Re: [pyfrmailinglist] Nvidia device not detected

2014-08-02 Thread Vincent, Peter E
Hi Ismael, Thanks for your interest in PyFR. If you run pyfr-sim -h you will get: usage: pyfr-sim [-h] [--verbose] [--backend BACKEND] [--progress] [--nansweep N] {run,restart} ... Runs a PyFR simulation positional arguments: {run,restart} sub-command

[pyfrmailinglist] New member!

2014-08-03 Thread Ismael D. Boureima
Hello everyone, thanks for having me on PyFR Best, Ismael -- You received this message because you are subscribed to the Google Groups PyFR Mailing List group. To unsubscribe from this group and stop receiving emails from it, send an email to pyfrmailinglist+unsubscr...@googlegroups.com.

Re: [pyfrmailinglist] Setting inflow with a variable expression?

2014-08-19 Thread Vincent, Peter E
Hi Anthony, Thanks for your interest in PyFR. I'm afraid this is not a feature at the moment - but it is definitely on our todo list! Cheers Peter On 19 Aug 2014, at 11:43, Anthony Ashley ash...@rpi.edumailto:ash...@rpi.edu wrote: Hello, I was wondering if it is possible to specify an

[pyfrmailinglist] PyFR v0.2.2

2014-09-01 Thread Vincent, Peter E
Dear All, Just to let you know we have released PyFR v0.2.2. PyFR v0.2.2 = PyFR v0.2.1 + mesh/solution re-partitioning + improved device selection for heterogeneous computing + improved documentation. http://www.pyfr.org/download.php Thanks again for your interest in the project. Peter Dr

Re: [pyfrmailinglist] pyfrmailinglist@googlegroups.com

2014-09-09 Thread Vincent, Peter E
Hi Zhang, Thanks for your interest in PyFR. If you run pyfr-sim -h you will get: usage: pyfr-sim [-h] [--verbose] [--backend BACKEND] [--progress] [--nansweep N] {run,restart} ... Runs a PyFR simulation positional arguments: {run,restart} sub-command

Re: [pyfrmailinglist] pyfrmailinglist@googlegroups.com

2014-09-09 Thread Zhang Wei
Dear Dr Peter: thanks for your reply. I tried to use parameter but it doesn't work. here is the error message: wxw@cu02 test]$ pyfr-sim run couette_flow_2d.pyfrm couette_flow_2d.ini -b openmp [cu02:30246] [[13141,1],0] ORTE_ERROR_LOG: Data for specified key not found in file

Re: [pyfrmailinglist] Computation of time step for FR

2014-10-20 Thread Freddie Witherden
On 20/10/14 12:01, Antonio Garcia-Uceda wrote: Dear All, My name is Antonio Garcia-Uceda, and I'm working on Flux Reconstruction. I'd like to know the way you compute the local time step in FR, for steady state solution. Originally I was using an approach inherited from FV (i.e. cellwise

Re: [pyfrmailinglist] Computation of time step for FR

2014-10-23 Thread Antonio Garcia-Uceda
Dear All, Thanks for the reply. Could you please indicate why exactly pyFR does not have local dt for steady state solutions? I mean, is there any constraint in FR different from the normal local dt used in FV? Cheers, Antonio On Monday, October 20, 2014 11:38:39 PM UTC+2, Vincent, Peter E

Re: [pyfrmailinglist] Computation of time step for FR

2014-10-23 Thread Freddie Witherden
On 23/10/2014 07:39, Antonio Garcia-Uceda wrote: Dear All, Thanks for the reply. Could you please indicate why exactly pyFR does not have local dt for steady state solutions? I mean, is there any constraint in FR different from the normal local dt used in FV? There is no technical reason

Re: [pyfrmailinglist] Computation of time step for FR

2014-10-23 Thread Antonio Garcia-Uceda
Thanks Freddie, once more, :). Btw, just curiosity, at the solution points, Do you store primitive variables, or conserved Variables x JacDet Value (i.e. u or bar_u as indicated in some papers)? Cheers, Antonio On Thursday, October 23, 2014 9:44:45 AM UTC+2, Freddie Witherden wrote: On

Re: [pyfrmailinglist] Extrapolate Variables to Flux Points on Faces

2014-10-29 Thread Vincent, Peter E
Yes, correct. The physical solution is stored at the solution points and extrapolated to the flux points. Cheers Peter Dr Peter Vincent MSci ARCS DIC PhD Senior Lecturer and EPSRC Early Career Fellow Department of Aeronautics Imperial College London South Kensington London SW7 2AZ UK web:

Re: [pyfrmailinglist] OpenCL Runtime Error

2014-11-02 Thread Freddie Witherden
Hi Zach, On 02/11/14 23:38, Zach Davis wrote: Hi Freddie, Setting the PYFR_LIBRARY_PATH environment variable now gets me to the point where clBLAS is found. I now get a status code of -54. Stack trace follows: Now we're getting somewhere! That error corresponds to -54 =

