Hi I didn't set SAGE_FAT_BINARY on either.
Actually, I have atlas on muizenberg not snapperkob: 0 root@muizenberg:~#dpkg -l |grep atlas ii libatlas3-base 3.10.1-4 amd64 Automatically Tuned Linear Algebra Software, generic shared 0 root@muizenberg:~# 1 jan@snapperkob:~/sage-6.4$dpkg -l |grep atlas 1 jan@snapperkob:~/sage-6.4$ Regards, Jan On 21 November 2014 14:54, Volker Braun <[email protected]> wrote: > You didn't set SAGE_FAT_BINARY=yes I guess since in that case we configure > R --without-ICU > > I take it you have Ubuntu's version of ATLAS installed on snapperkob and > not on muizenberg? > > > > On Friday, November 21, 2014 8:21:28 AM UTC, pipedream wrote: > >> Hi Volker, >> >> I repeated on snapperkob, not via buildbot just as my own user: >> >> real 125m41.153s >> user 208m24.169s >> sys 20m6.421s >> *************************************************************** >> Error building Sage. >> >> The following package(s) may have failed to build: >> >> package: r-3.1.1.p0 >> log file: /home/jan/sage-6.4/logs/pkgs/r-3.1.1.p0.log >> build directory: /home/jan/sage-6.4/local/var/tmp/sage/build/r-3.1.1.p0 >> >> The build directory may contain configuration files and other potentially >> helpful information. WARNING: if you now run 'make' again, the build >> directory will, by default, be deleted. Set the environment variable >> SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this. >> >> make: *** [build] Error 1 >> 2 jan@snapperkob:~/sage-6.4$ >> >> I can try investigate what is different on muizenberg and snapperkob or >> my user on muizenberg & snapperkob. >> >> They are both Dell Optiplex, 64 bit, entirely up to date Ubuntu 14.04.1, >> though: >> >> snapperkob is a text-only server install >> muizenberg is a GUI full desktop install >> >> There is little difference underneath in ubuntu though. It is the same >> kernel. (the package linux-server depends on linux-generic which is also on >> the desktop, and depends on the actual kernel) >> >> They both have the Intel E8400 CPU. They both have 8G RAM. >> >> Comparing the logs for the two R builds, I found these differences in the >> configure parts, due to different packages available on the system: >> >> muizenberg (built successfully) >> >> R is now configured for x86_64-unknown-linux-gnu >> >> Source directory: . >> Installation directory: /srv/sysadm/sage/sage-6.4/local >> >> C compiler: gcc -std=gnu99 -g -O2 >> Fortran 77 compiler: gfortran -g -O2 >> >> C++ compiler: g++ >> C++ 11 compiler: g++ -std=c++11 >> Fortran 90/95 compiler: gfortran -g -O2 >> Obj-C compiler: >> >> Interfaces supported: >> External libraries: readline, ICU, lzma >> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo >> Options enabled: shared R library, shared BLAS, R profiling >> >> Recommended packages: yes >> >> >> And snapperkob (failed): >> >> R is now configured for x86_64-unknown-linux-gnu >> >> Source directory: . >> Installation directory: /home/jan/sage-6.4/local >> >> C compiler: gcc -std=gnu99 -g -O2 >> Fortran 77 compiler: gfortran -g -O2 >> >> C++ compiler: g++ >> C++ 11 compiler: g++ -std=c++11 >> Fortran 90/95 compiler: gfortran -g -O2 >> Obj-C compiler: >> >> Interfaces supported: X11, tcltk >> External libraries: readline, BLAS(ATLAS), LAPACK(generic), ICU >> Additional capabilities: PNG, JPEG, NLS, cairo >> Options enabled: shared R library, R profiling >> >> Recommended packages: yes >> >> >> Can you think what I can change on snapperkob to test? BLAS or LAPACK >> perhaps? >> >> Regards, >> Jan >> >> >> >> >> >> >> On 20 November 2014 20:35, Jan Groenewald <[email protected]> wrote: >> >>> Different machine: >>> >>> 0 root@muizenberg:/srv/sysadm/sage#dpkg -S /usr/lib/x86_64-linux-gnu/ >>> libgomp.so.* >>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1 >>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >>> 0 root@muizenberg:/srv/sysadm/sage#dpkg -l libgomp1 >>> Desired=Unknown/Install/Remove/Purge/Hold >>> | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/ >>> trig-aWait/Trig-pend >>> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) >>> ||/ Name Version >>> Architecture Description >>> +++-=======================================-================ >>> ========-========================-========================== >>> ========================================================= >>> ii libgomp1:amd64 4.8.2-19ubuntu1 >>> amd64 GCC OpenMP (GOMP) support library >>> 0 root@muizenberg:/srv/sysadm/sage# >>> >>> Same version: >>> >>> 0 jan@snapperkob:~/src$dpkg -S /usr/lib/x86_64-linux-gnu/libgomp.so.* >>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1 >>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >>> 0 jan@snapperkob:~/src$dpkg -l libgomp1 >>> Desired=Unknown/Install/Remove/Purge/Hold >>> | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/ >>> trig-aWait/Trig-pend >>> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) >>> ||/ Name Version >>> Architecture Description >>> +++-=======================================-================ >>> ========-========================-========================== >>> ========================================================= >>> ii libgomp1:amd64 4.8.2-19ubuntu1 >>> amd64 GCC OpenMP (GOMP) support library >>> 0 jan@snapperkob:~/src$ >>> >>> Regards, >>> Jan >>> >>> >>> >>> On 20 November 2014 18:32, Volker Braun <[email protected]> wrote: >>> >>>> Is this on "snapperkob" or on a different machine? Do you >>>> have /usr/lib/x86_64-linux-gnu/libgomp.so.