jit failing
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Emma Wolpert
May 9, 2021, 7:01:03 AM5/9/21
to hoomd-users
Hi
I'm compiling hoomd-blue (version 2.9) from source in order to install jit and it all seems to be working apart from when i do ctest I have 3 tests failing:
274/363 Test #274: enthalpic_interaction.py-cpu ......................***Failed 0.73 sec
Start 275: test_jit_external_field.py-cpu
275/363 Test #275: test_jit_external_field.py-cpu ....................***Failed 0.38 sec
Start 276: test_jit_external_field.py-mpi-cpu
276/363 Test #276: test_jit_external_field.py-mpi-cpu ................***Failed 2.38 sec
I'm keen on using the external field function of jit so was wondering if you have any pointers of how I might be debug this?
Thanks,
Emma
Tim Moore
May 9, 2021, 9:56:25 PM5/9/21
to hoomd...@googlegroups.com
Hi Emma,
It would be helpful to see the output of those tests...which specific tests are failing? In my experience, building against an incompatible version of LLVM can cause this. What version are you using?
Tim
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Tim Moore
Emma Wolpert
May 10, 2021, 3:05:32 AM5/10/21
to hoomd-users
Hi Tim,
I'm using version 6 of LLVM as I read somewhere that its compatible with version 5-9, please let me know if there is another version I'm meant to be using. Heres the output I get in the log file for the failed tests:
274/363 Testing: enthalpic_interaction.py-cpu
274/363 Test: enthalpic_interaction.py-cpu
Command: "/opt/homebrew/bin/python3" "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py" "--mode=cpu"
Directory: /Users/Emma/test/hoomd-blue/build/hoomd/hpmc/test-py
"enthalpic_interaction.py-cpu" start time: May 09 12:00 BST
Output:
----------------------------------------------------------
HOOMD-blue v2.9.6 DOUBLE HPMC_MIXED MPI
Compiled: 09/05/2021
Copyright (c) 2009-2019 The Regents of the University of Michigan.
-----
You are using HOOMD-blue. Please cite the following:
* J A Anderson, J Glaser, and S C Glotzer. "HOOMD-blue: A Python package for
high-performance molecular dynamics and hard particle Monte Carlo
simulations", Computational Materials Science 173 (2020) 109363
-----
-----
You are using HPMC. Please cite the following:
* J A Anderson, M E Irrgang, and S C Glotzer. "Scalable Metropolis Monte Carlo
for simulation of hard shapes", Computer Physics Communications 204 (2016) 21
--30
-----
HOOMD-blue is running on the CPU
test_head_to_tail_antiparallel (__main__.enthalpic_dipole_interaction) ... enthalpic_interaction.py:081 | init.read_snapshot(self.snapshot);
notice(2): Group "all" created containing 2 particles
enthalpic_interaction.py:082 | self.mc = hpmc.integrate.sphere(seed=10,a=0,d=0);
enthalpic_interaction.py:084 | self.patch = jit.patch.user(mc=self.mc,r_cut=self.r_cut, code=self.dipole_dipole);
**ERROR**: EvalFactory: error: expected ')' at end of argument list
define float @eval(%struct.vec3* nocapture nonnull readonly align 4 dereferenceable(12) %0, i32 %1, %struct.quat* nocapture nonnull readonly align 4 dereferenceable(16) %2, float %3, float %4, i32 %5, %struct.quat* nocapture nonnull readonly align 4 dereferenceable(16) %6, float %7, float %8) local_unnamed_addr #0 {
^
ERROR
ERROR
test_head_to_tail_parallel (__main__.enthalpic_dipole_interaction) ... enthalpic_interaction.py:051 | init.read_snapshot(self.snapshot);
**ERROR**: Cannot initialize more than once
ERROR
ERROR
test_head_to_tail_parallel_union (__main__.enthalpic_dipole_interaction) ... enthalpic_interaction.py:168 | init.read_snapshot(self.snapshot);
**ERROR**: Cannot initialize more than once
ERROR
ERROR
test_side_to_side_parallel (__main__.enthalpic_dipole_interaction) ... enthalpic_interaction.py:139 | init.read_snapshot(self.snapshot);
**ERROR**: Cannot initialize more than once
ERROR
ERROR
test_alphas (__main__.patch_alpha_user) ... enthalpic_interaction.py:223 | system = init.read_snapshot(snapshot);
**ERROR**: Cannot initialize more than once
ERROR
test_alphas (__main__.patch_alpha_user_union) ... enthalpic_interaction.py:296 | system = init.read_snapshot(snapshot);
**ERROR**: Cannot initialize more than once
ERROR
======================================================================
ERROR: test_head_to_tail_antiparallel (__main__.enthalpic_dipole_interaction)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 84, in test_head_to_tail_antiparallel
self.patch = jit.patch.user(mc=self.mc,r_cut=self.r_cut, code=self.dipole_dipole);
File "/Users/Emma/test/hoomd-blue/build/hoomd/jit/patch.py", line 158, in __init__
self.cpp_evaluator = _jit.PatchEnergyJIT(hoomd.context.exec_conf, llvm_ir, r_cut, array_size);
RuntimeError: Error compiling JIT code.