Re: [pyfrmailinglist] OpenCL Runtime Error

2014-11-03 Thread Freddie Witherden
Hi Zach, On 03/11/14 00:15, Zach Davis wrote: I'm giving your tuning idea a go. It appears to be a somewhat slow and compute intensive process. One question I have related to this tune executable is whether this process works on the installation, or those files compiled in the build

Re: [pyfrmailinglist] OpenCL Runtime Error

2014-11-03 Thread Zach Davis
Monday, 3 November 2014 Hi Freddie, I have another follow-up question for you. I was able to confirm that using the openmp backend, OS X was unable to compile the requisite kernel due to lack of clang OpenMP support as you mentioned. I found a post on stackoverflow referencing partial

Re: [pyfrmailinglist] OpenCL Runtime Error

2014-11-03 Thread Zach Davis
Monday, 3 November 2014 Hi Freddie, I’m still looking into the OpenCL backend, but I think I was finally able to get the OpenMP backend up and running under OS X. I’ve collected a few relative performance benchmark results that perhaps some in the community might be interested in. Ideally,

[pyfrmailinglist] Issue loading CBLAS library

2014-11-17 Thread Antonio Garcia-Uceda
Dear all, My name is Antonio Garcia-Uceda, and I'm a researcher on Flux Reconstruction methods. I'm using pyFR as part of my project. I'm trying to run pyFR with backend opemp, but I'm coming across some issues when using a CBLAS library. I get the following error message on the screen: Let me

Re: [pyfrmailinglist] PyFR Delta Wing Example Issue

2014-11-18 Thread Freddie Witherden
Hi Zach, On 17/11/2014 20:00, Zach Davis wrote: As you noted I included a pole in my mesh. I’ve gone another route with the meshing, and that seems to have resolved my initial issue. However, now during the course of simulation I get a runtime error indicating the “Minimum sized time step

[pyfrmailinglist] Mac mpi4py installation issue

2015-02-09 Thread Gabriel Gassem
I am using Python 2.7.5 and have installed openmpi-1.8.4. However when i try and build mpi4py-1.3.1 using *'$ python setup.py build'* in terminal as outlined in the file*'docs/source/usrman/install.rst'*, i get the error pasted in the text document attached. See below for the final few lines for

Re: [pyfrmailinglist] OS X PyFR origin/develop branch

2015-03-09 Thread Vincent, Peter E
Hi Zach, To avoid conflicts between different version of python and other dependencies I would suggest using virtualenv: http://docs.python-guide.org/en/latest/dev/virtualenvs/ I am planning to add something to the User Guide in the near future suggesting the use of virtualenvs. Cheers

Re: [pyfrmailinglist] OS X PyFR origin/develop branch

2015-03-09 Thread Vincent, Peter E
Hi Zach, Can you try with Sphinx 1.3b3 and see if that fixes things? Cheers Peter Sent from my iPhone On 9 Mar 2015, at 22:51, Zach Davis z...@rescale.commailto:z...@rescale.com wrote: Hi Peter, That seems to have resolved my earlier issue—thanks! I’ve got another one with regards to

Re: [pyfrmailinglist] OS X PyFR origin/develop branch

2015-03-09 Thread Freddie Witherden
Hi Zach, On 09/03/15 22:51, Zach Davis wrote: That seems to have resolved my earlier issue—thanks! I’ve got another one with regards to generating the documentation: (venv)[zdavis@Minerva doc]$ make latexpdf sphinx-build -b latex -d build/doctrees src build/latex Making output

Re: [pyfrmailinglist] OS X PyFR origin/develop branch

2015-03-09 Thread Zach Davis
Hi Peter, That seems to have resolved my earlier issue—thanks! I’ve got another one with regards to generating the documentation: (venv)[zdavis@Minerva doc]$ make latexpdf sphinx-build -b latex -d build/doctrees src build/latex Making output directory... Running Sphinx v1.2.3 Exception

Re: [pyfrmailinglist] Example Datasets

2015-03-09 Thread Zach Davis
Hi Freddie, I was trying to run the same case with the OpenCL backend--I know, I know it's a bit more tenuous--and the simulation progress reached 98% before there was a pyopencl error which killed the MPI rank I had allocated for the GPU: (venv) [zdavis@Rahvin cubes]$ mpirun -np 5

Re: [pyfrmailinglist] How to profile PyFR?