* and if yes, which version? >>>> >>>> >>>> >>>> On Thursday, November 20, 2014 12:02:18 PM UTC, pipedream wrote: >>>>> >>>>> Hi >>>>> >>>>> I rebuilt sage from a cleanly unpacked source tree on Ubuntu 14.04, >>>>> and it still did not fail on R >>>>> >>>>> >>>>> export SAGE_INSTALL_GCC=yes >>>>> make >>>>> ... >>>>> Successfully installed r-3.1.1.p0 >>>>> >>>>> I'd like to assist running any tests to get this fixed. >>>>> >>>>> Regards, >>>>> Jan >>>>> >>>>> >>>>> On 19 November 2014 09:09, Jan Groenewald <[email protected]> wrote: >>>>> >>>>>> Hi >>>>>> >>>>>> I did >>>>>> >>>>>> $SAGE_INSTALL_GCC=yes make >>>>>> >>>>>> in the already built source tree, and it seemed to rebuild the >>>>>> relevant parts without failing. Is that enough or should I try it in a >>>>>> cleanly unpacked source tree? >>>>>> >>>>>> Regards, >>>>>> Jan >>>>>> >>>>>> >>>>>> On 18 November 2014 15:56, Jan Groenewald <[email protected]> wrote: >>>>>> >>>>>>> Will do. >>>>>>> >>>>>>> Regards, >>>>>>> Jan >>>>>>> >>>>>>> >>>>>>> On 18 November 2014 15:29, Volker Braun <[email protected]> wrote: >>>>>>> >>>>>>>> Try building with SAGE_INSTALL_GCC=yes, I'm pretty sure this is >>>>>>>> causing the problem. >>>>>>>> >>>>>>>> On Tuesday, November 18, 2014 11:56:03 AM UTC, pipedream wrote: >>>>>>>>> >>>>>>>>> Hi >>>>>>>>> >>>>>>>>> This is strange, the error I see is: >>>>>>>>> >>>>>>>>> /home/buildbot/build/sage/snapperkob/sage_git/build/local/var/tmp/sage/build/r-3.1.1.p0/src/bin/exec/R: >>>>>>>>> /usr/lib/x86_64-linux-gnu/libgomp.so.1: version `GOMP_4.0' not found >>>>>>>>> (required by >>>>>>>>> /home/buildbot/build/sage/snapperkob/sage_git/build/local/var/tmp/sage/build/r-3.1.1.p0/src/lib/libR.so) >>>>>>>>> >>>>>>>>> I have the same version of libgomp1 (4.8.2-19ubuntu1) installed on >>>>>>>>> my 14.04 64bit desktop as that builder (snapperkob) and yet sage 6.4 >>>>>>>>> built >>>>>>>>> succesfully on my desktop yesterday: >>>>>>>>> >>>>>>>>> "Successfully installed r-3.1.1.p0" >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> Jan >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On 18 November 2014 13:22, Volker Braun <[email protected]> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> The build failed because R insists on using openmp for some >>>>>>>>>> reason, but the openmp libraries are not installed (or of the wrong >>>>>>>>>> version): >>>>>>>>>> >>>>>>>>>> http://build.sagedev.org/release/builders/Zbin%20%20fast%20A >>>>>>>>>> IMS%20snapperkob%20%28Ubuntu%2014.04%20x86_64%29%20binary/ >>>>>>>>>> builds/1/steps/compile_2/logs/r-project >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tuesday, November 18, 2014 5:00:26 AM UTC, pipedream wrote: >>>>>>>>>>> >>>>>>>>>>> Hi >>>>>>>>>>> >>>>>>>>>>> I do not see the 14.04 Ubuntu binaries here. >>>>>>>>>>> http://boxen.math.washington.edu/home/sagemath/sage-mirror/l >>>>>>>>>>> inux/64bit/index.html >>>>>>>>>>> >>>>>>>>>>> Are they not automatically generated? >>>>>>>>>>> >>>>>>>>>>> Regards, >>>>>>>>>>> Jan >>>>>>>>>>> >>>>>>>>>>> On 17 November 2014 17:17, kcrisman <[email protected]> wrote: >>>>>>>>>>> >>>>>>>>>>>> The release notes have a broken link in them: >>>>>>>>>>>>> >>>>>>>>>>>>> http://boxen.math.washington.edu/home/release/sage-6.4/ >>>>>>>>>>>>> tickets.html >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> Yes, that has been reported before... >>>>>>>>>>>> >>>>>>>>>>>> By the way, Jeroen, I think I finished all the changes I'm >>>>>>>>>>>> going to for now. Long-term, it would be fun to do some database >>>>>>>>>>>> thingie >>>>>>>>>>>> to standardize names of a few very frequent contributors who have >>>>>>>>>>>> them in a >>>>>>>>>>>> couple different formats. >>>>>>>>>>>> >>>>>>>>>>>> >>>>> -- >>>>> .~. >>>>> /V\ Jan Groenewald >>>>> /( )\ www.aims.ac.za >>>>> ^^-^^ >>>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "sage-release" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at http://groups.google.com/group/sage-release. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> >>> >>> -- >>> .~. >>> /V\ Jan Groenewald >>> /( )\ www.aims.ac.za >>> ^^-^^ >>> >> >> >> >> -- >> .~. >> /V\ Jan Groenewald >> /( )\ www.aims.ac.za >> ^^-^^ >> > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/sage-release. > For more options, visit https://groups.google.com/d/optout. > -- .~. /V\ Jan Groenewald /( )\ www.aims.ac.za ^^-^^ -- You received this message because you are subscribed to the Google Groups "sage-release" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/sage-release. For more options, visit https://groups.google.com/d/optout.
