Hi I think I'm getting this the wrong way around. Is it not that
snapperkob build fails where there is NO system ATLAS installed, so it is using SAGE ATLAS. muizenberg works, where libatlas3-base is installed. How does a fix to NOT use the system ATLAS help, if the system ATLAS was not present on snapperkob? libx11-dev is installed on both. I am installaing libatlas3-base on snapperkob to try again. Note there is now load shedding in South Africa, and for the next three nights at 8pm South Africa time I expect snapperkob to be down for 2.5 hours. I hope this build finishes before that. Regards, Jan On 22 November 2014 01:09, Volker Braun <vbraun.n...@gmail.com> wrote: > I've added a commit to always use our ATLAS to > http://trac.sagemath.org/ticket/17349, if nothing else then this will let > us debug the issue in a sane way... > > > On Friday, November 21, 2014 10:24:22 PM UTC, Volker Braun wrote: >> >> R only uses our ATLAS if X development stuff is installed. The whole >> logic in the spkg-install is suspicious... >> >> >> >> >> On Friday, November 21, 2014 7:02:52 PM UTC, pipedream wrote: >>> >>> 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 <vbrau...@gmail.com> 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/t >>>>> mp/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 <j...@aims.ac.za> 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$dpkg -S /usr/lib/x86_64-linux-gnu/libg >>>>>> omp.so.* >>>>>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1 >>>>>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >>>>>> 0 jan@snapperkob:~/src$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 <vbrau...@gmail.com> 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 <j...@aims.ac.za> 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 <j...@aims.ac.za> wrote: >>>>>>>>> >>>>>>>>>> Will do. >>>>>>>>>> >>>>>>>>>> Regards, >>>>>>>>>> Jan >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 18 November 2014 15:29, Volker Braun <vbrau...@gmail.com> >>>>>>>>>> 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 <vbrau...@gmail.com> >>>>>>>>>>>> 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/bu >>>>>>>>>>>>> ilds/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 <kcri...@gmail.com> >>>>>>>>>>>>>> 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 sage-release...@googlegroups.com. >>>>>>> To post to this group, send email to sage-r...@googlegroups.com. >>>>>>> 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 sage-release...@googlegroups.com. >>>> To post to this group, send email to sage-r...@googlegroups.com. >>>> 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 sage-release+unsubscr...@googlegroups.com. > To post to this group, send email to sage-release@googlegroups.com. > 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. 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