2015-03-09 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 07/03/2015 06:43, Zhen Zhang wrote: Hi everyone! I am familiar with profiling C/C++ etc. program, but never profile any Python related stuff. What's more, PyFR uses a lot of modules and backends, which complicates it more. So, I want to

Re: [pyfrmailinglist] Example Datasets

2015-03-12 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Zach, On 11/03/2015 14:44, Zach Davis wrote: I can verify the changes that you made in your latest commit for PR-40 resolve the issue I was running into. I can also build the documentation without having to apply the 2to3 patch. Thanks for

Re: [pyfrmailinglist] Example Datasets

2015-03-10 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Zach, On 10/03/2015 05:36, Zach Davis wrote: I was trying to run the same case with the OpenCL backend--I know, I know it's a bit more tenuous--and the simulation progress reached 98% before there was a pyopencl error which killed the MPI rank

Re: [pyfrmailinglist] How to set Slip-BCs on PyFR

2015-04-24 Thread Antonio Garcia-Uceda
Dear Arvind, Indeed this is what I need, thanks. Do you know if these are also available in PyFR -0.2.4? Unfortunately I'm having troubles to install the libraries for python-0.3.0 and thus for the moment I keep using the previous version. Just one last thing: Would you have in hand the set-up

[pyfrmailinglist] Why non-parallel mode still needs MPI?

2015-04-24 Thread Zhen Zhang
Hi! My question is, if we are using PyFR with multiple processes, or in parallel execution, it is apparent that we needs MPI and launch with mpirun . But even the default launching as a single process, using the `pyfr run ...` directly, will launch MPI as well, even if there is only one

Re: [pyfrmailinglist] How to set Slip-BCs on PyFR

2015-04-24 Thread arvind iyer
unfortunately, you said the Slip BCs are only available on PyFR_0.3.0, right? Yes -- You received this message because you are subscribed to the Google Groups PyFR Mailing List group. To unsubscribe from this group and stop receiving emails from it, send an email to

Re: [pyfrmailinglist] Print out variables within the mako templates subroutines

2015-05-06 Thread Antonio Garcia-Uceda
Dear Freddie, Thanks a lot, it really helped. I managed to output the data inside the mako kernels as you indicated in the other posts. Is it also possible to print out as well the given sol/flux point in which the operation is going on? There's no index with this info inside the mako

Re: [pyfrmailinglist] Re: Print out variables within the mako templates subroutines

2015-05-06 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi Antonio, On 06/05/2015 08:48, Antonio Garcia-Uceda wrote: 1) whether it is possible to print out variables within the mako templates pointwise kernels, such as during the computation of inviscid/viscous fluxes. In terms of outputting

[pyfrmailinglist] PyFR v0.8.0

2015-05-07 Thread Vincent, Peter E
Dear All, We have released PyFR v0.8.0. New Features: - Shock capturing - Parallel .vtu output - Surface-force extraction Download: http://www.pyfr.org/download.php Thanks again for your interest in the project. Peter Dr Peter Vincent MSci ARCS DIC PhD Senior Lecturer and EPSRC

Re: [pyfrmailinglist] cPickle has me in a pickle

2015-07-01 Thread Dani Ruiz
Hi Freddie, Your change leaded again to the error with pickle... So I added the np.intp = np.int32 line to every file importing numpy module and that solved the issue. Anyhow, now I'm facing another problem with MPI (most probably related with mpi4py Python module) which I'm trying to solve

[pyfrmailinglist] Fw: 'pyfr run' KeyError for CUDA kernel

2015-07-06 Thread Tom Fogal
From: Tom Fogal Sent: Saturday, July 4, 2015 12:42 PM To: pyfrmailinglist@googlegroups.com Subject: 'pyfr run' KeyError for CUDA kernel Hi all, I've been upgrading/downgrading CUDA for other reasons on my system, and when I came back to my previously-working

Re: [pyfrmailinglist] Fw: 'pyfr run' KeyError for CUDA kernel

2015-07-06 Thread Freddie Witherden
Hi Tom, On 06/07/15 19:33, Tom Fogal wrote: I have tried with v1.0.0 and now 4ce740ff4d7ff3bd93b6f3ad00ee46815b6b810c to no avail. I am presently running with CUDA v6.5, PyCUDA 2014.1. Any ideas as to what I might have messed up? It takes a bit of work to unpick the various tracebacks

Re: [pyfrmailinglist] 'pyfr run' KeyError for CUDA kernel

2015-07-06 Thread Tom Fogal
Oh, I should take another look. I gave it a first spin last week, but dropped it when clean installs of pyFR inside it didn't fix my issue. If only I'd thought to do a clean install + all modules! Thanks, -tom On 07/06/2015 03:59 PM, Vincent, Peter E wrote: Hi Tom, Glad you got the

Re: [pyfrmailinglist] cPickle has me in a pickle

2015-06-30 Thread Dani Ruiz
Hi, Regarding the issue Miquel had, chaning the intp instances by int32 solves the problem with pickle on ARM 32 bits and, therefore, the application runs correctly with OpenMP backend. However, when running MPI+OpenMP it crashes again due to some key error with int32. Below the specific

Re: [pyfrmailinglist] RuntimeError: Mesh has 2 partitions but running with 1 MPI ranks, with OpenMPI

