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From: Rafael L. <ra...@de...> - 2019-09-09 08:43:04
|
* Mattias Johnsson <mat...@mq...> [2019-09-09 06:56]: > Thanks for the heads up. I'll install Debian testing and see if I can > reproduce and figure out what's going on. Thanks, Mattias. Note that the bug only manifests itself in Debian unstable. Best, Rafael |
From: Mattias J. <mat...@mq...> - 2019-09-09 06:56:38
|
Hi Rafael, Thanks for the heads up. I'll install Debian testing and see if I can reproduce and figure out what's going on. Cheers, Mattias ________________________________ From: Rafael Laboissière <ra...@de...> Sent: Monday, 9 September 2019 3:38 PM To: xmd...@li... <xmd...@li...> Subject: [xmds-devel] Debian package xmds2 fails to build with h5py 2.9.0-4 Dear XMDS developers, The xmds2 package in Debian is failing to build after the h5py package has been upgraded to version 2.9.0-4. You can find more details in the following bug report, filed against the xmds2 package: http://bugs.debian.org/938925<https://protect-au.mimecast.com/s/VYdyCBNqgBCMDJXGhjaba2?domain=bugs.debian.org> As far as I can tell, xmds2 itself is still working after the upgrade of h5py. What is not working is the run_tests.py script and this is causing the package build failure. I suspect that the problems arises in the code of function scriptTestingFunction, after the compilation and execution of unit test breakpoints_hdf.xmds, for which the data output in xsil files are compared against the hdf5 files. After that, all the subsequent units tests that need mpirun to be executed will then fail. This is the farthest that I could go in the diagnostics. I do not have time to debug further this problem. FYI, a library transition concerning h5py scheduled in Debian: https://release.debian.org/transitions/html/auto-hdf5.html<https://protect-au.mimecast.com/s/wb4RCD1vRkCnorL9clJvuI?domain=release.debian.org> If the bug in the run_tests.py script is not fixed, the xmds2 package will have to be removed from the testing distribution, and this will have a negative impact on the XMDS users of Debian and Ubuntu. Best regards, Rafael Laboissière _______________________________________________ xmds-devel mailing list xmd...@li... https://lists.sourceforge.net/lists/listinfo/xmds-devel<https://protect-au.mimecast.com/s/YXxYCE8wlRCglo87cQHFTr?domain=lists.sourceforge.net> |
From: Rafael L. <ra...@de...> - 2019-09-09 06:04:26
|
Dear XMDS developers, The xmds2 package in Debian is failing to build after the h5py package has been upgraded to version 2.9.0-4. You can find more details in the following bug report, filed against the xmds2 package: http://bugs.debian.org/938925 As far as I can tell, xmds2 itself is still working after the upgrade of h5py. What is not working is the run_tests.py script and this is causing the package build failure. I suspect that the problems arises in the code of function scriptTestingFunction, after the compilation and execution of unit test breakpoints_hdf.xmds, for which the data output in xsil files are compared against the hdf5 files. After that, all the subsequent units tests that need mpirun to be executed will then fail. This is the farthest that I could go in the diagnostics. I do not have time to debug further this problem. FYI, a library transition concerning h5py scheduled in Debian: https://release.debian.org/transitions/html/auto-hdf5.html If the bug in the run_tests.py script is not fixed, the xmds2 package will have to be removed from the testing distribution, and this will have a negative impact on the XMDS users of Debian and Ubuntu. Best regards, Rafael Laboissière |
From: Mattias J. <mat...@mq...> - 2019-08-26 06:21:11
|
Hi Saumil, I believe the worked example is correct. The terms on the right hand side of dW/dt = ... in the worked example script are not the Fourier transform of the terms like x * (partial^3 W / partial^2x / partial y). Rather, they are the terms in the original equation with the transverse derivatives (e.g. partial/partial x etc) replaced by operators corresponding to what they are in Fourier space. This means there is no need for you to Fourier transform your PDE by hand. So, for example, x * (partial^3 W / partial^2x / partial y) becomes x * i k_x * i k_x *i k_y. The reason for this is that when XMDS is evaluating that expression, it transforms W(x, y) into k-space, i.e. W(k_x, k_y), then multiplies that expression by i k_x * i k_x *i k_y to get W'(k_x, k_y), then transforms the result back to x,y space to get W'(x, y), and then multiplies that by x to get W''(x, y) = x*W'(x,y). (Note that XMDS's spectral methods use the Fourier transform rather than Laplace transform, which is why there is an "i" attached to the kx, ky etc operators.) Cheers, Mattias ________________________________ From: Saumil Shah <sam...