ArkoudaProject/community

Louis Jenkins

@LouisJenkinsCS

Chapel 1.25; I'm running on the headnode but 64GBs of RAM, didn't think I needed to reserve a compute node for compilation :(

machine info: Linux bluehive 3.10.0-1160.31.1.el7.x86_64 #1 SMP Wed May 26 20:18:08 UTC 2021 x86_64
CHPL_HOME: /scratch/ljenkin4/chapel-1.25.0 *
script location: /gpfs/fs2/scratch/ljenkin4/chapel-1.25.0/util/chplenv

CHPL_TARGET_PLATFORM: linux64
CHPL_TARGET_COMPILER: llvm
CHPL_TARGET_ARCH: x86_64
CHPL_TARGET_CPU: ivybridge *
CHPL_LOCALE_MODEL: flat
CHPL_COMM: gasnet *
  CHPL_COMM_SUBSTRATE: ibv *
  CHPL_GASNET_SEGMENT: large *
CHPL_TASKS: qthreads
CHPL_LAUNCHER: slurm-gasnetrun_ibv *
CHPL_TIMERS: generic
CHPL_UNWIND: none *
CHPL_MEM: jemalloc
CHPL_ATOMICS: cstdlib
  CHPL_NETWORK_ATOMICS: none
CHPL_GMP: bundled
CHPL_HWLOC: bundled
CHPL_RE2: bundled
CHPL_LLVM: bundled *
CHPL_AUX_FILESYS: none

glitch

@glitch

I'm running on a thinkpad with 16GB ram, Chapel 1.25.0, CHPL_COMM=none and typical times for me are 5-6 minutes

Louis Jenkins

@LouisJenkinsCS

I take it back, 256GBs of RAM

[ljenkin4@bluehive arkouda]$ free -h
              total        used        free      shared  buff/cache   available
Mem:           251G         38G         26G        4.6G        186G        199G
Swap:           31G        3.3G         28G

I think the machine is just really old, because my laptop builds Chapel and Arkouda relatively quickly as well

[ljenkin4@bluehive arkouda]$ grep MemTotal /proc/meminfo

MemTotal:       263519200 kB
[ljenkin4@bluehive arkouda]$ 
[ljenkin4@bluehive arkouda]$ lscpu
Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                72
On-line CPU(s) list:   0-71
Thread(s) per core:    2
Core(s) per socket:    18
Socket(s):             2
NUMA node(s):          2
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 79
Model name:            Intel(R) Xeon(R) CPU E5-2695 v4 @ 2.10GHz
Stepping:              1
CPU MHz:               2896.984
CPU max MHz:           3300.0000
CPU min MHz:           1200.0000
BogoMIPS:              4199.99
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              46080K
NUMA node0 CPU(s):     0-17,36-53
NUMA node1 CPU(s):     18-35,54-71
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single intel_ppin intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts

I'm wondering, is codegen following inlineFunctions? I.E. did it fail when trying to compile the output C code, or during earlier stage of compilation

Louis Jenkins

@LouisJenkinsCS

Also can confirm that Chapel compiler works for simple hello.chpl example, and runs, so I don't think it has to do with CHPL_TARGET_CPU or some kind of illegal opcode.

glitch

@glitch

Hmm.. this is a bit beyond my skills. I'd start with a really stripped down build and remove the gasnet / comm settings and see if you can get that built. Run top or something to watch system resources during the build and see if you can spot something off.
For comparison my resolve time is around 125s, the lowerIterators is 3s (and pretty much everything after that is low seconds until it makeBinary)

On the surface it almost looks like you ran into swap issues towards the end and the bus error leads me to believe something is wrong with your system's memory.

Louis Jenkins

@LouisJenkinsCS

I guess other people could be using the head node. I suppose I should reserve a compute node this time and have it handle compilation.

glitch

@glitch

If there is light usage now, I'd try kicking off another build and keeping an eye on the system resource usage. Honestly I'd expect it to take 10-15 minutes.