2015-05-24 Thread Freddie Witherden
Hi Pablo, On 24/05/15 04:33, Pablo Restrepo Henao wrote: I just installed PyFR 0.8.0. The 2d euler vortex example is working perfectly with Intel MPI 15, but I am having issues trying to run it with OpenMPI. (I tried with OpenMPI 1.8.5 and 1.8.1). When switching out MPI implementations it

[pyfrmailinglist] RuntimeError: Mesh has 2 partitions but running with 1 MPI ranks, with OpenMPI

2015-05-23 Thread Pablo Restrepo Henao
Hello, I just installed PyFR 0.8.0. The 2d euler vortex example is working perfectly with Intel MPI 15, but I am having issues trying to run it with OpenMPI. (I tried with OpenMPI 1.8.5 and 1.8.1). This is the error I am getting: bash-4.2$ pyfr import euler_vortex_2d.msh euler_vortex_2d.pyfrm

Re: [pyfrmailinglist] Some confusions about OPENMP backend

2015-06-29 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi, On 29/06/2015 06:34, CatDog wrote: 1. According to the output of clinfo (in the attachment), I have two OpenCL platform, in the NV GT 620 GPU platform. clinfo.out indicates I have 96 cores and ~256MB RAM. But in the output of nvidia-smi (in

Re: [pyfrmailinglist] Some confusions about OPENMP backend

2015-06-28 Thread CatDog
Hi, Freddie I still have some problem on the backends. 1. According to the output of clinfo (in the attachment), I have two OpenCL platform, in the NV GT 620 GPU platform. clinfo.out indicates I have 96 cores and ~256MB RAM. But in the output of nvidia-smi (in the following lines), I have

Re: [pyfrmailinglist] cPickle has me in a pickle

2015-06-30 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 On 30/06/2015 14:41, Dani Ruiz wrote: Hi, Regarding the issue Miquel had, chaning the intp instances by int32 solves the problem with pickle on ARM 32 bits and, therefore, the application runs correctly with OpenMP backend. However, when

Re: [pyfrmailinglist] PyFR 1.1.0 Documentations Issue

2015-10-23 Thread Zach Davis
Hi Peter, It appears my TeX distribution moved in OS X 10.11. After updating my shell environment’s path to this new location and re-installing the sphinx package in my virtual environment, things are working again. Apologies for any inconvenience due to my user-error. Best Regards, Zach

[pyfrmailinglist] PyFR v1.1.0

2015-10-23 Thread Vincent, Peter E
Dear All, We have released PyFR v1.1.0. New Features: - Residual plugin - More spatially/temporally varying boundary conditions - Viscous stresses from surface force plugin Download: http://www.pyfr.org/download.php Thanks again for your interest in the project. Peter Dr Peter

[pyfrmailinglist] Using PyFR for incompressible boundary layer solution

2015-10-26 Thread Dinesh Bhatia
Hi, I have just downloaded PyFR. I need an incompressible Navier-Stokes solution for a laminar boundary layer problem with the free-stream boundary condition to be a Neumann type. I have seen the basic types of BC options in PyFR and there is no direct way to apply such a BC. My

[pyfrmailinglist] Incompatibility with mpi4py 2

2015-10-29 Thread Freddie Witherden
Hi all, Last week version 2 of mpi4py was released. This release contains several backwards incompatible changes. Firstly, it is not currently possible to build h5py against this new version of mpi4py. Users are therefore recommended to stick with 1.3.1 until a new version of h5py is

Re: [pyfrmailinglist] Using PyFR for incompressible boundary layer solution

2015-10-29 Thread Vincent, Peter E
Hi Dinesh, Thanks for your interest in PyFR. Currently PyFR only has a compressible solver, but we seem to get good agreement with incompressible data by running with Ma = 0.1-0.2. You would probably want to try a characteristic BC (char-riem-inv) at the domain outlet in the first instance.

Re: [pyfrmailinglist] Using PyFR for incompressible boundary layer solution

2015-10-27 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi Dinesh, On 27/10/2015 00:22, Dinesh Bhatia wrote: > I have just downloaded PyFR. I need an incompressible > Navier-Stokes solution for a laminar boundary layer problem with > the free-stream boundary condition to be a Neumann type. PyFR is

Re: [pyfrmailinglist] Question about the compiler used in Mako template library

2015-11-13 Thread Antonio Garcia-Uceda
Thanks a lot for your reply Antonio On Friday, November 13, 2015 at 11:48:29 AM UTC+1, Freddie Witherden wrote: > > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA256 > > Hi Antonio, > > On 13/11/2015 10:33, Antonio Garcia-Uceda wrote: > > Thanks. I guess if not specified in the .ini file it

[pyfrmailinglist] Regarding PyFR on Multi GPU

2015-11-01 Thread Suraj Salvi
Hello Sir, I am working on Multi GPU implementation of CFD solver and i found that PyFR is providing such functionality. will you provide me data for PyFR Multi GPU support like steps to do so and basic installation of PyFR alos. Thanks and Regards, Suraj Salvi -- You received this message

