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Re: [scipion-users] [xmipp] xmipp run error with xmipp_mpi_transform_filter
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From: Pablo C. <pc...@cn...> - 2017-02-03 11:06:38
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Dear Yanfeng, My guess here is that there is a versions incompatibility between Scipion/Xmipp binaries (complied with openMPI 1.6, not sure, I'll check this) If this is the case we have 2 options: a:) Point to an openMPI 1.6 (for this please, edit the MPI_BINDIR, MPI_LIBDIR, and MPI_INCLUDE to point to a openMPI 1.6 version) b:) Use Scipion from sources, see https://github.com/I2PC/scipion/wiki/How-to-Install#installing-scipion-in-3-steps Let us know ho it goes, Kind regards , Pablo On 02/02/17 15:02, Zhou, Yanfeng wrote: > Hi Pablo, > > Thanks for the reply. I download the precompiled scipion file, and > xmipp folder is already there after I untar the install file. I > finish install with command like "scipion install spider --no-xmipp". > If I install with "scipion install", there is an error saying > imagej.tgz not exist. This error is described under > https://webcache.googleusercontent.com/search?q=cache:1yBKeY3aEKwJ:https://github.com/I2PC/scipion/issues/458+&cd=1&hl=en&ct=clnk&gl=us > > After my install with --no-xmipp, I can run xmipp applications without > xmipp_mpi_, either through scipion GUI or command line. The > MPI_BINDIR, MPI_LIBDIR, and MPI_INCLUDE are pointing to > /usr/lib64/openmpi folder by default. But newer versions of openmpi > no longer have libmpi.so.1 available. So I edit the xmipp.cfg to > point to an older version of MPI. > > I am running xmipp through scipion gui, but also test the command > line. Both give same error message when there is a xmipp_mpi_ in the > application. > > Please advise. > > Best, > Yanfeng > > > ------------------------------------------------------------------------ > *From:* Pablo Conesa [pc...@cn...] > *Sent:* Thursday, February 02, 2017 2:09 AM > *To:* Zhou, Yanfeng > *Cc:* jc...@cn... > *Subject:* Re: [xmipp] xmipp run error with xmipp_mpi_transform_filter > > Dear Yanfeng, > > by default "scipion install" compiles xmipp. > > So if you've run "scipion install" successfully, then xmipp is > compiled..unless you are working with binaries. > > Is that your case? > > Also, we do not change xmipp.cfg, although not sure if that makes any > difference. > > Are you running xmipp from the command line, without Scipion? > > > Best, Pablo. > > > > On 01/02/17 19:44, Carlos Oscar Sorzano wrote: >> >> Dear Yanfeng, >> >> I'm forwarding your message to the people more in charge of the >> installation issues. >> >> Kind regards, Carlos Oscar >> >> >> On 02/01/17 19:31, Zhou, Yanfeng wrote: >>> >>> Hi Carlos Oscar, >>> >>> Have another issue with xmipp distributed with scipion-v1.0.1, and I >>> failed to find a documentation on this topic. When I run commands >>> with mpi, like xmipp_mpi_run, it says >>> >>> Sorry! You were supposed to get help about: >>> >>> Opal_init:startup:internal-failure >>> >>> But I couldn’t open the help file: >>> >>> /software/lib/Linux-x86-64/openmpi-1.6.5-build3/share/openmpi/help-opal-runtime.txt: >>> No such file or directory. >>> >>> I have configured scipion.conf to point to openmpi directories >>> before scipion installation. After the install, openmpi directories >>> in xmipp.cfg are also edited. I could not find a documentation with >>> Scipion about how to successfully compile xmipp. Could you advise >>> or forward my message to someone who may know? >>> >>> Thank you, and I appreciate your input. >>> >>> Best, >>> >>> Yanfeng >>> >>> *From:*Carlos Oscar Sorzano [mailto:co...@cn...] >>> *Sent:* Tuesday, January 31, 2017 11:11 PM >>> *To:* Zhou, Yanfeng; xm...@cn... >>> *Subject:* Re: [xmipp] xmipp run error with xmipp_mpi_transform_filter >>> >>> Good to know. Thanks >>> >>> On 01/31/17 21:54, Zhou, Yanfeng wrote: >>> >>> Thanks for the help, Carlos Oscar. I have fixed it. >>> >>> Best, >>> >>> Yanfeng >>> >>> *From:*Carlos Oscar Sorzano [mailto:co...@cn...] >>> *Sent:* Friday, January 27, 2017 6:19 PM >>> *To:* Zhou, Yanfeng; xm...@cn... <mailto:xm...@cn...