@gm...> Sent: Friday, 23 August 2019 8:08:49 PM To: xmd...@li... <xmd...@li...>; xmd...@li... <xmd...@li...> Subject: [xmds-user] Mistake in worked examples Hello, greetings to fellow XMDS users. I think there is a mistake in the Wigner Function worked example. Please correct me if I am wrong, it uses Laplace Transform to go from W(x,y,t) to W(k_x,k_y,t). While x * (partial W / partial y) become i * x * k_y * W, I don't think x * (partial^3 W / partial^2x / partial y) becomes i^3 * x * k_x^2 * k_y. It is obvious if you write the integral with the Laplace kernel. Please let me know, Saumil |
From: Rafael L. <ra...@de...> - 2019-07-10 12:34:18
|
* Mattias Johnsson <mat...@mq...> [2019-07-07 23:56]: > XMDS3 isn't in the Ubuntu package repositories yet. I believe it has > been packaged for Debian, so I suspect the upcoming Ubuntu 19.10 will > have it. If you're using 18.04, XMDS 2.2.3 is definitely available if > you search for "xmds2" in the package manager. Indeed, version 3.0.0 of the xmds2 package has indeed be packages for Debian [1], but have only recently entered the "unstable" distribution. It has already migrate into Ubuntu (Eoan Ermine, under active development). [2] Best, Rafael Laboissière [1] https://tracker.debian.org/pkg/xmds2 [2] https://launchpad.net/ubuntu/+source/xmds2/3.0.0+dfsg-2 |
From: Mattias J. <mat...@mq...> - 2019-07-08 00:10:53
|
Hi Galaa, XMDS3 isn't in the Ubuntu package repositories yet. I believe it has been packaged for Debian, so I suspect the upcoming Ubuntu 19.10 will have it. If you're using 18.04, XMDS 2.2.3 is definitely available if you search for "xmds2" in the package manager. Regarding your pygments error, I am unable to reproduce this, although I note you're running Anaconda, and I've had bad interactions with XMDS and Anaconda before, as Anaconda seems to overwrite lots of python path stuff. Did you just run "./linux_install" or did you run it with some command switches, e.g. "./linux_install --develop"? Also, it looks like it failed at the stage of building the documentation, which is the last step. If you have the terminal output of everything before this error, right from when you ran the installer, could you sent it to me? Finally, if this is just some odd pygments error, it's possible that XMDS did indeed install. Could you check if it runs anyway? Cheers, Mattias ________________________________ From: Galaa Badrakh <gal...@gm...> Sent: Monday, 8 July 2019 7:29:59 AM To: xmd...@li... Subject: [xmds-devel] Fwd: An issue with installation Hi All, I am trying to install XMDS 3 on Ubuntu 18.04. First I have searched XMDS2 in the software center but could not find it. So I have installed with the linux_installer.sh but at the end of my installation, I got an error message which I have attached below. I have also tried to compile an example code, nlse.xmds, but failed. How can I fix this problem? Thanks in advance for your help. Regards, Galaa # Sphinx version: 1.8.5 # Python version: 3.7.3 (CPython) # Docutils version: 0.14 # Jinja2 version: 2.10 # Last messages: # Loaded extensions: Traceback (most recent call last): File "/home/galaa/anaconda3/lib/python3.7/site-packages/pygments/styles/__init__.py", line 64, in get_style_by_name mod = __import__('pygments.styles.' + mod, None, None, [cls]) ModuleNotFoundError: No module named 'pygments.styles.friendly_plus' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/cmd/build.py", line 303, in build_main args.tags, args.verbosity, args.jobs<https://protect-au.mimecast.com/s/gCh8CQnM1WflXQywFxprsr?domain=args.jobs>, args.keep_going) File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/application.py", line 263, in __init__ self._init_builder() File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/application.py", line 324, in _init_builder self.builder.init() File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/builders/html.py", line 330, in init self.init_highlighter() File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/builders/html.py", line 389, in init_highlighter self.highlighter = PygmentsBridge('html', style) File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/highlighting.py", line 83, in __init__ style = get_style_by_name(stylename) File "/home/galaa/anaconda3/lib/python3.7/site-packages/pygments/styles/__init__.py", line 67, in get_style_by_name (builtin and ", though it should be builtin") + ".") pygments.util.ClassNotFound: Could not find style module 'friendly_plus'. |
