sailfish-team / sailfish Goto Github PK

Lattice Boltzmann (LBM) simulation package for GPUs (CUDA, OpenCL)

Makefile 0.34% Python 41.59% Shell 0.67% Mako 10.01% C++ 31.75% Cuda 0.49% C 0.40% Elixir 0.89% HTML 13.74% CSS 0.05% Roff 0.07%

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VTK 6

Latest version of tvtk already supports VTK-6, however small changes should be conveniently implemented in sailfish to extend such feature.

It is working to me with the following patch:

diff --git a/sailfish/io.py b/sailfish/io.py
index 53b8aac..8c838a2 100644
--- a/sailfish/io.py
+++ b/sailfish/io.py
@@ -190,6 +190,7 @@ class VTKOutput(LBOutput):
         self.mask_nonfluid_nodes()
         os.environ['ETS_TOOLKIT'] = 'null'
         from tvtk.api import tvtk
+        from tvtk.common import configure_input
         idata = tvtk.ImageData(spacing=(1, 1, 1), origin=(0, 0, 0))

         first = True
@@ -204,7 +205,7 @@ class VTKOutput(LBOutput):
                 t = idata.point_data.add_array(field.flatten())
                 idata.point_data.get_array(t).name = name

-        idata.update()
+        idata.update_traits()
         dim = len(sample_field.shape)

         for name, field in self._vector_fields.iteritems():
@@ -223,7 +224,8 @@ class VTKOutput(LBOutput):
             idata.dimensions = list(reversed(sample_field.shape)) + [1]

         fname = filename(self.basename, self.digits, self.subdomain_id, i, suffix='.vti')
-        w = tvtk.XMLImageDataWriter(input=idata, file_name=fname)
+        w = tvtk.XMLImageDataWriter(file_name=fname)
+        configure_input(w, idata)
         w.write()

     # TODO: Implement this function.

Unfortunately I don't know if it would be incompatible with older versions of tvtk

ZMQError: Protocol not supported on Windows

I recently tried to get Sailfish running under Windows 10 and ran into a problem with the ZeroMQ.
Apparently the IPC protocol is unsupported under Windows and TCP should be used. The problem occurs at this line:

master_addr = 'ipc://{0}/sailfish-master-{1}_{2}'.format(
    tempfile.gettempdir(), os.getpid(), subdomain.id)

I expect this is low priority but would it be possible to make this implementation platform agnostic somehow? I am not familiar enough ZMQ to make PR for this myself; when changing the line to the TCP protocol located at '127.0.0.1:5555' i got pickle error about thread.locks.

Hanging during simulations

Xubuntu 15.10, sailfish from master (f111f6e), ATI R9 290

If I launch the Lid-Driven cavity, everything seems to be working fine... Unfortunately it is suddenly hanging:

[  1751  INFO Master/sobremesa] Machine master starting with PID 25192 at 2016-04-07 18:18:13 UTC
[  1751  INFO Master/sobremesa] Simulation started with: ./ldc_2d.py
[  1760  INFO Master/sobremesa] Sailfish version: f111f6e4a0953357f0871374aa825bc2eaafc2a0
[  1761  INFO Master/sobremesa] Handling subdomains: [0]
[  1761  INFO Master/sobremesa] Subdomain -> GPU map: {0: 0}
[  1764  INFO Master/sobremesa] Selected backend: opencl
[  2291  INFO Subdomain/0] Initializing subdomain.
[  2291  INFO Subdomain/0] Required memory: 
[  2291  INFO Subdomain/0] . distributions: 5 MiB
[  2291  INFO Subdomain/0] . fields: 0 MiB
[  2422  INFO Subdomain/0] On-GPU invalid result check disabled as the device does not support all required features.
/home/pepe/Downloads/sailfish/sailfish/backend_opencl.py:159: UserWarning: Received OpenCL source code in Unicode, should be ASCII string. Attempting conversion.
  return cl.Program(self.ctx, preamble + source).build() #'-cl-single-precision-constant -cl-fast-relaxed-math')
[  5056 WARNING Subdomain/0] Running infinite simulation.
[  5056  INFO Subdomain/0] Starting simulation.
[  5510  INFO Subdomain/0] iteration:2000  speed:277.77 MLUPS
[  5727  INFO Subdomain/0] iteration:3000  speed:295.56 MLUPS
[  5951  INFO Subdomain/0] iteration:4000  speed:288.61 MLUPS
[  6175  INFO Subdomain/0] iteration:5000  speed:288.83 MLUPS
[  6441  INFO Subdomain/0] iteration:6000  speed:243.48 MLUPS
[  6753  INFO Subdomain/0] iteration:7000  speed:208.11 MLUPS
[  7033  INFO Subdomain/0] iteration:8000  speed:230.93 MLUPS
[  7318  INFO Subdomain/0] iteration:9000  speed:227.47 MLUPS
[  7574  INFO Subdomain/0] iteration:10000  speed:252.54 MLUPS
[  7808  INFO Subdomain/0] iteration:11000  speed:276.91 MLUPS
[  8067  INFO Subdomain/0] iteration:12000  speed:250.54 MLUPS
[  8304  INFO Subdomain/0] iteration:13000  speed:273.10 MLUPS
[  8595  INFO Subdomain/0] iteration:14000  speed:222.76 MLUPS
[  8858  INFO Subdomain/0] iteration:15000  speed:246.14 MLUPS
[  9052  INFO Subdomain/0] iteration:16000  speed:333.59 MLUPS
[  9260  INFO Subdomain/0] iteration:17000  speed:311.17 MLUPS
[  9503  INFO Subdomain/0] iteration:18000  speed:266.69 MLUPS
[  9774  INFO Subdomain/0] iteration:19000  speed:238.98 MLUPS
[ 10013  INFO Subdomain/0] iteration:20000  speed:271.23 MLUPS
[ 10268  INFO Subdomain/0] iteration:21000  speed:253.38 MLUPS
[ 10535  INFO Subdomain/0] iteration:22000  speed:243.09 MLUPS
[ 10782  INFO Subdomain/0] iteration:23000  speed:262.50 MLUPS
[ 11032  INFO Subdomain/0] iteration:24000  speed:258.22 MLUPS
[ 11283  INFO Subdomain/0] iteration:25000  speed:258.77 MLUPS
[ 11527  INFO Subdomain/0] iteration:26000  speed:265.50 MLUPS
[ 11791  INFO Subdomain/0] iteration:27000  speed:245.31 MLUPS
[ 12058  INFO Subdomain/0] iteration:28000  speed:242.33 MLUPS
[ 12311  INFO Subdomain/0] iteration:29000  speed:255.68 MLUPS
[ 12564  INFO Subdomain/0] iteration:30000  speed:256.76 MLUPS
[ 12818  INFO Subdomain/0] iteration:31000  speed:254.30 MLUPS
[ 13066  INFO Subdomain/0] iteration:32000  speed:261.79 MLUPS
[ 13491  INFO Subdomain/0] iteration:33000  speed:152.45 MLUPS
[ 13741  INFO Subdomain/0] iteration:34000  speed:259.01 MLUPS
[ 14018  INFO Subdomain/0] iteration:35000  speed:233.74 MLUPS
[ 14260  INFO Subdomain/0] iteration:36000  speed:267.39 MLUPS
[ 14510  INFO Subdomain/0] iteration:37000  speed:258.93 MLUPS

If I cancel the job, it seems to be a synchronization problem between threads:

  File "./ldc_2d.py", line 41, in <module>
    ctrl.run()
  File "/home/pepe/Downloads/sailfish/sailfish/controller.py", line 793, in run
    return self._finish_simulation(subdomain_specs, summary_receiver)
  File "/home/pepe/Downloads/sailfish/sailfish/controller.py", line 708, in _finish_simulation
    self._simulation_process.join()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 145, in join
    res = self._popen.wait(timeout)
  File "/usr/lib/python2.7/multiprocessing/forking.py", line 154, in wait
    return self.poll(0)
  File "/usr/lib/python2.7/multiprocessing/forking.py", line 135, in poll
    pid, sts = os.waitpid(self.pid, flag)

However, if I launch the case with the following command:

./ldc_2d.py --debug_single_process

It is hanging again:

[  1718  INFO MainProcess] Machine master starting with PID 25261 at 2016-04-07 18:21:15 UTC
[  1718  INFO MainProcess] Simulation started with: ./ldc_2d.py --debug_single_process
[  1728  INFO MainProcess] Sailfish version: f111f6e4a0953357f0871374aa825bc2eaafc2a0
[  1729  INFO MainProcess] Handling subdomains: [0]
[  1729  INFO MainProcess] Subdomain -> GPU map: {0: 0}
[  1730  INFO MainProcess] Selected backend: opencl
[  2273  INFO MainProcess] Initializing subdomain.
[  2273  INFO MainProcess] Required memory: 
[  2273  INFO MainProcess] . distributions: 5 MiB
[  2273  INFO MainProcess] . fields: 0 MiB
[  2448  INFO MainProcess] On-GPU invalid result check disabled as the device does not support all required features.
/home/pepe/Downloads/sailfish/sailfish/backend_opencl.py:159: UserWarning: Received OpenCL source code in Unicode, should be ASCII string. Attempting conversion.
  return cl.Program(self.ctx, preamble + source).build() #'-cl-single-precision-constant -cl-fast-relaxed-math')
[  5546 WARNING MainProcess] Running infinite simulation.
[  5564  INFO MainProcess] Starting simulation.
[  6078  INFO MainProcess] iteration:2000  speed:266.26 MLUPS
[  6288  INFO MainProcess] iteration:3000  speed:304.68 MLUPS
[  6513  INFO MainProcess] iteration:4000  speed:287.41 MLUPS
[  6740  INFO MainProcess] iteration:5000  speed:285.69 MLUPS
[  6966  INFO MainProcess] iteration:6000  speed:286.89 MLUPS
[  7199  INFO MainProcess] iteration:7000  speed:278.13 MLUPS
[  7452  INFO MainProcess] iteration:8000  speed:255.82 MLUPS
[  7703  INFO MainProcess] iteration:9000  speed:257.62 MLUPS
[  7921  INFO MainProcess] iteration:10000  speed:297.96 MLUPS
[  8164  INFO MainProcess] iteration:11000  speed:266.58 MLUPS
[  8382  INFO MainProcess] iteration:12000  speed:296.28 MLUPS
[  8632  INFO MainProcess] iteration:13000  speed:259.16 MLUPS
[  8895  INFO MainProcess] iteration:14000  speed:246.05 MLUPS
[  9125  INFO MainProcess] iteration:15000  speed:282.82 MLUPS
[  9355  INFO MainProcess] iteration:16000  speed:281.31 MLUPS
[  9590  INFO MainProcess] iteration:17000  speed:275.48 MLUPS
[  9839  INFO MainProcess] iteration:18000  speed:260.35 MLUPS
[ 10076  INFO MainProcess] iteration:19000  speed:272.75 MLUPS
[ 10351  INFO MainProcess] iteration:20000  speed:235.59 MLUPS
[ 10625  INFO MainProcess] iteration:21000  speed:236.49 MLUPS
[ 11062  INFO MainProcess] iteration:22000  speed:148.00 MLUPS
[ 11284  INFO MainProcess] iteration:23000  speed:292.25 MLUPS
[ 11503  INFO MainProcess] iteration:24000  speed:295.61 MLUPS
[ 11764  INFO MainProcess] iteration:25000  speed:248.77 MLUPS
[ 12020  INFO MainProcess] iteration:26000  speed:252.55 MLUPS
[ 12274  INFO MainProcess] iteration:27000  speed:254.87 MLUPS
[ 12531  INFO MainProcess] iteration:28000  speed:252.07 MLUPS
[ 12779  INFO MainProcess] iteration:29000  speed:261.26 MLUPS

And this time I cannot cancel the job :-S

numpy 1.7 support

2a80b77 doesn't seem to quite fix it.

[kyle@desk01 examples]$ ./ldc_2d.py
[ 1883 INFO Master/desk01] Machine master starting with PID 4770
[ 1884 INFO Master/desk01] Handling subdomains: [0]
[ 1884 INFO Master/desk01] Subdomain -> GPU map: {0: 0}
[ 1951 INFO Subdomain/0] Initializing subdomain.
Process Subdomain/0:
Traceback (most recent call last):
File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(_self._args, *_self._kwargs)
File "/home/kyle/cfd/sailfish-cfd/sailfish/master.py", line 59, in _start_subdomain_runner
runner.run()
File "/home/kyle/cfd/sailfish-cfd/sailfish/subdomain_runner.py", line 1256, in run
self._sim.init_fields(self)
File "/home/kyle/cfd/sailfish-cfd/sailfish/lb_base.py", line 107, in init_fields
f = runner.make_scalar_field(name=field.name, async=True)
File "/home/kyle/cfd/sailfish-cfd/sailfish/subdomain_runner.py", line 243, in make_scalar_field
assert field.base is buf

(in reference to this comment to the Google group that should have been put here: https://groups.google.com/forum/?fromgroups=#!topic/sailfish-cfd/tbA5fhFCcMA)

Add MPI Support for distributed simulation

I've just downloaded the project and ran some of the examples. Looks good!

I'm interested in figuring out if it's plausible to support message passing (MPI) in order to set up distributed simulations. I wasn't able to figure out any other way to get in touch with you other than opening an issue, so if there was a better medium within which this communication can take place let me know. =)

From my (limited) investigation of the docs and code, it seems like distributed simulation works by having two nodes that can connect to each other over the network. At our institution we have a supercomputer where nodes communicate via MPI. There is a python project to support MPI in this way (http://pympi.sourceforge.net/), but I wasn't sure what the best way to go about adding it to sailfish is.

Any thoughts?

ModuleNotFoundError: No module named 'sympy.printing.ccode'

Hello, seems the repo is not under maintain.

