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Repo for the integrated Phylanx Jupyter Notebook Solution
Using my branch from #1, I can get fibonacci data back without any trouble, but in an effort to collect larger datasets for @sayefsakin, I'm a little lost on the best way to run something else.
Here's my attempt to adapt the LRA code from the phylanx example as follows:
from remote_run import remote_run, to_string, viz
from jetlag import Universal, RemoteJobWatcher
from knownsystems import *
import sys
uv = Universal()
uv.load(
backend=backend_tapis,
email="[email protected]",
jetlag_id='rostam-sbrandt',
)
def lra(file_name, xlo1, xhi1, ylo1, yhi1, xlo2, xhi2, ylo2, yhi2, alpha,
iterations, enable_output):
from phylanx.ast import file_read_csv, constant, shape, transpose, exp, dot
data = file_read_csv(file_name)
x = data[xlo1:xhi1, ylo1:yhi1]
y = data[xlo2:xhi2, ylo2]
weights = constant(0.0, shape(x, 1))
transx = transpose(x)
pred = constant(0.0, shape(x, 0))
error = constant(0.0, shape(x, 0))
gradient = constant(0.0, shape(x, 1))
step = 0
while step < iterations:
if enable_output:
print("step: ", step, ", ", weights)
pred = 1.0 / (1.0 + exp(-dot(x, weights)))
error = pred - y
gradient = dot(transx, error)
weights = weights - (alpha * gradient)
step += 1
return weights
job = remote_run(uv, lra, ("/phylanx-data/CSV/breast_cancer.csv", 0, 569, 0, 30, 0, 569, 30, 31, 1e-5, 750, 0), nodes=16, ppn=16)
job.wait()
print("result:",job.get_result())
try:
viz(job)
except:
print("Exception during viz step:",sys.exc_info()[0])
I get these errors in job-###/job.err
:
+ tar xzvf input.tgz
+ echo 'export AGAVE_JOB_NODE_COUNT=16'
+ echo 'export AGAVE_JOB_PROCESSORS_PER_NODE=1'
+ echo 'export nx=0'
+ echo 'export ny=0'
+ echo 'export nz=0'
+ cd ./run_dir
+ source ./runapp.sh
++ source ../.env
+++ export AGAVE_JOB_NODE_COUNT=16
+++ AGAVE_JOB_NODE_COUNT=16
+++ export AGAVE_JOB_PROCESSORS_PER_NODE=1
+++ AGAVE_JOB_PROCESSORS_PER_NODE=1
+++ export nx=0
+++ nx=0
+++ export ny=0
+++ ny=0
+++ export nz=0
+++ nz=0
+++ lscpu
+++ grep '^CPU(s):'
+++ cut -d: -f2
++ export 'CPUS= 32'
++ CPUS=' 32'
++ export APEX_OTF2=1
++ APEX_OTF2=1
++ export 'APEX_PAPI_METRICS=PAPI_TOT_CYC PAPI_BR_MSP PAPI_TOT_INS PAPI_BR_INS PAPI_LD_INS PAPI_SR_INS PAPI_L1_D
++ APEX_PAPI_METRICS='PAPI_TOT_CYC PAPI_BR_MSP PAPI_TOT_INS PAPI_BR_INS PAPI_LD_INS PAPI_SR_INS PAPI_L1_DCM PAPI
++ LD_LIBRARY_PATH=/home/jovyan/install/phylanx/lib64/phylanx:/home/jovyan/install/phylanx/lib64:/usr/local/lib6
++ export PYTHONPATH=/home/jovyan/.local/lib/python3.6/site-packages/phylanx-0.0.1-py3.6-linux-x86_64.egg
++ PYTHONPATH=/home/jovyan/.local/lib/python3.6/site-packages/phylanx-0.0.1-py3.6-linux-x86_64.egg
++ singularity exec /home/sbrandt/images/phylanx-test.simg python3 command.py
No RAPL events found.
Can't open fd for cpu0: Permission denied.
Traceback (most recent call last):
File "/home/jovyan/.local/lib/python3.6/site-packages/phylanx-0.0.1-py3.6-linux-x86_64.egg/phylanx/ast/physl.p
physl_db = db(_name_of_importing_file)
File "/home/jovyan/.local/lib/python3.6/site-packages/phylanx-0.0.1-py3.6-linux-x86_64.egg/phylanx/ast/physl_d
self.dbname, self.db, created = self.ensure_db(name, version)
File "/home/jovyan/.local/lib/python3.6/site-packages/phylanx-0.0.1-py3.6-linux-x86_64.egg/phylanx/ast/physl_d
os.makedirs(dbdir)
File "/usr/local/lib/python3.6/os.py", line 220, in makedirs
mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/__physlcache__'
I'm guessing this might have something to do with trying to sneakily use the data already on rostam under the /phylanx-data/CSV/breast_cancer.csv
directory?
Is there a better way to try to run something heavier through JetLag?
Test issue for Jetlag
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