_worker\": 1,\n",
" \"local_dir\": \"/scratch/\" + os.environ[\"USER\"],\n",
" \"template\": {\n",
" \"args\": [\n",
" \"--nthreads\", \"1\",\n",
" \"--local-directory\", \"/scratch/\" + os.environ[\"USER\"]\n",
" ],\n",
" \"jobEnvironment\": os.environ,\n",
" \"nativeSpecification\": \"-q normal\"\n",
" }\n",
"}\n",
"client_kwargs = {}\n",
"adaptive_kwargs = {\n",
" \"startup_cost\": \"12s\",\n",
" \"interval\": \"6s\",\n",
" \"minimum\": 0,\n",
" \"maximum\": int(os.environ.get(\"CORES\", cpu_count())) - 1\n",
" \"maximum\": 256\n",
"}"
]
},
Expand Down Expand Up @@ -1261,13 +1276,24 @@
"from psutil import cpu_count\n",
"\n",
"\n",
"ncores = int(os.environ.get(\"CORES\", cpu_count())) - 1\n",
"ncores = 32\n",
"\n",
"\n",
"dict_client = startup_distributed(\n",
" 1,\n",
" cluster_kwargs={\n",
" \"threads_per_worker\": ncores\n",
" \"preexec_commands\": (\n",
" \"singularity exec --bind /scratch --bind /misc ~/nanshe_workflow.simg \\\\\",\n",
" ),\n",
" \"template\":\n",
" {\n",
" \"args\": [\n",
" \"--nthreads\", str(ncores),\n",
" \"--local-directory\", \"/scratch/\" + os.environ[\"USER\"]\n",
" ],\n",
" \"jobEnvironment\": os.environ,\n",
" \"nativeSpecification\": \"-q normal -n %i\" % ncores,\n",
" },\n",
" },\n",
" client_kwargs={}\n",
")\n",
Expand Down