Exception when structural plasticity and multiple threads are used #629

sdiazpier · 2017-01-12T15:42:03Z

This PR addresses issue #290 by throwing a kernel exception when structural plasticity is enabled and multiple threads have been set for simulation.

…abled at the same time

sdiazpier · 2017-01-12T16:17:54Z

I suggest @heplesser, @jakobj and @sanjayankur31 as potential reviewers.

heplesser

@sdiazpier I approve this already, but you need to fix the conflict in test_all.py, which is due to the fact that I just merged #604.

jakobj

Nice, apart from the my small comment, so 👍

jakobj · 2017-01-12T20:00:14Z

nestkernel/sp_manager.cpp

+void
+nest::SPManager::enable_structural_plasticity()
+{
+  if ( kernel().vp_manager.get_num_threads() > 1 )


please add curly braces around the statement

jakobj · 2017-01-12T20:00:41Z

nestkernel/vp_manager.cpp

@@ -180,6 +180,10 @@ nest::VPManager::get_status( DictionaryDatum& d )
 void
 nest::VPManager::set_num_threads( nest::thread n_threads )
 {
+  if ( kernel().sp_manager.is_structural_plasticity_enabled()
+    && ( n_threads > 1 ) )
+    throw KernelException(


(see above)

jakobj · 2017-01-12T20:01:26Z

pynest/nest/tests/test_sp/test_enable_multithread.py

+        with self.assertRaises(nest.NESTError):
+            nest.SetKernelStatus(
+                {
+                    'resolution': 0.1,


why do you need to change resolution here?

heplesser · 2017-01-14T16:32:49Z

@sdiazpier There are some small code-formatting problems and the test for issue #578 now seems to work no longer:

 Weight Recorder Single Threaded ... ok
  ERROR: test_targets (nest.tests.test_sp.test_issue_578_sp.TestIssue578)
      raise _kernel.NESTError(encode(errorstring))
  NESTError: Structural plasticity can not be used with multiple threads in EnableStructuralPlasticity: 
  FAILED (SKIP=11, errors=1)

That test requires two threads (it is run as a single MPI process):

        nest.SetKernelStatus(
            {
                'resolution': 0.1,
                'total_num_virtual_procs': 2
            }
        )

So somehow that test and this PR seem orthogonal to each other?

…only when MPI is available.

heplesser

@sdiazpier Fine in principle, but some details need fixing.

heplesser · 2017-01-16T05:00:11Z

pynest/nest/tests/test_sp/test_all.py

+            call(["mpiexec", "-n", "2", "python", "test_sp/test_issue_578_sp.py"])
+        except:
+            print sys.exc_info()[0]
+            print "Test call with MPI ended in error"


print requires () to be Python3 compatible.

And shouldn't this exception propagate so that the test suite knows that the test failed? Currently, failing MPI will be registered as a working test.

heplesser · 2017-01-16T05:01:34Z

pynest/nest/tests/test_sp/test_all.py

+    from mpi4py import MPI
+except ImportError:
+    # Test without MPI
+    print "Tests without MPI"


print needs () in Python3.

heplesser · 2017-01-16T05:01:57Z

pynest/nest/tests/test_sp/test_all.py

+else:
+    # Test with MPI
+    mpi_test = 1
+    print "Testing with MPI"


print needs () in Python3.

heplesser · 2017-01-16T05:02:30Z

pynest/nest/tests/test_sp/test_all.py

+except ImportError:
+    # Test without MPI
+    print "Tests without MPI"
+    mpi_test = 0


If MPI is not available, post a skipping message.

heplesser · 2017-01-16T05:03:02Z

pynest/nest/tests/test_sp/test_all.py

+    # MPI tests
+    if mpi_test:
+        try:
+            call(["mpiexec", "-n", "2", "python", "test_sp/test_issue_578_sp.py"])


It would be best to pick up the MPI-invocation rule from .nestrc.

