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Re: [xmds-devel] XMDS and h5py serial vs. mpi
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From: Mattias J. <mat...@mq...> - 2023-10-12 03:11:05
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Hi Rafael, I'm not that familiar with the test suite, but I can see no reason why it should need the MPI version of h5py. In fact, I see I've only got the python3-h5py-serial package installed on my machine, and everything seems fine. My understanding is that while MPI may be used for the simulation, the end result is a set of data files that are then processed serially using the xsil2graphics2 command, which is what uses the XSILFile.py code. That's certainly how end users will use it outside of the test suite anyway. Could you help me by explaining what tests are demanding the MPI version of h5py, and whether they would still be fine if they used the serial version instead? If this issue can be fixed simply by having XMDS2 only depend on python3-h5py-serial, that would seem to be the easiest solution. Regards, Mattias ________________________________ From: Rafael Laboissière <ra...@de...> Sent: Thursday, 12 October 2023 7:19 AM To: XMDS devel list <xmd...@li...> Cc: Nilesh Patra <ni...@ri...>; Drew Parsons <dpa...@de...> Subject: [xmds-devel] XMDS and h5py serial vs. mpi Dear XMDS developers, For some context in what follows, please see Bug#1053314, filed against the xmds2 package of the Debian distribution. https://bugs.debian.org/1053314<https://bugs.debian.org/1053314> This “bug” was caused by recent changes in the packaging for the h5py module for Python in Debian, as regards the serial and mpi variants. You can find more context on this here: https://salsa.debian.org/science-team/h5py/-/blob/master/debian/README.Debian<https://salsa.debian.org/science-team/h5py/-/blob/master/debian/README.Debian> Apparently, some of the tests in the unit tests suite of XMDS needs the MPI (not serial) version of h5py. Since h5py is accessed through the generic API in XSILFile.py, it may happen that the serial version h5py is used, instead of the MPI version. In order to “fix” the problem, I introduced the following patch to the xmds2 Debian package: https://salsa.debian.org/science-team/xmds2/-/blob/master/debian/patches/h5py-always-use-mpi.patch<https://salsa.debian.org/science-team/xmds2/-/blob/master/debian/patches/h5py-always-use-mpi.patch> The question we are asking ourselves regards the intentions of the XMDS upstream developers with h5py and MPI. I am adding Drew Parsons and Nilesh Patra in Cc to this message. They might wish to correct some of my assertions above or add comments on the issue. Best, Rafael Laboissière _______________________________________________ xmds-devel mailing list xmd...@li... https://lists.sourceforge.net/lists/listinfo/xmds-devel<https://lists.sourceforge.net/lists/listinfo/xmds-devel> |