======================================================================
ERROR: test_head_to_tail_antiparallel (__main__.enthalpic_dipole_interaction)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 194, in tearDown
del self.patch;
AttributeError: patch
======================================================================
ERROR: test_head_to_tail_parallel (__main__.enthalpic_dipole_interaction)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 51, in test_head_to_tail_parallel
init.read_snapshot(self.snapshot);
File "/Users/Emma/test/hoomd-blue/build/hoomd/init.py", line 236, in read_snapshot
raise RuntimeError("Error initializing");
RuntimeError: Error initializing
======================================================================
ERROR: test_head_to_tail_parallel (__main__.enthalpic_dipole_interaction)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 193, in tearDown
del self.mc;
AttributeError: mc
======================================================================
ERROR: test_head_to_tail_parallel_union (__main__.enthalpic_dipole_interaction)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 168, in test_head_to_tail_parallel_union
init.read_snapshot(self.snapshot);
File "/Users/Emma/test/hoomd-blue/build/hoomd/init.py", line 236, in read_snapshot
raise RuntimeError("Error initializing");
RuntimeError: Error initializing
======================================================================
ERROR: test_head_to_tail_parallel_union (__main__.enthalpic_dipole_interaction)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 193, in tearDown
del self.mc;
AttributeError: mc
======================================================================
ERROR: test_side_to_side_parallel (__main__.enthalpic_dipole_interaction)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 139, in test_side_to_side_parallel
init.read_snapshot(self.snapshot);
File "/Users/Emma/test/hoomd-blue/build/hoomd/init.py", line 236, in read_snapshot
raise RuntimeError("Error initializing");
RuntimeError: Error initializing
======================================================================
ERROR: test_side_to_side_parallel (__main__.enthalpic_dipole_interaction)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 193, in tearDown
del self.mc;
AttributeError: mc
======================================================================
ERROR: test_alphas (__main__.patch_alpha_user)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 223, in setUp
system = init.read_snapshot(snapshot);
File "/Users/Emma/test/hoomd-blue/build/hoomd/init.py", line 236, in read_snapshot
raise RuntimeError("Error initializing");
RuntimeError: Error initializing
======================================================================
ERROR: test_alphas (__main__.patch_alpha_user_union)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/enthalpic_interaction.py", line 296, in setUp
system = init.read_snapshot(snapshot);
File "/Users/Emma/test/hoomd-blue/build/hoomd/init.py", line 236, in read_snapshot
raise RuntimeError("Error initializing");
RuntimeError: Error initializing
----------------------------------------------------------------------
Ran 6 tests in 0.335s
FAILED (errors=10)
<end of output>
Test time = 0.73 sec
----------------------------------------------------------
Test Failed.
"enthalpic_interaction.py-cpu" end time: May 09 12:00 BST
"enthalpic_interaction.py-cpu" time elapsed: 00:00:00
----------------------------------------------------------
275/363 Testing: test_jit_external_field.py-cpu
275/363 Test: test_jit_external_field.py-cpu
Command: "/opt/homebrew/bin/python3" "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/test_jit_external_field.py" "--mode=cpu"
Directory: /Users/Emma/test/hoomd-blue/build/hoomd/hpmc/test-py
"test_jit_external_field.py-cpu" start time: May 09 12:00 BST
Output:
----------------------------------------------------------
HOOMD-blue v2.9.6 DOUBLE HPMC_MIXED MPI
Compiled: 09/05/2021
Copyright (c) 2009-2019 The Regents of the University of Michigan.