Re: [pyfrmailinglist] Re: BLAS libraries used in PyFR

2015-11-03 Thread Freddie Witherden
Hi Antonio, On 03/11/15 13:52, Antonio Garcia-Uceda wrote: > I managed to build and link the ATLAS library. I've run some tests but > it gives me lower performance than I expected: OpenBLAS > (single-threaded) outperforms ATLAS by 20-30%. > > I know that the peformance of BLAS is

Re: [pyfrmailinglist] Re: BLAS libraries used in PyFR

2015-11-03 Thread Antonio Garcia-Uceda
Dear Freddie, I managed to build and link the ATLAS library. I've run some tests but it gives me lower performance than I expected: OpenBLAS (single-threaded) outperforms ATLAS by 20-30%. I know that the peformance of BLAS is platform-dependent and that your good experience with ATLAS is not

Re: [pyfrmailinglist] BLAS libraries used in PyFR

2015-10-19 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi Antonio, On 19/10/2015 11:32, Antonio Garcia-Uceda wrote: > My name is Antonio Garcia-Uceda, and I'm working on Flux > Reconstruction. > > Could you please let me know which BLAS-type library do you use > with PyFR? And according to your

Re: [pyfrmailinglist] Question about the compiler used in Mako template library

2015-11-13 Thread Antonio Garcia-Uceda
Dear Peter, Thanks. I guess if not specified in the .ini file it catches the one set by default in "gcc", right? I have another question: Do you know whether it's possible to set in Mako to keep the c++ files (they are tmp.c I think) somewhere and not to delete them after the PyFR launch is

[pyfrmailinglist] HPCWire Readers Choice Awards 2015

2015-09-10 Thread Vincent, Peter E
Hi All, Just to let you know that PyFR has been nominated for several HPCWire Readers Choice Awards: 12. Best HPC Software Product or Technology 18. Best HPC Collaboration Between Academia & Industry 20. Top 5 New Products or Technologies to Watch

Re: [pyfrmailinglist] Node ordering for Flux Reconstruction

2015-10-05 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi Kunal, On 05/10/2015 15:22, Kunal Puri wrote: > Hi. Does the flux reconstruction approach on triangles require a > specific node ordering? Consider two neighboring elements (A & B) > with the nodes numbered as follows: > > Element "A" is a

Re: [pyfrmailinglist] A couple of additional questions...

2016-01-02 Thread Jon Pandolfini
I had the same problem but did fix it. I found the easiest solution was to use synaptic package manager and install the libmetis-dev. This will install everything you need and set the path. On Thursday, June 19, 2014 at 12:38:51 PM UTC-5, Freddie Witherden wrote: > > -BEGIN PGP SIGNED

[pyfrmailinglist] Output solution on the bounraries with PyFR

2015-11-23 Thread Antonio Garcia-Uceda
Dear all, I'd like to ask you whether PyFR is able to output the solution on specific boundaries, such as pressure on a solid boundary. I know with the "[soln-plugin-sampler]" one can output the solution at specific locations, but it'd be tedious to define the boudnary point by point. If

[pyfrmailinglist] How to contribute to development?

2015-11-23 Thread René Hommel
Dear all, I am new at PyFR, highly interested to learn more and to apply the package. However, I did not find any information on the web sites how one can contribute to the development. I have a few things may be of interest (mesh converter, export capabilities). Any suggestions where to

Re: [pyfrmailinglist] Issues to compile PyFR-1.4.0

2016-06-22 Thread Antonio Garcia-Uceda
Hi Freddie, Indeed it manages to create a .egg file (seemingly binary) under the directory dist/. So you say I should copy manually this file to the drectory / *lib/python3.3/site-packages*, right? However I still need the executable pyfr in the directory /*bin, *which is created later at

Re: [pyfrmailinglist] Issues to compile PyFR-1.4.0

2016-06-22 Thread Antonio Garcia-Uceda
Dear Freddie, Thanks a lot for you reply. Indeed the workng directory is under a networking file system. I can't tell you details though since I;m not aware of it, but I can ask. Please let me know whether you need any further info. Thanks once more. Best regards, Antonio On Wednesday, June

[pyfrmailinglist] Issues to compile PyFR-1.4.0

2016-06-22 Thread Antonio Garcia-Uceda
Dear all, I'd be very grateful if you could help me out with the following: I'm trying to compile the last version PyFR-1.4.0, by launching the "setup.py" script. However at some point it crashes with the output shown below. In my understanding, the problem comes when trying to install the

Re: [pyfrmailinglist] Issues to compile PyFR-1.4.0

2016-06-22 Thread Freddie Witherden
Hi Antonio, On 22/06/2016 06:53, Antonio Garcia-Uceda wrote: > I'd be very grateful if you could help me out with the following: > > I'm trying to compile the last version PyFR-1.4.0, by launching the > "setup.py" script. However at some point it crashes with the output > shown below. > > In