> >>> *Subject:* Re: [xmipp] xmipp run error with >>> xmipp_mpi_transform_filter >>> >>> Dear Yanfeng, >>> >>> currently Xmipp is distributed along with Scipion. You may >>> follow Scipion installation instructions at >>> https://github.com/I2PC/scipion/wiki/How-to-Install. >>> >>> Kind regards, Carlos Oscar >>> >>> On 25/01/2017 15:12, Zhou, Yanfeng wrote: >>> >>> Thanks for the information, Carlos Oscar. Could you briefly >>> advise me how to recompile Xmipp and link libmpi.so from >>> LD_LIBRARY_PATH? My Linux experience is limited, and >>> basically I am learning and editing with Google. It seems >>> not to help much. >>> >>> Best, >>> >>> Yanfeng >>> >>> *From:*Carlos Oscar Sorzano [mailto:co...@cn...] >>> *Sent:* Monday, January 23, 2017 6:21 PM >>> *To:* Zhou, Yanfeng; xm...@cn... >>> *Subject:* Re: [xmipp] xmipp run error with >>> xmipp_mpi_transform_filter >>> >>> Dear Yanfeng, >>> >>> I can think of two reasons for this error. The 1st one is >>> that Xmipp has not been compiled in your machine, so that >>> Xmipp binaries have been downloaded, which were compiled in >>> a machine with libmpi.so.1 and you have a newer version. >>> Recompiling Xmipp should solve the issue. The 2nd one is >>> that you have the library but there is no link called >>> libmpi.so pointing to it, making such a link at a place >>> accessible from the LD_LIBRARY_PATH should solve it. >>> >>> Kind regards, Carlos Oscar >>> >>> On 01/23/17 22:07, Zhou, Yanfeng wrote: >>> >>> Dear Xmipp developer, >>> >>> This is Yanfeng from Shire in Lexington, MA. I am >>> testing classaverages with xmipp 3.1 under red hat >>> enterprise linux 7 system. I get error in command: >>> >>> mpirun –np 8 –bynode ‘which xmip_mpi_transform_filter’ >>> –I Images/imported/run_001/images.xmd –bad_pixels >>> outliers 3.5 –xmipp_protocol_script >>> >>> It says error while loading shared libraries: libmpi.so.1. >>> >>> I installed Xmipp 3.1 for CentOS 64bit, and openmpi was >>> configured properly. I included the LD_LIBRARY path in >>> my .bashrc file. Could you advise what could be the >>> issue? Should I download the installer for generic >>> system instead of CentOS? >>> >>> Thank you! >>> >>> Best, >>> >>> Yanfeng >>> >>> *Yanfeng Zhou, Ph.D.* >>> >>> Senior Scientist, >>> >>> Analytical Research, Discovery Therapeutics >>> >>> Shire >>> >>> 300 Shire Way >>> >>> Lexington, MA 02421 >>> >>> Phone: +1(781)869-7789 >>> >>> Email: Yan...@Sh... >>> <mailto:Yan...@Sh...> >>> >>> >>> ****************************************************** >>> Shire plc, the ultimate parent of the Shire Group of >>> companies, is registered in Jersey No. 99854 >>> Registered Office: 22 Grenville Street, St Helier, >>> Jersey JE4 8PX >>> ****************************************************** >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> This email and any files transmitted with it are >>> confidential and >>> may be legally privileged and are intended solely for >>> the use of >>> the individual or entity to whom they are addressed. If >>> you are >>> not the intended recipient please note that any disclosure, >>> distribution, or copying of this email is strictly >>> prohibited and may >>> be unlawful. If received in error, please delete this >>> email and any >>> attachments and confirm this to the sender. >>> >>> >>> >>> >>> >>> -- >>> >>> ------------------------------------------------------------------------ >>> >>> Carlos Oscar Sánchez Sorzano e-mail:co...@cn... <mailto:co...@cn...> >>> >>> Biocomputing unithttp://biocomp.cnb.csic.es >>> >>> National Center of Biotechnology (CSIC) >>> >>> c/Darwin, 3 >>> >>> Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 >>> >>> 28049 MADRID (SPAIN) Fax: 34-91-585 4506 >>> >>> ------------------------------------------------------------------------ >>> >>> >>> ****************************************************** >>> Shire plc, the ultimate parent of the Shire Group of >>> companies, is registered in Jersey No. 99854 >>> Registered Office: 22 Grenville Street, St Helier, Jersey >>> JE4 8PX >>> ****************************************************** >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> This email and any files transmitted with it are >>> confidential and >>> may be legally privileged and are intended solely for the use of >>> the individual or entity to whom they are addressed. If you are >>> not the intended recipient please note that any disclosure, >>> distribution, or copying of this email is strictly >>> prohibited and may >>> be unlawful. If received in error, please delete this email >>> and any >>> attachments and confirm this to the sender. >>> >>> >>> >>> >>> -- >>> >>> ------------------------------------------------------------------------ >>> >>> Carlos Oscar Sánchez Sorzano e-mail:co...