From: Galaa B. <gal...@gm...> - 2019-07-07 21:30:03
|
Hi All, I am trying to install XMDS 3 on Ubuntu 18.04. First I have searched XMDS2 in the software center but could not find it. So I have installed with the linux_installer.sh but at the end of my installation, I got an error message which I have attached below. I have also tried to compile an example code, nlse.xmds, but failed. How can I fix this problem? Thanks in advance for your help. Regards, Galaa # Sphinx version: 1.8.5 # Python version: 3.7.3 (CPython) # Docutils version: 0.14 # Jinja2 version: 2.10 # Last messages: # Loaded extensions: Traceback (most recent call last): File "/home/galaa/anaconda3/lib/python3.7/site-packages/pygments/styles/__init__.py", line 64, in get_style_by_name mod = __import__('pygments.styles.' + mod, None, None, [cls]) ModuleNotFoundError: No module named 'pygments.styles.friendly_plus' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/cmd/build.py", line 303, in build_main args.tags, args.verbosity, args.jobs, args.keep_going) File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/application.py", line 263, in __init__ self._init_builder() File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/application.py", line 324, in _init_builder self.builder.init() File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/builders/html.py", line 330, in init self.init_highlighter() File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/builders/html.py", line 389, in init_highlighter self.highlighter = PygmentsBridge('html', style) File "/home/galaa/anaconda3/lib/python3.7/site-packages/sphinx/highlighting.py", line 83, in __init__ style = get_style_by_name(stylename) File "/home/galaa/anaconda3/lib/python3.7/site-packages/pygments/styles/__init__.py", line 67, in get_style_by_name (builtin and ", though it should be builtin") + ".") pygments.util.ClassNotFound: Could not find style module 'friendly_plus'. |
From: Rafael L. <ra...@de...> - 2019-05-23 06:20:54
|
* Mattias Johnsson <mat...@mq...> [2019-05-22 23:47]: > There was no patch attached? If you did attach it, the list must have > stripped it. I probably did something wrong when I attached the file. > This error is in upstream waf code we ship as part of the waf build > system but don't actually use, which is why our testing didn't spot it. > If your patch was just dropping the "L" in "0x80000000L" let me know > and I'll make the change and put up a new tarball. The patch is now part of the debian package and can be found here: https://salsa.debian.org/science-team/xmds2/blob/master/debian/patches/compile-with-python3.patch > As a side question, are you subscribed to the > xmd...@li...? If so, did you get the 3.0 release > announcement a few days ago? Some people didn't get it and we're trying > to figure out why. I was not subscribed to this mailing list. I just tried to do it trough the SF web interface, but did not received the confirmation email back. Is there anything wrong with this mailing list? Best, Rafael |
From: Mattias J. <mat...@mq...> - 2019-05-22 23:47:42
|
Hi Rafael, There was no patch attached? If you did attach it, the list must have stripped it. This error is in upstream waf code we ship as part of the waf build system but don't actually use, which is why our testing didn't spot it. If your patch was just dropping the "L" in "0x80000000L" let me know and I'll make the change and put up a new tarball. As a side question, are you subscribed to the xmd...@li...? If so, did you get the 3.0 release announcement a few days ago? Some people didn't get it and we're trying to figure out why. Thanks for spotting this and all your hard work packaging XMDS2! Cheers, Mattias ________________________________ From: Rafael Laboissière <ra...@de...> Sent: Wednesday, 22 May 2019 8:31:11 PM To: xmd...@li... Subject: [xmds-devel] Script in 3.0.0 tarball does not compile against Python 3 Dear developers, The file xpdeint/waf/waflib/extras/subprocess.py in the 3.0.0 tarball does not compile against Python 3: $ python3 -m py_compile xpdeint/waf/waflib/extras/subprocess.py File "xpdeint/waf/waflib/extras/subprocess.py", line 314 if (GetVersion() >= 0x80000000L or ^ SyntaxError: invalid syntax This causes a installation problem of the xmds2 package in Debian: https://bugs.debian.org/929148<https://protect-au.mimecast.com/s/yv4YC81Vq2CYnNqXi2Mb50?domain=bugs.debian.org> The patch attached to this message fixes the problem. Best regards, Rafael Laboissière _______________________________________________ xmds-devel mailing list xmd...@li... https://lists.sourceforge.net/lists/listinfo/xmds-devel<https://protect-au.mimecast.com/s/61EGC91W8rC2o4qzcOALGA?domain=lists.sourceforge.net> |