-----
You are using HOOMD-blue. Please cite the following:
* J A Anderson, J Glaser, and S C Glotzer. "HOOMD-blue: A Python package for
high-performance molecular dynamics and hard particle Monte Carlo
simulations", Computational Materials Science 173 (2020) 109363
-----
HOOMD-blue is running on the CPU
test_gravity (__main__.jit_external_field)
This test simulates a sedimentation experiment by using an elongated ... -----
You are using HPMC. Please cite the following:
* J A Anderson, M E Irrgang, and S C Glotzer. "Scalable Metropolis Monte Carlo
for simulation of hard shapes", Computer Physics Communications 204 (2016) 21
--30
-----
test_jit_external_field.py:000 | """This module contains the operation functions for this project."""
from __future__ import print_function, division, absolute_import
import unittest
import hoomd
hoomd.context.initialize()
class jit_external_field(unittest.TestCase):
def test_gravity(self):
"""This test simulates a sedimentation experiment by using an elongated
box in the z-dimension and adding an effective gravitational
potential with a wall. Note that it is technically probabilistic in
nature, but we use enough particles and a strong enough gravitational
potential that the probability of particles rising in the simulation is
vanishingly small."""
from hoomd import hpmc, jit
import numpy as np
# Just creating a simple cubic lattice # is fine here.
system = hoomd.init.create_lattice(hoomd.lattice.sc(
test_jit_external_field.py:000 | """This module contains the operation functions for this project."""
from __future__ import print_function, division, absolute_import
import unittest
import hoomd
hoomd.context.initialize()
class jit_external_field(unittest.TestCase):
def test_gravity(self):
"""This test simulates a sedimentation experiment by using an elongated
box in the z-dimension and adding an effective gravitational
potential with a wall. Note that it is technically probabilistic in
nature, but we use enough particles and a strong enough gravitational
potential that the probability of particles rising in the simulation is
vanishingly small."""
from hoomd import hpmc, jit
import numpy as np
# Just creating a simple cubic lattice # is fine here.
system = hoomd.init.create_lattice(hoomd.lattice.sc(
notice(2): Group "all" created containing 125 particles
test_jit_external_field.py:026 | mc = hpmc.integrate.sphere(80391, d=0.1, a=0.1)
test_jit_external_field.py:027 | mc.overlap_checks.set('A', 'A', False)
test_jit_external_field.py:000 | """This module contains the operation functions for this project."""
from __future__ import print_function, division, absolute_import
import unittest
import hoomd
hoomd.context.initialize()
class jit_external_field(unittest.TestCase):
def test_gravity(self):
"""This test simulates a sedimentation experiment by using an elongated
box in the z-dimension and adding an effective gravitational
potential with a wall. Note that it is technically probabilistic in
nature, but we use enough particles and a strong enough gravitational
potential that the probability of particles rising in the simulation is
vanishingly small."""
from hoomd import hpmc, jit
import numpy as np
# Just creating a simple cubic lattice # is fine here.
system = hoomd.init.create_lattice(hoomd.lattice.sc(
1), n=5)
mc = hpmc.integrate.sphere(80391, d=0.1, a=0.1)
mc.overlap_checks.set('A', 'A', False)
mc.shape_param.set('A', diameter=1)
# Expand system, add walls, and add gravity
hoomd.update.box_resize(Lx=system.box.Lx*1.5, Ly = system.box.Ly*1.5,
test_jit_external_field.py:034 | wall = hpmc.field.wall(mc)
test_jit_external_field.py:035 | wall.add_plane_wall([0, 0, 1], [0, 0, -system.box.Lz/2])
test_jit_external_field.py:036 | gravity_field = hoomd.jit.external.user(mc=mc, code="return 1000*(r_i.z + box.getL().z/2);")
**ERROR**: ExternalFieldEvalFactory: error: expected ')' at end of argument list
define float @eval(%struct.BoxDim* nocapture nonnull readonly align 8 dereferenceable(123) %0, i32 %1, %struct.vec3* nocapture readonly %2, %struct.quat* nocapture nonnull readnone align 8 dereferenceable(32) %3, double %4, double %5) local_unnamed_addr #0 {
^
ERROR
======================================================================
ERROR: test_gravity (__main__.jit_external_field)
This test simulates a sedimentation experiment by using an elongated
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/test_jit_external_field.py", line 36, in test_gravity
gravity_field = hoomd.jit.external.user(mc=mc, code="return 1000*(r_i.z + box.getL().z/2);")
File "/Users/Emma/test/hoomd-blue/build/hoomd/jit/external.py", line 142, in __init__
self.cpp_compute = cls(hoomd.context.current.system_definition,
RuntimeError: Error compiling JIT code.