@cn... <mailto:co...@cn...> >>> >>> Biocomputing unithttp://biocomp.cnb.csic.es >>> >>> National Center of Biotechnology (CSIC) >>> >>> c/Darwin, 3 >>> >>> Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 >>> >>> 28049 MADRID (SPAIN) Fax: 34-91-585 4506 >>> >>> ------------------------------------------------------------------------ >>> >>> >>> ****************************************************** >>> Shire plc, the ultimate parent of the Shire Group of companies, >>> is registered in Jersey No. 99854 >>> Registered Office: 22 Grenville Street, St Helier, Jersey JE4 8PX >>> ****************************************************** >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> This email and any files transmitted with it are confidential and >>> may be legally privileged and are intended solely for the use of >>> the individual or entity to whom they are addressed. If you are >>> not the intended recipient please note that any disclosure, >>> distribution, or copying of this email is strictly prohibited >>> and may >>> be unlawful. If received in error, please delete this email and any >>> attachments and confirm this to the sender. >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Carlos Oscar Sánchez Sorzano e-mail:co...@cn... <mailto:co...@cn...> >>> Biocomputing unithttp://biocomp.cnb.csic.es >>> National Center of Biotechnology (CSIC) >>> c/Darwin, 3 >>> Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 >>> 28049 MADRID (SPAIN) Fax: 34-91-585 4506 >>> ------------------------------------------------------------------------ >>> >>> ****************************************************** >>> Shire plc, the ultimate parent of the Shire Group of companies, is >>> registered in Jersey No. 99854 >>> Registered Office: 22 Grenville Street, St Helier, Jersey JE4 8PX >>> ****************************************************** >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> This email and any files transmitted with it are confidential and >>> may be legally privileged and are intended solely for the use of >>> the individual or entity to whom they are addressed. If you are >>> not the intended recipient please note that any disclosure, >>> distribution, or copying of this email is strictly prohibited and may >>> be unlawful. If received in error, please delete this email and any >>> attachments and confirm this to the sender. >> >> -- >> ------------------------------------------------------------------------ >> Carlos Oscar Sánchez Sorzano e-mail:co...@cn... >> Biocomputing unithttp://biocomp.cnb.csic.es >> National Center of Biotechnology (CSIC) >> c/Darwin, 3 >> Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 >> 28049 MADRID (SPAIN) Fax: 34-91-585 4506 >> ------------------------------------------------------------------------ > > > ****************************************************** > Shire plc, the ultimate parent of the Shire Group of companies, is > registered in Jersey No. 99854 > Registered Office: 22 Grenville Street, St Helier, Jersey JE4 8PX > ****************************************************** > > > Please consider the environment before printing this e-mail > > This email and any files transmitted with it are confidential and > may be legally privileged and are intended solely for the use of > the individual or entity to whom they are addressed. If you are > not the intended recipient please note that any disclosure, > distribution, or copying of this email is strictly prohibited and may > be unlawful. If received in error, please delete this email and any > attachments and confirm this to the sender. |