From: Rafael L. <ra...@de...> - 2019-05-22 10:31:20
|
Dear developers, The file xpdeint/waf/waflib/extras/subprocess.py in the 3.0.0 tarball does not compile against Python 3: $ python3 -m py_compile xpdeint/waf/waflib/extras/subprocess.py File "xpdeint/waf/waflib/extras/subprocess.py", line 314 if (GetVersion() >= 0x80000000L or ^ SyntaxError: invalid syntax This causes a installation problem of the xmds2 package in Debian: https://bugs.debian.org/929148 The patch attached to this message fixes the problem. Best regards, Rafael Laboissière |
From: Rafael L. <ra...@de...> - 2018-05-08 06:48:42
|
* Mattias Johnsson <mat...@mq...> [2018-05-08 01:52]: > These directories have been empty for ages due to reorganisations of > the codebase in the past. I've now deleted them from our repository and > future release tarballs won't contain them. Great, thanks! > Thanks for spotting this! Lintian spotted it, not I. :-) Best, Rafael |
From: Mattias J. <mat...@mq...> - 2018-05-08 02:07:43
|
Hi Rafael, These directories have been empty for ages due to reorganisations of the codebase in the past. I've now deleted them from our repository and future release tarballs won't contain them. Thanks for spotting this! Cheers, Mattias ________________________________ From: Rafael Laboissière <ra...@de...> Sent: Friday, 4 May 2018 3:41:41 PM To: xmd...@li... Subject: [xmds-devel] Empty directories in XMDS2 tarball Dear maintainers, Is here any specific reason why the current XMDS2 tarball contains the following empty directories? xpdeint/Features/Noises/DSFMT/ xpdeint/Features/Noises/MKL/ xpdeint/Features/Noises/POSIX/ xpdeint/Features/Noises/Solirte/ xpdeint/support/waflib/Tools/ xpdeint/support/waflib/extras/ xpdeint/wafadmin/Tools/ It is a pedantic issue, but it is triggering a Lintian warning for the Debian package xmds2: https://lintian.debian.org/full/deb...@li...ml#xmds2_2.2.3_x2bdfsg-5<https://protect-au.mimecast.com/s/Pq4iCWLVn6iZWWmSniExM?domain=lintian.debian.org> Best, Rafael Laboissière ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot<https://protect-au.mimecast.com/s/YMQwCXLW6Dijzzotm36GV?domain=sdm.link> _______________________________________________ xmds-devel mailing list xmd...@li... https://lists.sourceforge.net/lists/listinfo/xmds-devel<https://protect-au.mimecast.com/s/Wvz-CYW86Esm442tZphUk?domain=lists.sourceforge.net> |
From: Rafael L. <ra...@de...> - 2018-05-04 06:17:27
|
Dear maintainers, Is here any specific reason why the current XMDS2 tarball contains the following empty directories? xpdeint/Features/Noises/DSFMT/ xpdeint/Features/Noises/MKL/ xpdeint/Features/Noises/POSIX/ xpdeint/Features/Noises/Solirte/ xpdeint/support/waflib/Tools/ xpdeint/support/waflib/extras/ xpdeint/wafadmin/Tools/ It is a pedantic issue, but it is triggering a Lintian warning for the Debian package xmds2: https://lintian.debian.org/full/deb...@li...ml#xmds2_2.2.3_x2bdfsg-5 Best, Rafael Laboissière |
From: Mattias J. <mat...@mq...> - 2018-02-01 07:39:21
|
Hi Oliver, Unfortunately at the moment there is no way to do this. The problem is that the parser doesn't know how to decide between whether the argument is the name of a file or a variable containing the name of a file. Maybe it could be allowable using the <validation kind="run-time"> feature and passing in the filename as a command line argument, but right now that's not set up. And even in that case it could get tricky if there was a file with the same name as the variable name. I have a think about it and add it to the list of things to do. Cheers, Mattias ________________________________ From: Oliver Sandberg <oli...@uq...> Sent: Thursday, 1 February 2018 3:02 PM To: xmd...@li... Subject: [xmds-devel] Input filename at runtime Hi XMDS devs, In a recent project, I've imported h5 data using <initialisation kind="hdf5"> <filename> func.h5 </filename> which works fine. However, it seems like there's no way to pass in the filename as an input argument at runtime. Is there a particular reason for this? Strings are supported and work fine, as in the examples in the documentation to specify a pulse shape. It looks like whatever is entered between <filename> tags is always interpreted as a string. Thanks for all the great work that you do! Cheers, Oliver Sandberg ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ xmds-devel mailing list xmd...@li... https://lists.sourceforge.net/lists/listinfo/xmds-devel |