…mmand creation from nestrc file

sdiazpier · 2017-01-16T10:26:03Z

Hi dear @heplesser, I have addressed most of your comments. I am not very acquainted with the format of the .nestrc file so I read the command in the most generic way I could with the knowledge that I have from it. Maybe I am not considering certain aspects of the format so If you have a better way or suggestion to make it easier/more robust please let me know.

sdiazpier · 2017-01-18T08:45:31Z

Dear @jougs, could you please take a look at this PR and let me know your opinion on handling the nestrc file to obtain the mpi execution command?

jougs

@sdiazpier: thanks for the PR. I've added some suggestions to make handling of the MPI command line more robust. I'll have a look again once you've addressed those.

jougs · 2017-01-24T05:36:48Z

pynest/nest/tests/test_sp/test_all.py

+            print ("MPI test command: " + line)
+            nestrcf.close()
+            return line
+


There's no need to parse and modify the line from .nestrc manually here as this is anyway a SLI function, which gives you the invocation line for a given number of processes, an executable and a script file. I suggest to replace the function signature by

def getMPITestCommand(np, script):

and the function body by something like this:

return nest.sli_func("mpirun", np, "python", script)

This is much safer, as it works for all possible definitions of mpirun in the .nestrc file.

jougs · 2017-01-24T05:38:40Z

pynest/nest/tests/test_sp/test_all.py

+            command = getMPITestCommand()
+            command = command.replace(
+                "  scriptfile", "test_sp/mpitest_issue_578_sp.py")
+            print ("Executing test with command: " + command)


Given the changes to the getMPITestCommand function detailed below, you can replace lines 53-55 by just

command = getMPITestCommand(2, "test_sp/mpitest_issue_578_sp.py")

sdiazpier · 2017-01-25T10:18:13Z

Hi dear @jougs I have made the changes you suggested. Could you please take a look at it and let me know if anything is missing?

… GSL is not enabled for this test and for the weight recorder test

sdiazpier · 2017-01-25T15:58:21Z

Dear @jougs I implemented the changes we talked about and added the check for GSL in the test. Please let me know if anything else is needed.

jougs

Many thanks for your changes. This looks very nice now.

sdiazpier added 2 commits January 12, 2017 15:55

Exception thrown in structural plasticity and multiple threads are en…

a1d5d14

…abled at the same time

Format for python test

e2ed98e

heplesser approved these changes Jan 12, 2017

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heplesser added this to the NEST 2.12 milestone Jan 12, 2017

heplesser assigned sdiazpier Jan 12, 2017

jakobj approved these changes Jan 12, 2017

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sdiazpier added 2 commits January 13, 2017 13:29

Added curly brackets and removed unnecessary setting of resolution

74bcfbb

Merged with master

417be50

Fixed small formatting issues and problem calling test for issue 578 …

153f932

…only when MPI is available.

heplesser requested changes Jan 16, 2017

View reviewed changes

sdiazpier added 2 commits January 16, 2017 11:11

Solved formatting, printing compatible with Python 3 and added mpi co…

9bd7afd

…mmand creation from nestrc file

Made some format corrections for the mpi command definition

a439624

sdiazpier added 2 commits January 17, 2017 23:15

Changed mpi call from unittest for structural plasticity with pynest

bb05859

Merge branch 'master' into sp_threads_exception

2b6f78c

sdiazpier mentioned this pull request Jan 19, 2017

Follow up on structural plasticity with multi-threaded simulations not working correctly #633

Open

jougs requested changes Jan 24, 2017

View reviewed changes

Changes in the function that gathers the mpi command from nestrc.

be331a0

Reduced the mpi call for the test on issue 578. Added a skip check if…

ed80994

… GSL is not enabled for this test and for the weight recorder test

heplesser approved these changes Jan 25, 2017

View reviewed changes

jougs approved these changes Jan 25, 2017

View reviewed changes

jougs merged commit 9bf42d7 into nest:master Jan 25, 2017

heplesser mentioned this pull request Jan 26, 2017

Problem updating connections with structural plasticity and multiple threads #290

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Exception when structural plasticity and multiple threads are used #629

Exception when structural plasticity and multiple threads are used #629

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Exception when structural plasticity and multiple threads are used #629

Exception when structural plasticity and multiple threads are used #629

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