----------------------------------------------------------------------
Ran 1 test in 0.112s
FAILED (errors=1)
<end of output>
Test time = 0.38 sec
----------------------------------------------------------
Test Failed.
"test_jit_external_field.py-cpu" end time: May 09 12:00 BST
"test_jit_external_field.py-cpu" time elapsed: 00:00:00
----------------------------------------------------------
276/363 Testing: test_jit_external_field.py-mpi-cpu
276/363 Test: test_jit_external_field.py-mpi-cpu
Command: "/opt/homebrew/bin/mpiexec" "-n" "2" "/opt/homebrew/bin/python3" "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/test_jit_external_field.py" "--mode=cpu"
Directory: /Users/Emma/test/hoomd-blue/build/hoomd/hpmc/test-py
"test_jit_external_field.py-mpi-cpu" start time: May 09 12:00 BST
Output:
----------------------------------------------------------
HOOMD-blue v2.9.6 DOUBLE HPMC_MIXED MPI
Compiled: 09/05/2021
Copyright (c) 2009-2019 The Regents of the University of Michigan.
-----
You are using HOOMD-blue. Please cite the following:
* J A Anderson, J Glaser, and S C Glotzer. "HOOMD-blue: A Python package for
high-performance molecular dynamics and hard particle Monte Carlo
simulations", Computational Materials Science 173 (2020) 109363
-----
Ranks 0-1: HOOMD-blue is running on the CPU
test_gravity (__main__.jit_external_field)
This test simulates a sedimentation experiment by using an elongated ... test_gravity (__main__.jit_external_field)
This test simulates a sedimentation experiment by using an elongated ... -----
You are using HPMC. Please cite the following:
* J A Anderson, M E Irrgang, and S C Glotzer. "Scalable Metropolis Monte Carlo
for simulation of hard shapes", Computer Physics Communications 204 (2016) 21
--30
-----
test_jit_external_field.py:000 | """This module contains the operation functions for this project."""
from __future__ import print_function, division, absolute_import
import unittest
import hoomd
hoomd.context.initialize()
class jit_external_field(unittest.TestCase):
def test_gravity(self):
"""This test simulates a sedimentation experiment by using an elongated
box in the z-dimension and adding an effective gravitational
potential with a wall. Note that it is technically probabilistic in
nature, but we use enough particles and a strong enough gravitational
potential that the probability of particles rising in the simulation is
vanishingly small."""
from hoomd import hpmc, jit
import numpy as np
# Just creating a simple cubic lattice # is fine here.
system = hoomd.init.create_lattice(hoomd.lattice.sc(
test_jit_external_field.py:000 | """This module contains the operation functions for this project."""
from __future__ import print_function, division, absolute_import
import unittest
import hoomd
hoomd.context.initialize()
class jit_external_field(unittest.TestCase):
def test_gravity(self):
"""This test simulates a sedimentation experiment by using an elongated
box in the z-dimension and adding an effective gravitational
potential with a wall. Note that it is technically probabilistic in
nature, but we use enough particles and a strong enough gravitational
potential that the probability of particles rising in the simulation is
vanishingly small."""
from hoomd import hpmc, jit
import numpy as np
# Just creating a simple cubic lattice # is fine here.
system = hoomd.init.create_lattice(hoomd.lattice.sc(
HOOMD-blue is using domain decomposition: n_x = 1 n_y = 1 n_z = 2.
1 x 1 x 2 local grid on 1 nodes
notice(2): Group "all" created containing 125 particles
test_jit_external_field.py:026 | mc = hpmc.integrate.sphere(80391, d=0.1, a=0.1)
test_jit_external_field.py:027 | mc.overlap_checks.set('A', 'A', False)
test_jit_external_field.py:000 | """This module contains the operation functions for this project."""
from __future__ import print_function, division, absolute_import
import unittest
import hoomd
hoomd.context.initialize()
class jit_external_field(unittest.TestCase):
def test_gravity(self):
"""This test simulates a sedimentation experiment by using an elongated
box in the z-dimension and adding an effective gravitational
potential with a wall. Note that it is technically probabilistic in
nature, but we use enough particles and a strong enough gravitational
potential that the probability of particles rising in the simulation is
vanishingly small."""