Re: [pyfrmailinglist] Issues to compile PyFR-1.4.0

2016-06-22 Thread Freddie Witherden
Hi Antonio, On 22/06/2016 07:11, Antonio Garcia-Uceda wrote: > Thanks a lot for you reply. > > Indeed the workng directory is under a networking file system. I can't > tell you details though since I;m not aware of it, but I can ask. > > Please let me know whether you need any further info. My

Re: [pyfrmailinglist] Problem converting Gmsh file to PyFR file

2016-02-05 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi Andrew, On 05/02/2016 17:44, Andrew Holt wrote: > I defined the physical surface for the fluid region and physical > lines for the boundaries (see .msh file). However I keep getting > the below error when I try to import the GMSH file into PyFR:

Re: [pyfrmailinglist] Problem converting Gmsh file to PyFR file

2016-02-05 Thread Andrew Holt
Hi I defined the physical surface for the fluid region and physical lines for the boundaries (see .msh file). However I keep getting the below error when I try to import the GMSH file into PyFR: ValueError: Malformed physical entity I have tried defining physical lines for all boundaries, and

Re: [pyfrmailinglist] units for mass, length and time

2016-02-01 Thread Vincent, Peter E
Hi Paul, Thanks for your interest in PyFR. A current feature of PyFR is that it can operate in any consistent system of units. Yes. Would it be possible to add the ability to use a specific system of units; SI, for example? I believe that this capability is a subset of the above? If you

Re: [pyfrmailinglist] units for mass, length and time

2016-02-01 Thread Freddie Witherden
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi Paul, On 01/02/2016 11:52, Paul Garlick wrote: > A current feature of PyFR is that it can operate in any consistent > system of units. Would it be possible to add the ability to use a > specific system of units; SI, for example? > > At

[pyfrmailinglist] units for mass, length and time

2016-02-01 Thread Paul Garlick
Hi Developers, A current feature of PyFR is that it can operate in any consistent system of units. Would it be possible to add the ability to use a specific system of units; SI, for example? At present, any scale factors used to non-dimensionalize a given PyFR case must be recorded

Re: [pyfrmailinglist] OpenMP backend error

2016-02-29 Thread 'Leo Allen' via PyFR Mailing List
Hi Freddie, After commenting out the prefork enabling, I made the following changes to util.py on the call function, from line 21. def __call__(self, *args, **kwargs): instance = args[0] print("") print(self) print("--self") print(*args)

Re: [pyfrmailinglist] OpenMP backend error

2016-02-24 Thread Freddie Witherden
Hi Leo, On 24/02/16 16:17, 'Leo Allen' via PyFR Mailing List wrote: > Hello, I've been using PyFR on a windows laptop with Cygwin 64bit, and > after upgrading pyfr to 1.3, I get an error which seems to persist even > when I downgrade back to 1.2. Nothing substantial changed between v1.2.0 and

Re: [pyfrmailinglist] cblas openmp error

2016-03-31 Thread Vincent, Peter E
Hi Emre, Thanks for your interest in PyFR. configparser.NoOptionError: No option 'cblas' in section: 'backend-openmp’ Seems like you have not set cblas in the ini file (as per the User Guide http://www.pyfr.org/user_guide.php) Cheers Peter Dr Peter Vincent MSci ARCS DIC PhD Senior Lecturer

[pyfrmailinglist] cblas openmp error

2016-03-30 Thread emre
Hi, I am a newbie to Linux and to PyFr. I have to work on a virtual machine for the moment. And for the time being I try to use PyFR with OpenMp but no chance so far. This is the error I get: /Documents/examples/couette_flow_2d$ sudo pyfr run -b openmp -p couette_flow_2d.pyfrm

Re: Özel iletinin konusu: [pyfrmailinglist] OpenMP backend error

2016-04-11 Thread Freddie Witherden
Hi Emre, On 11/04/2016 07:42, emre wrote: > I am sorry I could not thank you sooner, for your reply. Unfortunately I > could not do what you suggested "run a C code with the arguments given > in the error". I do not know C. But I worked on python installation > thinking that it might be related

Re: Özel iletinin konusu: [pyfrmailinglist] OpenMP backend error

2016-04-11 Thread emre
Hi Freddie, Do you have any suggestion how to do it? I tried cc = icl (intel c compiler code for windows corresponding to icc of linux) I tried cc = full path\icl.exe I tried to launch pyfr from Intel compiler command window. Each time I get this error: The first part with OpenMp Kernel

Re: [pyfrmailinglist] OpenMP backend error

2016-03-31 Thread emre
Hi Freddie, I have a similar problem. I installed Anaconda distribution, therefore I am not sure about the compiler but mpi4py seems to work only with Intel MPI. At first it was installing using MS MPI with wrong directories, then I corrected them with correct MS MPI. But the result of

