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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...@ub...> - 2021-02-24 06:06:01
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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 environment 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 though it's making incompatibilities. I hope it will help. Cheers, <http://ucm.es/> _____ Dr. David Maluenda Niubó dma...@ub...<mailto:dma...@ub...> - (+34) 619 029 310 Wavefront Engineering Group<https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA> Applied Physics - UB<https://www.ub.edu/portal/web/dp-fisica-aplicada> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Tue, Feb 23, 2021 at 8:55 PM Hoover, David (NIH/CIT) [E] via scipion-users <sci...@li...<mailto:sci...@li...>> wrote: 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...<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)> 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> 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> 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:Email%3Ah...@hp...> >> >> >> _______________________________________________ >> 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 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. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver. Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener. This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account. 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. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver. Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener. This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account. |