Looking at my output stats, resolve and makeBinary are really the spots that take the majority of the time.

Louis Jenkins

@LouisJenkinsCS

I'm running it again on a compute node this time.

glitch

@glitch

So it's been over 45 minutes, did it complete yet? If not what does the memory usage look like?

Louis Jenkins

@LouisJenkinsCS

Took only 10 min

I used a compute node this time

Turns out the problem was the headnode

glitch

@glitch

:thumbsup:

Louis Jenkins

@LouisJenkinsCS

Thanks for the help!

Louis Jenkins

@LouisJenkinsCS

This message was deleted

tests/categorical_test.py .F......FFF... [ 5%]
tests/check.py ................... [ 12%]
tests/client_test.py ......... [ 15%]
tests/coargsort_test.py ...... [ 18%]
tests/compare_test.py ............... [ 23%]
tests/datetime_test.py ............. [ 28%]
tests/dtypes_tests.py ........... [ 32%]
tests/groupby_test.py .............. [ 37%]
tests/nan_test.py . [ 38%]
tests/io_test.py F.F.FF.FFF..FF.FF.sF.. [ 46%]
tests/io_util_test.py ... [ 47%]
tests/join_test.py ....... [ 50%]
tests/logger_test.py ....... [ 53%]
tests/message_test.py .... [ 54%]
tests/numeric_test.py .......F..... [ 59%]
tests/operator_tests.py ............. [ 64%]
tests/pdarray_creation_test.py .......F...F.F.F.F.. [ 71%]
tests/regex_test.py ........ [ 74%]
tests/registration_test.py ................ [ 80%]
tests/security_test.py .... [ 82%]
tests/setops_test.py ...... [ 84%]
tests/sort_test.py ....

So the "F" means failure? "s" means?

glitch

@glitch

correct, s means skipped, currently there should only be 1 skipped test

Louis Jenkins

@LouisJenkinsCS

Is each test different or are these trials?

glitch

@glitch

they are all individual, you should have gotten a listing of the specific tests that failed

Louis Jenkins

@LouisJenkinsCS

Gotcha, I'll wait until they finish then.

glitch

@glitch

The make test target is really running pytest under the hood which you can invoke manually. i.e.

python3 -m pytest tests/numeric_test.py

You can run a specific one via

python3 -m pytest tests/numeric_test.py::NumericTest::testHistogram

Passing the -s option will also write all of the output to stdout

You can see other optoins etc. in the pytest.ini configuration file

Louis Jenkins

@LouisJenkinsCS

Gotcha. I ran make test-all but right now I'm waiting on the test suite to complete so I can see precisely which tests failed; its stalling right now

I'm wondering, will it fail if it times out? Also, does it create/shutdown the server in each test? I.E. is it possible that it fails because it takes too long to start the server in each test?

glitch

@glitch

From past experience if you're running in multi-locale mode and you think it stalled, do a ps -ef|grep arkouda_server to see if anything is running. Chances are the server process died out and the client in the test is waiting to reconnect ... which is never going to happen.

Everything should pass and it looks like you have enough failures where I'd kill the make test-all process and then re-run just one of the test files manually with the -soption to see what's going on.

Louis Jenkins

@LouisJenkinsCS

Weird its hanging but... ps -ef|grep arkouda_server yields a running server

Categorial Test, which ran perfectly the first time around, hangs on the 4th test

Oh nvm its still running even after the test ended

OH NVM

I was looking at the command itself; the server did indeed die

How do I handle this issue? Is it killed due to default timeout?

glitch

@glitch

No, the server likely seg-faulted during the test. I'd start with a single test class and single test and run it with the -s option so you can see the output