Here's a bug report, from python 3.10.

    from sailfish.controller import LBSimulationController
  File "F:\envs\lattuce-23071401\lib\site-packages\sailfish-2013.1-py3.10.egg\sailfish\controller.py", line 35, in <module>
    from sailfish import codegen, config, io, util
  File "F:\envs\lattuce-23071401\lib\site-packages\sailfish-2013.1-py3.10.egg\sailfish\codegen.py", line 16, in <module>
    from sailfish.lb_base import LBMixIn
  File "F:\envs\lattuce-23071401\lib\site-packages\sailfish-2013.1-py3.10.egg\sailfish\lb_base.py", line 4, in <module>
    from sailfish import sym, util
  File "F:\envs\lattuce-23071401\lib\site-packages\sailfish-2013.1-py3.10.egg\sailfish\sym.py", line 15, in <module>
    from sailfish import sym_codegen
  File "F:\envs\lattuce-23071401\lib\site-packages\sailfish-2013.1-py3.10.egg\sailfish\sym_codegen.py", line 11, in <module>
    from sympy.printing.ccode import C99CodePrinter
ModuleNotFoundError: No module named 'sympy.printing.ccode'

OpenCL backend doesn't work with pyopencl >= 2018.2

I tried to run Sailfish on a Conda environment with the latest version of pyopencl, but it seems backend_opencl.py use copy aliases. Checking the pyopencl repository I found that copy aliases were removed in v2018.2:

inducer/pyopencl@a9a14a4

Copy aliases were replaced by the enqueue_copy function.

It would be fine to update backend_opencl.py or edit pyopencl version in setup.py to pyopencl >= 2013.2, < 2018.2.

Poiseuille_3d and Womersley example error

The 'pressure' driving force option in 3d poiseuille example fails with and error because self.channel_length does not return a value. womersley is affected by bug because it inherites from poiseuille.

Further development and maintainance (not an issue)

Dear Developers,
I am have been developing multiphysics open source project based on lattice Boltzmann method for pore scale simulation called Yantra and also made publications with it (https://www.researchgate.net/profile/Ravi_Patel31). We have a long term goal in maintaining Yantra along with providing training for the software. Last Novemeber one such training was organized.

Yantra uses layered approach which allows it to easily integrate with external solver. I have studied the code of salfish partly and I am very much interested in integrating Yantra with Salfish for gpu applications rather than developing new functionality from start. As Salfish is also written in python I can support seamless integration between two tools. However, looking at the state of repository and google forum I am not sure if this project is actively maintained or not. If not I am willing to volunteer to learn internals of salfish and help maintaining it along with Yantra. For further discussions my email address is [email protected]
best regards
Ravi

lbm

How to monitor the velocity along the center line of a cavity?

Develop an IPython tutorial for Sailfish

article deposition calculations on the human lung

Dear sailfish Users and Developers!
I’ve been trying to simulate the particle deposition calculations on the human lung,The human trachea has a complex shape and tiny branches and I was wondering if this program could meet such a need.
Many thanks,
Guo Weiqi

ImportError: No module named skimage.morphology

ImportError: No module named skimage.morphology
ztdep@linux-9owh:~/Downloads/Sailfish/examples> sudo pip install scikit-image
Requirement already satisfied: scikit-image in /usr/lib64/python3.6/site-packages (0.17.2)
Requirement already satisfied: tifffile>=2019.7.26 in /usr/lib/python3.6/site-packages (from scikit-image) (2020.9.3)
Requirement already satisfied: matplotlib!=3.0.0,>=2.0.0 in /usr/lib64/python3.6/site-packages (from scikit-image) (3.2.2)
Requirement already satisfied: scipy>=1.0.1 in /usr/lib64/python3.6/site-packages (from scikit-image) (1.2.0)
Requirement already satisfied: pillow!=7.1.0,!=7.1.1,>=4.3.0 in /usr/lib64/python3.6/site-packages (from scikit-image) (5.0.0)
Requirement already satisfied: numpy>=1.15.1 in /usr/lib64/python3.6/site-packages (from scikit-image) (1.19.2)
Requirement already satisfied: imageio>=2.3.0 in /usr/lib/python3.6/site-packages (from scikit-image) (2.9.0)
Requirement already satisfied: PyWavelets>=1.1.1 in /usr/lib64/python3.6/site-packages (from scikit-image) (1.1.1)
Requirement already satisfied: networkx>=2.0 in /usr/lib/python3.6/site-packages (from scikit-image) (2.5)
Requirement already satisfied: python-dateutil>=2.1 in /usr/lib/python3.6/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image) (2.7.3)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/lib64/python3.6/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image) (1.2.0)
Requirement already satisfied: cycler>=0.10 in /usr/lib/python3.6/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/lib/python3.6/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image) (2.2.0)
Requirement already satisfied: decorator>=4.3.0 in /usr/lib/python3.6/site-packages (from networkx>=2.0->scikit-image) (4.4.2)
Requirement already satisfied: six>=1.5 in /usr/lib/python3.6/site-packages (from python-dateutil>=2.1->matplotlib!=3.0.0,>=2.0.0->scikit-image) (1.11.0)

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