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Re: [scipion-users] Fwd: Re: make externally compiled HDF5 available for xmipp compile
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From: David M. <dma...@gm...> - 2021-02-24 00:36:49
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Hi there, Just to explore another possibility, if you didn't try it yet. If you installed Scipion/Xmipp under conda, there is the chance to install hdf5 via conda. It's just to activate the Scipion's conda environ and, then 'conda install hdf5 -y -c defaults'. Xmipp tries to install it in this way when hdf5 is not found in the system. Perhaps, in your case that installation was not triggered because Xmipp found a hdf5 installation in the system, even it's making incompatibilities. I hope it will helps. Cheers, _____ Dr. David Maluenda Niubó (+34) 619.029.310 - dma...@ub... Wavefront Engineering Group Applied Physics (UB) El mar., 23 feb. 2021 20:55, Hoover, David (NIH/CIT) [E] via scipion-users < sci...@li...> escribió: > Unfortunately, I did not save the errors, but they were indicative of an > misunderstood API call. Bottom line, xmipp requires 1.8.x API; our local > install of HDF5 v1.10.x or v1.6.x broke the xmipp compilation. That's my > burden of hosting a spectrum of versions for every library and > application. I assume you all don't see this because HDF5 comes from a > standard yum or apt-get package. > > David > > On 2/23/2021 2:17 PM, Carlos Oscar Sorzano wrote: > > 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...> > >> Reply-To: Mailing list for Scipion users < > sci...@li...> > >> To: sci...@li... > >> CC: Hoover, David (NIH/CIT) [E] <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)> > 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...> 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> team* > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> scipion-users mailing list > >>>>> sci...@li... > >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users > >>>>> > >>>> > >>> -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > >>> > >>> > >>> _______________________________________________ > >>> scipion-users mailing list > >>> 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... > >> > >> > >> _______________________________________________ > >> scipion-users mailing list > >> 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... > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir > informació confidencial o protegida legalment i s’adreça exclusivament a la > persona o entitat destinatària. 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