From: Oliver S. <oli...@uq...> - 2018-02-01 04:35:53
|
Hi XMDS devs, In a recent project, I've imported h5 data using <initialisation kind="hdf5"> <filename> func.h5 </filename> which works fine. However, it seems like there's no way to pass in the filename as an input argument at runtime. Is there a particular reason for this? Strings are supported and work fine, as in the examples in the documentation to specify a pulse shape. It looks like whatever is entered between <filename> tags is always interpreted as a string. Thanks for all the great work that you do! Cheers, Oliver Sandberg |
From: Voit, M. <m....@ja...> - 2018-01-24 10:03:43
|
Dear List, due to a current project I'd be interested in adding an integration stepper to xmds2 which implements exponential time differencing methods [0]. I have already found the developer information [1]. Still, since this is not a small task, I wanted to ask for your expertise and comments. Right now, I'm not quite clear whether it is even possible since the methods are semilinear. Thus the linear and the nonlinear part need to be separated for different treatment, probably already separately specified by the user. Aside from that a big thank you for all the work you put into xmds2! Best, Max [0] Cox, S.M., and P.C. Matthews. “Exponential Time Differencing for Stiff Systems.” Journal of Computational Physics 176, no. 2 (March 2002): 430–55. https://doi.org/10.1006/jcph.2002.6995. [1] http://www.xmds.org/developer.html#how-to-introduce-a-new-integrator-stepper-into-the-xmds2-environment |
From: Mattias J. <mat...@mq...> - 2017-12-29 05:02:29
|
Hi Rafael, Yes, we are currently in the process of porting XMDS2 to Python 3. Joe, what's the status with this? Cheers, Mattias ________________________________ From: Rafael Laboissière <ra...@de...> Sent: Friday, 29 December 2017 8:37:48 AM To: xmd...@li... Subject: [xmds-devel] Plans to support Python 3? Dear XMDS2 developers, The Debian package xmds2 is doing fine but, when it is built, a Lintian warning is triggered, reminding that the end of life of Python 2 is approaching. Are you planning to make XMDS2 work with Python 3? Best, Rafael Laboissière [*] https://lintian.debian.org/tags/dependency-on-python-version-marked-for-end-of-life.html ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ xmds-devel mailing list xmd...@li... https://lists.sourceforge.net/lists/listinfo/xmds-devel |
From: Rafael L. <ra...@de...> - 2017-12-28 22:01:45
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Dear XMDS2 developers, The Debian package xmds2 is doing fine but, when it is built, a Lintian warning is triggered, reminding that the end of life of Python 2 is approaching. Are you planning to make XMDS2 work with Python 3? Best, Rafael Laboissière [*] https://lintian.debian.org/tags/dependency-on-python-version-marked-for-end-of-life.html |
From: Mattias J. <mat...@mq...> - 2017-08-15 01:35:09
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Hi Noah, Joe, I never wrote or committed any code to fix that initial bug, since I was under the impression that the people who found it were going to fix it and Joe only wanted me to confirm it was in fact a bug (Joe, see our email chain on 8th and 9th of June; your Gmail account). Regarding the issue of storing spare random numbers, yep, you're right. I'm not sure it's actually a problem, since a random number is a random number, but yes. I'd be tempted just to dump that optimization. I added it when I was in an optimization frenzy, but I think the effect was pretty minor and I have yet to find anyone who uses XMDS in single precision mode rather than double precision mode anyway. Not to mention that bit-twiddling code is horrible. So, yeah, go ahead and chuck it. Cheers, Mattias ________________________________ From: Noah via xmds-devel <xmd...@li...> Sent: Monday, 14 August 2017 9:32:52 PM To: xmd...