Also you should probably re-compile Arkouda with the ARKOUDA_DEVELOPER flag turned on (i.e. export ARKOUDA_DEVELOPER=1)

glitch

@glitch

This should display the name of the test running, which can help narrow down to a specific test that is hanging and then we can debug from there:

python3 -m pytest tests/categorical_test.py::CategoricalTest -v

Louis Jenkins

@LouisJenkinsCS

E       AssertionError: 'type[32 chars] of (Categorical, str, str_); got int instead' != 'type[32 chars] of (arkouda.categorical.Categorical, str, num[21 chars]tead'
E       - type of argument "other" must be one of (Categorical, str, str_); got int instead
E       + type of argument "other" must be one of (arkouda.categorical.Categorical, str, numpy.str_); got int instead

Hmm

========================================================================================== FAILURES ==========================================================================================
_________________________________________________________________________________ CategoricalTest.testBinop __________________________________________________________________________________

self = <categorical_test.CategoricalTest testMethod=testBinop>

    def testBinop(self):
        cat = self._getCategorical()
        catDupe = self._getCategorical()
        catNonDupe = self._getRandomizedCategorical()


        self.assertTrue((cat._binop(catDupe,'==')).all())
        self.assertTrue((cat._binop(catNonDupe,'!=')).all())

        self.assertTrue((ak.array([True,True,True,True,True,True,True,
                                   True,True,True]) == cat._binop(catDupe,'==')).all())

        self.assertTrue((ak.array([False,False,False,False,False,False,
                                   False,False,False,False]) == cat._binop(catDupe,'!=')).all())

        self.assertTrue((ak.array([True,False,False,False,False,False,
                                   False,False,False,False]) ==
                                   cat._binop('string 1', '==')).all())
        self.assertTrue((ak.array([True,False,False,False,False,False,
                                   False,False,False,False]) ==
                                   cat._binop(np.str_('string 1'), '==')).all())

        self.assertTrue((ak.array([False,True,True,True,True,True,True,True,True,True]) ==
                   cat._binop('string 1', '!=')).all())
        self.assertTrue((ak.array([False,True,True,True,True,True,True,True,True,True]) ==
                   cat._binop(np.str_('string 1'), '!=')).all())

        with self.assertRaises(NotImplementedError):
            cat._binop('string 1', '===')

        with self.assertRaises(TypeError) as cm:
            cat._binop(1, '==')
>       self.assertEqual(('type of argument "other" must be one of (Categorical, str, str_);' +
                          ' got int instead'),
                         cm.exception.args[0])
E       AssertionError: 'type[32 chars] of (Categorical, str, str_); got int instead' != 'type[32 chars] of (arkouda.categorical.Categorical, str, num[21 chars]tead'
E       - type of argument "other" must be one of (Categorical, str, str_); got int instead
E       + type of argument "other" must be one of (arkouda.categorical.Categorical, str, numpy.str_); got int instead
E       ?                                          ++++++++++++++++++++                  ++++++

tests/categorical_test.py:129: AssertionError
================================================================================== short test summary info ===================================================================================

7c180623e234acc691e04947c5a5faf3b0812faf

Hash is above

glitch

@glitch

What's your version of numpy?

Louis Jenkins

@LouisJenkinsCS

Name: numpy
Version: 1.20.1
Summary: NumPy is the fundamental package for array computing with Python.
Home-page: https://www.numpy.org
Author: Travis E. Oliphant et al.
Author-email: None
License: BSD
Location: /home/users/p02405/anaconda3/lib/python3.8/site-packages
Requires: 
Required-by: tifffile, tables, statsmodels, seaborn, scipy, scikit-learn, scikit-image, PyWavelets, pyerfa, patsy, pandas, numexpr, numba, mkl-random, mkl-fft, matplotlib, imageio, hdflow, h5py, Bottleneck, bokeh, bkcharts, astropy

glitch

@glitch

Ah, ok, we're not compatible with 1.20.x yet (Bears-R-Us/arkouda#670), you'll need to downgrade to the 1.19.x line

Louis Jenkins

@LouisJenkinsCS

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