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Re: [scipion-users] Fwd: Re: Fwd: Re: make externally compiled HDF5 available for xmipp compile
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From: David <dst...@cn...> - 2021-02-24 08:28:37
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Hi David, recommended approach is to use HDF5 distributed via standard channels, e.g. via apt on Ubuntu machines: sudo apt install libhdf5-dev Other tested option is to install it via conda in your virtual environment, provided you use it (as written already by David M.): activate your Scipion's conda environment and, then: conda install hdf5 -y -c defaults On Ubuntu 20.04LTS, apt will fetch version /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103.0.0 (as written by Pablo). It indeed seems to be version 1.10.4 (https://packages.ubuntu.com/focal/libhdf5-103), though I have to admit that I'm lost in this versioning name convention. Conda will fetch version 1.12, which goes to libhdf5_cpp.so.200.0.0 I have no experience with locally compiled version. You should not see any compilation errors (related to HDF5 or not) :) Based on your compiler and Cuda version, you might see some compilation warnings though. Hope this helps. If your problem persist, let us know and we can schedule a call. KR, David Strelak > > ---------- Původní e-mail ---------- > Od: Carlos Oscar Sorzano <co...@cn...> > Komu: Pablo Conesa <pc...@cn...>, hoo...@hp..., > Mailing list for Scipion users <sci...@li...>, > David Střelák <Dav...@se...> > Datum: 23. 2. 2021 20:20:18 > Předmět: Re: Fwd: Re: [scipion-users] make externally compiled HDF5 > available for xmipp compile > > > Dear David, > > this compilation issue really goes out of my expertise. Which are > the compilation errors you see? If they are solved by using > different functions from Xmipp, we may try to solve them. If you > want, we could have a separate call to see these errors in detail. > > Kind regards, Carlos Oscar > > On 2/23/21 12:40 PM, Pablo Conesa wrote: > > > > -------- Forwarded Message -------- > Subject: Re: [scipion-users] make externally compiled HDF5 > available for xmipp compile > Date: Fri, 19 Feb 2021 11:22:13 -0500 > From: Hoover, David (NIH/CIT) [E] via scipion-users > <sci...@li...> > <mailto:sci...@li...> > Reply-To: Mailing list for Scipion users > <sci...@li...> > <mailto:sci...@li...> > To: sci...@li... > <mailto:sci...@li...> > CC: Hoover, David (NIH/CIT) [E] <hoo...@hp...> > <mailto:hoo...@hp...> > > > > Was it compiled with 1.8.x API compatibility macros? I am > seeing errors unless I compile HDF5 with > --with-default-api-version=v18 option. > > https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html > > David > > On 2/19/2021 9:43 AM, Pablo Conesa wrote: > > Mine is linked to : > > libhdf5_serial.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 > (0x00007f354a368000) > libhdf5_cpp.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 > (0x00007f354a2eb000) > > I think is 1.10.4 > > On 19/2/21 14:31, Hoover, David (NIH/CIT) [E] via > scipion-users wrote: > > One more question: what version of HDF5 does xmipp > require? > > David > > On 2/19/2021 2:26 AM, Pablo Conesa wrote: > > Thanks Jason. > > There is a detailed "custom xmipp installation" > page > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> > where you can adapt xmipp to your system, > providing default installation does not work. > > > On 19/2/21 1:13, Jason Key wrote: > > Hi David, > > On Thu, Feb 18, 2021 at 12:42 PM Hoover, David > (NIH/CIT) [E] via > scipion-users<sci...@li...> > <mailto:sci...@li...> > wrote: > > Is there any way of making HDF5 headers > and libraries available for compiling xmipp? > That is, must I install HDF5 with yum or > apt-get into /usr/lib and /usr/include, or > is there an environment variable or > configuration setting that can be set to > force the compile to look elsewhere for > the header and library files? > > I was able to do this by adding INCDIRFLAGS > and LIBDIRFLAGS variables > to the xmipp.conf file in > "software/em/xmippSrc-v3.20.07". > > Best, > Jason > > -- Pablo Conesa - *Madrid Scipion > <http://scipion.i2pc.es> <http://scipion.i2pc.es> > team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> > <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > -- > David Hoover, Ph.D. > Computational Biologist > High Performance Computing Services, > Center for Information Technology, > National Institutes of Health > 12 South Dr., Rm 2N207 > Bethesda, MD 20892, USA > TEL: (+1) 301-435-2986 > Email:hoo...@hp... <mailto:hoo...@hp...> > > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