Re: [pyfrmailinglist] OpenMP backend error

2016-03-31 Thread Freddie Witherden
Hi Emre, On 31/03/2016 17:24, emre wrote: > I have a similar problem. > > I installed Anaconda distribution, therefore I am not sure about the > compiler but mpi4py seems to work only with Intel MPI. At first it was > installing using MS MPI with wrong directories, then I corrected them > with

Re: [pyfrmailinglist] cblas openmp error

2016-03-31 Thread emre
Thank you Peter, I was so focused on Linux (what package is missing) that I did not pay any attention to ini file. After reading mailinglist and checking out ini files, I noticed my mistake and ran the example. Now, I will focus on Windows. This seems to be the difficult part. Thanks again,

Re: [pyfrmailinglist] minor issue related to [soln-plugin-residual] nstep - pyfr-1.4.0

2016-04-28 Thread Vincent, Peter E
Hi Piotr, Thanks for the feedback. We can add a note indicating nsteps > 1. But I don’t think nsteps has to be even? Cheers Peter Dr Peter Vincent MSci ARCS DIC PhD Senior Lecturer and EPSRC Early Career Fellow Department of Aeronautics Imperial College London South Kensington London SW7 2AZ

[pyfrmailinglist] pyfr version and the output

2016-04-27 Thread Piotr Prusiński
Hello, Just a silly idea, but I believe there is one thing that could be useful at some point of the development. I mean, maybe it would be wise to add an information about the pyfr version somewhere in the output of the simulation, that could help to either track and compare the scalability

Re: [pyfrmailinglist] pyfr version and the output

2016-04-27 Thread Freddie Witherden
Hi Matthieu, On 27/04/2016 06:13, Masquelet, Matthieu (GE Global Research, US) wrote: > How about storing the git hash and the output of git diff? If you are > on a public branch that might be a good compromise and a valid > reference no? We did consider this a couple of years back. It is a

Re: [pyfrmailinglist] pyfr version and the output

2016-04-27 Thread Vincent, Peter E
Hi Piotr, Thanks for the suggestion. This is something we have discussed quite a lot. One issue is that you can never be sure that the version that is run is exactly the same as a release. The user may have made some ‘small tweaks’ (or even bigger changes), and the code would still tag results

Re: [pyfrmailinglist] What version of OpenMPI is supported?

2016-05-04 Thread Victor Major
Thanks Freddie, that was helpful. The error was in my environment settings. I do in fact only have openmpi installed, but the environment is not set up exactly right, apparently. when I execute PyFr with /opt/openmpi-1.8.3/bin/mpirun -np 1 pyfr run -b cuda it runs. I now have another

Re: [pyfrmailinglist] What version of OpenMPI is supported?

2016-05-04 Thread Freddie Witherden
Hi Victor, On 04/05/2016 00:20, Victor Major wrote: > I am trying to run the Euler vortex example, but I am stymied with the > following error: > > ..//python3.4/site-packages/mpi4py/MPI.cpython-34m.so: undefined symbol: > ompi_mpi_op_no_op > > I am guessing that this has to do with OpenMPI

Re: [pyfrmailinglist] Adapting to Changes in Recent PyFR Releases

2016-05-05 Thread Freddie Witherden
Hi Zach, On 05/05/2016 16:00, Zach Davis wrote: > I was attempting to run a case using PyFR—it’s been awhile and a few > things have change—but it appears that PyFR doesn’t like my clBLAS > library any more under OS X. The pyopencl module seems to have compiled > fine when I installed it, and

[pyfrmailinglist] What version of OpenMPI is supported?

2016-05-04 Thread Victor Major
I am trying to run the Euler vortex example, but I am stymied with the following error: ..//python3.4/site-packages/mpi4py/MPI.cpython-34m.so: undefined symbol: ompi_mpi_op_no_op I am guessing that this has to do with OpenMPI version against which mpi4py configured itself. I am running

[pyfrmailinglist] PyFR v1.4.0

2016-04-20 Thread Vincent, Peter E
Dear All, We have released PyFR v1.4.0. New Features: - CGNS mesh importer - MIC backend for Intel Xeon Phi co-processors Download: http://www.pyfr.org/download.php Thanks again for your interest in the project. Peter Dr Peter Vincent MSci ARCS DIC PhD Senior Lecturer and EPSRC Early

[pyfrmailinglist] two utility scripts for PyFR

2016-05-25 Thread Paul Garlick
Hi All, I have written two utility scripts to use with PyFR. One is for pre-processing and one is for post-processing. The scripts are available to download, or clone, from the repository at cgit.tourbillion-technology.com/pyfrUtils . The pre-processing script, *pyfrm2xdmf*, takes as input

Re: [pyfrmailinglist] GPU Computing Out of Memory

2016-07-28 Thread 'Arif Andira' via PyFR Mailing List
Thanks a lot Dr Peter E Vincent, glad to get the answer from you. It works with second and third order. May i ask you something else? Can run PyFR with multi-core in single processor ( in this case i use 1 CPU Intel i7 with 8 cores(4cores hyperthreading)) + GPU ( Nvidia GTX460 )