@li... Subject: [xmds-devel] Issue in DSFMTGenerator.tmpl Hi XMDS developers, I've come across an issue in the file `DSFMTGenerator.tmpl`, in the method template `generate_float_close1_open2_via_dsfmt<https://sourceforge.net/p/xmds/code/HEAD/tree/trunk/xpdeint/xpdeint/Stochastic/Generators/DSFMTGenerator.tmpl#l107>`, where the method creates two random numbers and stores one for the next time it is called. When the method is called twice and passed two different generators, it will return a random number generated with the first input both times. Some possible fixes include generating the method for every noise vector (would have to do the same for `generate_float_array_close0_open1` as well), checking if the input has changed, or simply removing the optimisation. Also, Joe informed me that the issue of `generate_float_array_close0_open1<https://sourceforge.net/p/xmds/code/HEAD/tree/trunk/xpdeint/xpdeint/Stochastic/Generators/DSFMTGenerator.tmpl#l140>` (in the same file) not using its parameters has been addressed, but it doesn't seem to have been pushed yet. Thanks for the help, Noah |
From: Noah <noa...@pr...> - 2017-08-14 11:33:15
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Hi XMDS developers, I've come across an issue in the file `DSFMTGenerator.tmpl`, in the method template `[generate_float_close1_open2_via_dsfmt](https://sourceforge.net/p/xmds/code/HEAD/tree/trunk/xpdeint/xpdeint/Stochastic/Generators/DSFMTGenerator.tmpl#l107)`, where the method creates two random numbers and stores one for the next time it is called. When the method is called twice and passed two different generators, it will return a random number generated with the first input both times. Some possible fixes include generating the method for every noise vector (would have to do the same for `generate_float_array_close0_open1` as well), checking if the input has changed, or simply removing the optimisation. Also, Joe informed me that the issue of `[generate_float_array_close0_open1](https://sourceforge.net/p/xmds/code/HEAD/tree/trunk/xpdeint/xpdeint/Stochastic/Generators/DSFMTGenerator.tmpl#l140)` (in the same file) not using its parameters has been addressed, but it doesn't seem to have been pushed yet. Thanks for the help, Noah |
From: Rafael L. <ra...@de...> - 2017-01-21 15:45:26
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* Mattias Johnsson <mat...@mq...> [2017-01-21 14:04]: > Hmm, I can't reproduce this. > > The only thing I can think of at the moment is that the test script is > trying to assign more processors (3) to the MPI job than your machine > has, and your MPI setup doesn't allow oversubscription. > > Are you using a dual core processor? If so, you could try changing the > line in io/mpi_xsilloading_hdf5.xmds that says > > mpirun -n 3 ./mpi_xsilloading_hdf5 > > to > > mpirun -n 2 ./mpi_xsilloading_hdf5 > > and see if that allows that test to pass. If it does, great. If not, > I'll think about it some more tomorrow. I build the package in a virtual machine with two core processors. Indeed, the change above fixes the problem for that particular unit test. Just forget about this. This is actually a non-issue as regards the Debian package. Best, Rafael |
From: Mattias J. <mat...@mq...> - 2017-01-21 14:04:57
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Hmm, I can't reproduce this. The only thing I can think of at the moment is that the test script is trying to assign more processors (3) to the MPI job than your machine has, and your MPI setup doesn't allow oversubscription. Are you using a dual core processor? If so, you could try changing the line in io/mpi_xsilloading_hdf5.xmds that says mpirun -n 3 ./mpi_xsilloading_hdf5 to mpirun -n 2 ./mpi_xsilloading_hdf5 and see if that allows that test to pass. If it does, great. If not, I'll think about it some more tomorrow. Cheers, Mattias ________________________________ From: Rafael Laboissière <ra...@de...> Sent: Sunday, 22 January 2017 12:21:49 AM To: xmd...@li... Subject: Re: [xmds-devel] Several unit tests failures * Mattias Johnsson <mat...@mq...> [2017-01-21 10:50]: > I take it this was the email that was delayed in the moderation queue, > and has only just now appeared? These errors were fixed by your patch > already, right? (And thanks again for that!) As I wrote in the subsequent message, the issues in CodeParser.py and XSILFile.py are fixed by patches. Otherwise, there is still a warning reported: features/halt_non_finite.xmds ... ./run_tests.py:64: RuntimeWarning: invalid value encountered in less_equal return numpy.logical_or(numpy.logical_or(numpy.abs(diff) <= 0.5 * relTol * (numpy.abs(array2) + numpy.abs(array1)), numpy.abs(diff) <= absTol), numpy.isnan(array2)).all() ok and several errors like the following: ====================================================================== FAIL: test_mpi_xsilloading_hdf5 (__main__.ScriptTestCase) io/mpi_xsilloading_hdf5.xmds ---------------------------------------------------------------------- Traceback (most recent call last): File "./run_tests.py", line 247, in newfunc return func(*(args + fargs), **newkeywords) File "./run_tests.py", line 151, in scriptTestingFunction self.assert_(returnCode == 0, "Failed to execute compiled simulation correctly. Got returnCode %(returnCode)i;\nstdout = %(stdout)s;\nstderr = %(stderr)s\n" % locals()) AssertionError: Failed to execute compiled simulation correctly. Got returnCode 1; stdout = ; stderr = -------------------------------------------------------------------------- There are not enough slots available in the system to satisfy the 3 slots that were requested by the application: ./mpi_xsilloading_hdf5 Either request fewer slots for your application, or make more slots available for use. -------------------------------------------------------------------------- I do not know how to cope with them. Best, Rafael ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ xmds-devel mailing list xmd...@li... https://lists.sourceforge.net/lists/listinfo/xmds-devel |
From: Rafael L. <ra...@de...> - 2017-01-21 13:21:57
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* Mattias Johnsson <mat...@mq...> [2017-01-21 10:50]: > I take it this was the email that was delayed in the moderation queue, > and has only just now appeared? These errors were fixed by your patch > already, right? (And thanks again for that!) As I wrote in the subsequent message, the issues in CodeParser.py and XSILFile.py are fixed by patches. Otherwise, there is still a warning reported: features/halt_non_finite.xmds ... ./run_tests.py:64: RuntimeWarning: invalid value encountered in less_equal return numpy.logical_or(numpy.logical_or(numpy.abs(diff) <= 0.5 * relTol * (numpy.abs(array2) + numpy.abs(array1)), numpy.abs(diff) <= absTol), numpy.isnan(array2)).all() ok and several errors like the following: ====================================================================== FAIL: test_mpi_xsilloading_hdf5 (__main__.ScriptTestCase) io/mpi_xsilloading_hdf5.xmds ---------------------------------------------------------------------- Traceback (most recent call last): File "./run_tests.py", line 247, in newfunc return func(*(args + fargs), **newkeywords) File "./run_tests.py", line 151, in scriptTestingFunction self.assert_(returnCode == 0, "Failed to execute compiled simulation correctly. Got returnCode %(returnCode)i;\nstdout = %(stdout)s;\nstderr = %(stderr)s\n" % locals()) AssertionError: Failed to execute compiled simulation correctly. Got returnCode 1; stdout = ; stderr = -------------------------------------------------------------------------- There are not enough slots available in the system to satisfy the 3 slots that were requested by the application: ./mpi_xsilloading_hdf5 Either request fewer slots for your application, or make more slots available for use. -------------------------------------------------------------------------- I do not know how to cope with them. Best, Rafael |
From: Mattias J. <mat...@mq...> - 2017-01-21 10:50:59
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Hi Rafael, I take it this was the email that was delayed in the moderation queue, and has only just now appeared? These errors were fixed by your patch already, right? (And thanks again for that!) Cheers, Mattias ________________________________ From: Rafael Laboissière <ra...@de...> Sent: Sunday, 15 January 2017 1:57:44 PM To: xmd...@li... Subject: [xmds-devel] Several unit tests failures I am trying to build xmds2 package for Debian with the latest versions of python2 (2.7.13-1) and numpy (1.12.0~rc2-1) in unstable. Several unit tests fail. An excerpt of the build log is attached below. Does anyone know how to fix this? Best, Rafael |
From: Mattias J. <mat...@mq...> - 2017-01-16 23:33:01
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Okay, that should be fine. I intend to do the release this week. Cheers, Mattias ________________________________ From: Rafael Laboissière <ra...@de...> Sent: Tuesday, 17 January 2017 10:31:36 AM To: xmd...@li... Subject: Re: [xmds-devel] Several unit tests failures * Mattias Johnsson <mat...@mq...> [2017-01-16 23:22]: > If we make the release quickly enough, could you get it into Debian > 9.0? If so, when would that be? The package for the new version must be uploaded until February 5. Rafael ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ xmds-devel mailing list xmd...@li... https://lists.sourceforge.net/lists/listinfo/xmds-devel |