from hoomd import hpmc, jit
import numpy as np
# Just creating a simple cubic lattice # is fine here.
system = hoomd.init.create_lattice(hoomd.lattice.sc(
1), n=5)
mc = hpmc.integrate.sphere(80391, d=0.1, a=0.1)
mc.overlap_checks.set('A', 'A', False)
mc.shape_param.set('A', diameter=1)
# Expand system, add walls, and add gravity
hoomd.update.box_resize(Lx=system.box.Lx*1.5, Ly = system.box.Ly*1.5,
test_jit_external_field.py:034 | wall = hpmc.field.wall(mc)
test_jit_external_field.py:035 | wall.add_plane_wall([0, 0, 1], [0, 0, -system.box.Lz/2])
test_jit_external_field.py:036 | gravity_field = hoomd.jit.external.user(mc=mc, code="return 1000*(r_i.z + box.getL().z/2);")
ERROR
ERROR
======================================================================
ERROR: test_gravity (__main__.jit_external_field)
This test simulates a sedimentation experiment by using an elongated
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/test_jit_external_field.py", line 36, in test_gravity
gravity_field = hoomd.jit.external.user(mc=mc, code="return 1000*(r_i.z + box.getL().z/2);")
File "/Users/Emma/test/hoomd-blue/build/hoomd/jit/external.py", line 142, in __init__
self.cpp_compute = cls(hoomd.context.current.system_definition,
RuntimeError: Error compiling JIT code.
----------------------------------------------------------------------
Ran 1 test in 0.123s
FAILED (errors=1)
======================================================================
ERROR: test_gravity (__main__.jit_external_field)
This test simulates a sedimentation experiment by using an elongated
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/Emma/test/hoomd-blue/hoomd/hpmc/test-py/test_jit_external_field.py", line 36, in test_gravity
gravity_field = hoomd.jit.external.user(mc=mc, code="return 1000*(r_i.z + box.getL().z/2);")
File "/Users/Emma/test/hoomd-blue/build/hoomd/jit/external.py", line 142, in __init__
self.cpp_compute = cls(hoomd.context.current.system_definition,
RuntimeError: Error compiling JIT code.
----------------------------------------------------------------------
Ran 1 test in 0.123s
FAILED (errors=1)
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[3968,1],1]
Exit code: 1
--------------------------------------------------------------------------
<end of output>
Test time = 2.38 sec
----------------------------------------------------------
Test Failed.
"test_jit_external_field.py-mpi-cpu" end time: May 09 12:00 BST
"test_jit_external_field.py-mpi-cpu" time elapsed: 00:00:02
----------------------------------------------------------
Thanks for taking a look.
Emma
Joshua Anderson
May 10, 2021, 8:42:34 AM5/10/21
to hoomd...@googlegroups.com
Emma,
The relevant error message in your output is this:
```**ERROR**: ExternalFieldEvalFactory: error: expected ')' at end of argument list
I would guess that the `clang` executable on your PATH is not compatible with the LLVM library you linked to when building HOOMD. These should match.
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
> To view this discussion on the web visit https://groups.google.com/d/msgid/hoomd-users/5d419e4b-31ae-4839-8b6c-3f1a348668b9n%40googlegroups.com.
The relevant error message in your output is this:
```**ERROR**: ExternalFieldEvalFactory: error: expected ')' at end of argument list
define float @eval(%struct.BoxDim* nocapture nonnull readonly align 8 dereferenceable(123) %0, i32 %1, %struct.vec3* nocapture readonly %2, %struct.quat* nocapture nonnull readnone align 8 dereferenceable(32) %3, double %4, double %5) local_unnamed_addr #0 {
```
I would guess that the `clang` executable on your PATH is not compatible with the LLVM library you linked to when building HOOMD. These should match.
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Luis Rivera-Rivera
May 10, 2021, 9:02:17 AM5/10/21
to hoomd...@googlegroups.com
Emma,
I've seen this error before and as Josh guessed above, it is most definitely a clang-LLVM mismatch issue. Try passing a different clang executable to the jit.patch.user class via the clang_exec argument.
To view this discussion on the web visit https://groups.google.com/d/msgid/hoomd-users/490935E3-E589-40A6-B6C1-7815D348C3CA%40umich.edu.
Luis Y. Rivera-Rivera
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