Re: [pyfrmailinglist] GPU Computing Out of Memory

2016-07-29 Thread 'Arif Andira' via PyFR Mailing List
Thanks a lot Dr Peter E Vincent, glad to get the answer from you. It works with second and third order. Does it mean that cuda backend cannot solve the relatively heavy case with 1 GB GPU memory ? May i ask you something else? Can i run PyFR with multi-core in single processor ( in this case i

Re: [pyfrmailinglist] GPU Computing Out of Memory

2016-07-29 Thread Zach Davis
Hi Arif, Freddie has answered how to go about setting up a heterogeneous run using both CPU and GPU configurations in the PyFR mailing list. The thread with detailed instructions can be found at: https://groups.google.com/forum/#!topic/pyfrmailinglist/3-WhWBeH2ok

Re: [pyfrmailinglist] Running in Single Core

2016-07-29 Thread Freddie Witherden
Hi, On 27/07/2016 18:52, 'DODO marto' via PyFR Mailing List wrote: > Is it weird? The single core processing led to fastest calculation time. > Is there a need to match the case with the backend? I mean some simple > cases maybe are suitable with low hardware configuration while more > complex

[pyfrmailinglist] Knowing number of floating point operations for pointwise kernels n PyFR

2017-02-06 Thread Antonio Garcia-Uceda
Dear all, I'm Antonio Garcia-Uceda, researcher on Flux Reconstruction methods. I'd like to ask you whether you could provide me with a estimation of the number of floating point operations needed for the different pointwise operators in PyFR (separately if possible). In particular, the

Re: [pyfrmailinglist] Time step and nb iterations for the simulations in the paper "Towards Green Aviation with Python at Petascale"

2017-02-06 Thread Antonio Garcia-Uceda
Hi Arvind, Thanks a lot for your reply. Antonio On Friday, January 27, 2017 at 6:21:37 PM UTC+1, arvind iyer wrote: > > Hi, > The simulation > * used a fixed time step of dt = 0.000150 non-dimensional time units > * spanned 9 non-dimensional time units ~2.7 flows over chord > * used RK45 time

Re: [pyfrmailinglist] Knowing number of floating point operations for pointwise kernels n PyFR

2017-02-07 Thread Freddie Witherden
Hi Antonio, On 06/02/17 07:42, Antonio Garcia-Uceda wrote: > I'd like to ask you whether you could provide me with a estimation > of the number of floating point operations needed for the different > pointwise operators in PyFR (separately if possible). In particular, > the computation of

Re: [pyfrmailinglist] dual timestepping error: metaclass conflict?

2017-01-22 Thread Freddie Witherden
Hi, On 22/01/2017 18:11, CatDog wrote: > [solver-time-integrator] > formuation =dual > scheme =bdf2 > pseudo-scheme =euler > tstart =0.0 > tend =100.0 > dt =0.005 > pseudo-dt =0.001 > controller =none > pseudo-niters-max =20 > pseudo-niters-min =5 > pseudo-aresid =1e-5 > pseudo-rresid =1e-5 It

Re: [pyfrmailinglist] dual timestepping error: metaclass conflict?

2017-01-23 Thread CatDog
I AM SO SORRY... On Monday, January 23, 2017 at 2:14:59 PM UTC+8, Freddie Witherden wrote: > > Hi, > > On 22/01/2017 18:11, CatDog wrote: > > [solver-time-integrator] > > formuation =dual > > scheme =bdf2 > > pseudo-scheme =euler > > tstart =0.0 > > tend =100.0 > > dt =0.005 > >

[pyfrmailinglist] Minimum step sized rejected and NaNs problem.

2017-01-26 Thread Cristale Garnica
Dear all, My name is Cristale Garnica. I am working on implementing FR algorithm to simulate a Wall-jet configuration. I created a simple mesh to start and an .ini file, but I have been getting NaNs problems when I don't use a controller and error 'Minimum sized time step rejected' while

Re: [pyfrmailinglist] Time step and nb iterations for the simulations in the paper "Towards Green Aviation with Python at Petascale"

2017-01-26 Thread Freddie Witherden
Hi Antonio, On 26/01/17 08:30, Antonio Garcia-Uceda wrote: > Dear all, > > I'd like to know whether it'd be possible to obtain the following info > about the physics simulations in the paper "Towards Green Aviation with > Python at Petascale" worth of the Gordom Bell Prize: > > * approx.

Re: [pyfrmailinglist] Minimum step sized rejected and NaNs problem.

2017-01-28 Thread Vincent, Peter E
Hi Cristale, You only appear to have two P2 elements over the entire jet as it enters the domain - so it is likely under-resolved. You probably need to make the mesh finer there as a starting point. Also, the jet appears to enter parallel and adjacent to a no-slip wall. Is that by design?

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